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Sample records for genotyping faecal samples

  1. Improved Methods of Carnivore Faecal Sample Preservation, DNA Extraction and Quantification for Accurate Genotyping of Wild Tigers

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    Harika, Katakam; Mahla, Ranjeet Singh; Shivaji, Sisinthy

    2012-01-01

    Background Non-invasively collected samples allow a variety of genetic studies on endangered and elusive species. However due to low amplification success and high genotyping error rates fewer samples can be identified up to the individual level. Number of PCRs needed to obtain reliable genotypes also noticeably increase. Methods We developed a quantitative PCR assay to measure and grade amplifiable nuclear DNA in feline faecal extracts. We determined DNA degradation in experimentally aged faecal samples and tested a suite of pre-PCR protocols to considerably improve DNA retrieval. Results Average DNA concentrations of Grade I, II and III extracts were 982pg/µl, 9.5pg/µl and 0.4pg/µl respectively. Nearly 10% of extracts had no amplifiable DNA. Microsatellite PCR success and allelic dropout rates were 92% and 1.5% in Grade I, 79% and 5% in Grade II, and 54% and 16% in Grade III respectively. Our results on experimentally aged faecal samples showed that ageing has a significant effect on quantity and quality of amplifiable DNA (pDNA degradation occurs within 3 days of exposure to direct sunlight. DNA concentrations of Day 1 samples stored by ethanol and silica methods for a month varied significantly from fresh Day 1 extracts (p0.05). DNA concentrations of fresh tiger and leopard faecal extracts without addition of carrier RNA were 816.5pg/µl (±115.5) and 690.1pg/µl (±207.1), while concentrations with addition of carrier RNA were 49414.5pg/µl (±9370.6) and 20982.7pg/µl (±6835.8) respectively. Conclusions Our results indicate that carnivore faecal samples should be collected as freshly as possible, are better preserved by two-step method and should be extracted with addition of carrier RNA. We recommend quantification of template DNA as this facilitates several downstream protocols. PMID:23071624

  2. Genotyping faecal samples of Bengal tiger Panthera tigris tigris for population estimation: A pilot study

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    Singh Lalji

    2006-10-01

    Full Text Available Abstract Background Bengal tiger Panthera tigris tigris the National Animal of India, is an endangered species. Estimating populations for such species is the main objective for designing conservation measures and for evaluating those that are already in place. Due to the tiger's cryptic and secretive behaviour, it is not possible to enumerate and monitor its populations through direct observations; instead indirect methods have always been used for studying tigers in the wild. DNA methods based on non-invasive sampling have not been attempted so far for tiger population studies in India. We describe here a pilot study using DNA extracted from faecal samples of tigers for the purpose of population estimation. Results In this study, PCR primers were developed based on tiger-specific variations in the mitochondrial cytochrome b for reliably identifying tiger faecal samples from those of sympatric carnivores. Microsatellite markers were developed for the identification of individual tigers with a sibling Probability of Identity of 0.005 that can distinguish even closely related individuals with 99.9% certainty. The effectiveness of using field-collected tiger faecal samples for DNA analysis was evaluated by sampling, identification and subsequently genotyping samples from two protected areas in southern India. Conclusion Our results demonstrate the feasibility of using tiger faecal matter as a potential source of DNA for population estimation of tigers in protected areas in India in addition to the methods currently in use.

  3. Reliable genotyping of the koala (Phascolarctos cinereus) using DNA isolated from a single faecal pellet.

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    Wedrowicz, Faye; Karsa, Mawar; Mosse, Jennifer; Hogan, Fiona E

    2013-07-01

    The koala, an Australian icon, has been added to the threatened species list. Rationale for the listing includes proposed declines in population size, threats to populations (e.g. disease) and loss and fragmentation of habitat. There is now an urgent need to obtain accurate data to assess the status of koala populations in Australia, to ensure the long-term viability of this species. Advances in genetic techniques have enabled DNA analysis to study and inform the management of wild populations; however, sampling of individual koalas is difficult in tall, often remote, eucalypt forest. The collection of faecal pellets (scats) from the forest floor presents an opportunistic sampling strategy, where DNA can be collected without capturing or even sighting an individual. Obtaining DNA via noninvasive sampling can be used to rapidly sample a large proportion of a population; however, DNA from noninvasively collected samples is often degraded. Factors influencing DNA quality and quantity include environmental exposure, diet and methods of sample collection, storage and DNA isolation. Reduced DNA quality and quantity can introduce genotyping errors and provide inaccurate DNA profiles, reducing confidence in the ability of such data to inform management/conservation strategies. Here, we present a protocol that produces a reliable individual koala genotype from a single faecal pellet and highlight the importance of optimizing DNA isolation and analysis for the species of interest. This method could readily be adapted for genetic studies of mammals other than koalas, particularly those whose diet contains high proportions of volatile materials that are likely to induce DNA damage. © 2013 John Wiley & Sons Ltd.

  4. Assessment of helminth load in faecal samples of free range ...

    African Journals Online (AJOL)

    Helminths load in faecal sample of free range indigenous chicken in Port Harcourt Metropolis was examined. Faecal samples were collected from 224 birds in 15 homesteads and 4 major markets - Mile 3, Mile 1, Borokiri and Eneka Village market where poultry birds are gathered for sale. 0.2-0.5g of feacal sample was ...

  5. Integrity of the Human Faecal Microbiota following Long-Term Sample Storage.

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    Elahe Kia

    Full Text Available In studies of the human microbiome, faecal samples are frequently used as a non-invasive proxy for the study of the intestinal microbiota. To obtain reliable insights, the need for bacterial DNA of high quality and integrity following appropriate faecal sample collection and preservation steps is paramount. In a study of dietary mineral balance in the context of type 2 diabetes (T2D, faecal samples were collected from healthy and T2D individuals throughout a 13-day residential trial. These samples were freeze-dried, then stored mostly at -20°C from the trial date in 2000/2001 until the current research in 2014. Given the relative antiquity of these samples (~14 years, we sought to evaluate DNA quality and comparability to freshly collected human faecal samples. Following the extraction of bacterial DNA, gel electrophoresis indicated that our DNA extracts were more sheared than extracts made from freshly collected faecal samples, but still of sufficiently high molecular weight to support amplicon-based studies. Likewise, spectrophotometric assessment of extracts revealed that they were of high quality and quantity. A subset of bacterial 16S rRNA gene amplicons were sequenced using Illumina MiSeq and compared against publicly available sequence data representing a similar cohort analysed by the American Gut Project (AGP. Notably, our bacterial community profiles were highly consistent with those from the AGP data. Our results suggest that when faecal specimens are stored appropriately, the microbial profiles are preserved and robust to extended storage periods.

  6. Cow-specific diet digestibility predictions based on near-infrared reflectance spectroscopy scans of faecal samples.

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    Mehtiö, T; Rinne, M; Nyholm, L; Mäntysaari, P; Sairanen, A; Mäntysaari, E A; Pitkänen, T; Lidauer, M H

    2016-04-01

    This study was designed to obtain information on prediction of diet digestibility from near-infrared reflectance spectroscopy (NIRS) scans of faecal spot samples from dairy cows at different stages of lactation and to develop a faecal sampling protocol. NIRS was used to predict diet organic matter digestibility (OMD) and indigestible neutral detergent fibre content (iNDF) from faecal samples, and dry matter digestibility (DMD) using iNDF in feed and faecal samples as an internal marker. Acid-insoluble ash (AIA) as an internal digestibility marker was used as a reference method to evaluate the reliability of NIRS predictions. Feed and composite faecal samples were collected from 44 cows at approximately 50, 150 and 250 days in milk (DIM). The estimated standard deviation for cow-specific organic matter digestibility analysed by AIA was 12.3 g/kg, which is small considering that the average was 724 g/kg. The phenotypic correlation between direct faecal OMD prediction by NIRS and OMD by AIA over the lactation was 0.51. The low repeatability and small variability estimates for direct OMD predictions by NIRS were not accurate enough to quantify small differences in OMD between cows. In contrast to OMD, the repeatability estimates for DMD by iNDF and especially for direct faecal iNDF predictions were 0.32 and 0.46, respectively, indicating that developing of NIRS predictions for cow-specific digestibility is possible. A data subset of 20 cows with daily individual faecal samples was used to develop an on-farm sampling protocol. Based on the assessment of correlations between individual sample combinations and composite samples as well as repeatability estimates for individual sample combinations, we found that collecting up to three individual samples yields a representative composite sample. Collection of samples from all the cows of a herd every third month might be a good choice, because it would yield a better accuracy. © 2015 Blackwell Verlag GmbH.

  7. Measuring the gut microbiome in birds: Comparison of faecal and cloacal sampling.

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    Videvall, Elin; Strandh, Maria; Engelbrecht, Anel; Cloete, Schalk; Cornwallis, Charlie K

    2018-05-01

    The gut microbiomes of birds and other animals are increasingly being studied in ecological and evolutionary contexts. Numerous studies on birds and reptiles have made inferences about gut microbiota using cloacal sampling; however, it is not known whether the bacterial community of the cloaca provides an accurate representation of the gut microbiome. We examined the accuracy with which cloacal swabs and faecal samples measure the microbiota in three different parts of the gastrointestinal tract (ileum, caecum, and colon) using a case study on juvenile ostriches, Struthio camelus, and high-throughput 16S rRNA sequencing. We found that faeces were significantly better than cloacal swabs in representing the bacterial community of the colon. Cloacal samples had a higher abundance of Gammaproteobacteria and fewer Clostridia relative to the gut and faecal samples. However, both faecal and cloacal samples were poor representatives of the microbial communities in the caecum and ileum. Furthermore, the accuracy of each sampling method in measuring the abundance of different bacterial taxa was highly variable: Bacteroidetes was the most highly correlated phylum between all three gut sections and both methods, whereas Actinobacteria, for example, was only strongly correlated between faecal and colon samples. Based on our results, we recommend sampling faeces, whenever possible, as this sample type provides the most accurate assessment of the colon microbiome. The fact that neither sampling technique accurately portrayed the bacterial community of the ileum nor the caecum illustrates the difficulty in noninvasively monitoring gut bacteria located further up in the gastrointestinal tract. These results have important implications for the interpretation of avian gut microbiome studies. © 2017 John Wiley & Sons Ltd.

  8. Detection of Campylobacter in human faecal samples in Fiji.

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    Devi, Aruna; Wilkinson, Jenny; Mahony, Timothy; Vanniasinkam, Thiru

    2014-01-01

    Data on campylobacteriosis in developed countries are well documented; in contrast, few studies on campylobacteriosis have been conducted in developing countries. This study was undertaken to test for Campylobacter in human faecal samples sent to the two major pathology laboratories in Fiji. A total of 408 diarrhoeal faecal samples were collected from the two major hospital pathology laboratories in Central Fiji (Suva) and Western Fiji (Lautoka) between December 2012 and February 2013 and from June to July 2013. Samples were analysed for the presence of Campylobacter using polymerase chain reaction (PCR) based methods. Campylobacter was detected in 241/408 (59.1%) of samples tested using PCR. Samples from children aged less than five accounted for 21.6% of positive cases. Campylobacter was detected in 59.1% of diarrhoeal samples collected from the two main laboratories in Fiji. A high proportion of children under five years with Campylobacter has been reported in other countries and could be due to parents being more likely to seek medical attention. Further studies are required to confirm the species of Campylobacter that are predominantly associated with gastroenteritis in Fiji.

  9. Two-step multiplex polymerase chain reaction improves the speed and accuracy of genotyping using DNA from noninvasive and museum samples.

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    Arandjelovic, M; Guschanski, K; Schubert, G; Harris, T R; Thalmann, O; Siedel, H; Vigilant, L

    2009-01-01

    Many studies in molecular ecology rely upon the genotyping of large numbers of low-quantity DNA extracts derived from noninvasive or museum specimens. To overcome low amplification success rates and avoid genotyping errors such as allelic dropout and false alleles, multiple polymerase chain reaction (PCR) replicates for each sample are typically used. Recently, two-step multiplex procedures have been introduced which drastically increase the success rate and efficiency of genotyping. However, controversy still exists concerning the amount of replication needed for suitable control of error. Here we describe the use of a two-step multiplex PCR procedure that allows rapid genotyping using at least 19 different microsatellite loci. We applied this approach to quantified amounts of noninvasive DNAs from western chimpanzee, western gorilla, mountain gorilla and black and white colobus faecal samples, as well as to DNA from ~100-year-old gorilla teeth from museums. Analysis of over 45 000 PCRs revealed average success rates of > 90% using faecal DNAs and 74% using museum specimen DNAs. Average allelic dropout rates were substantially reduced compared to those obtained using conventional singleplex PCR protocols, and reliable genotyping using low (< 25 pg) amounts of template DNA was possible. However, four to five replicates of apparently homozygous results are needed to avoid allelic dropout when using the lowest concentration DNAs (< 50 pg/reaction), suggesting that use of protocols allowing routine acceptance of homozygous genotypes after as few as three replicates may lead to unanticipated errors when applied to low-concentration DNAs. © 2008 The Authors. Journal compilation © 2008 Blackwell Publishing Ltd.

  10. Contamination of faecal coliforms in ice cubes sampled from food outlets in Kubang Kerian, Kelantan.

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    Noor Izani, N J; Zulaikha, A R; Mohamad Noor, M R; Amri, M A; Mahat, N A

    2012-03-01

    The use of ice cubes in beverages is common among patrons of food outlets in Malaysia although its safety for human consumption remains unclear. Hence, this study was designed to determine the presence of faecal coliforms and several useful water physicochemical parameters viz. free residual chlorine concentration, turbidity and pH in ice cubes from 30 randomly selected food outlets in Kubang Kerian, Kelantan. Faecal coliforms were found in ice cubes in 16 (53%) food outlets ranging between 1 CFU/100mL to >50 CFU/ 100mL, while in the remaining 14 (47%) food outlets, in samples of tap water as well as in commercially bottled drinking water, faecal coliforms were not detected. The highest faecal coliform counts of >50 CFU/100mL were observed in 3 (10%) food outlets followed by 11-50 CFU/100mL and 1-10 CFU/100mL in 7 (23%) and 6 (20%) food outlets, respectively. All samples recorded low free residual chlorine concentration (contamination by faecal coliforms was not detected in 47% of the samples, tap water and commercially bottled drinking water, it was concluded that (1) contamination by faecal coliforms may occur due to improper handling of ice cubes at the food outlets or (2) they may not be the water sources used for making ice cubes. Since low free residual chlorine concentrations were observed (food outlets, including that of ice cube is crucial in ensuring better food and water for human consumption.

  11. Impact of a new sampling buffer on faecal haemoglobin stability in a colorectal cancer screening programme by the faecal immunochemical test.

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    Grazzini, Grazia; Ventura, Leonardo; Rubeca, Tiziana; Rapi, Stefano; Cellai, Filippo; Di Dia, Pietro P; Mallardi, Beatrice; Mantellini, Paola; Zappa, Marco; Castiglione, Guido

    2017-07-01

    Haemoglobin (Hb) stability in faecal samples is an important issue in colorectal cancer screening by the faecal immunochemical test (FIT) for Hb. This study evaluated the performance of the FIT-Hb (OC-Sensor Eiken) used in the Florence screening programme by comparing two different formulations of the buffer, both in an analytical and in a clinical setting. In the laboratory simulation, six faecal pools (three in each buffer type) were stored at different temperatures and analysed eight times in 10 replicates over 21 days. In the clinical setting, 7695 screenees returned two samples, using both the old and the new specimen collection device (SCD). In the laboratory simulation, 5 days from sample preparation with the buffer of the old SCD, the Hb concentration decreased by 40% at room temperature (25°C, range 22-28°C) and up to 60% at outside temperature (29°C, range 16-39°C), whereas with the new one, Hb concentration decreased by 10%. In the clinical setting, a higher mean Hb concentration with the new SCD compared with the old one was found (6.3 vs. 5.0 µg Hb/g faeces, respectively, Pbuffer under laboratory conditions, but no difference was found in the clinical performance. In our study, only marginal advantages arise from the new buffer. Improvements in sample stability represent a significant target in the screening setting.

  12. Characterization of Staphylococcus aureus isolates from faecal samples of the Straw-Coloured Fruit Bat (Eidolon helvum) in Obafemi Awolowo University (OAU), Nigeria.

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    Akobi, Babatunji; Aboderin, Oladipo; Sasaki, Takashi; Shittu, Adebayo

    2012-11-26

    Bats (Chiroptera) are one of the most diverse groups of mammals which carry out important ecological and agricultural functions that are beneficial to humans. However, they are increasingly recognized as natural vectors for a number of zoonotic pathogens and favourable hosts for zoonotic infections. Large populations of the Straw-Coloured Fruit Bat (Eidolon helvum) colonize the main campus of the Obafemi Awolowo University (OAU), Ile-Ife, Nigeria, but the public health implications of faecal contamination and pollution by these flying mammals is unknown. This study characterized S. aureus obtained from faecal samples of these migratory mammals with a view to determining the clonal types of the isolates, and to investigate the possibility of these flying animals as potential reservoir for zoonotic S. aureus infections. One hundred and seven (107) S. aureus isolates were recovered from 560 faecal samples in eleven roosting sites from January 2008 to February 2010. A large proportion of the isolates were susceptible to antibiotics, and molecular characterization of 70 isolates showed that 65 (92.9%) were assigned in coagulase type VI, while accessory gene typing classified 69 isolates into the following: type I (12; 17.1%), type II (3; 4.3%), type III (1; 1.4%) and type IV (53; 75.7%). On the whole, the isolates were grouped in five (A-E) main genotypes. Of the ten representative isolates selected for multilocus sequence typing (MLST), nine isolates were assigned with new sequence types: ST1725, ST1726, ST1727, ST2463-ST2467 and ST2470. Phylogenetic analysis provided evidence that S. aureus isolates in group C were closely related with ST1822 and associated clones identified in African monkeys, and group D isolates with ST75, ST883 and ST1223. The two groups exhibited remarkable genetic diversity compared to the major S. aureus clade. Antibiotic resistance in faecal S. aureus isolates of E. helvum is low and multiple unique S. aureus lineages co-existed with E. helvum

  13. Population size estimation in Yellowstone wolves with error-prone noninvasive microsatellite genotypes.

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    Creel, Scott; Spong, Goran; Sands, Jennifer L; Rotella, Jay; Zeigle, Janet; Joe, Lawrence; Murphy, Kerry M; Smith, Douglas

    2003-07-01

    Determining population sizes can be difficult, but is essential for conservation. By counting distinct microsatellite genotypes, DNA from noninvasive samples (hair, faeces) allows estimation of population size. Problems arise because genotypes from noninvasive samples are error-prone, but genotyping errors can be reduced by multiple polymerase chain reaction (PCR). For faecal genotypes from wolves in Yellowstone National Park, error rates varied substantially among samples, often above the 'worst-case threshold' suggested by simulation. Consequently, a substantial proportion of multilocus genotypes held one or more errors, despite multiple PCR. These genotyping errors created several genotypes per individual and caused overestimation (up to 5.5-fold) of population size. We propose a 'matching approach' to eliminate this overestimation bias.

  14. [Occurrence of Giardia species and genotypes in humans and animals in Wielkopolska region, Poland].

    Science.gov (United States)

    Solarczyk, Piotr

    2009-01-01

    Giardia is the most common intestinal protozoan parasite found in humans and animals worldwide. Although it has been known for three hundred years, the nomenclature, taxonomy, host specificity, and pathogenicity of Giardia still arouse numerous controversies and ambiguities. Giardia is classified into six species, that are characterised by various ranges of hosts. The most dubious species is G. intestinalis, which includes a dozen or so genotypes, and only two of them (genotype A and B) have wide ranges of hosts, including humans. Moreover, in some genotype assemblages of G. intestinalis certain subgenotypes were distinguished and it was proven that in the same host species various subgenotypes of this parasite may occur. Bearing in mind the significant genetic heterogeneity of G. intestinalis and the fact that various genotypes and subgenotypes of this parasite are characterised by the broad or narrow host specificity, the data concerning the frequency of giardiosis occurrence are insufficient. It is necessary to use molecular biology techniques in order to define the genotype and/or the subgenotype of G. intestinalis that are found in humans and in certain animal species. Furthermore, since more and more pieces of evidence connected with a possibility of the sexual recombination of Giardia are gathered, it is unknown if genotypes and subgenotypes of this parasite are stable in time. The aim of this thesis was to define the frequency of Giardia occurrence in humans and animals in Wielkopolska region, to identify species and genotypes of Giardia that occur in humans and animals, as well as to obtain an axenic culture of the chosen isolates of Giardia from animals and to compare the sequence of the beta-giardin gene fragment obtained from the DNA isolated from cysts and trophozoites in order to check if the axenisation of G. intestinalis leads to the selection of genotypes or if Giardia genotypes are stable in time. Altogether, 2183 faecal samples were examined for

  15. Evaluation of a microwave method for dry matter determination in faecal samples from weaned pigs with or without clinical diarrhoea.

    Science.gov (United States)

    Pedersen, Ken Steen; Stege, Helle; Nielsen, Jens Peter

    2011-07-01

    Microwave drying as a procedure for determination of faecal dry matter in weaned pigs was evaluated and clinical relevant cut-off values between faecal consistency scores were determined. Repeatability and reproducibility were evaluated. Overall coefficient of variation was 0.03. The 95% confidence limits for any future faecal subsample examined by any operator in any replica were ± 0.85% faecal dry matter. Robustness in relation to weight of wet faeces was evaluated. The weight categories were 0.5, 1.0, 1.5, 2.0 and 3.0 g. Samples of 0.5 g gave significantly different mean faecal dry matter content compared to weighing of 1.0-3.0 g. Agreement with freeze-drying was evaluated. Lin's concordance correlation coefficient was 0.94. On average the faecal dry matter values was 1.7% (SD=1.99%) higher in freeze dried compared to micro waved samples. Non-parametric ROC analyses were used to determine optimal faecal dry matter cut-off values for clinical faecal consistency scores. The 4 consistency scores were score 1=firm and shaped, score 2=soft and shaped, score 3=loose and score 4=watery. The cut-off values were score 1: faecal dry matter content >19.5%, score 2: faecal dry matter content ≤ 19.5% and >18.0%, score 3: faecal dry matter content ≤ 18.0% and >11.3%, score 4: faecal dry matter content ≤ 11.3%. In conclusion, the microwave procedure has an acceptable repeatability/reproducibility and good agreement with freeze drying can be expected. A minimum of 1.0 g of wet faeces must be used for analyses. Faecal dry matter cut-off values between 4 different clinical consistency scores were determined. © 2011 Elsevier B.V. All rights reserved.

  16. The contribution of simple random sampling to observed variations in faecal egg counts.

    Science.gov (United States)

    Torgerson, Paul R; Paul, Michaela; Lewis, Fraser I

    2012-09-10

    It has been over 100 years since the classical paper published by Gosset in 1907, under the pseudonym "Student", demonstrated that yeast cells suspended in a fluid and measured by a haemocytometer conformed to a Poisson process. Similarly parasite eggs in a faecal suspension also conform to a Poisson process. Despite this there are common misconceptions how to analyse or interpret observations from the McMaster or similar quantitative parasitic diagnostic techniques, widely used for evaluating parasite eggs in faeces. The McMaster technique can easily be shown from a theoretical perspective to give variable results that inevitably arise from the random distribution of parasite eggs in a well mixed faecal sample. The Poisson processes that lead to this variability are described and illustrative examples of the potentially large confidence intervals that can arise from observed faecal eggs counts that are calculated from the observations on a McMaster slide. Attempts to modify the McMaster technique, or indeed other quantitative techniques, to ensure uniform egg counts are doomed to failure and belie ignorance of Poisson processes. A simple method to immediately identify excess variation/poor sampling from replicate counts is provided. Copyright © 2012 Elsevier B.V. All rights reserved.

  17. First detection and genotyping of Giardia intestinalis in stool samples collected from children in Ghazni Province, eastern Afghanistan and evaluation of the PCR assay in formalin-fixed specimens.

    Science.gov (United States)

    Lass, Anna; Karanis, Panagiotis; Korzeniewski, Krzysztof

    2017-08-01

    It is estimated that faecal-orally transmitted diseases are common in Afghanistan, as a consequence of poor hygienic standards of life and widespread contamination of water and food with both human and animal faeces. However, there is little information in the literature concerning infections caused by intestinal parasites in the Afghan population. In this study, we report the occurrence of Giardia intestinalis assemblages (A and B) in formalin-fixed stool samples collected from 245 Afghan schoolchildren living in Ghazni Province in eastern Afghanistan. Detection of the parasite's DNA and genotyping was performed using real-time PCR, specific to the β-giardin gene of G. intestinalis. Positive results were recorded in 52 (21.2%) samples. Genotyping was successful in 39 faecal samples and showed the predominance of assemblage B of G. intestinalis in this population (15 assemblage A and 24 assemblage B). Co-infection with both genotypes A and B was detected in four samples. Additionally, we evaluated the effect of 10% buffered formalin fixative on the detection of G. intestinalis DNA using real-time PCR and nested PCR characterised by different lengths of PCR products (74 and 479 bp, respectively). The human faeces containing the Giardia cysts were tested for 16 weeks. Amplification of G. intestinalis DNA with real-time PCR was possible up to 6 weeks of preservation of stool sample in formalin, compared to only 2 weeks with nested PCR. This suggests that real-time PCR is a more suitable tool in cases where stool samples have to be kept in formalin for longer periods of time.

  18. PCR Screening of Antibiotic Resistance Genes in Faecal Samples from Australian and Chinese Children.

    Science.gov (United States)

    Ravensdale, Joshua T; Xian, Darren Ten Wei; Wei, Chooi Ming; Lv, Quanjun; Wen, Xiajian; Guo, Jing; Coorey, Ranil; LeSouëf, Peter; Lu, Fengmin; Zhang, Brad; Dykes, Gary A

    2018-03-31

    Recent public awareness campaigns on the risk of antibiotic resistance in pathogenic microbes has placed pressure on governments to enforce stricter antimicrobial stewardship policies on the hospital and agricultural industry. This study aimed to screen faecal samples from Australian and Chinese children for the presence of antibiotic resistance genes to identify demographics at risk of carriage of these genes and examine antimicrobial stewardship policies from the two countries which may influence carriage. Faecal samples from 46 Australian and 53 Chinese children were screened for the presence of six clinically relevant antibiotic resistance genes using PCR. Clinical and demographic data was also collected from each patient. Over 90% of faecal samples from Chinese children tested positive for β-lactam, macrolide, tetracycline, and aminoglycoside resistance genes, which was substantially higher than Australian samples. Besides country of origin, no clear trend could be seen to predict carriage of resistance genes. The exception to this was Chinese born children who immigrated to Australia having higher rates of carriage for bla TEM and tetM genes than children born and still living in Australia. These data indicated that Chinese children were more likely to carry certain antibiotic resistance genes than Australian children. The Chinese government has recently implemented strict policies to control the overuse of antibiotics in hospitals. However, many of these policies do not extend to the agricultural industry which could explain the differences seen in this study. Copyright © 2018. Published by Elsevier Ltd.

  19. Identification of the origin of faecal contamination in estuarine oysters using Bacteroidales and F-specific RNA bacteriophage markers.

    Science.gov (United States)

    Mieszkin, S; Caprais, M P; Le Mennec, C; Le Goff, M; Edge, T A; Gourmelon, M

    2013-09-01

    The aim of this study was to identify the origin of faecal pollution impacting the Elorn estuary (Brittany, France) by applying microbial source tracking (MST) markers in both oysters and estuarine waters. The MST markers used were as follows: (i) human-, ruminant- and pig-associated Bacteroidales markers by real-time PCR and (ii) human genogroup II and animal genogroup I of F-specific RNA bacteriophages (FRNAPH) by culture/genotyping and by direct real-time reverse-transcriptase PCR. The higher occurrence of the human genogroup II of F-specific RNA bacteriophages using a culture/genotyping method, and human-associated Bacteroidales marker by real-time PCR, allowed the identification of human faecal contamination as the predominant source of contamination in oysters (total of 18 oyster batches tested) and waters (total of 24 water samples tested). The importance of using the intravalvular liquids instead of digestive tissues, when applying host-associated Bacteroidales markers in oysters, was also revealed. This study has shown that the application of a MST toolbox of diverse bacterial and viral methods can provide multiple lines of evidence to identify the predominant source of faecal contamination in shellfish from an estuarine environment. Application of this MST toolbox is a useful approach to understand the origin of faecal contamination in shellfish harvesting areas in an estuarine setting. © 2013 The Society for Applied Microbiology.

  20. First report of Echinococcus granulosus (genotype G6) in a dog in Bamako, Mali.

    Science.gov (United States)

    Mauti, S; Traoré, A; Crump, L; Zinsstag, J; Grimm, F

    2016-02-15

    Cystic echinococcosis is one of the most widespread and important helminthic zoonoses, caused by the larval stage of Echinococcus granulosus sensu lato. However, to date there is little information about the disease in West Africa. Faecal and fur samples from 193 dogs, the main final hosts, were collected in 2010 and 2011 in Bamako, Mali. Taeniid eggs were found microscopically in 28/118 (24%) and 80/223 (36%) faecal and fur samples, respectively. One faecal and one fur sample from the same dog were positive for E. granulosus s. l. DNA. In the remaining 27 faecal (96%) and 77 fur samples (96%) only Taenia DNA was detected. Three microscopically positive fur samples were negative by PCR. Sequence analysis of part of the NADH dehydrogenase subunit 1 gene identified the parasite as E. granulosus (genotype G6; Echinococcus canadensis). This is the first study to focus on the final host of E. granulosus s. l. in Mali and the first report of E. canadensis in Mali. Copyright © 2016 Elsevier B.V. All rights reserved.

  1. Travel-associated faecal colonization with ESBL-producing Enterobacteriaceae: incidence and risk factors.

    Science.gov (United States)

    Ostholm-Balkhed, Ase; Tärnberg, Maria; Nilsson, Maud; Nilsson, Lennart E; Hanberger, Håkan; Hällgren, Anita

    2013-09-01

    To study the acquisition of extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-PE) among the faecal flora during travel, with a focus on risk factors, antibiotic susceptibility and ESBL-encoding genes. An observational prospective multicentre cohort study of individuals attending vaccination clinics in south-east Sweden was performed, in which the submission of faecal samples and questionnaires before and after travelling outside Scandinavia was requested. Faecal samples were screened for ESBL-PE by culturing on ChromID ESBL and an in-house method. ESBL-PE was confirmed by phenotypic and genotypic methods. Susceptibility testing was performed with the Etest. Individuals who acquired ESBL-PE during travel (travel-associated carriers) were compared with non-carriers regarding risk factors, and unadjusted and adjusted ORs after manual stepwise elimination were calculated using logistic regression. Of 262 enrolled individuals, 2.4% were colonized before travel. Among 226 evaluable participants, ESBL-PE was detected in the post-travel samples from 68 (30%) travellers. The most important risk factor in the final model was the geographic area visited: Indian subcontinent (OR 24.8, P Asia (OR 8.63, P < 0.001) and Africa north of the equator (OR 4.94, P = 0.002). Age and gastrointestinal symptoms also affected the risk significantly. Multiresistance was seen in 77 (66%) of the ESBL-PE isolates, predominantly a combination of reduced susceptibility to third-generation cephalosporins, trimethoprim/sulfamethoxazole and aminoglycosides. The most common species and ESBL-encoding gene were Escherichia coli (90%) and CTX-M (73%), respectively. Acquisition of multiresistant ESBL-PE among the faecal flora during international travel is common. The geographical area visited has the highest impact on ESBL-PE acquisition.

  2. Cost-effectiveness of one versus two sample faecal immunochemical testing for colorectal cancer screening

    NARCIS (Netherlands)

    S.L. Goede (Luuk); A.H.C. Roon (Aafke); J.C.I.Y. Reijerink (Jacqueline); A.J. van Vuuren (Hanneke); I. Lansdorp-Vogelaar (Iris); J.D.F. Habbema (Dik); E.J. Kuipers (Ernst); M.E. van Leerdam (Monique); M. van Ballegooijen (Marjolein)

    2013-01-01

    textabstractObjective The sensitivity and specificity of a single faecal immunochemical test (FIT) are limited. The performance of FIT screening can be improved by increasing the screening frequency or by providing more than one sample in each screening round. This study aimed to evaluate if

  3. Novel Cryptosporidium bat genotypes III and IV in bats from the USA and Czech Republic.

    Science.gov (United States)

    Kváč, Martin; Hořická, Anna; Sak, Bohumil; Prediger, Jitka; Salát, Jiří; Širmarová, Jana; Bartonička, Tomáš; Clark, Mark; Chelladurai, Jeba Rose Jennifer Jesudoss; Gillam, Erin; McEvoy, John

    2015-10-01

    Bats from the families Rhinolophidae (n = 90) and Vespertilionidae (n = 191) in the USA and Czech Republic were screened for the presence of Cryptosporidium by microscopic and molecular analysis of faecal samples collected from rectum of dissected animals and from the ground beneath roosting sites. Cryptosporidium oocysts were not detected in any of the 281 faecal specimens examined using the aniline-carbol-methyl violet staining method. Nested PCR amplification, sequencing and phylogenetic analysis of the small ribosomal subunit rRNA and actin genes were used to identify isolates and infer evolutionary relationships. Cryptosporidium parvum was identified in a western small-footed bat (Myotis ciliolabrum) from the USA and a common pipistrelle bats (Pipistrellus pipistrellus) from the Czech Republic. Two novel genotypes were identified and named Cryptosporidium bat genotype III and IV. Bat genotype III was found in two big brown bats (Eptesicus fuscus) from the USA. Bat genotype IV was detected in two common pipistrelle bats from the Czech Republic.

  4. Ancylostoma caninum: calibration and comparison of diagnostic accuracy of flotation in tube, McMaster and FLOTAC in faecal samples of dogs.

    Science.gov (United States)

    Cringoli, Giuseppe; Rinaldi, Laura; Maurelli, Maria Paola; Morgoglione, Maria Elena; Musella, Vincenzo; Utzinger, Jürg

    2011-05-01

    We performed a calibration of flotation in tube, McMaster and FLOTAC to determine the optimal flotation solution (FS) and the influence of faecal preservation for the diagnosis of Ancylostoma caninum in dogs, and compared the accuracy of the three copromicroscopic techniques. Among nine different FS, sodium chloride and sodium nitrate performed best for detection and quantification of A. caninum eggs. Faecal samples, either fresh or preserved in formalin 5%, resulted in higher A. caninum egg counts, compared to frozen samples or preserved in formalin 10% or sodium acetate-acetic acid-formalin. FLOTAC consistently resulted in higher A. caninum eggs per gram of faeces (EPG) and lower coefficient of variation (CV) than McMaster and flotation in tube. The best results in terms of mean faecal egg counts (highest value, i.e. 117.0EPG) and CV (lowest value, i.e. 4.8%) were obtained with FLOTAC using sodium chloride and faecal samples preserved in formalin 5%. Our findings suggest that the FLOTAC technique should be considered for the diagnosis of A. caninum in dogs. Copyright © 2011 Elsevier Inc. All rights reserved.

  5. Uncertainty on faecal analysis on dose assessment

    Energy Technology Data Exchange (ETDEWEB)

    Juliao, Ligia M.Q.C.; Melo, Dunstana R.; Sousa, Wanderson de O.; Santos, Maristela S.; Fernandes, Paulo Cesar P. [Instituto de Radioprotecao e Dosimetria, Comissao Nacional de Energia Nuclear, Av. Salvador Allende s/n. Via 9, Recreio, CEP 22780-160, Rio de Janeiro, RJ (Brazil)

    2007-07-01

    Monitoring programmes for internal dose assessment may need to have a combination of bioassay techniques, e.g. urine and faecal analysis, especially in workplaces where compounds of different solubilities are handled and also in cases of accidental intakes. Faecal analysis may be an important data for assessment of committed effective dose due to exposure to insoluble compounds, since the activity excreted by urine may not be detectable, unless a very sensitive measurement system is available. This paper discusses the variability of the daily faecal excretion based on data from just one daily collection; collection during three consecutive days: samples analysed individually and samples analysed as a pool. The results suggest that just 1 d collection is not appropriate for dose assessment, since the 24 h uranium excretion may vary by a factor of 40. On the basis of this analysis, the recommendation should be faecal collection during three consecutive days, and samples analysed as a pool, it is more economic and faster. (authors)

  6. Effect of vacuum packing and temperature on survival and hatching of strongyle eggs in faecal samples

    DEFF Research Database (Denmark)

    Sengupta, Mita Eva; Thapa, Sundar; Thamsborg, Stig Milan

    2016-01-01

    Strongyle eggs of helminths of livestock usually hatch within a few hours or days after deposition with faeces. This poses a problem when faecal sampling is performed in the field. As oxygen is needed for embryonic development, it is recommended to reduce air supply during transport and refrigerate....... The present study therefore investigated the combined effect of vacuum packing and temperature on survival of strongyle eggs and their subsequent ability to hatch and develop into L3. Fresh faecal samples were collected from calves infected with Cooperia oncophora, pigs infected with Oesophagostomum dentatum......, and horses infected with Strongylus vulgaris and cyathostomins. The samples were allocated into four treatments: vacuum packing and storage at 5 °C or 20 °C (5 V and 20 V); normal packing in plastic gloves closed with a loose knot and storage at 5 °C or 20 °C (5 N and 20 N). The number of eggs per gram...

  7. Scrambled eggs: A highly sensitive molecular diagnostic workflow for Fasciola species specific detection from faecal samples.

    Directory of Open Access Journals (Sweden)

    Nichola Eliza Davies Calvani

    2017-09-01

    Full Text Available Fasciolosis, due to Fasciola hepatica and Fasciola gigantica, is a re-emerging zoonotic parasitic disease of worldwide importance. Human and animal infections are commonly diagnosed by the traditional sedimentation and faecal egg-counting technique. However, this technique is time-consuming and prone to sensitivity errors when a large number of samples must be processed or if the operator lacks sufficient experience. Additionally, diagnosis can only be made once the 12-week pre-patent period has passed. Recently, a commercially available coprological antigen ELISA has enabled detection of F. hepatica prior to the completion of the pre-patent period, providing earlier diagnosis and increased throughput, although species differentiation is not possible in areas of parasite sympatry. Real-time PCR offers the combined benefits of highly sensitive species differentiation for medium to large sample sizes. However, no molecular diagnostic workflow currently exists for the identification of Fasciola spp. in faecal samples.A new molecular diagnostic workflow for the highly-sensitive detection and quantification of Fasciola spp. in faecal samples was developed. The technique involves sedimenting and pelleting the samples prior to DNA isolation in order to concentrate the eggs, followed by disruption by bead-beating in a benchtop homogeniser to ensure access to DNA. Although both the new molecular workflow and the traditional sedimentation technique were sensitive and specific, the new molecular workflow enabled faster sample throughput in medium to large epidemiological studies, and provided the additional benefit of speciation. Further, good correlation (R2 = 0.74-0.76 was observed between the real-time PCR values and the faecal egg count (FEC using the new molecular workflow for all herds and sampling periods. Finally, no effect of storage in 70% ethanol was detected on sedimentation and DNA isolation outcomes; enabling transport of samples from endemic

  8. Scrambled eggs: A highly sensitive molecular diagnostic workflow for Fasciola species specific detection from faecal samples

    Science.gov (United States)

    Calvani, Nichola Eliza Davies; Windsor, Peter Andrew; Bush, Russell David

    2017-01-01

    Background Fasciolosis, due to Fasciola hepatica and Fasciola gigantica, is a re-emerging zoonotic parasitic disease of worldwide importance. Human and animal infections are commonly diagnosed by the traditional sedimentation and faecal egg-counting technique. However, this technique is time-consuming and prone to sensitivity errors when a large number of samples must be processed or if the operator lacks sufficient experience. Additionally, diagnosis can only be made once the 12-week pre-patent period has passed. Recently, a commercially available coprological antigen ELISA has enabled detection of F. hepatica prior to the completion of the pre-patent period, providing earlier diagnosis and increased throughput, although species differentiation is not possible in areas of parasite sympatry. Real-time PCR offers the combined benefits of highly sensitive species differentiation for medium to large sample sizes. However, no molecular diagnostic workflow currently exists for the identification of Fasciola spp. in faecal samples. Methodology/Principal findings A new molecular diagnostic workflow for the highly-sensitive detection and quantification of Fasciola spp. in faecal samples was developed. The technique involves sedimenting and pelleting the samples prior to DNA isolation in order to concentrate the eggs, followed by disruption by bead-beating in a benchtop homogeniser to ensure access to DNA. Although both the new molecular workflow and the traditional sedimentation technique were sensitive and specific, the new molecular workflow enabled faster sample throughput in medium to large epidemiological studies, and provided the additional benefit of speciation. Further, good correlation (R2 = 0.74–0.76) was observed between the real-time PCR values and the faecal egg count (FEC) using the new molecular workflow for all herds and sampling periods. Finally, no effect of storage in 70% ethanol was detected on sedimentation and DNA isolation outcomes; enabling

  9. Scrambled eggs: A highly sensitive molecular diagnostic workflow for Fasciola species specific detection from faecal samples.

    Science.gov (United States)

    Calvani, Nichola Eliza Davies; Windsor, Peter Andrew; Bush, Russell David; Šlapeta, Jan

    2017-09-01

    Fasciolosis, due to Fasciola hepatica and Fasciola gigantica, is a re-emerging zoonotic parasitic disease of worldwide importance. Human and animal infections are commonly diagnosed by the traditional sedimentation and faecal egg-counting technique. However, this technique is time-consuming and prone to sensitivity errors when a large number of samples must be processed or if the operator lacks sufficient experience. Additionally, diagnosis can only be made once the 12-week pre-patent period has passed. Recently, a commercially available coprological antigen ELISA has enabled detection of F. hepatica prior to the completion of the pre-patent period, providing earlier diagnosis and increased throughput, although species differentiation is not possible in areas of parasite sympatry. Real-time PCR offers the combined benefits of highly sensitive species differentiation for medium to large sample sizes. However, no molecular diagnostic workflow currently exists for the identification of Fasciola spp. in faecal samples. A new molecular diagnostic workflow for the highly-sensitive detection and quantification of Fasciola spp. in faecal samples was developed. The technique involves sedimenting and pelleting the samples prior to DNA isolation in order to concentrate the eggs, followed by disruption by bead-beating in a benchtop homogeniser to ensure access to DNA. Although both the new molecular workflow and the traditional sedimentation technique were sensitive and specific, the new molecular workflow enabled faster sample throughput in medium to large epidemiological studies, and provided the additional benefit of speciation. Further, good correlation (R2 = 0.74-0.76) was observed between the real-time PCR values and the faecal egg count (FEC) using the new molecular workflow for all herds and sampling periods. Finally, no effect of storage in 70% ethanol was detected on sedimentation and DNA isolation outcomes; enabling transport of samples from endemic to non

  10. Prevalence of Endoparasites in Faecal Samples of Cracids Bred in Captivity at the Parque Dois Irmãos, Recife, Pernambuco, Brazil

    Directory of Open Access Journals (Sweden)

    A. L. B. Cunha

    2008-01-01

    Full Text Available Among the many problems arising from poor sanitation that can affect wild birds maintained in captivity, parasitic afflictions are among the most frequent, and their effects can range from subclinical infections to death. Some of the most common cases involve endoparasites, principally if the species under consideration exists at a high population density. This being so, the aim of the current work was to report on the prevalence of endoparasites in faecal samples from cracids (curassows and allies bred in captivity at the Parque Dois Irmãos, Recife, Pernambuco state in Brazil. To do this, faecal and sand samples were collected from the enclosures of birds of the family Cracidae belonging to the collection from the Parque Dois Irmãos, which originated from private collections from the Metropolitan Region and Forest Zone of the State of Pernambuco. Four lots of faecal and sand samples were collected over a 60-day period, giving a total of 84 faecal samples from 58 individuals of 21 species of cracids. The material collected was submitted for coproparasitological tests using the right method and spontaneous sedimentation. The results obtained were positive for Strongyloides sp., Ascaridia sp., Capillaria sp. and cysts of Entamoeba coli, as well as eggs belonging to the superfamily Strongyloidea.

  11. Faecal carriage of Staphylococcus aureus in the hospital and community setting: a systematic review

    Directory of Open Access Journals (Sweden)

    Shantelle eClaassen-Weitz

    2016-05-01

    Full Text Available Background and rationale: Staphylococcus aureus faecal carriage has been identified as a potential source for nosocomial transmission and a risk factor for disease development. This systematic review determined the overall S. aureus (including methicillin susceptible and resistant S. aureus (MSSA and MRSA faecal carriage rates within the community and healthcare settings.Methodology: Peer-reviewed articles indexed in Medline, Scopus, Academic Search Premier, Africa-Wide Information, CINAHL, and Web of Science were identified using applicable and controlled vocabulary through to 11 November 2015. Eligible studies were ascertained by three independent reviewers. Random-effects meta-analyses of proportions were performed to determine S. aureus, MSSA and MRSA faecal carriage rates reported by eligible studies.Results: Twenty six studies were included in this review. The pooled estimates for S. aureus, MSSA and MRSA faecal carriage were 26 % (95 % confidence interval (CI: 16.8 % - 36.3 %, 86 % (95 % confidence interval (CI: 65.9 % - 97.9 % and 10 % (95 % CI: 0.7 % - 27.0 %, respectively. Faecal S. aureus carriage rates increased on average from 10 % to 65 % during the first eight weeks of life, followed by an average carriage rate of 64 % at six months and 46 % at one year of life. Genotyping techniques were employed mainly in studies conducted in developed countries and comprised largely of gel-based techniques. Six studies reported on the role of S. aureus faecal strains in diarrhoea (n = 2 and the risk for acquiring infections (n = 4. Eight of the 26 studies included in this review performed antibiotic susceptibility testing of S. aureus faecal isolates.Conclusion: This study provides evidence that screening for S. aureus faecal carriage, at least in populations at high risk, could be an effective measure for the prevention of S. aureus transmission and infection in the healthcare and community setting. More well-structured studies need to be

  12. Droplet digital PCR improves absolute quantification of viable lactic acid bacteria in faecal samples.

    Science.gov (United States)

    Gobert, Guillaume; Cotillard, Aurélie; Fourmestraux, Candice; Pruvost, Laurence; Miguet, Jean; Boyer, Mickaël

    2018-03-14

    Analysing correlations between the observed health effects of ingested probiotics and their survival in digestive tract allows adapting their preparations for food. Tracking ingested probiotic in faecal samples requires accurate and specific tools to quantify live vs dead cells at strain level. Traditional culture-based methods are simpler to use but they do not allow quantifying viable but non-cultivable (VBNC) cells and they are poorly discriminant below the species level. We have set up a viable PCR (vPCR) assay combining propidium monoazide (PMA) treatment and either real time quantitative PCR (qPCR) or droplet digital PCR (ddPCR) to quantify a Lactobacillus rhamnosus and two Lactobacillus paracasei subsp. paracasei strains in piglet faeces. Adjustments of the PMA treatment conditions and reduction of the faecal sample size were necessary to obtain accurate discrimination between dead and live cells. The study also revealed differences of PMA efficiency among the two L. paracasei strains. Both PCR methods were able to specifically quantify each strain and provided comparable total bacterial counts. However, quantification of lower numbers of viable cells was best achieved with ddPCR, which was characterized by a reduced lower limit of quantification (improvement of up to 1.76 log 10 compared to qPCR). All three strains were able to survive in the piglets' gut with viability losses between 0.78 and 1.59 log 10 /g faeces. This study shows the applicability of PMA-ddPCR to specific quantification of small numbers of viable bacterial cells in the presence of an important background of unwanted microorganisms, and without the need to set up standard curves. It also illustrates the need to adapt PMA protocols according to the final matrix and target strain, even for closely related strains. The PMA-ddPCR approach provides a new tool to quantify bacterial survival in faecal samples from a preclinical and clinical trial. Copyright © 2018 The Authors. Published by

  13. Enhancing faecal sludge management in peri-urban areas of Lusaka through faecal sludge valorisation: challenges and opportunities

    Science.gov (United States)

    Tembo, J. M.; Nyirenda, E.; Nyambe, I.

    2017-03-01

    Lusaka, the capital city of Zambia, has two million inhabitants with 70% residing in peri-urban areas. Ninety (90) % of this population employ pit latrines for excretion generating approximately 22,680 tons of faecal sludge per annum. This sludge is inadequately managed hence of the generated amount, over 60% remains within the residential environment thereby compromising both the environment and public health. To foster a solution to this problem, a study was commissioned to assess faecal sludge valorisation potential and how it would impact on Faecal Sludge Management. The study evaluated policy, institutional and regulatory frameworks, sanitation practices including latrine construction and usage aspects and also characterised the faecal sludge for selected parameters relevant to valorisation. Four peri-urban areas were adopted as study sites. Policy issues together with existing institutional and regulatory frameworks were assessed through literature review. Sanitation practices were evaluated through physical observations, focus group discussions, interviews and questionnaire administration. Faecal sludge characterisation was through sampling and analysis. It was observed that there are policy gaps in fostering faecal sludge valorisation. Sanitation practices and latrines construction also do not favour valorisation. The quality of the raw sludge has potential for valorisation though again, some parameters like solid waste content require drastic changes in sanitation practices in order not to compromise the reuse potential of the sludge. It was concluded that if faecal sludge management is to be enhanced through valorisation, there is need to have policies promoting pit latrine faecal sludge reuse and strengthened regulatory and institutional frameworks in this respect.

  14. Use of real-time PCR on faecal samples for detection of sub-clinical Salmonella infection in cattle did not improve the detection sensitivity compared to conventional bacteriology

    DEFF Research Database (Denmark)

    Jensen, Annette Nygaard; Nielsen, L.R.; Baggesen, Dorte Lau

    2013-01-01

    bacteriological culture-reference method (BCRM) on cattle faecal samples for detection of sub-clinical Salmonella infections in cattle. Thirty faecal samples were artificially contaminated with either 10 or 50CFU of one of five strains of S. Dublin (SD) and S. Typhimurium (ST). The overall detection sensitivity...... of both rt-PCR and BCRM was 100% for ST and 78% for SD. Furthermore, 163 faecal samples from cattle herds with suspected Salmonella infection were tested to compare the relative performance of rt-PCR to BCRM on samples from naturally infected herds. The relative sensitivity of rt-PCR was 20% (3/15 BCRM...... positive samples) while the relative specificity and accuracy was 99% and 92%, respectively. Both methods had limitations for detecting low levels of SD (...

  15. Mycobacterium ulcerans DNA not detected in faecal samples from Buruli ulcer patients: results of a pilot study.

    Directory of Open Access Journals (Sweden)

    Fred S Sarfo

    Full Text Available It has recently been shown that in a Buruli ulcer (BU endemic region of southeastern Australia, significant numbers of possums (native tree-dwelling marsupials have clinical BU disease. Furthermore, based on quantitative PCR (qPCR analysis, animals with BU lesions (and some without shed M. ulcerans DNA in their faeces, indicative of bacterial loads of up to 10(8 organisms/gram. These findings led us to propose that humans might also harbour M. ulcerans in their gastrointestinal tract and shed the bacterium in their faeces. We conducted a pilot study and collected faecal swabs from 26 patients with confirmed BU and 31 healthy household controls. Faecal samples were also collected from 10 healthy controls from non-endemic regions in Ghana. All 67 specimens were negative when tested by IS2404 PCR. The detection sensitivity of this method was ≥10(4 bacteria per gram (wet-weight of human faecal material. We conclude that the human gastrointestinal tract is unlikely to be a significant reservoir of M. ulcerans.

  16. Rapid Salmonella detection in experimentally inoculated equine faecal and veterinary hospital environmental samples using commercially available lateral flow immunoassays.

    Science.gov (United States)

    Burgess, B A; Noyes, N R; Bolte, D S; Hyatt, D R; van Metre, D C; Morley, P S

    2015-01-01

    Salmonella enterica is the most commonly reported cause of outbreaks of nosocomial infections in large animal veterinary teaching hospitals and the closure of equine hospitals. Rapid detection may facilitate effective control practices in equine populations. Shipping and laboratory testing typically require ≥48 h to obtain results. Lateral flow immunoassays developed for use in food-safety microbiology provide an alternative that has not been evaluated for use with faeces or environmental samples. We aimed to identify enrichment methods that would allow commercially available rapid Salmonella detection systems (lateral flow immunoassays) to be used in clinical practice with equine faecal and environmental samples, providing test results in 18-24 h. In vitro experiment. Equine faecal and environmental samples were inoculated with known quantities of S. enterica serotype Typhimurium and cultured using 2 different enrichment techniques for faeces and 4 enrichment techniques for environmental samples. Samples were tested blindly using 2 different lateral flow immunoassays and plated on agar media for confirmatory testing. In general, commercial lateral flow immunoassays resulted in fewer false-negative test results with enrichment of 1 g faecal samples in tetrathionate for 18 h, while all environmental sample enrichment techniques resulted in similar detection rates. The limit of detection from spiked samples, ∼4 colony-forming units/g, was similar for all methods evaluated. The lateral flow immunoassays evaluated could reliably detect S. enterica within 18 h, indicating that they may be useful for rapid point-of-care testing in equine practice applications. Additional evaluation is needed using samples from naturally infected cases and the environment to gain an accurate estimate of test sensitivity and specificity and to substantiate further the true value of these tests in clinical practice. © 2014 EVJ Ltd.

  17. Faecal Campylobacter shedding among dogs in animal shelters across Texas.

    Science.gov (United States)

    Leahy, A M; Cummings, K J; Rodriguez-Rivera, L D; Hamer, S A; Lawhon, S D

    2017-12-01

    Epidemiologic studies on faecal Campylobacter shedding among dogs in the United States have been limited, despite evidence that the incidence of human campylobacteriosis has increased over the last decade. Our objectives were to estimate the prevalence of faecal Campylobacter shedding among shelter dogs in Texas, to estimate the specific prevalence of Campylobacter jejuni and Campylobacter coli shedding, and to identify risk factors for Campylobacter-positive status. Using a cross-sectional study design, we collected faecal samples from dogs in six animal shelters across Texas between May and December, 2014. Quantitative PCR protocols were used to detect Campylobacter in samples and to specifically identify C. jejuni and C. coli. The prevalence of faecal Campylobacter shedding among sampled dogs was 75.7% (140/185). Prevalence varied significantly by shelter (p = .03), ranging from 57% to 93%. There was a marginal association (p = .06) between abnormal faecal consistency and positive Campylobacter status, after controlling for shelter as a random effect. However, approximately 70% of Campylobacter-positive dogs had grossly normal faeces. Campylobacter prevalence did not vary significantly by age group or sex. The prevalence of C. jejuni-positive samples was 5.4% (10/185), but C. coli was not detected in any samples. Dogs are a potential source of zoonotic Campylobacter transmission. © 2017 Blackwell Verlag GmbH.

  18. Sewage reflects the distribution of human faecal Lachnospiraceae

    Science.gov (United States)

    McLellan, Sandra L.; Newton, Ryan J.; Vandewalle, Jessica L.; Shanks, Orin C.; Huse, Susan M.; Eren, A. Murat; Sogin, Mitchell L.

    2014-01-01

    Summary Faecal pollution contains a rich and diverse community of bacteria derived from animals and humans, many of which might serve as alternatives to the traditional enterococci and Escherichia coli faecal indicators. We used massively parallel sequencing (MPS) of the 16S rRNA gene to characterize microbial communities from wastewater treatment plant (WWTP) influent sewage from 12 cities geographically distributed across the USA. We examined members of the Clostridiales, which included the families Clostridiaceae, Lachnospiraceae and Ruminococcaceae for their potential as sewage indicators. Lachnospiraceae was one of the most abundant groups of faecal bacteria in sewage, and several Lachnospiraceae high-abundance sewage pyrotags occurred in at least 46 of 48 human faecal samples. Clone libraries targeting Clostridium coccoides (C. coccoides) in sewage samples demonstrated that Lachnospiraceae-annotated V6 pyrotags encompassed the previously reported C. coccoides group. We used oligotyping to profile the genus Blautia within Lachnospiraceae and found oligotypes comprised of 24 entropy components that showed patterns of host specificity. These findings suggest that indicators based on Blautia might have the capacity to discriminate between different faecal pollution sources. Development of source-specific alternative indicators would enhance water quality assessments, which leads to improved ecosystem health and reduced human health risk due to waterborne disease. PMID:23438335

  19. Parasitology and urban livestock farming in Nigeria : prevalence of ova in faecal and soil samples and animal ectoparasites in Makurdi

    Directory of Open Access Journals (Sweden)

    E.A. Omudu

    2007-05-01

    Full Text Available Domestic environmental pollution resulting from urban livestock farming was investigated in Makurdi using parasitological techniques. The test tube flotation technique was used for the parasitological analysis of animal faecal matter and soil samples collected from residential premises. Ectoparasitic fauna of dogs, goats, sheep and cattle cohabiting with humans within the same residential compound were also collected and identified. The hand-picking and body brushing methods were employed to search for ticks, fleas, lice and mites. Of the 150 soil samples examined, 55 (36.7 % were positive for 1 or more eggs of helminth parasites. There was no significant difference in the distribution of eggs in the soil samples from the 3 areas sampled (c2=0.046, df=2, P>0.05. Ascaris species were the dominant parasite eggs found. Of the 180 faecal samples examined, 107 (59.4 % were positive for 1 or more eggs of helminth parasites. Chi-square analysis showed no significant difference in the level of infection of different animal faeces sampled (c2=5.74, df=4, P>0.05. Ascaris species were again the dominating helminth parasite eggs found. There was also no significant difference in the prevalence of helminth eggs in the animal faecal samples from the 3 areas sampled (c2=5.99, df=4, P>0.05. A total of 1908 ectoparasites was recovered (ticks: 32.80 %; lice: 22.43 %; fleas: 22.06% and mite: 22.69 %. There was no significant difference in infestation animals between sexes (c2=0.10, df=4, P>0.05. The predominant genus encountered for ticks were Amblyomma, while Linognathus (43.90%, Ctenocephalides (97.38% and Sarcoptes (58.89 % were most predominant for lice, fleas and mites respectively. The public health implications of the findings, especially as these relate to the increasing incidence and prevalence of zoonotic infections, are discussed.

  20. Evaluation of two automated enzyme-immunoassays for detection of thermophilic campylobacters in faecal samples from cattle and swine

    DEFF Research Database (Denmark)

    Hoorfar, Jeffrey; Nielsen, E.M.; Stryhn, H.

    1999-01-01

    We evaluated the performance of two enzyme-immunoassays (EIA) for the detection of naturally occurring, thermophilic Campylobacter spp. found in faecal samples from cattle (n = 21 and n = 26) and swine (n = 43) relative to the standard culture method, and also assuming that none of the tests...

  1. Microbial population analysis improves the evidential value of faecal traces in forensic investigations.

    Science.gov (United States)

    Quaak, Frederike C A; de Graaf, Mei-Lan M; Weterings, Rob; Kuiper, Irene

    2017-01-01

    The forensic science community has a growing interest in microbial population analysis, especially the microbial populations found inside and on the human body. Both their high abundance, microbes outnumber human cells by a factor 10, and their diversity, different sites of the human body harbour different microbial communities, make them an interesting tool for forensics. Faecal material is a type of trace evidence which can be found in a variety of criminal cases, but is often being ignored in forensic investigations. Deriving a human short tandem repeat (STR) profile from a faecal sample can be challenging. However, the microbial communities within faecal material can be of additional criminalistic value in linking a faecal trace to the possible donor. We present a microarray technique in which the faecal microbial community is used to differentiate between faecal samples and developed a decision model to predict the possible common origin of questioned samples. The results show that this technique may be a useful additional tool when no or only partial human STR profiles can be generated.

  2. Longitudinal prevalence and faecal shedding of Chlamydia pecorum in sheep.

    Science.gov (United States)

    Yang, Rongchang; Jacobson, Caroline; Gardner, Graham; Carmichael, Ian; Campbell, Angus J D; Ryan, Una

    2014-09-01

    The prevalence and faecal shedding of Chlamydia spp. in sheep in Australia has not been well described. Two species-specific quantitative PCRs (qPCRs) targeting the chlamydial outer membrane protein cell surface antigen gene (ompA) were validated and used to determine the prevalence and faecal shedding of C. abortus and C. pecorum from faecal samples of lambs at three sampling times (weaning, post-weaning and pre-slaughter) from eight farms in South Australia, New South Wales, Victoria and Western Australia. A total of 3412 faecal samples were collected and screened from approximately 1189 lambs across the four states. C. abortus was not detected in any of the samples screened. The overall prevalence of C. pecorum was 1027/3412 (30.1%) and median bacterial concentrations at weaning, post-weaning and pre-slaughter were 1.8 × 10(7), 1.2 × 10(7) and 9.6 × 10(5)/g faeces, respectively. A subset of C. pecorum positive samples from each farm, (n = 48) was sequenced to confirm their identity. The present study demonstrates that C. pecorum is prevalent in Australian sheep, highlighting a need for further research on the impact of this bacterium on production. Copyright © 2014 Elsevier Ltd. All rights reserved.

  3. Examination of anonymous canine faecal samples provides data on endoparasite prevalence rates in dogs for comparative studies.

    Science.gov (United States)

    Hinney, Barbara; Gottwald, Michaela; Moser, Jasmine; Reicher, Bianca; Schäfer, Bhavapriya Jasmin; Schaper, Roland; Joachim, Anja; Künzel, Frank

    2017-10-15

    Several endoparasites of dogs cannot only be detrimental to their primary host but might also represent a threat to human health because of their zoonotic potential. Due to their high dog population densities, metropolitan areas can be highly endemic for such parasites. We aimed to estimate the prevalence of endoparasites in dogs in the Austrian capital of Vienna by examining a representative number of canine faecal samples and to compare the prevalences with two neighbouring peri-urban and rural regions. In addition we analysed whether the density of dog populations and cleanliness of dog zones correlated with parasite occurrence. We collected 1001 anonymous faecal samples from 55 dog zones from all 23 districts of the federal state of Vienna, as well as 480 faecal samples from the Mödling district and Wolkersdorf with a peri-urban and rural character, respectively. Faeces were examined by flotation and by Baermann technique. Additionally we evaluated 292 Viennese, 102 peri-urban and 50 rural samples for Giardia and Cryptosporidium by GiardiaFASTest ® and CryptoFASTest ® . Samples from "clean" dog zones were compared to samples from "dirty" zones. The infection rate of Toxocara was surprisingly low, ranging from 0.6% to 1.9%. Trichuris was the most frequent helminth (1.8-7.5%) and Giardia the most frequent protozoan (4.0-10.8%). Ancylostomatidae, Crenosoma, Capillaria, Taeniidae, Cystoisospora and Sarcocystis were found in 1.8-2.2%, 0-0.9%, 0-0.9%, 0-0.6%, 0.3-3.1% and 0-0.6% of the samples, respectively. Samples from "dirty" dog zones in Vienna showed a significantly higher rate of parasites overall (p=0.003) and of Trichuris (p=0.048) compared to samples from "clean" dog zones. There were no statistically significant differences in densely vs. less densely populated areas of Vienna. Samples from the rural region of Wolkersdorf had significantly higher overall parasite, Trichuris and Cystoisospora prevalences than the peri-urban Mödling district and Vienna (p

  4. Assessment of reagent effectiveness and preservation methods for equine faecal samples

    Directory of Open Access Journals (Sweden)

    Eva Vavrouchova

    2015-03-01

    Full Text Available The aim of our study was to identify the most suitable flotation solution and effective preservation method for the examination of equine faeces samples using the FLOTAC technique. Samples from naturally infected horses were transported to the laboratory andanalysed accordingly. The sample from each horse was homogenized and divided into four parts: one was frozen, another two were preserved in different reagents such as sodium acetate-acetic-acid–formalin (SAF or 5% formalin.The last part was examined as a fresh sample in three different flotation solutions (Sheather´s solution, sodium chloride and sodium nitrate solution, all with a specific gravity 1.200. The preserved samples were examined in the period from 14 to21days after collection. According to our results, the sucrose solution was the most suitable flotation solution for fresh samples (small strongyle egg per gram was 706 compared to 360 in sodium chlorid and 507 in sodium nitrate and the sodium nitrate solution was the most efficient for the preserved samples (egg per gram was 382 compared to 295 in salt solution and 305 in sucrose solution. Freezing appears to be the most effective method of sample preservation, resulting in minimal damage to fragile strongyle eggs and therefore it is the most simple and effective preservation method for the examination of large numbers of faecal samples without the necessity of examining them all within 48 hours of collection. Deep freezing as a preservation method for equine faeces samples has not, according to our knowledge, been yet published.

  5. Interpreting faecal analysis results for monitoring exposure to uranium

    International Nuclear Information System (INIS)

    Berard, P.; Rongier, E.; Faure, M.L.; Auriol, B.; Estrabaud, M.; Mazeyrat, C.

    1996-01-01

    Radiotoxicological monitoring of workers exposed to non-transferable forms of uranium requires six-monthly examinations. These examinations are prescribed according to the kind of product manipulated and tO the industrial risk attached to the workplace. The range of examinations that are useful for this kind of monitoring includes whole body counting examinations, urine analyses and in-line faecal sampling: whole body examinations, which are fundamental to monitoring, provide a lung retention value. However, the detection limit of lung examinations is not low enough for chronic operational monitoring; urine examinations are extremely sensitive to alpha activity (1 mBq per isotope) but the fraction detected in the urine after incorporation by inhalation is very small; in-line 24-hour faecal sampling allows avoiding any workplace exclusion. The authors intend to present their experience acquired over a six year period in the field of systematic faecal examinations after chronic inhalation of the different uranium compounds. They also present results of a study carried out to determine normal uranium concentrations in the faeces of a non-exposed population, the uranium content in drinking waters and the consequences on faecal excretion. Establishing the isotopic content of uranium in the faeces makes it possible to determine practical investigation levels for occupational monitoring. Even if faecal sampling may be critically perceived by the personnel, the authors' experience highlights the value of this kind of analysis which allows to track down the industrial reality of the exposure. Internal dosimetry calculations cannot, however, be carried out, because the physical parameters of the inhaled aerosols are not always known. (author)

  6. Identifying avian sources of faecal contamination using sterol analysis.

    Science.gov (United States)

    Devane, Megan L; Wood, David; Chappell, Andrew; Robson, Beth; Webster-Brown, Jenny; Gilpin, Brent J

    2015-10-01

    Discrimination of the source of faecal pollution in water bodies is an important step in the assessment and mitigation of public health risk. One tool for faecal source tracking is the analysis of faecal sterols which are present in faeces of animals in a range of distinctive ratios. Published ratios are able to discriminate between human and herbivore mammal faecal inputs but are of less value for identifying pollution from wildfowl, which can be a common cause of elevated bacterial indicators in rivers and streams. In this study, the sterol profiles of 50 avian-derived faecal specimens (seagulls, ducks and chickens) were examined alongside those of 57 ruminant faeces and previously published sterol profiles of human wastewater, chicken effluent and animal meatwork effluent. Two novel sterol ratios were identified as specific to avian faecal scats, which, when incorporated into a decision tree with human and herbivore mammal indicative ratios, were able to identify sterols from avian-polluted waterways. For samples where the sterol profile was not consistent with herbivore mammal or human pollution, avian pollution is indicated when the ratio of 24-ethylcholestanol/(24-ethylcholestanol + 24-ethylcoprostanol + 24-ethylepicoprostanol) is ≥0.4 (avian ratio 1) and the ratio of cholestanol/(cholestanol + coprostanol + epicoprostanol) is ≥0.5 (avian ratio 2). When avian pollution is indicated, further confirmation by targeted PCR specific markers can be employed if greater confidence in the pollution source is required. A 66% concordance between sterol ratios and current avian PCR markers was achieved when 56 water samples from polluted waterways were analysed.

  7. Seroprevalence and genotype of Chlamydia in pet parrots in China.

    Science.gov (United States)

    Zhang, N-Z; Zhang, X-X; Zhou, D-H; Huang, S-Y; Tian, W-P; Yang, Y-C; Zhao, Q; Zhu, X-Q

    2015-01-01

    Parrots are one of the most popular pet birds in China, and can harbour Chlamydia which has significance for human and animal health. We investigated, by indirect haemagglutination assay, the seroprevalence of Chlamydia infection in four species of parrots, namely budgerigars (Melopsittacus undulatus), lovebirds (Agapornis sp.), cockatiels (Nymphicus hollandicus) and Alexandrine parakeets (Psittacula eupatria) that were collected from Weifang and Beijing cities, North China and explored the association between potential risk factors and chlamydial seropositivity. We further determined the genotype of Chlamydia in 21 fresh faecal samples based on the ompA sequence by reconstruction of phylogenetic relationships. Of the 311 parrots examined, 35·37% (95% confidence interval 30·06-40·68) were seropositive, and species, gender, age, season and geographical location were identified as risk factors. Two PCR-positive samples represented Chlamydia psittaci genotype A. The occurrence of C. psittaci genotype A in the droppings of two pet parrots in China suggests potential environmental contamination with Chlamydiaceae and may raise a public health concern.

  8. Scrambled eggs: A highly sensitive molecular diagnostic workflow for Fasciola species specific detection from faecal samples

    OpenAIRE

    Calvani, Nichola Eliza Davies; Windsor, Peter Andrew; Bush, Russell David; Šlapeta, Jan

    2017-01-01

    Background Fasciolosis, due to Fasciola hepatica and Fasciola gigantica, is a re-emerging zoonotic parasitic disease of worldwide importance. Human and animal infections are commonly diagnosed by the traditional sedimentation and faecal egg-counting technique. However, this technique is time-consuming and prone to sensitivity errors when a large number of samples must be processed or if the operator lacks sufficient experience. Additionally, diagnosis can only be made once the 12-week pre-pat...

  9. Estimation of endogenous faecal calcium in buffalo (BOS bubalis) by isotope dilution technique

    International Nuclear Information System (INIS)

    Singh, S.; Sareen, V.K.; Marwaha, S.R.; Sekhon, B.; Bhatia, I.S.

    1973-01-01

    Detailed investigations on the isotope-dilution technique for the estimation of endogenous faecal calcium were conducted with buffalo calves fed on growing ration. The ration consisted of wheat straw, green lucerne and concentrate mix. The endogenous faecal calcium was 3.71 g/day, which is 17.8 percent of the total faecal calcium. The apparent and true digestibilities of Ca were calculated as 51 and 60 percent respectively. The endogenous faecal calcium can be estimated in buffalo calves by giving single subcutaneous injection of Ca 45 and collecting blood samples on 12th and 21st days only, and representative sample from the faeces collected from 13th through 22nd day after the injection. (author)

  10. Faecal excretion of brush border membrane enzymes in patients with clostridium difficile diarrhoea

    Directory of Open Access Journals (Sweden)

    Katyal R

    2002-01-01

    Full Text Available PURPOSE: To look for the presence of intestinal brush border membrane (BBM enzymes in the faecal samples of patients with Clostridium difficile association. METHODS: One hundred faecal samples were investigated for C.difficile toxin (CDT. Simultaneous assays for faecal excretion of intestinal BBM enzymes viz., disaccharidases, alkaline phosphatase (AP and leucine aminopeptidase (LAP were also done. RESULTS: C.difficile toxin was detected in 25 (25% of the samples with a titre ranging from 10 to 160. No significant difference (p>0.05 was seen between the CDT positive and negative groups with any of the disaccharidases studied. However, significant increase (pC.difficile diarrhoea.

  11. Pattern of faecal 20-oxopregnane and oestrogen concentrations during pregnancy in wild plains zebra mares.

    Science.gov (United States)

    Ncube, Hlengisizwe; Duncan, Patrick; Grange, Sophie; Cameron, Elissa Z; Barnier, Florian; Ganswindt, Andre

    2011-07-01

    Regulative endocrine mechanisms influence the reproductive behaviour and success of mammals, but they have been studied predominantly in domestic and captive animals. The study aims at describing the pattern of faecal 20-oxopregnane and oestrogen concentrations during pregnancy in wild plains zebra Equus quagga chapmani. Data were collected during wet and dry seasons 2007-2009. Enzyme Immunoassays were used to determine 20-oxopregnane and oestrogen concentrations in faecal samples (n=74) collected from individual mares (n=32) whose dates of foaling were known through long-term monitoring. Hormonal profiles were described with a General Additive Model (GAM: Hormone ∼ Days to Foaling). Faecal 20-oxopregnanes have a complex cycle during pregnancy (GAM, n=70, R(2)=0.616, p200 ng/g DW) of faecal 20-oxopregnanes associated with high (>160 ng/g DW) faecal oestrogen levels indicate mid-pregnancy in c.90% of cases (16/17). High faecal 20-oxopregnanes (>200 ng/g DW) and low faecal oestrogen levels (<160 ng/g DW) indicate late pregnancy, again in c.90% of cases. Two faecal samples would allow the stage of pregnancy to be determined with confidence. Copyright © 2011 Elsevier Inc. All rights reserved.

  12. Use of Sequenom sample ID Plus® SNP genotyping in identification of FFPE tumor samples.

    Directory of Open Access Journals (Sweden)

    Jessica K Miller

    Full Text Available Short tandem repeat (STR analysis, such as the AmpFlSTR® Identifiler® Plus kit, is a standard, PCR-based human genotyping method used in the field of forensics. Misidentification of cell line and tissue DNA can be costly if not detected early; therefore it is necessary to have quality control measures such as STR profiling in place. A major issue in large-scale research studies involving archival formalin-fixed paraffin embedded (FFPE tissues is that varying levels of DNA degradation can result in failure to correctly identify samples using STR genotyping. PCR amplification of STRs of several hundred base pairs is not always possible when DNA is degraded. The Sample ID Plus® panel from Sequenom allows for human DNA identification and authentication using SNP genotyping. In comparison to lengthy STR amplicons, this multiplexing PCR assay requires amplification of only 76-139 base pairs, and utilizes 47 SNPs to discriminate between individual samples. In this study, we evaluated both STR and SNP genotyping methods of sample identification, with a focus on paired FFPE tumor/normal DNA samples intended for next-generation sequencing (NGS. The ability to successfully validate the identity of FFPE samples can enable cost savings by reducing rework.

  13. Detection of picobirnavirus and rotavirus in diarrhoeic faecal samples of cattle and buffalo calves in Mumbai metropolis, Western India

    Directory of Open Access Journals (Sweden)

    Anjan Mondal

    2013-12-01

    Full Text Available In this study 113 diarrhoeic faecal samples obtained from buffalo (n = 68 and cattle (n = 45 calves under 1 years of age were analysed in order to determine the presence of rotavirus infection and the frequency of picobirnavirus excretion. Eleven (9.73% samples positive for group A rotavirus were identified through RNA-polyacrylamide gel electrophoresis (RNA-PAGE, while 4 (3.53% samples showed a bisegmented genome with a typical picobirnavirus pattern. This is the first report of picobirnavirus in cattle and buffalo calves from Western India.

  14. Evaluation of culture methods for rapid screening of swine faecal samples for Yersinia enterocolitica O : 3 biotype 4

    DEFF Research Database (Denmark)

    Hoorfar, Jeffrey; Holmvig, C.B.F.

    1999-01-01

    In two studies, seven different culture protocols were compared to test naturally contaminated faecal samples from pigs for isolation of Y. enterocolitica serotype O; 3/biotype 4( n = 70 and n = 79). Four of the protocols were based on the Nordic Committee on Food Analysis (NMKL protocols), while...... indicate possibilities of shortening the culture methods by replacing most of the biochemical tests with an agglutination test based on a monoclonal antibody....

  15. Cystic fibrosis transmembrane conductance regulator (CFTR allelic variants relate to shifts in faecal microbiota of cystic fibrosis patients.

    Directory of Open Access Journals (Sweden)

    Serena Schippa

    Full Text Available INTRODUCTION: In this study we investigated the effects of the Cystic Fibrosis Transmembrane conductance Regulator (CFTR gene variants on the composition of faecal microbiota, in patients affected by Cystic Fibrosis (CF. CFTR mutations (F508del is the most common lead to a decreased secretion of chloride/water, and to mucus sticky secretions, in pancreas, respiratory and gastrointestinal tracts. Intestinal manifestations are underestimated in CF, leading to ileum meconium at birth, or small bowel bacterial overgrowth in adult age. METHODS: Thirty-six CF patients, fasting and under no-antibiotic treatment, were CFTR genotyped on both alleles. Faecal samples were subjected to molecular microbial profiling through Temporal Temperature Gradient Electrophoresis and species-specific PCR. Ecological parameters and multivariate algorithms were employed to find out if CFTR variants could be related to the microbiota structure. RESULTS: Patients were classified by two different criteria: 1 presence/absence of F508del mutation; 2 disease severity in heterozygous and homozygous F508del patients. We found that homozygous-F508del and severe CF patients exhibited an enhanced dysbiotic faecal microbiota composition, even within the CF cohort itself, with higher biodiversity and evenness. We also found, by species-specific PCR, that potentially harmful species (Escherichia coli and Eubacterium biforme were abundant in homozygous-F508del and severe CF patients, while beneficial species (Faecalibacterium prausnitzii, Bifidobacterium spp., and Eubacterium limosum were reduced. CONCLUSIONS: This is the first report that establishes a link among CFTR variants and shifts in faecal microbiota, opening the way to studies that perceive CF as a 'systemic disease', linking the lung and the gut in a joined axis.

  16. Cystic fibrosis transmembrane conductance regulator (CFTR) allelic variants relate to shifts in faecal microbiota of cystic fibrosis patients.

    Science.gov (United States)

    Schippa, Serena; Iebba, Valerio; Santangelo, Floriana; Gagliardi, Antonella; De Biase, Riccardo Valerio; Stamato, Antonella; Bertasi, Serenella; Lucarelli, Marco; Conte, Maria Pia; Quattrucci, Serena

    2013-01-01

    In this study we investigated the effects of the Cystic Fibrosis Transmembrane conductance Regulator (CFTR) gene variants on the composition of faecal microbiota, in patients affected by Cystic Fibrosis (CF). CFTR mutations (F508del is the most common) lead to a decreased secretion of chloride/water, and to mucus sticky secretions, in pancreas, respiratory and gastrointestinal tracts. Intestinal manifestations are underestimated in CF, leading to ileum meconium at birth, or small bowel bacterial overgrowth in adult age. Thirty-six CF patients, fasting and under no-antibiotic treatment, were CFTR genotyped on both alleles. Faecal samples were subjected to molecular microbial profiling through Temporal Temperature Gradient Electrophoresis and species-specific PCR. Ecological parameters and multivariate algorithms were employed to find out if CFTR variants could be related to the microbiota structure. Patients were classified by two different criteria: 1) presence/absence of F508del mutation; 2) disease severity in heterozygous and homozygous F508del patients. We found that homozygous-F508del and severe CF patients exhibited an enhanced dysbiotic faecal microbiota composition, even within the CF cohort itself, with higher biodiversity and evenness. We also found, by species-specific PCR, that potentially harmful species (Escherichia coli and Eubacterium biforme) were abundant in homozygous-F508del and severe CF patients, while beneficial species (Faecalibacterium prausnitzii, Bifidobacterium spp., and Eubacterium limosum) were reduced. This is the first report that establishes a link among CFTR variants and shifts in faecal microbiota, opening the way to studies that perceive CF as a 'systemic disease', linking the lung and the gut in a joined axis.

  17. Genotyping of Toxoplasma Gondii Isolates from Soil Samples in Tehran, Iran

    Directory of Open Access Journals (Sweden)

    M Tavalla

    2013-06-01

    Full Text Available Background: The protozoan parasite Toxoplasma gondii can infect any warm blooded nucleated cells. One of the ways for human infection is ingestion of oocysts directly from soil or via infected fruits or vegetables. To survey the potential role of T. gondii oocyst in soil samples, the present study was conducted in Tehran City, Iran.Methods: A total of 150 soil samples were collected around rubbish dumps, children's play ground, parks and public places. Oocysts recovery was performed by sodium nitrate flotation method on soil samples. For molecular detection, PCR reaction targeting B1 gene was performed and then, the posi­tive results were confirmed using repetitive 529 bp DNA fragment in other PCR reaction. Finally, the positive samples were genotyped at the SAG2 locus.Results: Toxoplasma DNA was found in 13 soil samples. After genotyping and RFLP analysis in SAG2 locus, nine positive samples were revealed type III, one positive sample was type I whereas three samples revealed mixed infection (type, I & III.Conclusion: The predominant genotype in Tehran soil samples is type III.

  18. Occurrence and genotype characterization of Giardia duodenalis in goat kids from the Canary Islands, Spain.

    Science.gov (United States)

    Ruiz, Antonio; Foronda, Pilar; González, Jorge F; Guedes, Aránzazu; Abreu-Acosta, Néstor; Molina, José M; Valladares, Basilio

    2008-06-14

    Giardia duodenalis (syn. Giardia lamblia, Giardia intestinalis) is a wide-spread intestinal protozoa of both humans and animals. Although giardiosis in goat is commonly asymptomatic, young kids may bear an enteric disease associated with persistent diarrhoea and delayed weight gain. In the present study we have analysed the occurrence of Giardia in 315 young goat kids (2-6 months old) from Gran Canaria Island (Spain) through visualization of faecal cysts. The identification of genotypes of G. duodenalis among the farms was attained by nested PCR of the triophosphate isomerase (TPI) and single PCR of beta-giardin genes and subsequent sequencing. Positive samples were found in 42.2% of the animals and 95.5% of the farms. Goat faecal specimens were positive for only livestock-associated G. duodenalis assemblage E genotype for both TPI and beta-giardin genes. The genetic analysis of these two loci revealed the presence of different haplotypes among the farms included in the survey and high homology with homologous genes from cattle and sheep. Altogether, the data presented here provide additional information to the prevalence and genetic characterization of Giardia isolates. The absence of assemblages A and B in this study suggests that zoonotic transmission of Giardia from goats could be of low epidemiological significance, although these findings should be validated in studies including other geographical areas, age groups and larger number of samples.

  19. Assessing radiocaesium bioavailability in birds separation of urates from faecal pellets

    Energy Technology Data Exchange (ETDEWEB)

    Clapp, J.; Beresford, N.A [Centre for Ecology and Hydrology, Lancaster, Environment Centre, Lancaster (United Kingdom)

    2004-07-01

    Concomitant analyses of urine and faeces present a methodology whereby the bioavailability of dietary radionuclides can be estimated. Whilst the collection of urine from most wild animals is impractical, birds excrete urine in a semi-solid state making field collection possible. In birds the end product of nitrogen metabolism is uric acid which is combined with albumin, calcium and potassium cations as a laminated sphere 0.5 to 15 {mu}m in size. Urate spheres are passed as a colloidal suspension in a proteinaceous fluid composed predominantly of water, albumin and electrolytes giving the characteristic white dollop' to avian guano. Some herbivorous bird species (e.g. Lagopus spp.) excrete comparatively dry-pelleted guano with distinct urate (white) and faecal (brown) components. These are readily separable as they form the predominant constituents of the opposite ends of the cylindrically shaped pellet. This raises the hypothesis that the separation and analyses of the faecal and urate component of herbivorous bird pellets presents a possible methodology to estimate the bioavailability of ingested radionuclides (i.e. as the apparent absorption coefficient). Preliminary sampling and analyses determined that the radiocaesium content of the urate component of Lagopus spp. guano was consistently higher than the faecal tip. The results of a field sampling programme to test this hypothesis are discussed. Lagopus Lagopus scoticus (Red grouse) guano (separated into urate and faecal components), Calluna vulgaris (predominant dietary component of L. lagopus) and soil samples were collected over a period one year from an upland area in northern England. Comparison of the urate to faecal radiocaesium activity concentrations is used to investigate potential changes in the dietary radiocaesium of L. lagopus throughout the year. (author)

  20. Assessing radiocaesium bioavailability in birds separation of urates from faecal pellets

    International Nuclear Information System (INIS)

    Clapp, J.; Beresford, N.A

    2004-01-01

    Concomitant analyses of urine and faeces present a methodology whereby the bioavailability of dietary radionuclides can be estimated. Whilst the collection of urine from most wild animals is impractical, birds excrete urine in a semi-solid state making field collection possible. In birds the end product of nitrogen metabolism is uric acid which is combined with albumin, calcium and potassium cations as a laminated sphere 0.5 to 15 μm in size. Urate spheres are passed as a colloidal suspension in a proteinaceous fluid composed predominantly of water, albumin and electrolytes giving the characteristic white dollop' to avian guano. Some herbivorous bird species (e.g. Lagopus spp.) excrete comparatively dry-pelleted guano with distinct urate (white) and faecal (brown) components. These are readily separable as they form the predominant constituents of the opposite ends of the cylindrically shaped pellet. This raises the hypothesis that the separation and analyses of the faecal and urate component of herbivorous bird pellets presents a possible methodology to estimate the bioavailability of ingested radionuclides (i.e. as the apparent absorption coefficient). Preliminary sampling and analyses determined that the radiocaesium content of the urate component of Lagopus spp. guano was consistently higher than the faecal tip. The results of a field sampling programme to test this hypothesis are discussed. Lagopus Lagopus scoticus (Red grouse) guano (separated into urate and faecal components), Calluna vulgaris (predominant dietary component of L. lagopus) and soil samples were collected over a period one year from an upland area in northern England. Comparison of the urate to faecal radiocaesium activity concentrations is used to investigate potential changes in the dietary radiocaesium of L. lagopus throughout the year. (author)

  1. Rectal motility after sacral nerve stimulation for faecal incontinence

    DEFF Research Database (Denmark)

    Michelsen, H B; Worsøe, J; Krogh, K

    2010-01-01

    Sacral nerve stimulation (SNS) is effective against faecal incontinence, but the mode of action is obscure. The aim of this study was to describe the effects of SNS on fasting and postprandial rectal motility. Sixteen patients, 14 women age 33-73 (mean 58), with faecal incontinence of various...... contractions, total time with cyclic rectal contractions, the number of aborally and orally propagating contractions, the number of anal sampling reflexes or rectal wall tension during contractions. Postprandial changes in rectal tone were significantly reduced during SNS (P

  2. Interpretation of serum antibody response to Anoplocephala perfoliata in relation to parasite burden and faecal egg count

    DEFF Research Database (Denmark)

    Kjaer, L.N.; Lungholt, M.M.; Nielsen, M.K.

    2007-01-01

    of development and gross pathological mucosal lesions were recorded and compared with serum antibody responses and faecal egg counts. Faecal egg counts were determined in samples from A. perfoliata infected horses using a semi-quantitative centrifugation/flotation technique. Blood samples collected at slaughter...

  3. Prevalence of faecal incontinence in community-dwelling older people in Bali, Indonesia.

    Science.gov (United States)

    Suyasa, I Gede Putu Darma; Xiao, Lily Dongxia; Lynn, Penelope Ann; Skuza, Pawel Piotr; Paterson, Jan

    2015-06-01

    To explore the prevalence rate of faecal incontinence in community-dwelling older people, associated factors, impact on quality of life and practices in managing faecal incontinence. Using a cross-sectional design, 600 older people aged 60+ were randomly selected from a population of 2916 in Bali, Indonesia using a simple random sampling technique. Three hundred and three participants were interviewed (response rate 51%). The prevalence of faecal incontinence was 22.4% (95% confidence interval (CI) 18.0-26.8). Self-reported constipation (odds ratio (OR) 3.68, 95% CI 1.87-7.24) and loose stools (OR 2.66, 95% CI 1.47-4.78) were significantly associated with faecal incontinence. There was a strong positive correlation between total bowel control score and total quality-of-life score (P Bali. © 2014 ACOTA.

  4. Faecal microbiota transplantation

    DEFF Research Database (Denmark)

    Jørgensen, Simon M D; Hansen, Mette Mejlby; Erikstrup, Christian

    2017-01-01

    BACKGROUND: Faecal microbiota transplantation (FMT) is currently being established as a second-line treatment for recurrent Clostridium difficile infection. FMT is further being considered for other infectious and inflammatory conditions. Safe and reproducible methods for donor screening, laborat......BACKGROUND: Faecal microbiota transplantation (FMT) is currently being established as a second-line treatment for recurrent Clostridium difficile infection. FMT is further being considered for other infectious and inflammatory conditions. Safe and reproducible methods for donor screening...

  5. Occurrence of faecal contamination in households along the US-Mexico border.

    Science.gov (United States)

    Carrasco, L; Mena, K D; Mota, L C; Ortiz, M; Behravesh, C B; Gibbs, S G; Bristol, J R; Mayberry, L; Cardenas, V M

    2008-06-01

    The study aim was to determine the presence of total and faecal coliforms on kitchen surfaces, in tap water and on the hands of caregivers in households on both sides of the US-Mexico border. Samples were collected in 135 randomly selected households in Ciudad Juarez, Mexico, and El Paso, Texas. Different surfaces throughout the kitchen and head of households' hands were sampled using sterile cotton swabs moistened in D/E neutralizing solution. Sponge/dishcloth and drinking water samples were also obtained. Total and faecal coliforms were enumerated on m-Endo LES and mFC respectively. Total coliforms and Escherichia coli in drinking water samples were enumerated in accordance with the Quanti-Tray method. Sponge/dishcloth samples were the most commonly contaminated kitchen sites, followed by countertops and cutting boards. We recovered faecal coliforms from 14% of the hands of child caregivers, and this indicator was moderately associated with self-reported failure to wash hands after using the toilet (OR = 3.2; 95% CI: 0.9, 11.1). Hand washing should continue to be emphasized, and additional interventions should be directed to specific kitchen areas, such as sponges/dishcloths, tables/countertops and cutting boards. There is a need for additional interventions regarding kitchen sanitation.

  6. CMV genotyping using different samples in post renal transplant recipients with CMV disease

    Directory of Open Access Journals (Sweden)

    Ramya Barani

    2017-10-01

    Full Text Available CMV is the most common viral infection which occurs in post renal transplant recipients (PTR. There are four different gB genotypes (gB1 to gB4 which exist in CMV. Studies have reported that mixed infection with different genotypes will cause severe clinical manifestations as well as co-infection with other herpesvirus including Epstein-Barr virus (EBV [1]. CMV can cause compartmentalized disease involving different organs with different genotypes. There are reports in immuno compromised individuals with different genotypes [2, 3]. Institutional ethics committee approval was obtained prior to conduct of the study (IEC-NI/08/DEC/07/46. Whole blood, saliva and urine were collected from PTR. DNA were extracted (Qiagen DNA mini kit and CMV quantitative PCR targeting ppUL83 gene was performed with CMV R-gene™ using an ABI 7900 Fast real time PCR (SDS Version: 2.4. PTR who had high viral load (>1000 copies/ml in any three or two samples were included for CMV genotyping PCR targeting gB region (410-bp [2]. DNA sequencing was performed in ABI 3730 GA platform by Sanger method and sequences were analyzed by reference strains. A total of 24 samples were collected from 9 PTR. Among these four PTR had high viral load in all three samples (whole blood, urine & saliva and those with high viral load (n=5 in 2 samples (Whole blood & urine/saliva were screened for CMV genotyping. Majority of the strains belonged to genotype B1 and only one PTR was infected with genotype B2 in three samples. In PTR with genotype B1, gastro intestinal infection (GI was predominantly found in 78% (n=7 followed by graft dysfunction (GDF in 56% (n=5 of the PTR. PTR who detected with genotype B2 was associated with fever, leukopenia (CMV syndrome, GDF and also found with EBV infection. Co-infection with EBV was observed in 44% (n=4; VZV and HSV type 1 was also observed. Genotypes are associated with the severity of the disease and co-infection with other herpes virus infections. In

  7. Comparative phenotypic and genotypic analyses of Salmonella Rissen that originated from food animals in Thailand and United States.

    Science.gov (United States)

    Pornsukarom, S; Patchanee, P; Erdman, M; Cray, P F; Wittum, T; Lee, J; Gebreyes, W A

    2015-03-01

    Salmonella enterica serovar Rissen has been recognized as one of the most common serovar among humans and pork production systems in different parts of the world, especially Asia. In the United States, this serovar caused outbreaks but its epidemiologic significance remains unknown. The objectives of this study were to compare the phenotypic (antimicrobial susceptibility) and genotypic attributes of Salmonella Rissen isolated in Thailand (Thai) and the United States (US). All the Thai isolates (n = 30) were recovered from swine faecal samples. The US isolates (n = 35) were recovered from swine faecal samples (n = 29), cattle (n = 2), chicken (n = 2), dog (n = 1) and a ready-to-eat product (n = 1). The antimicrobial susceptibility of isolates was determined using the Kirby-Bauer disk diffusion method with a panel of 12 antimicrobials. Pulse-field gel electrophoresis (PFGE) was used to determine the genotypic diversity of isolates. All Thai isolates showed multidrug resistance (MDR) with the most frequent antibiotic resistance shown against ampicillin (100%), sulfisoxazole (96.7%), tetracycline (93.3%), streptomycin (90%) and chloramphenicol (30%). About half of the isolates of USA origin were pan-susceptible and roughly 30% were resistant to only tetracycline (R-type: Te). Salmonella Rissen isolated from Thailand and the USA in this study were found to be clonally unrelated. Genotypic analyses indicated that isolates were clustered primarily based on the geographic origin implying the limited clonality among the strains. Clonal relatedness among different host species within the same geography (USA) was found. We found genotypic similarity in Thai and US isolates in few instances but with no epidemiological link. Further studies to assess propensity for increased inter-regional transmission and dissemination is warranted. © 2014 Blackwell Verlag GmbH.

  8. Cost-effectiveness of one versus two sample faecal immunochemical testing for colorectal cancer screening.

    Science.gov (United States)

    Goede, S Lucas; van Roon, Aafke H C; Reijerink, Jacqueline C I Y; van Vuuren, Anneke J; Lansdorp-Vogelaar, Iris; Habbema, J Dik F; Kuipers, Ernst J; van Leerdam, Monique E; van Ballegooijen, Marjolein

    2013-05-01

    The sensitivity and specificity of a single faecal immunochemical test (FIT) are limited. The performance of FIT screening can be improved by increasing the screening frequency or by providing more than one sample in each screening round. This study aimed to evaluate if two-sample FIT screening is cost-effective compared with one-sample FIT. The MISCAN-colon microsimulation model was used to estimate costs and benefits of strategies with either one or two-sample FIT screening. The FIT cut-off level varied between 50 and 200 ng haemoglobin/ml, and the screening schedule was varied with respect to age range and interval. In addition, different definitions for positivity of the two-sample FIT were considered: at least one positive sample, two positive samples, or the mean of both samples being positive. Within an exemplary screening strategy, biennial FIT from the age of 55-75 years, one-sample FIT provided 76.0-97.0 life-years gained (LYG) per 1000 individuals, at a cost of € 259,000-264,000 (range reflects different FIT cut-off levels). Two-sample FIT screening with at least one sample being positive provided 7.3-12.4 additional LYG compared with one-sample FIT at an extra cost of € 50,000-59,000. However, when all screening intervals and age ranges were considered, intensifying screening with one-sample FIT provided equal or more LYG at lower costs compared with two-sample FIT. If attendance to screening does not differ between strategies it is recommended to increase the number of screening rounds with one-sample FIT screening, before considering increasing the number of FIT samples provided per screening round.

  9. Whole-genome comparison of urinary pathogenic Escherichia coli and faecal isolates of UTI patients and healthy controls

    DEFF Research Database (Denmark)

    Nielsen, Karen Leth; Stegger, Marc; Kiil, Kristoffer

    2017-01-01

    The faecal flora is a common reservoir for urinary tract infection (UTI), and Escherichia coli (E. coli) is frequently found in this reservoir without causing extraintestinal infection. We investigated these E. coli reservoirs by whole-genome sequencing a large collection of E. coli from healthy...... controls (faecal), who had never previously had UTI, and from UTI patients (faecal and urinary) sampled from the same geographical area. We compared MLST types, phylogenetic relationship, accessory genome content and FimH type between patient and control faecal isolates as well as between UTI and faecal......-only isolates, respectively. Comparison of the accessory genome of UTI isolates to faecal isolates revealed 35 gene families which were significantly more prevalent in the UTI isolates compared to the faecal isolates, although none of these were unique to one of the two groups. Of these 35, 22 belonged...

  10. Development and Use of a Real-Time Quantitative PCR Method for Detecting and Quantifying Equol-Producing Bacteria in Human Faecal Samples and Slurry Cultures

    Directory of Open Access Journals (Sweden)

    Lucía Vázquez

    2017-06-01

    Full Text Available This work introduces a novel real-time quantitative PCR (qPCR protocol for detecting and quantifying equol-producing bacteria. To this end, two sets of primers targeting the dihydrodaidzein reductase (ddr and tetrahydrodaidzein reductase (tdr genes, which are involved in the synthesis of equol, were designed. The primers showed high specificity and sensitivity when used to examine DNA from control bacteria, such as Slackia isoflavoniconvertens, Slackia equolifaciens, Asaccharobacter celatus, Adlercreutzia equolifaciens, and Enterorhabdus mucosicola. To demonstrate the validity and reliability of the protocol, it was used to detect and quantify equol-producing bacteria in human faecal samples and their derived slurry cultures. These samples were provided by 18 menopausal women under treatment of menopause symptoms with a soy isoflavone concentrate, among whom three were known to be equol-producers given the prior detection of the molecule in their urine. The tdr gene was detected in the faeces of all these equol-producing women at about 4–5 log10 copies per gram of faeces. In contrast, the ddr gene was only amplified in the faecal samples of two of these three women, suggesting the presence in the non-amplified sample of reductase genes unrelated to those known to be involved in equol formation and used for primer design in this study. When tdr and ddr were present in the same sample, similar copy numbers of the two genes were recorded. However, no significant increase in the copy number of equol-related genes along isoflavone treatment was observed. Surprisingly, positive amplification for both tdr and ddr genes was obtained in faecal samples and derived slurry cultures from two non-equol producing women, suggesting the genes could be non-functional or the daidzein metabolized to other compounds in samples from these two women. This novel qPCR tool provides a technique for monitoring gut microbes that produce equol in humans. Monitoring equol

  11. Monitoring bacterial faecal contamination in waters using multiplex ...

    African Journals Online (AJOL)

    Monitoring of sanitary quality or faecal pollution in water is currently based on quantifying some bacterial indicators such as Escherichia coli and faecal enterococci. Using a multiplex real-time PCR assay for faecal enterococci and Bacteroides spp., the detection of faecal contamination in non-treated water can be done in a ...

  12. Evaluation of a high resolution genotyping method for Chlamydia trachomatis using routine clinical samples.

    Directory of Open Access Journals (Sweden)

    Yibing Wang

    2011-02-01

    Full Text Available Genital chlamydia infection is the most commonly diagnosed sexually transmitted infection in the UK. C. trachomatis genital infections are usually caused by strains which fall into two pathovars: lymphogranuloma venereum (LGV and the genitourinary genotypes D-K. Although these genotypes can be discriminated by outer membrane protein gene (ompA sequencing or multi-locus sequence typing (MLST, neither protocol affords the high-resolution genotyping required for local epidemiology and accurate contact-tracing.We evaluated variable number tandem repeat (VNTR and ompA sequencing (now called multi-locus VNTR analysis and ompA or "MLVA-ompA" to study local epidemiology in Southampton over a period of six months. One hundred and fifty seven endocervical swabs that tested positive for C. trachomatis from both the Southampton genitourinary medicine (GUM clinic and local GP surgeries were tested by COBAS Taqman 48 (Roche PCR for the presence of C. trachomatis. Samples tested as positive by the commercial NAATs test were genotyped, where possible, by a MLVA-ompA sequencing technique. Attempts were made to isolate C. trachomatis from all 157 samples in cell culture, and 68 (43% were successfully recovered by repeatable passage in culture. Of the 157 samples, 93 (i.e. 59% were fully genotyped by MLVA-ompA. Only one mixed infection (E & D in a single sample was confirmed. There were two distinct D genotypes for the ompA gene. Most frequent ompA genotypes were D, E and F, comprising 20%, 41% and 16% of the type-able samples respectively. Within all genotypes we detected numerous MLVA sub-types.Amongst the common genotypes, there are a significant number of defined MLVA sub-types, which may reflect particular background demographics including age group, geography, high-risk sexual behavior, and sexual networks.

  13. High Prevalence of Faecal Carriage of ESBL-Producing Enterobacteriaceae among Children in Dar es Salaam, Tanzania.

    Science.gov (United States)

    Tellevik, Marit G; Blomberg, Bjørn; Kommedal, Øyvind; Maselle, Samuel Y; Langeland, Nina; Moyo, Sabrina J

    2016-01-01

    Faecal carriage of ESBL-producing bacteria is a potential risk for transmission and infection. Little is known about faecal carriage of antibiotic resistance in Tanzania. This study aimed to investigate the prevalence of faecal carriage of ESBL-producing Enterobacteriaceae and to identify risk factors for carriage among young children in Tanzania. From August 2010 to July 2011, children below 2 years of age were recruited in Dar es Salaam, including healthy community children (n = 250) and children hospitalized due to diarrhoea (n = 250) or other diseases (n = 103). ChromID ESBL agar and ChromID CARBA SMART agar were used for screening. Antimicrobial susceptibility testing was performed by the disk diffusion method. ESBL genotypes were identified by Real-Time PCR and sequencing. The overall prevalence of ESBL carriage was 34.3% (207/ 603). The prevalence of ESBL carriage was significantly higher among hospitalized children (50.4%), compared to community children (11.6%; P Enterobacteriaceae among children below 2 years of age in Tanzania, particularly those with HIV-infection. Resistance to a majority of the available antimicrobials commonly used for children in Tanzania leaves few treatment options for infections when caused by these bacteria.

  14. Subclinical laminitis and its association with pO2 and faecal alterations: Isikli, Aydin experience

    Directory of Open Access Journals (Sweden)

    Ibrahim Akin

    2015-05-01

    Full Text Available ABSTRACT Objective. The aim of this field trial was to investigate the relationships among subclinical laminitis, hematological, ruminal and faecal alterations. Materials and Methods. To this extent dairy cows presenting subclinical laminitis (n=11 and to those of other healthy cows without laminitis (n=10 were enrolled and assigned into two groups. All animals were receiving the same daily ration formulated to contain 47% cornsilage and 18% hay, mainly. Effects of subclinical laminitis challenges on measurements of feces, and blood samples, were investigated to determine which of these measurements may aid in the diagnosis. pH changes in ruminal fluid collected via rumenocentesis were measured. Besides the following parameters were also measured; blood pH, faecal pH and faecal scoring. Blinded investigators performed the sample collection. Results. No statistical differences between the groups were detected for blood gas values studied regarding pCO2, HCO3, BE, indeed mean that pO2 values decreased statistically (p<0.05 and faecal pH was significantly decreased (p<0.05 in cows with subclinical laminitis in contrast to healthy controls. Conclusions. pO2 values and faecal pH may be valuable as indirect indicators of subclinical laminitis in cattle.

  15. A standardised faecal collection protocol for intestinal helminth egg counts in Asian elephants, Elephas maximus

    Directory of Open Access Journals (Sweden)

    Carly L. Lynsdale

    2015-12-01

    Full Text Available The quantitative assessment of parasite infection is necessary to measure, manage and reduce infection risk in both wild and captive animal populations. Traditional faecal flotation methods which aim to quantify parasite burden, such as the McMaster egg counting technique, are widely used in veterinary medicine, agricultural management and wildlife parasitology. Although many modifications to the McMaster method exist, few account for systematic variation in parasite egg output which may lead to inaccurate estimations of infection intensity through faecal egg counts (FEC. To adapt the McMaster method for use in sampling Asian elephants (Elephas maximus, we tested a number of possible sources of error regarding faecal sampling, focussing on helminth eggs and using a population of over 120 semi-captive elephants distributed across northern Myanmar. These included time of day of defecation, effects of storage in 10% formalin and 10% formol saline and variation in egg distribution between and within faecal boluses. We found no significant difference in the distribution of helminth eggs within faecal matter or for different defecation times, however, storage in formol saline and formalin significantly decreased egg recovery. This is the first study to analyse several collection and storage aspects of a widely-used traditional parasitology method for helminth parasites of E. maximus using known host individuals. We suggest that for the modified McMaster technique, a minimum of one fresh sample per elephant collected from any freshly produced bolus in the total faecal matter and at any point within a 7.5 h time period (7.30am–2.55 pm will consistently represent parasite load. This study defines a protocol which may be used to test pre-analytic factors and effectively determine infection load in species which produce large quantities of vegetative faeces, such as non-ruminant megaherbivores.

  16. Development of real-time PCR and hybridization methods for detection and identification of thermophilic Campylobacter spp. in pig faecal samples

    DEFF Research Database (Denmark)

    Jensen, Annette Nygaard; Andersen, M. T.; Dalsgaard, Anders

    2005-01-01

    species-specific detection of Campylobacter spp. in naturally infected pig faecal samples after an enrichment step, whereas the hybridization approach enhanced the specific isolation of C. jejuni (present in minority to C. coli) from pigs. Conclusions: The rt-PCR was specific for Campylobacter jejuni, C...... by phenotypic methods and the developed rt-PCR provides an easy and fast method for such differentiation. Detection of C. jejuni by colony hybridization may increase the isolation rate of this species from pig faeces....

  17. Extraction of DNA from Forensic Biological Samples for Genotyping.

    Science.gov (United States)

    Stray, J E; Liu, J Y; Brevnov, M G; Shewale, J G

    2010-07-01

    Biological forensic samples constitute evidence with probative organic matter. Evidence believed to contain DNA is typically processed for extraction and purification of its nucleic acid content. Forensic DNA samples are composed of two things, a tissue and the substrate it resides on. Compositionally, a sample may contain almost anything and for each, the type, integrity, and content of both tissue and substrate will vary, as will the contaminant levels. This fact makes the success of extraction one of the most unpredictable steps in genotypic analysis. The development of robust genotyping systems and analysis platforms for short tandem repeat (STR) and mitochondrial DNA sequencing and the acceptance of results generated by these methods in the court system, resulted in a high demand for DNA testing. The increasing variety of sample submissions created a need to isolate DNA from forensic samples that may be compromised or contain low levels of biological material. In the past decade, several robust chemistries and isolation methods have been developed to safely and reliably recover DNA from a wide array of sample types in high yield and free of PCR inhibitors. In addition, high-throughput automated workflows have been developed to meet the demand for processing increasing numbers of samples. This review summarizes a number of the most widely adopted methods and the best practices for DNA isolation from forensic biological samples, including manual, semiautomated, and fully automated platforms. Copyright © 2010 Central Police University.

  18. Intracommunity relationships, dispersal pattern and paternity success in a wild living community of Bonobos (Pan paniscus) determined from DNA analysis of faecal samples.

    Science.gov (United States)

    Gerloff, U; Hartung, B; Fruth, B; Hohmann, G; Tautz, D

    1999-06-07

    Differences in social relationships among community members are often explained by differences in genetic relationships. The current techniques of DNA analysis allow explicit testing of such a hypothesis. Here, we have analysed the genetic relationships for a community of wild bonobos (Pan paniscus) using nuclear and mitochondrial DNA markers extracted from faecal samples. Bonobos show an opportunistic and promiscuous mating behaviour, even with mates from outside the community. Nonetheless, we find that most infants were sired by resident males and that two dominant males together attained the highest paternity success. Intriguingly, the latter males are the sons of high-ranking females, suggesting an important influence of mothers on the paternity success of their sons. The molecular data support previous inferences on female dispersal and male philopatry. We find a total of five different mitochondrial haplotypes among 15 adult females, suggesting a frequent migration of females. Moreover, for most adult and subadult males in the group we find a matching mother, while this is not the case for most females, indicating that these leave the community during adolescence. Our study demonstrates that faecal samples can be a useful source for the determination of kinship in a whole community.

  19. Otter Lutra lutra movements assessed by genotyped spraints in southern Italy

    Directory of Open Access Journals (Sweden)

    Claudio Prigioni

    2006-09-01

    Full Text Available Abstract
    This paper analyses some otter (Lutra lutra spatial data, obtained by the location of genetically typed spraints in the Pollino national park and surrounding areas (southern Italy. A sample of 214 otter spraints was collected (27 faeces in 2001-02 and 187 in 2004 along 10 streams of the park, and their location was digitalized by a Geographic Information System (Arcview 3.1 for spatial analysis. DNA was extracted using the GuSCN/silica method and each faecal sample was genotyped by PCR amplification of twelve microsatellite loci. Finally, 103 (48.1% spraints yielded a reliable genotype, providing the identification of 31 otters. The maximum distance, measured along watercourses between the genotyped faecal samples of each individual identified by at least two faeces, varied from 0.02 to 34.8 km. On the whole, our results outlined a ranging pattern based on the occupation by one otter of a long stretch of watercourse (21.6 and 34.8 km, including 4-6 partially overlapped short stretches (from 0.02 to 14.1 km occupied by as many animals. RIASSUNTO – Spostamenti della Lontra Lutra lutra valutati mediante analisi genetica delle feci in Italia meridionale. Tramite l’estrazione del DNA da feci “fresche” e la succes- siva amplificazione di 12 loci microsatellite, da un campione di 214 feci di Lontra raccolto lungo 10 corsi idrici del Parco Nazionale del Pollino e aree limitrofe (27 feci nel 2001-02 e 187 nel 2004 sono stati ottenuti 103 genotipi affidabili (48,1%, consentendo l’identifi- cazione di 31 individui. La localizzazione delle feci genotipizzate è stata stabilita mediante GPS (Global Positioning System e trasferita su una mappa digitalizzata (scala 1:10000 tramite GIS (Geographic Information System. La distanza massima, misurata lungo i corsi idrici investigati, tra i campioni fecali tipizzati di ciascun individuo è variata da 0,02 a 34,8 km. Nel complesso, i risultati ottenuti hanno

  20. Faecal analysis suggests generalist diets in three species of ...

    African Journals Online (AJOL)

    The overlap in other arthropod taxa ingested was low across species and seasons, suggesting an opportunistic component to their foraging behaviour. We distinguished plant matter in faecal samples of all species in all seasons, reflecting either voluntary or accidental ingestion. The results of this study suggest that the ...

  1. Plasma and faecal testosterone and estradiol in chicken

    International Nuclear Information System (INIS)

    Mekchay, S.; Apichartsrungkoon, T.; Pongpiachan, P.

    1996-01-01

    Identification of sex in some kind of fowls can not be done by using their external appearances. Sex steroid hormone levels may be used as an indicator of sexual dimorphism in birds. The objective of this investigation was to measure plasma and faecal testosterone and estradiol concentrations in 8 male and 15 female chickens by using radioimmunoassay (RIA) technique. The relationship between plasma and faecal testosterone, and plasma and faecal estradiol are positively correlated. The correlation coefficients (r 2 ) between plasma and faecal steroids concentration were 0.621 (p<0.05) for testosterone and 0.692 (p<0.05) for estradiol. The average plasma and faecal sex steroid concentrations in male and female chickens were 10.05 ± 1.97 ng/ml and 511.50 ± 95.89 ng/g (for male testosterone), 24.85 ± 1.60 pg/ml and 49.65 ± 6.01 ng/g (for male estradiol), 0.79 ± 0.05 ng/ml and 134.20 ± 14.70 ng/ml (for female testosterone), 129.91 ± 19.30 pg/ml and 334.80 ± 15.62 ng/g (for female estradiol), respectively. Plasma and faecal testosterone and estradiol levels in male and female chickens are significant difference (p<0.01, p<0.01, p<0.001 and p<0.001 respectively). The results of this investigation suggested that plasma or faecal sex steroid concentrations can be used to discriminate sex of chicken which is show the possibility to use the plasma or faecal sex steroids for identification of sex in other bird species

  2. Antimicrobial resistance in the Bacteroides fragilis group in faecal samples from patients receiving broad-spectrum antibiotics

    DEFF Research Database (Denmark)

    Møller Hansen, Kia Cirkeline; Ferløv-Schwensen, Simon Andreas; Henriksen, Daniel Pilsgaard

    2017-01-01

    Members of the Bacteroides fragilis group are opportunistic pathogens and cause severe infections including bacteraemia. As increased levels of antimicrobial resistance in B. fragilis group bacteria can be detected years after administration of specific antibiotics, monitoring antimicrobial...... susceptibility in the gut microbiota could be important. The objectives of this study were to 1) investigate the distribution of species and the occurrence of reduced antimicrobial susceptibility in the B. fragilis group from patients treated at departments with a high level of antibiotic use, 2) to determine...... the prevalence of the carbapenem resistance gene cfiA in B. fragilis in this patient group, and 3) to determine the association between previous antibiotic treatment and reduced susceptibility to clindamycin, meropenem, metronidazole, and piperacillin-tazobactam. Consecutive faecal samples (n = 197) were...

  3. Faecal incontinence in rural and regional northern Queensland community-dwelling adults.

    Science.gov (United States)

    Bartlett, Lynne M; Nowak, Madeleine J; Ho, Yikhong

    2013-01-01

    In Australia, faecal incontinence, the involuntary loss of liquid or solid stool with or without a person's awareness, has been reported in 8% of the South Australian and 11% of the urban New South Wales community-dwelling populations. Studies conducted in 2004 and 2005 reported faecal incontinence in more than 20% of colorectal and urogynaecological clinic patients at Townsville Hospital (a referral centre serving rural North Queensland). This prompted concern regarding the level of faecal incontinence in the community. The aim of this study was to investigate the prevalence of faecal incontinence in the North and Far North Queensland urban and rural communities. The sample size was based on the New South Wales postal surveys (11% prevalence). Higher rates were expected in North/Far North Queensland, so prevalence there was estimated at 12.1% (confidence interval ± 2%, ie the true level to be between 10.1% and 14.1%). The sample for each of the Townsville, Cairns (in Far North Queensland) and rural/remote settings was calculated at 1022. The database for the present study was compiled using a systematic randomised process selecting two private names from each column on each page of the Cairns and Townsville White Pages® (Cairns: 1112 urban, 481 rural, 226 remote; Townsville: 1049 urban, 432 rural, 320 remote). The questionnaire covered personal demographics, health/risk factors, bowel habits, nutrition (fibre and fluid intake) and physical activity. Faecal incontinence was defined as accidental leakage of solid or liquid stool in the past 12 months that was not caused by a virus, medication or contaminated food. To improve the response rate a participation incentive of a chance to win a $250 voucher or one of ten $50 vouchers was offered in the initial mail-out. The initial survey was mailed out in July 2007; two follow-up surveys were mailed out to non-responders in September 2007 and January 2008. One hundred randomly selected non-responders were telephoned in

  4. Hepatitis C virus genotyping of organ donor samples to aid in transplantation of HCV-positive organs.

    Science.gov (United States)

    Gentile, Caren; Van Deerlin, Vivianna M; Goldberg, David S; Reese, Peter P; Hasz, Richard D; Abt, Peter; Blumberg, Emily; Farooqi, Midhat S

    2018-02-01

    Given the availability of new highly efficacious anti-HCV therapies, some clinicians have advocated for wider use of kidneys from hepatitis C virus-positive (HCV+) donors, including transplanting them into HCV-negative recipients. As treatment regimens for HCV are commonly guided by genotype, pretransplant HCV genotyping of tissue donors would be beneficial. To our knowledge, donor HCV genotyping has never been reported. We retrieved archived frozen plasma samples for 17 previous organ donors through a local organ procurement organization. We performed HCV genotyping using the eSensor HCVg Direct Test (GenMark Diagnostics) and also by Sanger sequencing, for confirmation (Retrogen). In addition, viral loads were measured using the COBAS AmpliPrep/TaqMan system (Roche Diagnostics). We found that most of the samples (n = 14) were HCV Genotype 1a with the remainder being Genotype 2b (n = 1) or Genotype 3 (n = 2). All genotyping results were concordant with Sanger sequencing. The average HCV viral load in the sample group was ~ 1.6 million IU/mL (range: ~16 000 IU/mL to 7 million IU/mL). We demonstrate that viral RNA from organ donor plasma can be successfully genotyped for HCV. This ability suggests that transplantation of HCV+ kidneys into HCV-negative recipients, followed by genotype-guided antiviral therapy, could be feasible. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  5. Whole-genome comparison of urinary pathogenic Escherichia coli and faecal isolates of UTI patients and healthy controls.

    Science.gov (United States)

    Nielsen, Karen Leth; Stegger, Marc; Kiil, Kristoffer; Godfrey, Paul A; Feldgarden, Michael; Lilje, Berit; Andersen, Paal S; Frimodt-Møller, Niels

    2017-12-01

    The faecal flora is a common reservoir for urinary tract infection (UTI), and Escherichia coli (E. coli) is frequently found in this reservoir without causing extraintestinal infection. We investigated these E. coli reservoirs by whole-genome sequencing a large collection of E. coli from healthy controls (faecal), who had never previously had UTI, and from UTI patients (faecal and urinary) sampled from the same geographical area. We compared MLST types, phylogenetic relationship, accessory genome content and FimH type between patient and control faecal isolates as well as between UTI and faecal-only isolates, respectively. Comparison of the accessory genome of UTI isolates to faecal isolates revealed 35 gene families which were significantly more prevalent in the UTI isolates compared to the faecal isolates, although none of these were unique to one of the two groups. Of these 35, 22 belonged to a genomic island and three putatively belonged to a type VI secretion system (T6SS). MLST types and SNP phylogeny indicated no clustering of the UTI or faecal E. coli from patients distinct from the control faecal isolates, although there was an overrepresentation of UTI isolates belonging to clonal lineages CC73 and CC12. One combination of mutations in FimH, N70S/S78N, was significantly associated to UTI, while phylogenetic analysis of FimH and fimH identified no signs of distinct adaptation of UTI isolates compared to faecal-only isolates not causing UTI. In summary, the results showed that (i) healthy women who had never previously had UTI carried faecal E. coli which were overall closely related to UTI and faecal isolates from UTI patients; (ii) UTI isolates do not cluster separately from faecal-only isolates based on SNP analysis; and (iii) 22 gene families of a genomic island, putative T6SS proteins as well as specific metabolism and virulence associated proteins were significantly more common in UTI isolates compared to faecal-only isolates and (iv) evolution of fim

  6. Diet, faecal pH and colorectal cancer

    NARCIS (Netherlands)

    Dokkum, W. van; Boer, B.C.J. de; Faassen, A. van; Pikaar, N.A.; Hermus, R.J.J.

    1983-01-01

    We suggest that a lower faecal pH may be correlated with a lower mortality of large-bowel cancer and that faecal pH should always be considered in epidemiological studies on the role of diet in colon carcinogenesis.

  7. Discordant genotyping results using DNA isolated from anti-doping control urine samples.

    Science.gov (United States)

    Choong, Eva; Schulze, Jenny J; Ericsson, Magnus; Rane, Anders; Ekström, Lena

    2017-07-01

    The UGT2B17 gene deletion polymorphism is known to correlate to urinary concentration of testosterone-glucuronide and hence this genotype exerts a large impact on the testosterone/epitestosterone (T/E) ratio, a biomarker for testosterone doping. The objective of this study was to assess if DNA isolated from athletes' urine samples (n = 713) obtained in routine doping controls could be targeted for genotyping analysis for future integration in the athlete's passport. A control population (n = 21) including both urine and blood DNA was used for genotyping concordance test. Another aim was to study a large group (n = 596) of authentic elite athletes in respect of urinary steroid profile in relation to genetic variation. First we found that the genotype results when using urine-derived DNA did not correlate sufficiently with the genotype obtained from whole blood DNA. Secondly we found males with one or two UGT2B17 alleles had higher T/E (mean 1.63 ± 0.93) than females (mean 1.28 ± 1.08), p˂0.001. Unexpectedly, we found that several male del/del athletes in power sports had a T/E ˃1. If men in power sport exert a different urinary steroid profile needs to be further investigated. The other polymorphisms investigated in the CYP17A1, UGT2B7 and UGT2B15 genes did not show any associations with testosterone and epitestosterone concentrations. Our results show that genotyping using urine samples according to our method is not useful in an anti-doping setting. Instead, it is of importance for the anti-doping test programs to include baseline values in the ABP to minimize any putative impact of genotype. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

  8. Variation in faecal water content may confound estimates of gastro-intestinal parasite intensity in wild African herbivores.

    Science.gov (United States)

    Turner, W C; Cizauskas, C A; Getz, W M

    2010-03-01

    Estimates of parasite intensity within host populations are essential for many studies of host-parasite relationships. Here we evaluated the seasonal, age- and sex-related variability in faecal water content for two wild ungulate species, springbok (Antidorcas marsupialis) and plains zebra (Equus quagga). We then assessed whether or not faecal water content biased conclusions regarding differences in strongyle infection rates by season, age or sex. There was evidence of significant variation in faecal water content by season and age for both species, and by sex in springbok. Analyses of faecal egg counts demonstrated that sex was a near-significant factor in explaining variation in strongyle parasite infection rates in zebra (P = 0.055) and springbok (P = 0.052) using wet-weight faecal samples. However, once these intensity estimates were re-scaled by the percent of dry matter in the faeces, sex was no longer a significant factor (zebra, P = 0.268; springbok, P = 0.234). These results demonstrate that variation in faecal water content may confound analyses and could produce spurious conclusions, as was the case with host sex as a factor in the analysis. We thus recommend that researchers assess whether water variation could be a confounding factor when designing and performing research using faecal indices of parasite intensity.

  9. Environmental Monitoring and Analysis of Faecal Contamination in an Urban Setting in the City of Bari (Apulia Region, Italy: Health and Hygiene Implications

    Directory of Open Access Journals (Sweden)

    Maria Tempesta

    2010-11-01

    Full Text Available Few studies have been conducted in Italy to quantify the potential risk associated with dynamics and distribution of pathogens in urban settings. The aim of this study was to acquire data on the environmental faecal contamination in urban ecosystems, by assessing the presence of pathogens in public areas in the city of Bari (Apulia region, Italy. To determine the degree of environmental contamination, samples of dog faeces and bird guano were collected from different areas in the city of Bari (park green areas, playgrounds, public housing areas, parkways, and a school. A total of 152 canine faecal samples, in 54 pools, and two samples of pigeon guano from 66 monitored sites were examined. No samples were found in 12 areas spread over nine sites. Chlamydophila psittaci was detected in seven canine and two pigeon guano samples. Salmonella species were not found.  On the other hand, four of 54 canine faecal samples were positive for reovirus. Thirteen canine faecal samples were positive for parasite eggs: 8/54 samples contained Toxocara canis and Toxascaris leonina eggs and 5/54 samples contained Ancylostoma caninum eggs. Our study showed that public areas are often contaminated by potentially zoonotic pathogens.

  10. Group A rotavirus genotypes in hospital-acquired gastroenteritis in Italy, 2012-14.

    Science.gov (United States)

    Ianiro, G; Delogu, R; Fiore, L; Monini, M; Ruggeri, F M

    2017-07-01

    Group A rotaviruses (RVA) are the leading cause of acute gastroenteritis (AGE) in young (aged rotavirus are presently known, most RVA infections in humans worldwide are related to five major G/P combinations: G1P[8], G2P[4], G3P[8], G4P[8], and G9P[8]. To provide the hospitals of the Italian surveillance network with update information on RVA AGE. During RVA gastroenteritis surveillance in Italy in 2012-14, a total of 2341 RVA-positive faecal samples were collected from children hospitalized with AGE, and RVA strains were genotyped following standard EuroRotaNet protocols. Most strains analysed belonged to the five major human genotypes and 118 out of 2341 (5.0%) were reported to be hospital-acquired. Comparison of the distributions of the RVA genotypes circulating in the community or associated with nosocomial infections showed a different distribution of genotypes circulating inside the hospital wards, with respect to those observed in the community. G1P[8] and G9P[8] RVA strains were detected frequently, whereas G12P[8] caused a single large nosocomial outbreak. The information from this study will be useful to implement guidelines for preventing RVA AGE and optimizing the management of patients in hospital wards. Copyright © 2017 The Healthcare Infection Society. Published by Elsevier Ltd. All rights reserved.

  11. Use of faecal markers in screening for colorectal neoplasia: a European group on tumor markers position paper.

    LENUS (Irish Health Repository)

    Duffy, Michael J

    2012-02-01

    Several randomized controlled trials have shown that population-based screening using faecal occult blood testing (FOBT) can reduce mortality from colorectal neoplasia. Based on this evidence, a number of countries have introduced screening for colorectal cancer (CRC) and high-risk adenoma and many others are considering its introduction. The aim of this article is to critically review the current status of faecal markers as population-based screening tests for these neoplasia. Most of the available faecal tests involve the measurement of either occult blood or a panel of DNA markers. Occult blood may be measured using either the guaiac faecal occult blood test (gFOBT) or a faecal immunochemical test (iFOBT). Although iFOBT may require a greater initial investment, they have several advantages over gFOBT, including greater analytical sensitivity and specificity. Their use results in improved clinical performance and higher uptake rates. Importantly for population screening, some of the iFOBTs can be automated and provide an adjustable cutoff for faecal haemoglobin concentration. However, samples for iFOBT, may be less stable after collection than for gFOBT. For new centres undertaking FOBT for colorectal neoplasia, the European Group on Tumour Markers recommends use of a quantitative iFOBT with an adjustable cutoff point and high throughput analysis. All participants with positive FOBT results should be offered colonoscopy. The panel recommends further research into increasing the stability of iFOBT and the development of improved and affordable DNA and proteomic-based tests, which reduce current false negative rates, simplify sample transport and enable automated analysis.

  12. Faecal Waste Disposal and Environmental Health Status in a Nigerian Coastal Settlement of Oron

    Directory of Open Access Journals (Sweden)

    Edet E. Ikurekong

    2008-10-01

    Full Text Available AIM/BACKGROUND: This research investigated the relationship between faecal waste disposal and the environmental health status of the inhabitants of Oron LGA, of Akwa Ibom State, Nigeria. The objectives were to identify the methods of faecal disposal; identify the incidence of faecal waste related diseases and the pattern and types of diseases occurrence in the study area. METHOD: 400 households were randomly selected for interview from 17 villages of the study area. Ground and surface water samples were spatially collected and analysed to determine their quality. These include streams, boreholes pipe-borne, and rain and river water from the 17 villages. RESULTS: The result shows that both the qualitative and quantitative aspect of the major sources of drinking water supply are at variance with the established national and international standards. The stepwise multiple regression models applied proved the validity of population demographic characteristics, unhygienic environment and poor quality of water supply as factors that enhance the incidence and vulnerability of the population to faecal waste related disease occurrence. CONCLUSION: The study recommends sustainable strategies towards the management of human faecal waste and related diseases in the study area. [TAF Prev Med Bull 2008; 7(5.000: 363-368

  13. Effect of room temperature transport vials on DNA quality and phylogenetic composition of faecal microbiota of elderly adults and infants.

    LENUS (Irish Health Repository)

    Hill, Cian J

    2016-05-01

    Alterations in intestinal microbiota have been correlated with a growing number of diseases. Investigating the faecal microbiota is widely used as a non-invasive and ethically simple proxy for intestinal biopsies. There is an urgent need for collection and transport media that would allow faecal sampling at distance from the processing laboratory, obviating the need for same-day DNA extraction recommended by previous studies of freezing and processing methods for stool. We compared the faecal bacterial DNA quality and apparent phylogenetic composition derived using a commercial kit for stool storage and transport (DNA Genotek OMNIgene GUT) with that of freshly extracted samples, 22 from infants and 20 from older adults.

  14. Faecal bacterial composition in dairy cows shedding Mycobacterium avium subsp. paratuberculosis in faeces in comparison with nonshedding cows.

    Science.gov (United States)

    Kaevska, Marija; Videnska, Petra; Sedlar, Karel; Bartejsova, Iva; Kralova, Alena; Slana, Iva

    2016-06-01

    The aim of this study was to determine possible differences in the faecal microbiota of dairy cows infected with Mycobacterium avium subsp. paratuberculosis (Johne's disease) in comparison with noninfected cows from the same herds. Faecal samples from cows in 4 herds were tested for M. avium subsp. paratuberculosis by real-time PCR, and faecal bacterial populations were analysed by 454 pyrosequencing of the 16S rRNA gene. The most notable differences between shedding and nonshedding cows were an increase in the genus Psychrobacter and a decrease in the genera Oscillospira, Ruminococcus, and Bifidobacterium in cows infected with M. avium subsp. paratuberculosis. The present study is the first to report the faecal microbial composition in dairy cows infected with M. avium subsp. paratuberculosis.

  15. Occurrence and molecular characteristics of ESBL/AmpC-producing Escherichia coli in faecal samples from horses in an equine clinic.

    Science.gov (United States)

    Apostolakos, Ilias; Franz, Eelco; van Hoek, Angela H A M; Florijn, Alice; Veenman, Christiaan; Sloet-van Oldruitenborgh-Oosterbaan, Marianne M; Dierikx, Cindy; van Duijkeren, Engeline

    2017-07-01

    To investigate the occurrence and characteristics of ESBL/AmpC-producing Escherichia coli in faecal samples from horses at one equine clinic in the Netherlands. A total of 91 horses, including residents and patients, were sampled. ESBL/AmpC-producing E. coli were identified by a combination disc diffusion test. Phylogenetic groups and MLST were determined. ESBL/AmpC genes were analysed using PCR and sequencing. Plasmids were characterized by transformation and PCR-based replicon typing. Subtyping of plasmids was done by plasmid MLST. At least one E. coli isolate with a confirmed ESBL/AmpC gene was found in samples from 76 horses (84%). Although phylogenetic group B1 E. coli bla CTX-M-1 predominated, a diverse E. coli population was found, indicating that clonal nosocomial spread was not the only reason for the high occurrence found. MLST analysis revealed the presence of 47 E. coli STs, organized in four clusters of genetically related strains. ST10, ST641, ST1079 and ST1250 were most commonly found. With regard to the genes, bla CTX-M-1 was most prevalent ( n  =   91), followed by bla CTX-M-2 ( n  =   26). The most frequently found plasmid type was IncHI1, but plasmids belonging to the IncF, IncI1 and IncN groups were also identified. A high occurrence of ESBL-producing E. coli in faecal samples was found among horses in an equine clinic and the variety of STs, ESBL genes and plasmid types suggests nosocomial transmission. ESBL E. coli can cause difficult-to-treat infections in horses and prudent use of antimicrobials is warranted. A further assessment of the risks of transmission to persons in close contact with horses, such as caretakers or veterinarians, is crucial. © The Author 2017. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  16. Impact of faecal DM excretion on faecal calcium losses in dogs eating complete moist and dry pet foods - food digestibility is a major determinant of calcium requirements.

    Science.gov (United States)

    Kienzle, Ellen; Brenten, Thomas; Dobenecker, Britta

    2017-01-01

    The recommendations for the Ca supply for maintenance of dogs have been reduced by about 75 % in the last decades. An important factor for Ca requirements is faecal Ca losses. In previous studies with experimental diets faecal Ca losses depended on Ca intake and on faecal DM excretion. A predictive equation for faecal Ca losses in mg/kg body weight (BW) developed in a fibre model is: faecal losses = -33·8 + (13·6 faecal DM excretion (g/kg BW)) + (0·78 Ca intake (mg/kg BW)). The present study aimed at testing this equation in pet food with material from trials carried out for other purposes. Digestion trials with twenty-five dry and fifteen moist foods (326 observations in total) were evaluated retrospectively. Faecal DM excretion and faecal Ca losses were significantly correlated ( r 2  0·86; P  losses in a practical feeding situation. In conclusion, Ca requirements for maintenance may vary with food DM intake and digestibility.

  17. Streptococcus caviae sp. nov., isolated from guinea pig faecal samples.

    Science.gov (United States)

    Palakawong Na Ayudthaya, Susakul; Hilderink, Loes J; Oost, John van der; Vos, Willem M de; Plugge, Caroline M

    2017-05-01

    A novel cellobiose-degrading and lactate-producing bacterium, strain Cavy grass 6T, was isolated from faecal samples of guinea pigs (Cavia porcellus). Cells of the strain were ovalshaped, non-motile, non-spore-forming, Gram-stain-positive and facultatively anaerobic. The strain gr at 25-40 °C (optimum 37 °C) and pH 4.5-9.5 (optimum 8.0). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain Cavy grass 6T belongs to the genus Streptococcus with its closest relative being Streptococcus devriesei CCUG 47155T with only 96.5 % similarity. Comparing strain Cavy grass 6T and Streptococcus devriesei CCUG 47155T, average nucleotide identity and level of digital DNA-DNA hybridization dDDH were only 86.9 and 33.3 %, respectively. Housekeeping genes groEL and gyrA were different between strain Cavy grass 6T and other streptococci. The G+C content of strain Cavy grass 6T was 42.6±0.3 mol%. The major (>10 %) cellular fatty acids of strain Cavy grass 6T were C16:0, C20 : 1ω9c and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). Strain Cavy grass 6T ferment a range of plant mono- and disaccharides as well as polymeric carbohydrates, including cellobiose, dulcitol, d-glucose, maltose, raffinose, sucrose, l-sorbose, trehalose, inulin and dried grass extract, to lactate, formate, acetate and ethanol. Based on phylogenetic and physiological characteristics, Cavy grass 6T can be distinguished from other members of the genus Streptococcus. Therefore, a novel species of the genus Streptococcus, family Streptococcaceae, order Lactobacillales is proposed, Streptococcuscaviae sp. nov. (type strain Cavy grass 6T=TISTR 2371T=DSM 102819T).

  18. Using faecal profiling to assess the effects of different management ...

    African Journals Online (AJOL)

    We used faecal profiling to assess diet quality of animals under three different management types in a semi-arid savanna, northwest of Kimberley, Northern Cape, South Africa. The levels of faecal crude protein (FCP) and faecal phosphorus (FP) of freeranging springbok (Antidorcas marsupialis) and blue wildebeest ...

  19. Tracing Males From Different Continents by Genotyping JC Polyomavirus in DNA From Semen Samples.

    Science.gov (United States)

    Rotondo, John Charles; Candian, Tommaso; Selvatici, Rita; Mazzoni, Elisa; Bonaccorsi, Gloria; Greco, Pantaleo; Tognon, Mauro; Martini, Fernanda

    2017-05-01

    The human JC polyomavirus (JCPyV) is an ubiquitous viral agent infecting approximately 60% of humans. Recently, JCPyV sequences have been detected in semen samples. The aim of this investigation was to test whether semen JCPyV genotyping can be employed to trace the origin continent of males. Semen DNA samples (n = 170) from males of different Continents were investigated by PCR for the polymorphic JCPyV viral capsid protein 1 (VP1) sequences, followed by DNA sequencing. JCPyV sequences were detected with an overall prevalence of 27.6% (47/170). DNA sequencing revealed that European males carried JCPyV types 1A (71.4%), 4 (11.4%), 2B (2.9%), 2D1 (2.9%), and 3A (2.9%). Asians JCPyV type 2D1 (66.7%) and Africans JCPyV types 3A (33.3%) and 1A (33.3%). In 10.6% of males, two different JCPyV genotypes were detected, suggesting that the second JCPyV genotype was acquired in the destination country. This study indicates that the majority of semen samples found to be JCPyV-positive, were infected with the JCPyV genotype found in the geographic area of male origin. Therefore, semen JCPyV genotyping could be employed to trace the origin continent of males. Our findings could be applied to forensic investigations, in case of for instance sexual crimes. Indeed, JCPyV genotyping should enable investigators to make additional detailed profiling of the offender. J. Cell. Physiol. 232: 982-985, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  20. Plasma disposition and faecal excretion of oxfendazole, fenbendazole and albendazole following oral administration to donkeys.

    Science.gov (United States)

    Gokbulut, Cengiz; Akar, Ferda; McKellar, Quintin A

    2006-07-01

    Fenbendazole (FBZ), oxfendazole (fenbendazole sulphoxide, FBZSO), and albendazole (ABZ) were administered orally to donkeys at 10mg/kg bodyweight. Blood and faecal samples were collected from 1 to 120 h post-treatment. The plasma and faecal samples were analysed by high performance liquid chromatography (HPLC). The parent molecule and its sulphoxide and sulphone (FBZSO(2)) metabolites did not reach detectable concentrations in any plasma samples following FBZ administration. ABZ was also not detected in any plasma samples, but its sulphoxide and sulphone metabolites were detected, demonstrating that ABZ was completely metabolised by first-pass mechanisms in donkeys. Maximum plasma concentrations (C(max)) of FBZSO (0.49microg/mL) and FBZSO(2) (0.60microg/mL) were detected at (t(max)) 5.67 and 8.00h, respectively, following administration of FBZSO. The area under the curve (AUC) of the sulphone metabolite (10.33microg h/mL) was significantly higher than that of the parent drug FBZSO (5.17microg h/mL). C(max) of albendazole sulphoxide (ABZSO) (0.08g/mL) and albendazole sulphone (ABZSO(2)) (0.04microg/mL) were obtained at 5.71 and 8.00h, respectively, following ABZ administration. The AUC of the sulphoxide metabolite (0.84microg h/mL) of ABZ was significantly higher than that of the sulphone metabolite (0.50microg h/mL). The highest dry-faecal concentrations of parent molecules were detected at 32, 34 and 30h for FBZSO, FBZ and ABZ, respectively. The sulphide metabolite was significantly higher than the parent molecule after FBZSO administration. The parent molecule was predominant in the faecal samples following FBZ administration. After ABZ administration, the parent molecule was significantly metabolised, probably by gastrointestinal microflora, to its sulphoxide metabolite (ABZSO) that showed a similar excretion profile to the parent molecule in the faecal samples. The AUC of the parent FBZ was significantly higher than that of FBZSO and ABZ in faeces. It is

  1. Presence of faecal coliforms and selected heavy metals in ice cubes from food outlets in Taman Universiti, Johor Bahru, Malaysia.

    Science.gov (United States)

    Mahat, N A; Meor Ahmad, Z; Abdul Wahab, R

    2015-09-01

    Consumption of iced beverages is common in Malaysia although specific research focusing on its safety parameters such as presence of faecal coliforms and heavy metal elements remains scarce. A study conducted in Kelantan indicated that faecal coliforms were detected in the majority of the ice cube samples analyzed, largely attributable to improper handling. Hence, it was found pertinent to conduct similar study in other parts of the country such as Johor Bahru if the similar pattern prevailed. Therefore, this present cross sectional study which randomly sampled ice cubes from 30 permanent food outlets in Taman Universiti, Johor Bahru for detecting contamination by faecal coliforms and selected heavy metal elements (lead, copper, manganese and zinc) acquires significance. Faecal coliforms were detected in 11 (36.67%) of the samples, ranging between 1 CFU/100 mL to > 50 CFU/100 mL; two of the samples were grossly contaminated (>50 CFU/100 mL). Interestingly, while positive detection of lead was observed in 29 of the 30 ice cube samples (mean: 0.511±0.105 ppm; range: 0.489-0.674 ppm), copper, manganese and zinc were not detected. In addition, analysis on commercially bottled mineral water as well as in tap water samples did not detect such contaminations. Therefore, it appears that (1) contamination of faecal coliforms in ice cubes in food outlets in Malaysia may not be sporadic in pattern but rather prevalent and (2) the source of water used for manufacturing the ice cubes that contained significant amount of lead would suggest that (3) it was neither originated from the treated tap water supply nor bottled mineral water or (4) perhaps contaminated during manufacturing process. Further studies exploring the source of water used for manufacturing these ice cubes as well as the handling process among food operators deserve consideration.

  2. A semi-automated magnetic capture probe based DNA extraction and real-time PCR method applied in the Swedish surveillance of Echinococcus multilocularis in red fox (Vulpes vulpes) faecal samples.

    Science.gov (United States)

    Isaksson, Mats; Hagström, Åsa; Armua-Fernandez, Maria Teresa; Wahlström, Helene; Ågren, Erik Olof; Miller, Andrea; Holmberg, Anders; Lukacs, Morten; Casulli, Adriano; Deplazes, Peter; Juremalm, Mikael

    2014-12-19

    Following the first finding of Echinococcus multilocularis in Sweden in 2011, 2985 red foxes (Vulpes vulpes) were analysed by the segmental sedimentation and counting technique. This is a labour intensive method and requires handling of the whole carcass of the fox, resulting in a costly analysis. In an effort to reduce the cost of labour and sample handling, an alternative method has been developed. The method is sensitive and partially automated for detection of E. multilocularis in faecal samples. The method has been used in the Swedish E. multilocularis monitoring program for 2012-2013 on more than 2000 faecal samples. We describe a new semi-automated magnetic capture probe DNA extraction method and real time hydrolysis probe polymerase chain reaction assay (MC-PCR) for the detection of E. multilocularis DNA in faecal samples from red fox. The diagnostic sensitivity was determined by validating the new method against the sedimentation and counting technique in fox samples collected in Switzerland where E. multilocularis is highly endemic. Of 177 foxes analysed by the sedimentation and counting technique, E. multilocularis was detected in 93 animals. Eighty-two (88%, 95% C.I 79.8-93.9) of these were positive in the MC-PCR. In foxes with more than 100 worms, the MC-PCR was positive in 44 out of 46 (95.7%) cases. The two MC-PCR negative samples originated from foxes with only immature E. multilocularis worms. In foxes with 100 worms or less, (n = 47), 38 (80.9%) were positive in the MC-PCR. The diagnostic specificity of the MC-PCR was evaluated using fox scats collected within the Swedish screening. Of 2158 samples analysed, two were positive. This implies that the specificity is at least 99.9% (C.I. = 99.7-100). The MC-PCR proved to have a high sensitivity and a very high specificity. The test is partially automated but also possible to perform manually if desired. The test is well suited for nationwide E. multilocularis surveillance programs where sampling

  3. The prevalence and genotype of human papillomavirus on cervical samples from an Irish female population with external genital warts.

    LENUS (Irish Health Repository)

    Cremin, Suzanne M

    2012-07-01

    The aim of this study was to determine the cervical genotype profile of females who presented to an STI Clinic with external genital warts (EGW); and to determine the potential vaccine coverage prior to the uptake of the HPV vaccines. Sixty-one cervical scrapings were taken from females aged 18-35 y who had external genital warts or a history of external genital warts. The resulting 50 samples that were positive for HPV-DNA were subjected to genotype identification. Forty-six of these samples had detectable genotypes by LIPA analysis and most (78%, 36\\/46) had multiple low risk (LR) and high risk (HR) genotypes on the cervix. Twenty-five of these samples (54%) had more than 1 HR genotype. Of the 36 patients who had any HR genotypes, 18 (50%) were identified to have the most oncogenic HPV genotypes, namely 16 and 18. Three of these samples had both 16 and 18 on the cervix. The presence of multiple HR genotypes on the majority of cervical samples from a self-referred population of females with EGW is presented. This study is of importance since persistent HR-HPV is the necessary risk factor in the development of precancerous and cancerous lesions of the cervix. Gardisil, the quadrivalent HPV vaccine would have been useful in the prevention of 28% (13\\/46) of these infections.

  4. Rectal intussusception and unexplained faecal incontinence: findings of a proctographic study.

    Science.gov (United States)

    Collinson, R; Cunningham, C; D'Costa, H; Lindsey, I

    2009-01-01

    The aetiology of faecal incontinence is multifactorial, yet there remains an approach to assessment and treatment that focusses on the sphincter. Rectal intussusception (RI) is underdiagnosed and manifests primarily as obstructed defecation. Yet greater than 50% of these patients admit to faecal incontinence on closer questioning. We aimed to evaluate the incidence of RI at evacuation proctography selectively undertaken in the evaluation of patients with faecal incontinence. Patients with faecal incontinence seen in a pelvic floor clinic were evaluated with anorectal physiology and ultrasound. Where the faecal incontinence was not fully explained by physiology and ultrasound, evacuation proctography was undertaken. Studies were classified as 'normal', 'low-grade RI' (recto-rectal), 'high-grade RI' (recto-anal) or 'anismus'. Forty patients underwent evacuation proctography (33 women, 83%). Median age was 63 years (range 34-77 years). Seven patients (17%) had a normal proctogram. Three (8%) had recto-rectal RI. Twenty-five (63%) demonstrated recto-anal RI. Five patients (12%) had anismus. Recto-anal intussusception is common in patients undergoing selective evacuation proctography for investigation of faecal incontinence. The role of recto-anal intussusception in the multifactorial aetiology of faecal incontinence has been largely overlooked. Evacuation proctography should be considered as part of routine work-up of patients with faecal incontinence.

  5. Are carnivore digestive separation mechanisms revealed on structure-rich diets?: Faecal inconsistency in dogs (Canis familiaris fed day old chicks.

    Directory of Open Access Journals (Sweden)

    Annelies De Cuyper

    Full Text Available Pronounced variations in faecal consistency have been described anecdotally for some carnivore species fed a structure-rich diet. Typically two faecal consistencies are distinguished, namely hard and firm versus liquid and viscous faeces. It is possible that a separation mechanism is operating in the carnivore digestive tract, as in many herbivore species. Six beagle dogs were fed two experimental diets in a cross-over design of 7 days. Test diets consisted of chunked day old chicks differing only in particle size (fine = 7.8 mm vs coarse = 13 mm in order to vary dietary structure. Digestive retention time was measured using titanium oxide (TiO2 as marker. The total faecal output was scored for consistency and faecal fermentation profiles were evaluated through faecal short-chain fatty acid (SCFA and ammonia (NH3 analyses. A total of 181 faecal samples were collected. Dietary particle size did not affect faecal consistency, fermentative end products nor mean retention time (MRT. However, a faecal consistency dichotomy was observed with firm faeces (score 2-2.5 and soft faeces (score 4-4.5 being the most frequently occurring consistencies in an almost alternating pattern in every single dog. Firm and soft faeces differed distinctively in fermentative profiles. Although the structure difference between diets did not affect the faecal dichotomy, feeding whole prey provoked the occurrence of the latter which raises suspicion of a digestive separation mechanism in the canine digestive tract. Further faecal characterisation is however required in order to unravel the underlying mechanism.

  6. Intestinal parasites and genotyping of Giardia duodenalis in children: first report of genotype B in isolates from human clinical samples in Mexico

    Directory of Open Access Journals (Sweden)

    Julio César Torres-Romero

    2014-06-01

    Full Text Available Giardia duodenalis is one of the most prevalent enteroparasites in children. This parasite produces several clinical manifestations. The aim of this study was to determine the prevalence of genotypes of G. duodenalis causing infection in a region of southeastern Mexico. G. duodenalis cysts were isolated (33/429 from stool samples of children and molecular genotyping was performed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP analysis, targeting the triosephosphate isomerase ( tpi and glutamate dehydrogenase ( gdh genes. The tpi gene was amplified in all of the cyst samples, either for assemblage A (27 samples or assemblage B (6 samples. RFLP analysis classified the 27 tpi -A amplicons in assemblage A, subgenotype I. Samples classified as assemblage B were further analysed using PCR-RFLP of the gdh gene and identified as assemblage B, subgenotype III. To our knowledge, this is the first report of assemblage B of G. duodenalis in human clinical samples from Mexico.

  7. Faecal Escherichia coli from patients with E. coli urinary tract infection and healthy controls who have never had a urinary tract infection

    DEFF Research Database (Denmark)

    Nielsen, Karen L; Dynesen, Pia; Larsen, Preben

    2014-01-01

    Urinary tract infections (UTIs) are primarily caused by Escherichia coli with the patient's own faecal flora acting as a reservoir for the infecting E. coli. Here we sought to characterize the E. coli faecal flora of UTI patients and healthy controls who had never had a UTI. Up to 20 E. coli...... colonies from each rectal swab were random amplified polymorphic DNA (RAPD) typed for clonality, dominance in the sample and correlation to the infecting UTI isolate in patients. Each distinct clone was phylotyped and tested for antimicrobial susceptibility. Eighty-seven per cent of the UTI patients...... carried the infecting strain in their faecal flora, and faecal clones causing UTI were more often dominant in the faecal flora. Patients had a larger diversity of E. coli in their gut flora by carrying more unique E. coli clones compared to controls, and patient faecal clones were more often associated...

  8. Faecal Microbiota of Forage-Fed Horses in New Zealand and the Population Dynamics of Microbial Communities following Dietary Change

    Science.gov (United States)

    Fernandes, Karlette A.; Kittelmann, Sandra; Rogers, Christopher W.; Gee, Erica K.; Bolwell, Charlotte F.; Bermingham, Emma N.; Thomas, David G.

    2014-01-01

    The effects of abrupt dietary transition on the faecal microbiota of forage-fed horses over a 3-week period were investigated. Yearling Thoroughbred fillies reared as a cohort were exclusively fed on either an ensiled conserved forage-grain diet (“Group A”; n = 6) or pasture (“Group B”; n = 6) for three weeks prior to the study. After the Day 0 faecal samples were collected, horses of Group A were abruptly transitioned to pasture. Both groups continued to graze similar pasture for three weeks, with faecal samples collected at 4-day intervals. DNA was isolated from the faeces and microbial 16S and 18S rRNA gene amplicons were generated and analysed by pyrosequencing. The faecal bacterial communities of both groups of horses were highly diverse (Simpson’s index of diversity >0.8), with differences between the two groups on Day 0 (Phorses became similar to Group B within four days of feeding on pasture, whereas the structure of the archaeal community remained constant pre- and post-dietary change. The community structure of the faecal microbiota (bacteria, archaea and ciliate protozoa) of pasture-fed horses was also identified. The initial differences observed appeared to be linked to recent dietary history, with the bacterial community of the forage-fed horses responding rapidly to abrupt dietary change. PMID:25383707

  9. Distribution of sewage pollution around a maritime Antarctic research station indicated by faecal coliforms, Clostridium perfringens and faecal sterol markers

    Energy Technology Data Exchange (ETDEWEB)

    Hughes, Kevin A.; Thompson, Anu

    2004-02-01

    This study describes the distribution of sewage pollution markers (faecal coliforms, Clostridium perfringens and faecal sterols) in seawater and marine sediments around Rothera Research Station, Antarctic Peninsula. Untreated sewage waste has been released from this site since 1975, creating the potential for long-term contamination of the benthic environment. Faecal coliform concentrations in seawater reached background levels within 300 m of the outfall. In sediment cores, both C. perfringens and faecal coliform concentrations declined with distance from the outfall, though C. perfringens persisted at greater depths in the sediment. High concentrations of 5{beta}(H)-cholestan-3{beta}-ol (coprostanol) relative to the corresponding 5{alpha}-epimer (cholestanol), indicative of sewage pollution, were only found in sediments within 200 m of the sewage outfall. This study has shown that sewage contamination is limited to the immediate vicinity of the sewage outfall. Nevertheless, a sewage treatment plant was installed in February 2003 to reduce this contamination further. - Sewage contamination of seawater and marine sediments near Rothera Research Station (Antarctic Peninsula) was limited to the immediate vicinity of the outfall.

  10. Distribution of sewage pollution around a maritime Antarctic research station indicated by faecal coliforms, Clostridium perfringens and faecal sterol markers

    International Nuclear Information System (INIS)

    Hughes, Kevin A.; Thompson, Anu

    2004-01-01

    This study describes the distribution of sewage pollution markers (faecal coliforms, Clostridium perfringens and faecal sterols) in seawater and marine sediments around Rothera Research Station, Antarctic Peninsula. Untreated sewage waste has been released from this site since 1975, creating the potential for long-term contamination of the benthic environment. Faecal coliform concentrations in seawater reached background levels within 300 m of the outfall. In sediment cores, both C. perfringens and faecal coliform concentrations declined with distance from the outfall, though C. perfringens persisted at greater depths in the sediment. High concentrations of 5β(H)-cholestan-3β-ol (coprostanol) relative to the corresponding 5α-epimer (cholestanol), indicative of sewage pollution, were only found in sediments within 200 m of the sewage outfall. This study has shown that sewage contamination is limited to the immediate vicinity of the sewage outfall. Nevertheless, a sewage treatment plant was installed in February 2003 to reduce this contamination further. - Sewage contamination of seawater and marine sediments near Rothera Research Station (Antarctic Peninsula) was limited to the immediate vicinity of the outfall

  11. Canine faecal contamination and parasitic risk in the city of Naples (southern Italy

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    Veneziano Vincenzo

    2006-09-01

    Full Text Available Abstract Background Dogs are associated with more than 60 zoonotic diseases among which, parasitosis and, in particular, helminthosis, can pose serious public-health concerns worldwide. Many canine gastrointestinal parasites eliminate their dispersion elements (eggs, larvae, oocysts by the faecal route. The quantity of canine faeces deposited on public and private property in cities worldwide is both a perennial nuisance and an important health issue. Public sites such as playgrounds, parks, gardens, public squares and sandpits may be an important source of human infection. The aim of this study was to evaluate the extent of both canine faecal contamination in the city of Naples (southern Italy, and presence of canine parasitic elements, with particular regard to those which are potential agents of zoonosis. A regular grid of sub-areas (1 km × 700 m was overlaid on the city map using a Geographical Information System (GIS. In each sub-area the straightest 1 km transect was drawn and digitalized on-screen in the GIS. Between February and May 2005 canine faeces were counted along the 1 km transects in 143 sub-areas, and 415 canine faecal samples were collected and submitted to coprological examinations. Negative binomial regression models and Gaussian random effects models were used to analyze the association between faeces count and human population density taking into account for extraPoisson variability. Logistic regression model was used to evaluate the association between positivity to parasitic elements and number of canine faeces. Results Out of the 143 studied sub-areas, 141 (98.6% contained canine faeces. There was a strong spatial gradient with 48% of the total variability accounted by between neighbourhood variability; a positive association between the number of faeces and the human population density was found. Seventy (over 415, 16.9% canine faecal samples were positive for parasitic elements. There was no association between

  12. Fluorescence hyper-spectral imaging to detecting faecal contamination on fresh tomatoes

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    Roberto Romaniello

    2016-03-01

    Full Text Available Faecal contamination of fresh fruits represents a severe danger for human health. Thus some techniques based on microbiological testing were developed to individuate faecal contaminants but those tests do not results efficient because their non-applicability on overall vegetable unity. In this work a methodology based on hyper-spectral fluorescence imaging was developed and tested to detecting faecal contamination on fresh tomatoes. Two image-processing methods were performed to maximise the contrast between the faecal contaminant and tomatoes skin: principal component analysis and band image ratio (BRI. The BRI method allows classifying correctly 70% of contaminated area, with no false-positives in all examined cases. Thus, the developed methodology can be employed for a fast and effective detection of faecal contamination on fresh tomatoes.

  13. Faecal contamination of household drinking water in Rwanda: A national cross-sectional study

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    Kirby, Miles A., E-mail: miles.kirby@lshtm.ac.uk [London School of Hygiene and Tropical Medicine, Keppel St, London WC1E 7HT (United Kingdom); Nagel, Corey L., E-mail: nagelc@ohsu.edu [Oregon Health and Science University, School of Nursing Portland Campus, 3455 SW US Veterans Hospital Road, SN-6S, Portland, OR 97239 (United States); Rosa, Ghislaine, E-mail: ghislaine.rosa@lshtm.ac.uk [London School of Hygiene and Tropical Medicine, Keppel St, London WC1E 7HT (United Kingdom); Iyakaremye, Laurien, E-mail: laurieniyakaremye1@gmail.com [DelAgua Health Rwanda Implementation, Ltd., 3rd Fl KG 19 Avenue, Kibagabaga Rd, Kigali (Rwanda); Zambrano, Laura Divens, E-mail: laura.zambrano@emory.edu [Emory University Rollins School of Public Health, 1518 Clifton Road, NE, Atlanta, GA 30322 (United States); Clasen, Thomas F., E-mail: thomas.f.clasen@emory.edu [London School of Hygiene and Tropical Medicine, Keppel St, London WC1E 7HT (United Kingdom); Emory University Rollins School of Public Health, 1518 Clifton Road, NE, Atlanta, GA 30322 (United States)

    2016-11-15

    Unsafe drinking water is a leading cause of morbidity and mortality, especially among young children in low-income settings. We conducted a national survey in Rwanda to determine the level of faecal contamination of household drinking water and risk factors associated therewith. Drinking water samples were collected from a nationally representative sample of 870 households and assessed for thermotolerant coliforms (TTC), a World Health Organization (WHO)-approved indicator of faecal contamination. Potential household and community-level determinants of household drinking water quality derived from household surveys, the 2012 Rwanda Population and Housing Census, and a precipitation dataset were assessed using multivariate logistic regression. Widespread faecal contamination was present, and only 24.9% (95% CI 20.9–29.4%, n = 217) of household samples met WHO Guidelines of having no detectable TTC contamination, while 42.5% (95% CI 38.0–47.1%, n = 361) of samples had > 100 TTC/100 mL and considered high risk. Sub-national differences were observed, with poorer water quality in rural areas and Eastern province. In multivariate analyses, there was evidence for an association between detectable contamination and increased open waste disposal in a sector, lower elevation, and water sources other than piped to household or rainwater/bottled. Risk factors for intermediate/high risk contamination (> 10 TTC/100 mL) included low population density, increased open waste disposal, lower elevation, water sources other than piped to household or rainwater/bottled, and occurrence of an extreme rain event the previous day. Modelling suggests non-household-based risk factors are determinants of water quality in this setting, and these results suggest a substantial proportion of Rwanda's population are exposed to faecal contamination through drinking water. - Graphical abstract: Household drinking water quality (thermotolerant coliform colony forming units/100 m

  14. Faecal contamination of household drinking water in Rwanda: A national cross-sectional study

    International Nuclear Information System (INIS)

    Kirby, Miles A.; Nagel, Corey L.; Rosa, Ghislaine; Iyakaremye, Laurien; Zambrano, Laura Divens; Clasen, Thomas F.

    2016-01-01

    Unsafe drinking water is a leading cause of morbidity and mortality, especially among young children in low-income settings. We conducted a national survey in Rwanda to determine the level of faecal contamination of household drinking water and risk factors associated therewith. Drinking water samples were collected from a nationally representative sample of 870 households and assessed for thermotolerant coliforms (TTC), a World Health Organization (WHO)-approved indicator of faecal contamination. Potential household and community-level determinants of household drinking water quality derived from household surveys, the 2012 Rwanda Population and Housing Census, and a precipitation dataset were assessed using multivariate logistic regression. Widespread faecal contamination was present, and only 24.9% (95% CI 20.9–29.4%, n = 217) of household samples met WHO Guidelines of having no detectable TTC contamination, while 42.5% (95% CI 38.0–47.1%, n = 361) of samples had > 100 TTC/100 mL and considered high risk. Sub-national differences were observed, with poorer water quality in rural areas and Eastern province. In multivariate analyses, there was evidence for an association between detectable contamination and increased open waste disposal in a sector, lower elevation, and water sources other than piped to household or rainwater/bottled. Risk factors for intermediate/high risk contamination (> 10 TTC/100 mL) included low population density, increased open waste disposal, lower elevation, water sources other than piped to household or rainwater/bottled, and occurrence of an extreme rain event the previous day. Modelling suggests non-household-based risk factors are determinants of water quality in this setting, and these results suggest a substantial proportion of Rwanda's population are exposed to faecal contamination through drinking water. - Graphical abstract: Household drinking water quality (thermotolerant coliform colony forming units/100 mL) nationally and

  15. Assessment of faecal glucocorticoid metabolite excretion in captive female fishing cats (Prionailurus viverinus) in Thailand.

    Science.gov (United States)

    Khonmee, Jaruwan; Vorawattanatham, Narathip; Pinyopummin, Anuchai; Thitaram, Chatchote; Somgird, Chaleamchat; Punyapornwithaya, Veerasak; Brown, Janine L

    2016-01-01

    There is little information on the endocrinology of fishing cats (Prionailurus viverinus), an endangered species in Southeast Asia, especially that pertaining to adrenal function. This study characterized faecal glucocorticoid metabolites in female fishing cats housed at Chiang Mai Night Safari to investigate seasonal and age relationships in hormone patterns. Faecal samples were collected 3 days/week for 1 year from seven females ranging in age from 4.5 to 9.6 years. A corticosterone enzyme immunoassay was validated for fishing cats by showing increases (∼60%) in faecal glucocorticoid immunoactivity above pre-treatment baseline levels within 1-2 days after an adrenocorticotrophic hormone injection. Faecal glucocorticoid metabolite concentrations were not related to age (P > 0.05), but there was a seasonal effect, with concentrations being higher (P fishing cats, and we found that glucocorticoid metabolite production was influenced by seasonal factors, but not by age. We conclude that weather patterns should be taken into consideration in future studies of glucocorticoid activity in this endangered species, especially those studies aimed at improving captive management to create self-sustaining and healthy populations.

  16. Household-based prevalence of helminths and parasitic protozoa in rural KwaZulu-Natal, South Africa, assessed from faecal vault sampling.

    Science.gov (United States)

    Trönnberg, Linda; Hawksworth, David; Hansen, Anette; Archer, Colleen; Stenström, Thor Axel

    2010-10-01

    This study was undertaken to examine the family-based prevalence of environmentally persistent parasites in two rural communities of KwaZulu-Natal, South Africa. Samples were collected from 120 urine-diversion family toilets and screened for selected protozoa and helminths with immunomagnetic separation and the ammonium bicarbonate (AMBIC) protocol respectively. The parasites found were Ascaris lumbricoides (59%), Giardia intestinalis (54%), Trichuris trichiura (48%), Cryptosporidium spp. (21%) and Taenia spp. (18%). Only 14% of the household toilets were negative for these pathogens. The occurrence of A. lumbricoides and T. trichiura was lower (Pparasites per gram was done for each sample and this provided realistic risk assessment data for the reuse of material from urine-diversion toilets. The high occurrence of parasites found in the two communities, in spite of sanitation and hygiene interventions in the areas, suggests an endemicity that will not be reduced without de-worming campaigns. Finally, the study showed that sampling directly from the deposited faecal material may be useful for parasitic prevalence estimations. Copyright © 2010 Royal Society of Tropical Medicine and Hygiene.

  17. Antimicrobial resistance in faecal samples from buffalo, wildebeest and zebra grazing together with and without cattle in Tanzania.

    Science.gov (United States)

    Katakweba, A A S; Møller, K S; Muumba, J; Muhairwa, A P; Damborg, P; Rosenkrantz, J T; Minga, U M; Mtambo, M M A; Olsen, J E

    2015-04-01

    The aim of this study was to determine whether the practice of co-grazing with cattle and wild life constitutes a risk of transmission of antibiotic resistant bacteria to wild ungulates. Faecal samples were collected from buffalo (n = 35), wildebeest (n = 40), zebra (n = 40) and cattle (N = 20) from Mikumi National Park, Tanzania (MNP), where cattle is prohibited and from Ngorongoro Conservation Area (NCA) where co-grazing is practiced. The number of coliforms and enterococci resistant to selected antibiotics was determined. Wild life generally harboured higher number of resistant Escherichia coli and Enterococci than cattle, but with no general influence in wild life of co-grazing with cattle. Vancomycin-resistant Enterococci were detected in wild life samples, and E. coli resistant to cefotaxime and enrofloxacin were observed among isolates from all wild life, but not from cattle. Culture independent estimates of the number of sulII gene copies obtained by qPCR did not differ between wild life from the two sample sites, while tetW was significantly higher in samples from MPN than from NCA. Antibiotic resistant bacteria were not more frequently found in ungulates grazing together with cattle than ungulates without this interaction. This study did not indicate that transmission of antibiotic resistant bacteria is a frequent event following co-grazing of wild life and cattle. © 2014 The Society for Applied Microbiology.

  18. Another one bites the dust: faecal silica levels in large herbivores correlate with high-crowned teeth

    Science.gov (United States)

    Hummel, Jürgen; Findeisen, Eva; Südekum, Karl-Heinz; Ruf, Irina; Kaiser, Thomas M.; Bucher, Martin; Clauss, Marcus; Codron, Daryl

    2011-01-01

    The circumstances of the evolution of hypsodonty (= high-crowned teeth) are a bone of contention. Hypsodonty is usually linked to diet abrasiveness, either from siliceous phytoliths (monocotyledons) or from grit (dusty environments). However, any empirical quantitative approach testing the relation of ingested silica and hypsodonty is lacking. In this study, faecal silica content was quantified as acid detergent insoluble ash and used as proxy for silica ingested by large African herbivores of different digestive types, feeding strategies and hypsodonty levels. Separate sample sets were used for the dry (n = 15 species) and wet (n = 13 species) season. Average faecal silica contents were 17–46 g kg−1 dry matter (DM) for browsing and 52–163 g kg−1 DM for grazing herbivores. No difference was detected between the wet (97.5 ± 14.4 g kg−1 DM) and dry season (93.5 ± 13.7 g kg−1 DM) faecal silica. In a phylogenetically controlled analysis, a strong positive correlation (dry season r = 0.80, p < 0.0005; wet season r = 0.74, p < 0.005) was found between hypsodonty index and faecal silica levels. While surprisingly our results do not indicate major seasonal changes in silica ingested, the correlation of faecal silica and hypsodonty supports a scenario of a dominant role of abrasive silica in the evolution of high-crowned teeth. PMID:21068036

  19. Faecal soiling: pathophysiology of postdefaecatory incontinence.

    Science.gov (United States)

    Pucciani, F

    2013-08-01

    Passive postdefaecatory incontinence is poorly understood and yet is an important clinical problem. The aim of this study was to characterize the pathophysiology of postdefaecatory incontinence in patients affected by faecal soiling. Seventy-two patients (30 women, age range 49-79 years; 42 men, age range, 53-75 years) affected by faecal passive incontinence with faecal soiling were included in the study. Two patient groups were identified: Group 1 comprised 42 patients with postdefaecatory incontinence and Group 2 had 30 patients without incontinence after bowel movements. After a preliminary clinical evaluation, including the Faecal Incontinence Severity Index (FISI) score and the obstructed defaecation syndrome (ODS) score, all patients of Groups 1 and 2 were studied by means of endoanal ultrasound and anorectal manometry. The results were compared with those from 20 healthy control subjects. A significantly higher ODS score was found in Group 1 (P IAS) in Group 2 (P IAS atrophy and the FISI score (ρs 0.78; P < 0.03). Anal resting pressure (Pmax and Pm ) was significantly lower in Group 2 (P < 0.04). The straining test was considered positive in 30 (71.4%) patients in Group 1, significantly greater than in Group 2 (P < 0.01). A significantly higher conscious rectal sensitivity threshold (CRST) was found in Group 1 patients (P < 0.01). The ODS score, a positive straining test and high CRST values suggest that postdefaecatory incontinence is secondary to impaired defaecation. Colorectal Disease © 2013 The Association of Coloproctology of Great Britain and Ireland.

  20. A comparison of modifications of the McMaster method for the enumeration of Ascaris suum eggs in pig faecal samples.

    Science.gov (United States)

    Pereckiene, A; Kaziūnaite, V; Vysniauskas, A; Petkevicius, S; Malakauskas, A; Sarkūnas, M; Taylor, M A

    2007-10-21

    The comparative efficacies of seven published McMaster method modifications for faecal egg counting were evaluated on pig faecal samples containing Ascaris suum eggs. Comparisons were made as to the number of samples found to be positive by each of the methods, the total egg counts per gram (EPG) of faeces, the variations in EPG obtained in the samples examined, and the ease of use of each of the methods. Each method was evaluated after the examination of 30 samples of faeces. The positive samples were identified by counting A. suum eggs in one, two and three sections of newly designed McMaster chamber. In the present study compared methods were reported by: I-Henriksen and Aagaard [Henriksen, S.A., Aagaard, K.A., 1976. A simple flotation and McMaster method. Nord. Vet. Med. 28, 392-397]; II-Kassai [Kassai, T., 1999. Veterinary Helminthology. Butterworth-Heinemann, Oxford, 260 pp.]; III and IV-Urquhart et al. [Urquhart, G.M., Armour, J., Duncan, J.L., Dunn, A.M., Jennings, F.W., 1996. Veterinary Parasitology, 2nd ed. Blackwell Science Ltd., Oxford, UK, 307 pp.] (centrifugation and non-centrifugation methods); V and VI-Grønvold [Grønvold, J., 1991. Laboratory diagnoses of helminths common routine methods used in Denmark. In: Nansen, P., Grønvold, J., Bjørn, H. (Eds.), Seminars on Parasitic Problems in Farm Animals Related to Fodder Production and Management. The Estonian Academy of Sciences, Tartu, Estonia, pp. 47-48] (salt solution, and salt and glucose solution); VII-Thienpont et al. [Thienpont, D., Rochette, F., Vanparijs, O.F.J., 1986. Diagnosing Helminthiasis by Coprological Examination. Coprological Examination, 2nd ed. Janssen Research Foundation, Beerse, Belgium, 205 pp.]. The number of positive samples by examining single section ranged from 98.9% (method I), to 51.1% (method VII). Only with methods I and II, there was a 100% positivity in two out of three of the chambers examined, and FEC obtained using these methods were significantly (pcoefficient

  1. Faecal D/L lactate ratio is a metabolic signature of microbiota imbalance in patients with short bowel syndrome.

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    Camille Mayeur

    Full Text Available Our objective was to understand the functional link between the composition of faecal microbiota and the clinical characteristics of adults with short bowel syndrome (SBS. Sixteen patients suffering from type II SBS were included in the study. They displayed a total oral intake of 2661±1005 Kcal/day with superior sugar absorption (83±12% than protein (42±13% or fat (39±26%. These patients displayed a marked dysbiosis in faecal microbiota, with a predominance of Lactobacillus/Leuconostoc group, while Clostridium and Bacteroides were under-represented. Each patient exhibited a diverse lactic acid bacteria composition (L. delbrueckii subsp. bulgaricus, L. crispatus, L. gasseri, L. johnsonii, L. reuteri, L. mucosae, displaying specific D and L-lactate production profiles in vitro. Of 16 patients, 9/16 (56% accumulated lactates in their faecal samples, from 2 to 110 mM of D-lactate and from 2 to 80 mM of L-lactate. The presence of lactates in faeces (56% patients was used to define the Lactate-accumulator group (LA, while absence of faecal lactates (44% patients defines the Non lactate-accumulator group (NLA. The LA group had a lower plasma HCO3(- concentration (17.1±2.8 mM than the NLA group (22.8±4.6 mM, indicating that LA and NLA groups are clinically relevant sub-types. Two patients, belonging to the LA group and who particularly accumulated faecal D-lactate, were at risk of D-encephalopathic reactions. Furthermore, all patients of the NLA group and those accumulating preferentially L isoform in the LA group had never developed D-acidosis. The D/L faecal lactate ratio seems to be the most relevant index for a higher D-encephalopathy risk, rather than D- and L-lactate faecal concentrations per se. Testing criteria that take into account HCO3(- value, total faecal lactate and the faecal D/L lactate ratio may become useful tools for identifying SBS patients at risk for D-encephalopathy.

  2. Plasma cortisol and faecal cortisol metabolites concentrations in stereotypic and non-stereotypic horses: do stereotypic horses cope better with poor environmental conditions?

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    Fureix Carole

    2013-01-01

    Full Text Available Abstract Background Stereotypic behaviours, i.e. repetitive behaviours induced by frustration, repeated attempts to cope and/or brain dysfunction, are intriguing as they occur in a variety of domestic and captive species without any clear adaptive function. Among the different hypotheses, the coping hypothesis predicts that stereotypic behaviours provide a way for animals in unfavourable environmental conditions to adjust. As such, they are expected to have a lower physiological stress level (glucocorticoids than non-stereotypic animals. Attempts to link stereotypic behaviours with glucocorticoids however have yielded contradictory results. Here we investigated correlates of oral and motor stereotypic behaviours and glucocorticoid levels in two large samples of domestic horses (NStudy1 = 55, NStudy2 = 58, kept in sub-optimal conditions (e.g. confinement, social isolation, and already known to experience poor welfare states. Each horse was observed in its box using focal sampling (study 1 and instantaneous scan sampling (study 2. Plasma samples (collected in study 1 but also non-invasive faecal samples (collected in both studies were retrieved in order to assess cortisol levels. Results Results showed that 1 plasma cortisol and faecal cortisol metabolites concentrations did not differ between horses displaying stereotypic behaviours and non-stereotypic horses and 2 both oral and motor stereotypic behaviour levels did not predict plasma cortisol or faecal cortisol metabolites concentrations. Conclusions Cortisol measures, collected in two large samples of horses using both plasma sampling as well as faecal sampling (the latter method minimizing bias due to a non-invasive sampling procedure, therefore do not indicate that stereotypic horses cope better, at least in terms of adrenocortical activity.

  3. Decomposition of oak leaf litter and millipede faecal pellets in soil under temperate mixed oak forest

    Science.gov (United States)

    Tajovský, Karel; Šimek, Miloslav; Háněl, Ladislav; Šantrůčková, Hana; Frouz, Jan

    2015-04-01

    The millipedes Glomeris hexasticha (Diplopoda, Glomerida) were maintained under laboratory conditions and fed on oak leaf litter collected from a mixed oak forest (Abieto-Quercetum) in South Bohemia, Czech Republic. Every fourth day litter was changed and produced faecal pellets were separated and afterwards analysed. Content of organic carbon and C:N ratio lowered in faecal pellets as compared with consumed litter. Changes in content of chemical elements (P, K, Ca, Mg, Na) were recognised as those characteristic for the first stage of degradation of plant material. Samples of faecal pellets and oak leaf litter were then exposed in mesh bags between the F and H layers of forest soil for up to one year, subsequently harvested and analysed. A higher rate of decomposition of exposed litter than that of faecal pellets was found during the first two weeks. After 1-year exposure, the weight of litter was reduced to 51%, while that of pellets to 58% only, although the observed activity of present biotic components (algae, protozoans, nematodes; CO2 production, nitrogenase activity) in faecal pellets was higher as compared with litter. Different micro-morphological changes were observed in exposed litter and in pellets although these materials originated from the same initial sources. Comparing to intact leaf litter, another structural and functional processes occurred in pellets due to the fragmentation of plant material by millipedes. Both laboratory and field experiments showed that the millipede faecal pellets are not only a focal point of biodegradation activity in upper soil layers, but also confirmed that millipede feces undergo a slower decomposition than original leaf litter.

  4. Antimicrobial resistance in equine faecal Escherichia coli isolates from North West England

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    Williams Nicola J

    2010-04-01

    Full Text Available Abstract Background Escherichia coli isolates of equine faecal origin were investigated for antibiotic resistance, resistance genes and their ability to perform horizontal transfer. Methods In total, 264 faecal samples were collected from 138 horses in hospital and community livery premises in northwest England, yielding 296 resistant E. coli isolates. Isolates were tested for susceptibility to antimicrobial drugs by disc diffusion and agar dilution methods in order to determine minimum inhibitory concentrations (MIC. PCR amplification was used to detect genes conferring resistance to: ampicillin (TEM and SHV beta-lactamase, chloramphenicol (catI, catII, catIII and cml, tetracycline (tetA, tetB, tetC, tetD, tet E and tetG, and trimethoprim (dfrA1, dfrA9, dfrA12, dfrA13, dfr7, and dfr17. Results The proportion of antibiotic resistant isolates, and multidrug resistant isolates (MDR was significantly higher in hospital samples compared to livery samples (MDR: 48% of hospital isolates; 12% of livery isolates, p dfr, TEM beta-lactamase, tet and cat, conferring resistance to trimethoprim, ampicillin, tetracycline and chloramphenicol, respectively. Within each antimicrobial resistance group, these genes occurred at frequencies of 93% (260/279, 91%, 86.8% and 73.5%, respectively; with 115/296 (38.8% found to be MDR isolates. Conjugation experiments were performed on selected isolates and MDR phenotypes were readily transferred. Conclusions Our findings demonstrate that E. coli of equine faecal origin are commonly resistant to antibiotics used in human and veterinary medicine. Furthermore, our results suggest that most antibiotic resistance observed in equine E. coli is encoded by well-known and well-characterized resistant genes common to E. coli from man and domestic animals. These data support the ongoing concern about antimicrobial resistance, MDR, antimicrobial use in veterinary medicine and the zoonotic risk that horses could potentially pose to

  5. Increasing Genome Sampling and Improving SNP Genotyping for Genotyping-by-Sequencing with New Combinations of Restriction Enzymes.

    Science.gov (United States)

    Fu, Yong-Bi; Peterson, Gregory W; Dong, Yibo

    2016-04-07

    Genotyping-by-sequencing (GBS) has emerged as a useful genomic approach for exploring genome-wide genetic variation. However, GBS commonly samples a genome unevenly and can generate a substantial amount of missing data. These technical features would limit the power of various GBS-based genetic and genomic analyses. Here we present software called IgCoverage for in silico evaluation of genomic coverage through GBS with an individual or pair of restriction enzymes on one sequenced genome, and report a new set of 21 restriction enzyme combinations that can be applied to enhance GBS applications. These enzyme combinations were developed through an application of IgCoverage on 22 plant, animal, and fungus species with sequenced genomes, and some of them were empirically evaluated with different runs of Illumina MiSeq sequencing in 12 plant species. The in silico analysis of 22 organisms revealed up to eight times more genome coverage for the new combinations consisted of pairing four- or five-cutter restriction enzymes than the commonly used enzyme combination PstI + MspI. The empirical evaluation of the new enzyme combination (HinfI + HpyCH4IV) in 12 plant species showed 1.7-6 times more genome coverage than PstI + MspI, and 2.3 times more genome coverage in dicots than monocots. Also, the SNP genotyping in 12 Arabidopsis and 12 rice plants revealed that HinfI + HpyCH4IV generated 7 and 1.3 times more SNPs (with 0-16.7% missing observations) than PstI + MspI, respectively. These findings demonstrate that these novel enzyme combinations can be utilized to increase genome sampling and improve SNP genotyping in various GBS applications. Copyright © 2016 Fu et al.

  6. Reliable discrimination of 10 ungulate species using high resolution melting analysis of faecal DNA.

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    Ana Ramón-Laca

    Full Text Available Identifying species occupying an area is essential for many ecological and conservation studies. Faecal DNA is a potentially powerful method for identifying cryptic mammalian species. In New Zealand, 10 species of ungulate (Order: Artiodactyla have established wild populations and are managed as pests because of their impacts on native ecosystems. However, identifying the ungulate species present within a management area based on pellet morphology is unreliable. We present a method that enables reliable identification of 10 ungulate species (red deer, sika deer, rusa deer, fallow deer, sambar deer, white-tailed deer, Himalayan tahr, Alpine chamois, feral sheep, and feral goat from swabs of faecal pellets. A high resolution melting (HRM assay, targeting a fragment of the 12S rRNA gene, was developed. Species-specific primers were designed and combined in a multiplex PCR resulting in fragments of different length and therefore different melting behaviour for each species. The method was developed using tissue from each of the 10 species, and was validated in blind trials. Our protocol enabled species to be determined for 94% of faecal pellet swabs collected during routine monitoring by the New Zealand Department of Conservation. Our HRM method enables high-throughput and cost-effective species identification from low DNA template samples, and could readily be adapted to discriminate other mammalian species from faecal DNA.

  7. Use of denaturing gradient gel electrophoresis to detect Actinobacteria associated with the human faecal microbiota.

    Science.gov (United States)

    Hoyles, Lesley; Clear, Jessica A; McCartney, Anne L

    2013-08-01

    With the exceptions of the bifidobacteria, propionibacteria and coriobacteria, the Actinobacteria associated with the human gastrointestinal tract have received little attention. This has been due to the seeming absence of these bacteria from most clone libraries. In addition, many of these bacteria have fastidious growth and atmospheric requirements. A recent cultivation-based study has shown that the Actinobacteria of the human gut may be more diverse than previously thought. The aim of this study was to develop a denaturing gradient gel electrophoresis (DGGE) approach for characterizing Actinobacteria present in faecal samples. Amount of DNA added to the Actinobacteria-specific PCR used to generate strong PCR products of equal intensity from faecal samples of five infants, nine adults and eight elderly adults was anti-correlated with counts of bacteria obtained using fluorescence in situ hybridization probe HGC69A. A nested PCR using Actinobacteria-specific and universal PCR-DGGE primers was used to generate profiles for the Actinobacteria. Cloning of sequences from the DGGE bands confirmed the specificity of the Actinobacteria-specific primers. In addition to members of the genus Bifidobacterium, species belonging to the genera Propionibacterium, Microbacterium, Brevibacterium, Actinomyces and Corynebacterium were found to be part of the faecal microbiota of healthy humans. Copyright © 2013 Elsevier Ltd. All rights reserved.

  8. Faecal microbiota of forage-fed horses in New Zealand and the population dynamics of microbial communities following dietary change.

    Science.gov (United States)

    Fernandes, Karlette A; Kittelmann, Sandra; Rogers, Christopher W; Gee, Erica K; Bolwell, Charlotte F; Bermingham, Emma N; Thomas, David G

    2014-01-01

    The effects of abrupt dietary transition on the faecal microbiota of forage-fed horses over a 3-week period were investigated. Yearling Thoroughbred fillies reared as a cohort were exclusively fed on either an ensiled conserved forage-grain diet ("Group A"; n = 6) or pasture ("Group B"; n = 6) for three weeks prior to the study. After the Day 0 faecal samples were collected, horses of Group A were abruptly transitioned to pasture. Both groups continued to graze similar pasture for three weeks, with faecal samples collected at 4-day intervals. DNA was isolated from the faeces and microbial 16S and 18S rRNA gene amplicons were generated and analysed by pyrosequencing. The faecal bacterial communities of both groups of horses were highly diverse (Simpson's index of diversity > 0.8), with differences between the two groups on Day 0 (P 003), CF231 (family Paraprevotellaceae; P = 0.004), and currently unclassified members within the order Clostridiales (P = 0.003) and within the family Lachnospiraceae (P = 0.006). The bacterial community of Group A horses became similar to Group B within four days of feeding on pasture, whereas the structure of the archaeal community remained constant pre- and post-dietary change. The community structure of the faecal microbiota (bacteria, archaea and ciliate protozoa) of pasture-fed horses was also identified. The initial differences observed appeared to be linked to recent dietary history, with the bacterial community of the forage-fed horses responding rapidly to abrupt dietary change.

  9. Assessment of faecal glucocorticoid metabolite excretion in captive female fishing cats (Prionailurus viverinus) in Thailand

    Science.gov (United States)

    Khonmee, Jaruwan; Vorawattanatham, Narathip; Pinyopummin, Anuchai; Thitaram, Chatchote; Somgird, Chaleamchat; Punyapornwithaya, Veerasak; Brown, Janine L.

    2016-01-01

    There is little information on the endocrinology of fishing cats (Prionailurus viverinus), an endangered species in Southeast Asia, especially that pertaining to adrenal function. This study characterized faecal glucocorticoid metabolites in female fishing cats housed at Chiang Mai Night Safari to investigate seasonal and age relationships in hormone patterns. Faecal samples were collected 3 days/week for 1 year from seven females ranging in age from 4.5 to 9.6 years. A corticosterone enzyme immunoassay was validated for fishing cats by showing increases (∼60%) in faecal glucocorticoid immunoactivity above pre-treatment baseline levels within 1–2 days after an adrenocorticotrophic hormone injection. Faecal glucocorticoid metabolite concentrations were not related to age (P > 0.05), but there was a seasonal effect, with concentrations being higher (P < 0.05) during the winter (1.54 ± 0.04 µg/g) and rainy season (1.43 ± 0.04 µg/g) compared with the summer (1.22 ± 0.05 µg/g). Significant relationships were found between faecal glucocorticoids and rainfall (positive) and day length (negative), but not a temperature–humidity index. This is the first study to assess adrenal steroidogenic activity in female fishing cats, and we found that glucocorticoid metabolite production was influenced by seasonal factors, but not by age. We conclude that weather patterns should be taken into consideration in future studies of glucocorticoid activity in this endangered species, especially those studies aimed at improving captive management to create self-sustaining and healthy populations. PMID:27293767

  10. Genotype X/C recombinant (putative genotype I) of hepatitis B virus is rare in Hanoi, Vietnam--genotypes B4 and C1 predominate.

    Science.gov (United States)

    Phung, Thi Bich Thuy; Alestig, Erik; Nguyen, Thanh Liem; Hannoun, Charles; Lindh, Magnus

    2010-08-01

    There are eight known genotypes of hepatitis B virus, A-H, and several subgenotypes, with rather well-defined geographic distributions. HBV genotypes were evaluated in 153 serum samples from Hanoi, Vietnam. Of the 87 samples that could be genotyped, genotype B was found in 67 (77%) and genotype C in 19 (22%). All genotype C strains were of subgenotype C1, and the majority of genotype B strains were B4, while a few were B2. The genotype X/C recombinant strain, identified previously in Swedish patients of indigenous Vietnamese origin, was found in one sample. This variant, proposed to be classified as genotype I, has been found recently also by others in Vietnam and Laos. The current study indicates that the genotype X/C recombinant may represent approximately 1% of the HBV strains circulating in Vietnam. (c) 2010 Wiley-Liss, Inc.

  11. Temporal Variability of Faecal Contamination from On-Site Sanitation Systems in the Groundwater of Northern Thailand

    Science.gov (United States)

    Chuah, C. Joon; Ziegler, Alan D.

    2018-06-01

    We investigated the impacts of on-site sanitation systems to local groundwater. In this year-long study, we monitored the response of faecal contamination levels to hydroclimatological factors including rainfall and groundwater table. Concentration of faecal indicators— E. coli (ESC), Enterococcus (ENT), nitrate—in thirteen pairs of shallow and deep wells were determined every 7-14 days. All samples from shallow wells were tested positive for faecal contamination (ESC and ENT > 1 MPN/100 mL) but concentration varies. A maximum of 24,000 MPN/100 mL were recorded in some shallow wells. Water from deep wells showed lower susceptibility to contamination with only 4 and 23% of samples tested positive for ESC and ENT, respectively. Concentrations of ESC and ENT were lower too, with a maximum of 5 MPN/100 mL and 28 MPN/100 mL, respectively. Fluctuation in contamination among the wells was described by four archetypal responses to hydroclimatological forcing: (i) flushing during the onset of wet season, (ii) dilution over the course of the wet season, (iii) concentration during the dry season, and (iv) synoptic response to storms. Previous studies attempting to link the prevalence of faecal/waterborne diseases and temporal factors (e.g., dry vs wet season) have produced differing outcomes. Our study may help explain the relevant hydrological mechanisms leading to these varying observations. Presently, most communities in Thailand have access to `improved' sanitation systems. However, due to the unsustainable implementation of these systems, the otherwise viable drinking-water resources in the form of the abundant local groundwater has become a genuine health hazard.

  12. Blinded comparison of faecal loading on plain radiography versus radio-opaque marker transit studies in the assessment of constipation

    Energy Technology Data Exchange (ETDEWEB)

    Cowlam, S. [Sunderland Royal Hospital, Sunderland (United Kingdom); Vinayagam, R.; Khan, U.; Marsden, S.; Minty, I.; Moncur, P.; Bain, I. [University Hospital of North Durham, Durham (United Kingdom); Yiannakou, Y.J. [University Hospital of North Durham, Durham (United Kingdom)], E-mail: yan.yiannakou@cddft.nhs.uk

    2008-12-15

    Aim: To compare faecal loading on plain radiography versus radio-opaque marker transit studies in the assessment of constipation. Methods: The study group was a convenience sample of patients attending the Durham Constipation Clinic. All patients underwent transit studies according to an established protocol, and severity of constipation was assessed contemporaneously using a validated questionnaire (PAC-SYM). Transit studies were performed using radio-opaque markers that were ingested over 3 consecutive days, with a radiograph taken on the fourth day. Digital images of the radiograph were digitally altered to remove all traces of the transit markers without affecting the underlying pattern of faecal loading. Four observers assessed faecal loading independently; two clinicians (C1 and C2) and two radiologists (R1 and R2). C1 and R1 used a previously described formal scoring method of assessing faecal loading, whereas C2 and R2 assessed the images as if they were in a clinic or reporting session, grading the faecal loading as mild, moderate, or severe. Results: One hundred patients were recruited out of 186 presenting in a 2-year period. All patients completed assessments. The correlation between observers was only fair to moderate (r ranging from 0.34-0.51). There were some surprisingly marked disagreements in 10-18% of assessments. The correlation between faecal loading and transit was weak for all observers (r ranging from 0.261-0.311). Symptom severity did not correlate with faecal loading. Conclusion: These results suggest that there is considerable inter-observer variation in the radiological assessment of faecal loading, irrespective of the training or method used by the observer, and that there is very poor correlation with colonic transit. The diagnosis of constipation, and the assessment of severity, is best performed clinically.

  13. Blinded comparison of faecal loading on plain radiography versus radio-opaque marker transit studies in the assessment of constipation

    International Nuclear Information System (INIS)

    Cowlam, S.; Vinayagam, R.; Khan, U.; Marsden, S.; Minty, I.; Moncur, P.; Bain, I.; Yiannakou, Y.J.

    2008-01-01

    Aim: To compare faecal loading on plain radiography versus radio-opaque marker transit studies in the assessment of constipation. Methods: The study group was a convenience sample of patients attending the Durham Constipation Clinic. All patients underwent transit studies according to an established protocol, and severity of constipation was assessed contemporaneously using a validated questionnaire (PAC-SYM). Transit studies were performed using radio-opaque markers that were ingested over 3 consecutive days, with a radiograph taken on the fourth day. Digital images of the radiograph were digitally altered to remove all traces of the transit markers without affecting the underlying pattern of faecal loading. Four observers assessed faecal loading independently; two clinicians (C1 and C2) and two radiologists (R1 and R2). C1 and R1 used a previously described formal scoring method of assessing faecal loading, whereas C2 and R2 assessed the images as if they were in a clinic or reporting session, grading the faecal loading as mild, moderate, or severe. Results: One hundred patients were recruited out of 186 presenting in a 2-year period. All patients completed assessments. The correlation between observers was only fair to moderate (r ranging from 0.34-0.51). There were some surprisingly marked disagreements in 10-18% of assessments. The correlation between faecal loading and transit was weak for all observers (r ranging from 0.261-0.311). Symptom severity did not correlate with faecal loading. Conclusion: These results suggest that there is considerable inter-observer variation in the radiological assessment of faecal loading, irrespective of the training or method used by the observer, and that there is very poor correlation with colonic transit. The diagnosis of constipation, and the assessment of severity, is best performed clinically

  14. Environmental impact on faecal glucocorticoid metabolite concentrations in Grevy's Zebra (Equus grevyi)

    OpenAIRE

    Yarnell, K; Walker, SL

    2017-01-01

    The non-invasive nature of faecal glucocorticoid metabolite (FGM) assessment means that sample collection is on an opportunistic basis and samples cannot always be collected immediately upon defection during field studies. Faeces that have been exposed to heat and moisturemay not accurately reflect levels of FGM. Our study exposed male (n=3) and female (n=3) Grevy's zebra (Equus grevyi) faeces to six environmental conditions to simulate a range of weather and seasonal patterns (temperate clim...

  15. The effect of dietary garlic supplementation on body weight gain, feed intake, feed conversion efficiency, faecal score, faecal coliform count and feeding cost in crossbred dairy calves.

    Science.gov (United States)

    Ghosh, Sudipta; Mehla, Ram K; Sirohi, S K; Roy, Biswajit

    2010-06-01

    Thirty-six crossbred calves (Holstein cross) of 5 days of age were used to study the effect of garlic extract feeding on their performance up to the age of 2 months (pre-ruminant stage). They were randomly allotted into treatment and control groups (18 numbers in each group). Performance was evaluated by measuring average body weight (BW) gain, feed intake (dry matter (DM), total digestible nutrient (TDN) and crude protein (CP)), feed conversion efficiency (FCE; DM, TDN and CP), faecal score, faecal coliform count and feeding cost. Diets were the same for the both groups. In addition, treatment group received garlic extract supplementation at 250 mg/kg BW per day per calf. Body weight measured weekly, feed intake measured twice daily, proximate analysis of feeds and fodders analysed weekly, faecal scores monitored daily and faecal coliform count done weekly. There was significant increase in average body weight gain, feed intake and FCE and significant decrease in severity of scours as measured by faecal score and faecal coliform count in the treatment group compared to the control group (P Feed cost per kilogramme BW gain was significantly lower in the treatment group compared to control group (P calves for better performance.

  16. High-throughput microsatellite genotyping in ecology: improved accuracy, efficiency, standardization and success with low-quantity and degraded DNA.

    Science.gov (United States)

    De Barba, M; Miquel, C; Lobréaux, S; Quenette, P Y; Swenson, J E; Taberlet, P

    2017-05-01

    Microsatellite markers have played a major role in ecological, evolutionary and conservation research during the past 20 years. However, technical constrains related to the use of capillary electrophoresis and a recent technological revolution that has impacted other marker types have brought to question the continued use of microsatellites for certain applications. We present a study for improving microsatellite genotyping in ecology using high-throughput sequencing (HTS). This approach entails selection of short markers suitable for HTS, sequencing PCR-amplified microsatellites on an Illumina platform and bioinformatic treatment of the sequence data to obtain multilocus genotypes. It takes advantage of the fact that HTS gives direct access to microsatellite sequences, allowing unambiguous allele identification and enabling automation of the genotyping process through bioinformatics. In addition, the massive parallel sequencing abilities expand the information content of single experimental runs far beyond capillary electrophoresis. We illustrated the method by genotyping brown bear samples amplified with a multiplex PCR of 13 new microsatellite markers and a sex marker. HTS of microsatellites provided accurate individual identification and parentage assignment and resulted in a significant improvement of genotyping success (84%) of faecal degraded DNA and costs reduction compared to capillary electrophoresis. The HTS approach holds vast potential for improving success, accuracy, efficiency and standardization of microsatellite genotyping in ecological and conservation applications, especially those that rely on profiling of low-quantity/quality DNA and on the construction of genetic databases. We discuss and give perspectives for the implementation of the method in the light of the challenges encountered in wildlife studies. © 2016 John Wiley & Sons Ltd.

  17. Peptoniphilus catoniae sp. nov., isolated from a human faecal sample from a traditional Peruvian coastal community.

    Science.gov (United States)

    Patel, Nisha B; Tito, Raul Y; Obregón-Tito, Alexandra J; O'Neal, Lindsey; Trujillo-Villaroel, Omar; Marin-Reyes, Luis; Troncoso-Corzo, Luzmila; Guija-Poma, Emilio; Lewis, Cecil M; Lawson, Paul A

    2016-05-01

    A novel Gram-stain-positive, coccus-shaped, obligately anaerobic bacterium was isolated from a faecal sample obtained from an individual in a traditional community located off the southern coast of Peru. Comparative 16S rRNA gene sequence analysis showed the novel bacterium belonged to the genus Peptoniphilus but showed no particular relationship with any species, demonstrating less than 91 % 16S rRNA gene sequence similarity with all members of the genus. The major cellular fatty acids of the novel isolate were determined to be C10 : 0, C14 : 0, C16 : 0, C18 : 1ω9c and C18 : 2ω6,9c/anteiso-C18 : 0. The DNA G+C content was 34.4 mol%. End-products of metabolism from peptone-yeast-glucose broth (PYG) were determined to be acetate and butyrate. Based on the phenotypic, chemotaxonomic and phylogenetic results, the organism represents a novel species of the genus Peptoniphilus, for which the name Peptoniphilus catoniae sp. nov. is proposed. The type strain is M6.X2DT ( = DSM 29874T = CCUG 66798T).

  18. Evaluation of Faecalibacterium 16S rDNA genetic markers for accurate identification of swine faecal waste by quantitative PCR.

    Science.gov (United States)

    Duan, Chuanren; Cui, Yamin; Zhao, Yi; Zhai, Jun; Zhang, Baoyun; Zhang, Kun; Sun, Da; Chen, Hang

    2016-10-01

    A genetic marker within the 16S rRNA gene of Faecalibacterium was identified for use in a quantitative PCR (qPCR) assay to detect swine faecal contamination in water. A total of 146,038 bacterial sequences were obtained using 454 pyrosequencing. By comparative bioinformatics analysis of Faecalibacterium sequences with those of numerous swine and other animal species, swine-specific Faecalibacterium 16S rRNA gene sequences were identified and Polymerase Chain Okabe (PCR) primer sets designed and tested against faecal DNA samples from swine and non-swine sources. Two PCR primer sets, PFB-1 and PFB-2, showed the highest specificity to swine faecal waste and had no cross-reaction with other animal samples. PFB-1 and PFB-2 amplified 16S rRNA gene sequences from 50 samples of swine with positive ratios of 86 and 90%, respectively. We compared swine-specific Faecalibacterium qPCR assays for the purpose of quantifying the newly identified markers. The quantification limits (LOQs) of PFB-1 and PFB-2 markers in environmental water were 6.5 and 2.9 copies per 100 ml, respectively. Of the swine-associated assays tested, PFB-2 was more sensitive in detecting the swine faecal waste and quantifying the microbial load. Furthermore, the microbial abundance and diversity of the microbiomes of swine and other animal faeces were estimated using operational taxonomic units (OTUs). The species specificity was demonstrated for the microbial populations present in various animal faeces. Copyright © 2016 Elsevier Ltd. All rights reserved.

  19. Correlation of bowel symptoms with colonic transit, length, and faecal load in functional faecal retention

    DEFF Research Database (Denmark)

    Raahave, Dennis; Christensen, Elsebeth; Loud, Franck B.

    2009-01-01

    INTRODUCTION: Abdominal pain, bloating, and defecation disturbances are common complaints in gastrointestinal functional disorders. This study explores whether bowel symptoms are correlated to colon transit time (CTT), faecal loading (coprostasis), and colon length; and whether prokinetic interve...

  20. Faecal microbiota of forage-fed horses in New Zealand and the population dynamics of microbial communities following dietary change.

    Directory of Open Access Journals (Sweden)

    Karlette A Fernandes

    Full Text Available The effects of abrupt dietary transition on the faecal microbiota of forage-fed horses over a 3-week period were investigated. Yearling Thoroughbred fillies reared as a cohort were exclusively fed on either an ensiled conserved forage-grain diet ("Group A"; n = 6 or pasture ("Group B"; n = 6 for three weeks prior to the study. After the Day 0 faecal samples were collected, horses of Group A were abruptly transitioned to pasture. Both groups continued to graze similar pasture for three weeks, with faecal samples collected at 4-day intervals. DNA was isolated from the faeces and microbial 16S and 18S rRNA gene amplicons were generated and analysed by pyrosequencing. The faecal bacterial communities of both groups of horses were highly diverse (Simpson's index of diversity > 0.8, with differences between the two groups on Day 0 (P < 0.017 adjusted for multiple comparisons. There were differences between Groups A and B in the relative abundances of four genera, BF311 (family Bacteroidaceae; P = 0.003, CF231 (family Paraprevotellaceae; P = 0.004, and currently unclassified members within the order Clostridiales (P = 0.003 and within the family Lachnospiraceae (P = 0.006. The bacterial community of Group A horses became similar to Group B within four days of feeding on pasture, whereas the structure of the archaeal community remained constant pre- and post-dietary change. The community structure of the faecal microbiota (bacteria, archaea and ciliate protozoa of pasture-fed horses was also identified. The initial differences observed appeared to be linked to recent dietary history, with the bacterial community of the forage-fed horses responding rapidly to abrupt dietary change.

  1. Microbial shifts and signatures of long-term remission in ulcerative colitis after faecal microbiota transplantation

    NARCIS (Netherlands)

    Fuentes Enriquez de Salamanca, Susana; Rossen, Noortje G.; Spek, van der Mirjam J.; Hartman, Jorn H.A.; Huuskonen, Laura; Korpela, Katri; Salojärvi, Jarkko; Aalvink, Steven; Vos, de Willem M.; Haens, D' Geert R.; Zoetendal, Erwin G.

    2017-01-01

    Faecal microbiota transplantation (FMT) may contribute towards disease remission in ulcerative colitis (UC), but it is unknown which factors determine long-term effect of treatment. Here, we aimed to identify bacterial signatures associated with sustained remission. To this end, samples from

  2. High quality copy number and genotype data from FFPE samples using Molecular Inversion Probe (MIP) microarrays

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Yuker; Carlton, Victoria E.H.; Karlin-Neumann, George; Sapolsky, Ronald; Zhang, Li; Moorhead, Martin; Wang, Zhigang C.; Richardson, Andrea L.; Warren, Robert; Walther, Axel; Bondy, Melissa; Sahin, Aysegul; Krahe, Ralf; Tuna, Musaffe; Thompson, Patricia A.; Spellman, Paul T.; Gray, Joe W.; Mills, Gordon B.; Faham, Malek

    2009-02-24

    A major challenge facing DNA copy number (CN) studies of tumors is that most banked samples with extensive clinical follow-up information are Formalin-Fixed Paraffin Embedded (FFPE). DNA from FFPE samples generally underperforms or suffers high failure rates compared to fresh frozen samples because of DNA degradation and cross-linking during FFPE fixation and processing. As FFPE protocols may vary widely between labs and samples may be stored for decades at room temperature, an ideal FFPE CN technology should work on diverse sample sets. Molecular Inversion Probe (MIP) technology has been applied successfully to obtain high quality CN and genotype data from cell line and frozen tumor DNA. Since the MIP probes require only a small ({approx}40 bp) target binding site, we reasoned they may be well suited to assess degraded FFPE DNA. We assessed CN with a MIP panel of 50,000 markers in 93 FFPE tumor samples from 7 diverse collections. For 38 FFPE samples from three collections we were also able to asses CN in matched fresh frozen tumor tissue. Using an input of 37 ng genomic DNA, we generated high quality CN data with MIP technology in 88% of FFPE samples from seven diverse collections. When matched fresh frozen tissue was available, the performance of FFPE DNA was comparable to that of DNA obtained from matched frozen tumor (genotype concordance averaged 99.9%), with only a modest loss in performance in FFPE. MIP technology can be used to generate high quality CN and genotype data in FFPE as well as fresh frozen samples.

  3. Bacterial indicators of faecal pollution of water supplies and public ...

    African Journals Online (AJOL)

    Bacterial indicators of faecal pollution of water supplies and their significance to public health are reviewed in this paper, to highlight their levels of general acceptability and suitability as safeguards against health hazards associated with water supplies. Regular bacteriological analysis with the sole aim of detecting faecal ...

  4. Spontaneous scrotal faecal fistula in a Nigerian adult: review of ...

    African Journals Online (AJOL)

    We report a 28-year-old Nigerian who presented with four days history of spontaneous scrotal ulceration and faecal discharge. This symptom was preceded by features of intestinal obstruction which got relieved after the faecal discharge from the scrotum. He was resuscitated and had segmental resection and anastomosis ...

  5. Influence of clinical and laboratory variables on faecal antigen ELISA results in dogs with canine parvovirus infection.

    Science.gov (United States)

    Proksch, A L; Unterer, S; Speck, S; Truyen, U; Hartmann, K

    2015-06-01

    False negative faecal canine parvovirus (CPV) antigen ELISA results in dogs with CPV infection are common, but the factors that lead to these false negative results are still unknown. The aim of this study was to investigate whether dogs with a false negative faecal CPV antigen ELISA result have milder clinical signs and laboratory changes, a lower faecal virus load, higher faecal and serum CPV antibody titres and a faster recovery than dogs with a positive result. Eighty dogs with CPV infection, confirmed by the presence of clinical signs and a positive faecal CPV polymerase chain reaction (PCR), were assigned to two groups according to their faecal antigen ELISA result. Time until presentation, severity of symptoms, laboratory parameters, faecal virus load, faecal and serum antibody titres, and CPV sequencing data were compared between both groups. In 38/80 dogs that were hospitalised until recovery, the time to recovery, mortality, and the course of the disease were compared between dogs with positive and negative faecal antigen ELISA results. Of the 80 dogs included, 41 (51.3%) had a false negative faecal antigen ELISA result. ELISA-negative dogs had a significantly shorter time until presentation, lower frequency of defaecation, lower faecal virus load, and higher serum antibody concentrations than ELISA-positive dogs. Laboratory changes, CPV shedding, and outcomes were not associated with faecal antigen ELISA results. In conclusion, low faecal CPV load and antibodies binding to CPV antigen in faeces are likely to be important reasons for false negative faecal antigen ELISA results. Dogs with clinical signs of CPV infection should be retested by faecal PCR. Copyright © 2015 Elsevier Ltd. All rights reserved.

  6. Comparisons of sampling procedures and time of sampling for the detection of Salmonella in Danish infected chicken flocks raised in floor systems

    DEFF Research Database (Denmark)

    Gradel, K.O.; Andersen, J.; Madsen, M.

    2002-01-01

    other within each flock: 1) 5 pairs of socks, analysed as 5 samples, 2) 2 pairs of socks, analysed as one sample, and 3) 60 faecal samples, analysed as one pooled sample. Agreement between sampling methods was evaluated by the following statistical tests: 'Kappa', 'The adjusted rand', McNemar"s test...... in detecting S. enterica as the 60 faecal samples. In broiler flocks, 5 pairs of socks were used both in the routine samples taken at about 3 weeks of age for the establishment of infection of the flock, and as one of the follow-up samples taken shortly before slaughter age, which means that the only notable...... for marginal symmetry, Proportion of agreement P-0, P-, P-, and Odds Ratio. The highest agreement was found between the 2 types of sock sampling, while the lowest agreement was found by comparing 60 faecal samples with 5 pairs of socks. Two pairs of socks analysed as one pool appeared to be just as effective...

  7. Measurement of faecal sludge in-situ shear strength and density ...

    African Journals Online (AJOL)

    Various mechanised technologies have been developed to facilitate pit emptying, which are currently either tested on faecal sludge or an 'ad-hoc' simulant that (in the opinion of the tester) approximately replicates the behaviour of faecal sludge. This ranges from a watery consistency in some pour-flush latrines to the strong ...

  8. Additional oligofructose/inulin does not increase faecal bifidobacteria in critically ill patients receiving enteral nutrition: a randomised controlled trial.

    Science.gov (United States)

    Majid, Hazreen A; Cole, Jayne; Emery, Peter W; Whelan, Kevin

    2014-12-01

    Patients with diarrhoea during enteral nutrition (EN) have been shown to have low faecal bifidobacteria concentrations. Oligofructose/inulin selectively stimulate the growth of bifidobacteria in healthy humans. This study investigates the effect of additional oligofructose/inulin on the gastrointestinal microbiota, short-chain fatty acids (SCFA) and faecal output in patients receiving EN. Adult patients in the intensive care unit (ICU) who were starting EN with a formula containing fibre were randomised to receive 7 g/d of additional oligofructose/inulin or an identically packaged placebo (maltodextrin). A fresh faecal sample was collected at baseline and following at least 7 days of supplementation. Faecal microbiota were analysed using fluorescent in-situ hybridisation and faecal output was monitored daily. Twenty-two patients (mean age 71 years) completed at least 7 days of intervention (mean 12 days). At the end of the intervention, there were no significant differences in the concentrations of bifidobacteria between the groups, after adjusting for baseline values (oligofructose/inulin 6.9 + 1.4, placebo 7.8 + 1.3 log10 cells/g dry faeces, P > 0.05), but there were significantly lower concentrations of Faecalibacterium prausnitzii (7.0 + 1.0 vs. 8.4 + 1.3 log10 cells/g, P = 0.01) and Bacteroides-Prevotella (9.1 + 1.0 vs. 9.9 + 0.9 log10 cells/g, P = 0.05) in patients receiving additional oligofructose/inulin. There were no differences in faecal concentrations of any SCFA, secretory IgA, daily faecal score or incidence of diarrhoea between the two groups. Additional oligofructose/inulin did not increase faecal bifidobacteria in critically ill patients receiving EN, although it did result in lower concentrations of F. prausnitzii and Bacteroides-Prevotella. This trial is registered at http://controlled-trials.com. Identifier: ISRCTN06446184. Copyright © 2013 Elsevier Ltd and European Society for Clinical Nutrition and Metabolism. All

  9. How genetic data improve the interpretation of results of faecal glucocorticoid metabolite measurements in a free-living population.

    Directory of Open Access Journals (Sweden)

    Maik Rehnus

    Full Text Available Measurement of glucocorticoid metabolites (GCM in faeces has become a widely used and effective tool for evaluating the amount of stress experienced by animals. However, the potential sampling bias resulting from an oversampling of individuals when collecting "anonymous" (unknown sex or individual faeces has rarely been investigated. We used non-invasive genetic sampling (NIGS to investigate potential interpretation errors of GCM measurements in a free-living population of mountain hares during the mating and post-reproductive periods. Genetic data improved the interpretation of results of faecal GCM measurements. In general GCM concentrations were influenced by season. However, genetic information revealed that it was sex-dependent. Within the mating period, females had higher GCM levels than males, but individual differences were more expressed in males. In the post-reproductive period, GCM concentrations were neither influenced by sex nor individual. We also identified potential pitfalls in the interpretation of anonymous faecal samples by individual differences in GCM concentrations and resampling rates. Our study showed that sex- and individual-dependent GCM levels led to a misinterpretation of GCM values when collecting "anonymous" faeces. To accurately evaluate the amount of stress experienced by free-living animals using faecal GCM measurements, we recommend documenting individuals and their sex of the sampled population. In stress-sensitive and elusive species, such documentation can be achieved by using NIGS and for diurnal animals with sexual and individual variation in appearance or marked individuals, it can be provided by a detailed field protocol.

  10. Increase of faecal tryptic activity relates to changes in the intestinal microbiome: analysis of Crohn's disease with a multidisciplinary platform.

    Directory of Open Access Journals (Sweden)

    Tore Midtvedt

    Full Text Available To investigate-by molecular, classical and functional methods-the microbiota in biopsies and faeces from patients with active Crohn's disease (CD and controls.The microbiota in biopsies was investigated utilizing a novel molecular method and classical cultivation technology. Faecal samples were investigated by classical technology and four functional methods, reflecting alterations in short chain fatty acids pattern, conversion of cholesterol and bilirubin and inactivation of trypsin.By molecular methods we found more than 92% similarity in the microbiota on the biopsies from the two groups. However, 4.6% of microbes found in controls were lacking in CD patients. Furthermore, NotI representation libraries demonstrate two different clusters representing CD patients and controls, respectively. Utilizing conventional technology, Bacteroides (alt. Parabacteroides was less frequently detected in the biopsies from CD patients than from controls. A similar reduction in the number of Bacteroides was found in faecal samples. Bacteroides is the only group of bacteria known to be able to inactivate pancreatic trypsin. Faecal tryptic activity was high in CD patients, and inversely correlated to the levels of Bacteroides.CD patients have compositional and functional alterations in their intestinal microbiota, in line with the global description hypothesis rather than the candidate microorganism theory. The most striking functional difference was high amount of faecal tryptic activity in CD patients, inversely correlated to the levels of Bacteroides in faeces.

  11. Factors affecting genotyping success in giant panda fecal samples.

    Science.gov (United States)

    Zhu, Ying; Liu, Hong-Yi; Yang, Hai-Qiong; Li, Yu-Dong; Zhang, He-Min

    2017-01-01

    Fecal samples play an important role in giant panda conservation studies. Optimal preservation conditions and choice of microsatellites for giant panda fecal samples have not been established. In this study, we evaluated the effect of four factors (namely, storage type (ethanol (EtOH), EtOH -20 °C, 2-step storage medium, DMSO/EDTA/Tris/salt buffer (DETs) and frozen at -20 °C), storage time (one, three and six months), fragment length, and repeat motif of microsatellite loci) on the success rate of microsatellite amplification, allelic dropout (ADO) and false allele (FA) rates from giant panda fecal samples. Amplification success and ADO rates differed between the storage types. Freezing was inferior to the other four storage methods based on the lowest average amplification success and the highest ADO rates ( P panda fecal preservation in microsatellite studies, and EtOH and the 2-step storage medium should be chosen on priority for long-term storage. We recommend candidate microsatellite loci with longer repeat motif to ensure greater genotyping success for giant panda fecal studies.

  12. Integrated community profiling indicates long-term temporal stability of the predominant faecal microbiota in captive cheetahs.

    Directory of Open Access Journals (Sweden)

    Anne A M J Becker

    Full Text Available Understanding the symbiotic relationship between gut microbes and their animal host requires characterization of the core microbiota across populations and in time. Especially in captive populations of endangered wildlife species such as the cheetah (Acinonyx jubatus, this knowledge is a key element to enhance feeding strategies and reduce gastrointestinal disorders. In order to investigate the temporal stability of the intestinal microbiota in cheetahs under human care, we conducted a longitudinal study over a 3-year period with bimonthly faecal sampling of 5 cheetahs housed in two European zoos. For this purpose, an integrated 16S rRNA DGGE-clone library approach was used in combination with a series of real-time PCR assays. Our findings disclosed a stable faecal microbiota, beyond intestinal community variations that were detected between zoo sample sets or between animals. The core of this microbiota was dominated by members of Clostridium clusters I, XI and XIVa, with mean concentrations ranging from 7.5-9.2 log10 CFU/g faeces and with significant positive correlations between these clusters (P<0.05, and by Lactobacillaceae. Moving window analysis of DGGE profiles revealed 23.3-25.6% change between consecutive samples for four of the cheetahs. The fifth animal in the study suffered from intermediate episodes of vomiting and diarrhea during the monitoring period and exhibited remarkably more change (39.4%. This observation may reflect the temporary impact of perturbations such as the animal's compromised health, antibiotic administration or a combination thereof, which temporarily altered the relative proportions of Clostridium clusters I and XIVa. In conclusion, this first long-term monitoring study of the faecal microbiota in feline strict carnivores not only reveals a remarkable compositional stability of this ecosystem, but also shows a qualitative and quantitative similarity in a defined set of faecal bacterial lineages across the five

  13. Sorbitol-fermenting Bifidobacteria are indicators of very recent human faecal pollution in streams and groundwater habitats in urban tropical lowlands

    Science.gov (United States)

    2010-01-01

    Sorbitol-fermenting Bifidobacteria (SFB) proved to be an excellent indicator of very recent human faecal pollution (hours to days) in the investigated tropical stream and groundwater habitats. SFB were recovered from human faeces and sources potentially contaminated with human excreta. SFB were undetectable in animal faeces and environmental samples not contaminated with human faeces. Microcosm studies demonstrated a rapid die-off rate in groundwater (T90 value 0.6 days) and stream water (T90 value 0.9–1.7 days). Discrimination sensitivity analysis, including E. coli, faecal coliforms, total coliforms and Clostridium perfringens spores, revealed high ability of SFB to distinguish differing levels of faecal pollution especially for streams although high background levels of interfering bacteria can complicate its recovery on the used medium. Due to its faster die-off, as compared to many waterborne pathogens, SFB cannot replace microbiological standard parameters for routine water quality monitoring but it is highly recommendable as a specific and complementary tool when human faecal pollution has to be localized or verified. Because of its exclusive faecal origin and human specificity it seems also worthwhile to include SFB in future risk evaluation studies at tropical water resources in order to evaluate under which situations risks of infection may be indicated. PMID:20375476

  14. PHYSIOTHERAPY MANAGEMENT OF FAECAL IMPACTION:

    African Journals Online (AJOL)

    Dr.MrsOdebode

    bowel above the rectum) leading to serious discomfort. This accumulation can also lead to generalized abdominal distention. Faecal impaction is more common in elderly people with limited ability to move (Saddler, 2005). Among the causes are medications like antacids, which have aluminium as an ingredient; calcium ...

  15. Impact of inter-genotypic recombination and probe cross-reactivity on the performance of the Abbott RealTime HCV Genotype II assay for hepatitis C genotyping.

    Science.gov (United States)

    Sridhar, Siddharth; Yip, Cyril C Y; Chan, Jasper F W; To, Kelvin K W; Cheng, Vincent C C; Yuen, Kwok-Yung

    2018-05-01

    The Abbott RealTime HCV Genotype II assay (Abbott-RT-HCV assay) is a real-time PCR based genotyping method for hepatitis C virus (HCV). This study measured the impact of inter-genotypic recombination and probe cross-reactivity on the performance of the Abbott-RT-HCV assay. 517 samples were genotyped using the Abbott-RT-HCV assay over a one-year period, 34 (6.6%) were identified as HCV genotype 1 without further subtype designation raising the possibility of inaccurate genotyping. These samples were subjected to confirmatory sequencing. 27 of these 34 (79%) samples were genotype 1b while five (15%) were genotype 6. One HCV isolate was an inter-genotypic 1a/4o recombinant. This is a novel natural HCV recombinant that has never been reported. Inter-genotypic recombination and probe cross-reactivity can affect the accuracy of the Abbott-RT-HCV assay, both of which have significant implications on antiviral regimen choice. Confirmatory sequencing of ambiguous results is crucial for accurate genotyping. Copyright © 2018 Elsevier Inc. All rights reserved.

  16. Circulating rotavirus genotypes in the Irish paediatric population prior to the introduction of the vaccination programme.

    Science.gov (United States)

    Yandle, Z; Coughlan, S; Drew, R J; O'Flaherty, N; O'Gorman, J; De Gascun, C

    2017-11-01

    Rotavirus is the leading cause of viral gastroenteritis in children, and it is anticipated that the introduction of the Rotarix™ vaccine (GlaxoSmithKline Biologicals S.A., Rixensart, Belgium) into the Irish immunisation schedule will result in a significant reduction of rotavirus-associated disease. In the pre- and post-vaccination eras, it is important to determine circulating strains of rotavirus to assess vaccine effectiveness, to monitor vaccine failures, and to detect potential emerging strains. This study was a collaboration between the Temple Street Children's University Hospital (TSCUH), Dublin, and the National Virus Reference Laboratory (NVRL), Dublin, to determine the then circulating rotavirus strains in a paediatric hospital. In the 2015/2016 period (July 2015-June 2016) 89 faecal samples from paediatric patients (53 from TSCUH, 36 from other hospitals) were characterised. The results showed G1P[8] to be the predominant genotype (57%), followed by G9P[8] (34%), G4P[8] (6%), G2P[4] (2%), and G12P[8] (1%). This distribution of genotypes is comparable to those found in other European countries prior to vaccination suggesting that the vaccine should be highly efficacious in the Irish population.

  17. Integrated Community Profiling Indicates Long-Term Temporal Stability of the Predominant Faecal Microbiota in Captive Cheetahs

    Science.gov (United States)

    Becker, Anne A. M. J.; Janssens, Geert P. J.; Snauwaert, Cindy; Hesta, Myriam; Huys, Geert

    2015-01-01

    Understanding the symbiotic relationship between gut microbes and their animal host requires characterization of the core microbiota across populations and in time. Especially in captive populations of endangered wildlife species such as the cheetah (Acinonyx jubatus), this knowledge is a key element to enhance feeding strategies and reduce gastrointestinal disorders. In order to investigate the temporal stability of the intestinal microbiota in cheetahs under human care, we conducted a longitudinal study over a 3-year period with bimonthly faecal sampling of 5 cheetahs housed in two European zoos. For this purpose, an integrated 16S rRNA DGGE-clone library approach was used in combination with a series of real-time PCR assays. Our findings disclosed a stable faecal microbiota, beyond intestinal community variations that were detected between zoo sample sets or between animals. The core of this microbiota was dominated by members of Clostridium clusters I, XI and XIVa, with mean concentrations ranging from 7.5-9.2 log10 CFU/g faeces and with significant positive correlations between these clusters (Pcheetahs. The fifth animal in the study suffered from intermediate episodes of vomiting and diarrhea during the monitoring period and exhibited remarkably more change (39.4%). This observation may reflect the temporary impact of perturbations such as the animal’s compromised health, antibiotic administration or a combination thereof, which temporarily altered the relative proportions of Clostridium clusters I and XIVa. In conclusion, this first long-term monitoring study of the faecal microbiota in feline strict carnivores not only reveals a remarkable compositional stability of this ecosystem, but also shows a qualitative and quantitative similarity in a defined set of faecal bacterial lineages across the five animals under study that may typify the core phylogenetic microbiome of cheetahs. PMID:25905625

  18. Detection of anthelmintic resistance in sheep and goat against fenbendazole by faecal egg count reduction test.

    Science.gov (United States)

    Singh, Ramandeep; Bal, M S; Singla, L D; Kaur, Paramjit

    2017-06-01

    Anthelmintic resistance against commonly used anthelmintic fenbendazole was evaluated by employing faecal egg count reduction test (FECRT) in naturally occurring gastrointestinal (GI) nematodes in the semi organized sheep and goat farms of Ludhiana and Amritsar districts. A total of 80 animals (20 each for sheep and goat in both districts) were randomly selected and their faecal samples were examined by qualitative and quantitative parasitological techniques. Results indicate presence of high level of resistance against fenbendazole in both sheep and goat population of Ludhiana and Amritsar districts. More resistance was observed in the GI nematodes from animals reared in Amritsar district as compared to Ludhiana district. The level of anthelmintic resistance observed was apparently more in sheep than goats.

  19. Integrated site-specific quantification of faecal bacteria and detection of DNA markers in faecal contamination source tracking as a microbial risk tracking tool in urban Lake ecosystems

    Science.gov (United States)

    Donde, Oscar Omondi; Tian, Cuicui; Xiao, Bangding

    2017-11-01

    The presence of feacal-derived pathogens in water is responsible for several infectious diseases and deaths worldwide. As a solution, sources of fecal pollution in waters must be accurately assessed, properly determined and strictly controlled. However, the exercise has remained challenging due to the existing overlapping characteristics by different members of faecal coliform bacteria and the inadequacy of information pertaining to the contribution of seasonality and weather condition on tracking the possible sources of pollution. There are continued efforts to improve the Faecal Contamination Source Tracking (FCST) techniques such as Microbial Source Tracking (MST). This study aimed to make contribution to MST by evaluating the efficacy of combining site specific quantification of faecal contamination indicator bacteria and detection of DNA markers while accounting for seasonality and weather conditions' effects in tracking the major sources of faecal contamination in a freshwater system (Donghu Lake, China). The results showed that the use of cyd gene in addition to lacZ and uidA genes differentiates E. coli from other closely related faecal bacteria. The use of selective media increases the pollution source tracking accuracy. BSA addition boosts PCR detection and increases FCST efficiency. Seasonality and weather variability also influence the detection limit for DNA markers.

  20. Novel genotype of Ehrlichia canis detected in samples of human blood bank donors in Costa Rica.

    Science.gov (United States)

    Bouza-Mora, Laura; Dolz, Gaby; Solórzano-Morales, Antony; Romero-Zuñiga, Juan José; Salazar-Sánchez, Lizbeth; Labruna, Marcelo B; Aguiar, Daniel M

    2017-01-01

    This study focuses on the detection and identification of DNA and antibodies to Ehrlichia spp. in samples of blood bank donors in Costa Rica using molecular and serological techniques. Presence of Ehrlichia canis was determined in 10 (3.6%) out of 280 blood samples using polymerase chain reaction (PCR) targeting the ehrlichial dsb conserved gene. Analysis of the ehrlichial trp36 polymorphic gene in these 10 samples revealed substantial polymorphism among the E. canis genotypes, including divergent tandem repeat sequences. Nucleotide sequences of dsb and trp36 amplicons revealed a novel genotype of E. canis in blood bank donors from Costa Rica. Indirect immunofluorescence assay (IFA) detected antibodies in 35 (35%) of 100 serum samples evaluated. Thirty samples showed low endpoint titers (64-256) to E. canis, whereas five sera yielded high endpoint titers (1024-8192); these five samples were also E. canis-PCR positive. These findings represent the first report of the presence of E. canis in humans in Central America. Copyright © 2016 Elsevier GmbH. All rights reserved.

  1. Monitoring the circulation of rotavirus among children after the introduction of the RotarixTM vaccine in Goiânia, Brazil

    Directory of Open Access Journals (Sweden)

    Ana Maria Tavares Borges

    2011-06-01

    Full Text Available The epidemiological features of rotavirus A (RVA infection differ between children from developing and developed countries which could result in differences in vaccine efficacy around the world. To evaluate the impact of RotarixTM on RVA prevalence, we monitored RVA genotypes circulating in Goiânia by monitoring virus in faecal samples from children that had or had not been previously vaccinated. From February-November of 2008, 220 faecal samples were collected from children in seven day-care centres. RVA detection was performed by two methodologies and the results were confirmed by polyacrylamide gel electrophoresis. From the 220 samples, eight were RVA-positive (3.6% and five were from children that had received either one or two doses of the vaccine. All positive samples were collected from children with diarrhoea during August and September. Genotyping of the RVA characterised five of the viral samples as genotype G2P[4] and one as G8P[4], suggesting that G2P[4] was the predominant circulating genotype in Goiânia during the study. The fact that vaccinated children were also infected by RVA suggests that the vaccine does not fully protect against infection by the G2[P4] RVA genotype.

  2. The composition and metabolism of faecal microbiota is specifically modulated by different dietary polysaccharides and mucin: an isothermal microcalorimetry study.

    Science.gov (United States)

    Adamberg, K; Kolk, K; Jaagura, M; Vilu, R; Adamberg, S

    2018-01-29

    The metabolic activity of colon microbiota is specifically affected by fibres with various monomer compositions, degree of polymerisation and branching. The supply of a variety of dietary fibres assures the diversity of gut microbial communities considered important for the well-being of the host. The aim of this study was to compare the impact of different oligo- and polysaccharides (galacto- and fructooligosaccharides, resistant starch, levan, inulin, arabinogalactan, xylan, pectin and chitin), and a glycoprotein mucin on the growth and metabolism of faecal microbiota in vitro by using isothermal microcalorimetry (IMC). Faecal samples from healthy donors were incubated in a phosphate-buffered defined medium with or without supplementation of a single substrate. The generation of heat was followed on-line, microbiota composition (V3-V4 region of the 16S rRNA using Illumina MiSeq v2) and concentrations of metabolites (HPLC) were determined at the end of growth. The multiauxic power-time curves obtained were substrate-specific. More than 70% of all substrates except chitin were fermented by faecal microbiota with total heat generation of up to 8 J/ml. The final metabolite patterns were in accordance with the microbiota changes. For arabinogalactan, xylan and levan, the fibre-affected distribution of bacterial taxa showed clear similarities (e.g. increase of Bacteroides ovatus and decrease of Bifidobacterium adolescentis). The formation of propionic acid, an important colon metabolite, was enhanced by arabinogalactan, xylan and mucin but not by galacto- and fructooligosaccharides or inulin. Mucin fermentation resulted in acetate, propionate and butyrate production in ratios previously observed for faecal samples, indicating that mucins may serve as major substrates for colon microbial population. IMC combined with analytical methods was shown to be an effective method for screening the impact of specific dietary fibres on functional changes in faecal microbiota.

  3. Faecal loading in the cecum as a new radiological sign of acute appendicitis

    International Nuclear Information System (INIS)

    Petroianu, Andy

    2005-01-01

    Purpose: Although the radiological features of acute appendicitis have been well documented, the value of the plain radiography has not been fully appreciated. The aim of this study was to determine the frequency of the association of acute appendicitis and images of faecal loading in the cecum. Methods: Plain abdominal radiographs of 100 consecutive adult patients operated on acute appendicitis were assessed. The presence of faecal loading was registered. Results: The presence of faecal loading in the cecum occurred in 97 of the cases of acute appendicitis. Conclusion: This study seems to demonstrate that the presence of radiological images of faecal loading in the cecum may be a useful sign of acute appendicitis

  4. Genotyping coronaviruses associated with feline infectious peritonitis.

    Science.gov (United States)

    Lewis, Catherine S; Porter, Emily; Matthews, David; Kipar, Anja; Tasker, Séverine; Helps, Christopher R; Siddell, Stuart G

    2015-06-01

    Feline coronavirus (FCoV) infections are endemic among cats worldwide. The majority of infections are asymptomatic or result in only mild enteric disease. However, approximately 5 % of cases develop feline infectious peritonitis (FIP), a systemic disease that is a frequent cause of death in young cats. In this study, we report the complete coding genome sequences of six FCoVs: three from faecal samples from healthy cats and three from tissue lesion samples from cats with confirmed FIP. The six samples were obtained over a period of 8 weeks at a single-site cat rescue and rehoming centre in the UK. We found amino acid differences located at 44 positions across an alignment of the six virus translatomes and, at 21 of these positions, the differences fully or partially discriminated between the genomes derived from the faecal samples and the genomes derived from the tissue lesion samples. In this study, two amino acid differences fully discriminated the two classes of genomes: these were both located in the S2 domain of the virus surface glycoprotein gene. We also identified deletions in the 3c protein ORF of genomes from two of the FIP samples. Our results support previous studies that implicate S protein mutations in the pathogenesis of FIP. © 2015 The Authors.

  5. Megarectumsigma underwent surgery for chronic faecal impact action

    International Nuclear Information System (INIS)

    Canessa, C.; Gomez del Valle, M.; Caraballo, M.

    2002-01-01

    Seven patients with megarectumsigma underwent surgery for chronic faecal impaction,reviewing clinical diagnosis, aetiology and medical and surgical management.It is suggested medical management of chronic faecal impaction trying to achieve elective surgery.The curative surgery should include the resection of all pathologic bowel, but in Duhamel procedure and its modifications distal rectal tran section should be at the peritoneal reflection.Habr-Gama modification has shown to be technically easier and it has been communicated good functional results.Local unfavourable conditions may be resolve by staged surgery,which allows outline definitive bowel reconstruction after functional assessment

  6. Molecular analysis of faecal samples from birds to identify potential crop pests and useful biocontrol agents in natural areas.

    Science.gov (United States)

    King, R A; Symondson, W O C; Thomas, R J

    2015-06-01

    Wild habitats adjoining farmland are potentially valuable sources of natural enemies, but also of pests. Here we tested the utility of birds as 'sampling devices', to identify the diversity of prey available to predators and particularly to screen for pests and natural enemies using natural ecosystems as refugia. Here we used PCR to amplify prey DNA from three sympatric songbirds foraging on small invertebrates in Phragmites reedbed ecosystems, namely the Reed Warbler (Acrocephalus scirpaceus), Sedge Warbler (Acrocephalus schoenobaenus) and Cetti's Warbler (Cettia cetti). A recently described general invertebrate primer pair was used for the first time to analyse diets. Amplicons were cloned and sequenced, then identified by reference to the Barcoding of Life Database and to our own sequences obtained from fresh invertebrates. Forty-five distinct prey DNA sequences were obtained from 11 faecal samples, of which 39 could be identified to species or genus. Targeting three warbler species ensured that species-specific differences in prey choice broadened the range of prey taken. Amongst the prey found in reedbeds were major pests (including the tomato moth Lacanobia oleracea) as well as many potentially valuable natural enemies including aphidophagous hoverflies and braconid wasps. Given the mobility of birds, this approach provides a practical way of sampling a whole habitat at once, providing growers with information on possible invasion by locally resident pests and the colonization potential of natural enemies from local natural habitats.

  7. Faecal microbiota composition in vegetarians: comparison with omnivores in a cohort of young women in southern India.

    Science.gov (United States)

    Kabeerdoss, Jayakanthan; Devi, R Shobana; Mary, R Regina; Ramakrishna, Balakrishnan S

    2012-09-28

    The effect of vegetarian diets on faecal microbiota has been explored largely through culture-based techniques. The present study compared the faecal microbiota of vegetarian and omnivorous young women in southern India. Faecal samples were obtained from thirty-two lacto-vegetarian and twenty-four omnivorous young adult women from a similar social and economic background. Macronutrient intake and anthropometric data were collected. Faecal microbiota of interest was quantified by real-time PCR with SYBR Green using primers targeting 16S rRNA genes of groups, including: Clostridium coccoides group (Clostridium cluster XIVa), Roseburia spp.-Eubacterium rectale, Bacteroides--Prevotella group, Bifidobacterium genus, Lactobacillus group, Clostridium leptum group (Clostridium cluster IV), Faecalibacterium prausnitzii, Ruminococcus productus--C. coccoides, Butyrivibrio, Enterococcus species and Enterobacteriaceae. The groups were matched for age, socio-economic score and anthropometric indices. Intake of energy, complex carbohydrates and Ca were significantly higher in the omnivorous group. The faecal microbiota of the omnivorous group was enriched with Clostridium cluster XIVa bacteria, specifically Roseburia-E. rectale. The relative proportions of other microbial communities were similar in both groups. The butyryl-CoA CoA-transferase gene, associated with microbial butyrate production, was present in greater amounts in the faeces of omnivores, and the levels were highly correlated with Clostridium cluster XIVa and Roseburia-E. rectale abundance and to a lesser extent with Clostridium leptum and F. prausnitzii abundance and with crude fibre intake. Omnivores had an increased relative abundance of Clostridium cluster XIVa bacteria and butyryl-CoA CoA-transferase gene compared with vegetarians, but we were unable to identify the components of the diet responsible for this difference.

  8. Hepatitis C genotype distribution in patient and blood donor samples in South Africa for the period 2008-2012.

    Science.gov (United States)

    Prabdial-Sing, N; Chirwa, T; Thaver, J; Smuts, H; Vermeulen, M; Suchard, M; Puren, A J

    2016-11-01

    There are limited molecular epidemiological studies of hepatitis C at a national level in South Africa. The introduction of newer treatment modalities for hepatitis C requires knowledge of the genotypes as these may have different prognostic and therapeutic implications. This retrospective study describes genotype distributions of patients attending specialist clinics and a blood donor group studied during the period 2008-2012 in South Africa. Residual samples from diagnostic viral load testing from specialist clinics in South Africa (n=941) and from the South African National Blood Service (n=294) were analysed quantitatively by real-time PCR and genotyped using the Versant line probe assay or sequencing. Genotype 1 was predominant in blood donors (34%), whilst genotype 5a was prevalent in patients (36%). In the blood donor group, genotype 4 was detected for the first time. Genotype 2 was rare in the patient group and not detected in blood donors. Genotype 1 was the predominant genotype in the younger age groups (less than 30 years), whereas genotype 5a was found at higher proportions in the older age groups for both the patient and blood donor groups, comprising more than 60% of genotypes in those older than 50 years. Genotypes 1 and 5 were at highest proportions across all provinces compared to other genotypes. In blood donors, genotype 1 was predominant among Caucasians (43%) and genotype 5a among Blacks (54%). Such information is required for planning the impact on the health sector with regard to newly emerging therapies for hepatitis C and burden of disease. © 2016 John Wiley & Sons Ltd.

  9. Genotyping of Mycobacterium leprae present on Ziehl-Neelsen-stained microscopic slides and in skin biopsy samples from leprosy patients in different geographic regions of Brazil

    Directory of Open Access Journals (Sweden)

    Amanda Nogueira Brum Fontes

    2012-12-01

    Full Text Available We analysed 16 variable number tandem repeats (VNTR and three single-nucleotide polymorphisms (SNP in Mycobacterium leprae present on 115 Ziehl-Neelsen (Z-N-stained slides and in 51 skin biopsy samples derived from leprosy patients from Ceará (n = 23, Pernambuco (n = 41, Rio de Janeiro (n = 22 and Rondônia (RO (n = 78. All skin biopsies yielded SNP-based genotypes, while 48 of the samples (94.1% yielded complete VNTR genotypes. We evaluated two procedures for extracting M. leprae DNA from Z-N-stained slides: the first including Chelex and the other combining proteinase and sodium dodecyl sulfate. Of the 76 samples processed using the first procedure, 30.2% were positive for 16 or 15 VNTRs, whereas of the 39 samples processed using the second procedure, 28.2% yielded genotypes defined by at least 10 VNTRs. Combined VNTR and SNP analysis revealed large variability in genotypes, but a high prevalence of SNP genotype 4 in the Northeast Region of Brazil. Our observation of two samples from RO with an identical genotype and seven groups with similar genotypes, including four derived from residents of the same state or region, suggest a tendency to form groups according to the origin of the isolates. This study demonstrates the existence of geographically related M. leprae genotypes and that Z-N-stained slides are an alternative source for M. leprae genotyping.

  10. Effect of Heat Stress on Concentrations of Faecal Cortisol Metabolites in Dairy Cows.

    Science.gov (United States)

    Rees, A; Fischer-Tenhagen, C; Heuwieser, W

    2016-06-01

    The negative impact of heat stress on health and productivity of dairy cows is well known. Heat stress can be quantified with the temperature-humidity index (THI) and is defined as a THI ≥ 72. Additionally, animal welfare is affected in cows living under heat stress conditions. Finding a way to quantify heat stress in dairy cows has been of increasing interest over the past decades. Therefore, the objective of this study was to evaluate concentrations of faecal glucocorticoid metabolites [i.e. 11,17-dioxoandrostanes (11,17-DOA)] as an indirect stress parameter in dairy cows without heat stress (DOA 0), with heat stress on a single day (acute heat stress, DOA 1) or with more than a single day of heat stress (chronic heat stress, DOA 2). Cows were housed in five farms under moderate European climates. Two statistical approaches (approach 1 and approach 2) were assessed. Using approach 1, concentrations of faecal 11,17-DOA were compared among DOA 0, DOA 1 and DOA 2 samples regardless of their origin (i.e. cow, unpaired comparison with a one-way anova). Using approach 2, a cow was considered as its own control; that is 11,17-DOA was treated as a cow-specific factor and only paired samples were included in the analysis for this approach (paired comparison with t-tests). In approach 1 (p = 0.006) and approach 2 (p = 0.038), 11,17-DOA values of cows under acute heat stress were higher compared to those of cows without heat stress. Our results also indicate that acute heat stress has to be considered as a confounder in studies measuring faecal glucocorticoid metabolites in cows to evaluate other stressful situations. © 2016 Blackwell Verlag GmbH.

  11. Success and failure rates of tumor genotyping techniques in routine pathological samples with non-small-cell lung cancer.

    Science.gov (United States)

    Vanderlaan, Paul A; Yamaguchi, Norihiro; Folch, Erik; Boucher, David H; Kent, Michael S; Gangadharan, Sidharta P; Majid, Adnan; Goldstein, Michael A; Huberman, Mark S; Kocher, Olivier N; Costa, Daniel B

    2014-04-01

    Identification of some somatic molecular alterations in non-small-cell lung cancer (NSCLC) has become evidence-based practice. The success and failure rate of using commercially available tumor genotyping techniques in routine day-to-day NSCLC pathology samples is not well described. We sought to evaluate the success and failure rate of EGFR mutation, KRAS mutation, and ALK FISH in a cohort of lung cancers subjected to routine clinical tumor genotype. Clinicopathologic data, tumor genotype success and failure rates were retrospectively compiled and analyzed from 381 patient-tumor samples. From these 381 patients with lung cancer, the mean age was 65 years, 61.2% were women, 75.9% were white, 27.8% were never smokers, 73.8% had advanced NSCLC and 86.1% had adenocarcinoma histology. The tumor tissue was obtained from surgical specimens in 48.8%, core needle biopsies in 17.9%, and as cell blocks from aspirates or fluid in 33.3% of cases. Anatomic sites for tissue collection included lung (49.3%), lymph nodes (22.3%), pleura (11.8%), bone (6.0%), brain (6.0%), among others. The overall success rate for EGFR mutation analysis was 94.2%, for KRAS mutation 91.6% and for ALK FISH 91.6%. The highest failure rates were observed when the tissue was obtained from image-guided percutaneous transthoracic core-needle biopsies (31.8%, 27.3%, and 35.3% for EGFR, KRAS, and ALK tests, respectively) and bone specimens (23.1%, 15.4%, and 23.1%, respectively). In specimens obtained from bone, the failure rates were significantly higher for biopsies than resection specimens (40% vs. 0%, p=0.024 for EGFR) and for decalcified compared to non-decalcified samples (60% vs. 5.5%, p=0.021 for EGFR). Tumor genotype techniques are feasible in most samples, outside small image-guided percutaneous transthoracic core-needle biopsies and bone samples from core biopsies with decalcification, and therefore expansion of routine tumor genotype into the care of patients with NSCLC may not require special

  12. Detection of Strongylus vulgaris in equine faecal samples by real-time PCR and larval culture - method comparison and occurrence assessment.

    Science.gov (United States)

    Kaspar, A; Pfister, K; Nielsen, M K; Silaghi, C; Fink, H; Scheuerle, M C

    2017-01-11

    Strongylus vulgaris has become a rare parasite in Germany during the past 50 years due to the practice of frequent prophylactic anthelmintic therapy. To date, the emerging development of resistance in Cyathostominae and Parascaris spp. to numerous equine anthelmintics has changed deworming management and the frequency of anthelmintic usage. In this regard, reliable detection of parasitic infections, especially of the highly pathogenic S. vulgaris is essential. In the current study, two diagnostic methods for the detection of infections with S. vulgaris were compared and information on the occurrence of this parasite in German horses was gained. For this purpose, faecal samples of 501 horses were screened for S. vulgaris with real-time PCR and an additional larval culture was performed in samples of 278 horses. A subset of 26 horses underwent multiple follow-up examinations with both methods in order to evaluate both the persistence of S. vulgaris infections and the reproducibility of each diagnostic method. The real-time PCR revealed S. vulgaris-DNA in ten of 501 investigated equine samples (1.9%). The larval culture demonstrated larvae of S. vulgaris in three of the 278 samples (1.1%). A direct comparison of the two methods was possible in 321 samples including 43 follow-up examinations with the result of 11 S. vulgaris-positive samples by real-time PCR and 4 S. vulgaris-positive samples by larval culture. The McNemar's test (p-value = 0.016) revealed a significant difference and the kappa values (0.525) showed a moderate agreement between real-time PCR and larval culture. The real-time PCR detected a significantly higher proportion of positives of S. vulgaris compared to larval culture and should thus be considered as a routine diagnostic method for the detection of S. vulgaris in equine samples.

  13. Sigmoid Colonic Perforation with Faecal Peritonitis due to Faecaloma

    Directory of Open Access Journals (Sweden)

    Ibrahim Khalil

    2014-09-01

    Full Text Available Colon perforation is an uncommon event usually caused by malignancy, diverticular disease, amoebic colitis, steroid therapy, trauma and ulcerative colitis, but stercoral perforation is very rare. Severe chronic constipation is considered to be the main causative factor in development of stercoral perforation of colon. Sometimes it can also produce catastrophic complications like colonic obstruction, faecal peritonitis and septicaemia. We report a rare case of sigmoid colonic perforation with faecal peritonitis and pneumoperitonium due to faecaloma which was diagnosed after exploratory laparotomy.

  14. Impact of animal density on cattle nutrition in dry Mediterranean rangelands: a faecal near-IR spectroscopy-aided study.

    Science.gov (United States)

    Landau, S Y; Dvash, L; Yehuda, Y; Muklada, H; Peleg, G; Henkin, Z; Voet, H; Ungar, E D

    2018-02-01

    In the context of determining the sustainable carrying capacity of dry-Mediterranean herbaceous rangelands, we examined the effect of animal density on cattle nutrition, which is fundamental to animal performance and welfare. The effects on dietary components of low (0.56 cows/ha; L) and high (1.11 cows/ha; H) animal densities were monitored for three consecutive years in grazing beef cows. In the dry season (summer and early autumn), cows had free access to N-rich poultry litter (PL) given as a dietary supplement. In each season, near-IR spectroscopy (NIRS) was used to predict the chemical composition of herbage samples (ash, NDF, CP, in vitro dry matter digestibility (IVDMD) and metabolizable energy (ME) content from IVDMD). Near-IR spectroscopy was applied also to faecal samples to determine the chemical composition of the diet selected by the animal, as well as the contents of ash, NDF and CP in the faeces themselves. A faecal-NIRS equation was applied to estimate the dietary proportion of PL. Seasonal categories were green, dry without PL supplementation and dry with it. We found no effects of animal density on nutrition during the green season but effects were apparent when cows consumed dry pasture. Ash content predicted by faecal NIRS was higher in the diet than in plant samples clipped from pasture, which infers that cows ingested soil. Dietary and faecal ash contents were higher (Panimals. During the dry period, dietary contents of ME were higher in L than in H (Panimal health, the above results cast doubts on the long-term sustainability of the higher of the animal densities tested. Although it may be sustainable vis-à-vis the vegetation, treatment H may have exceeded the boundaries of what is acceptable for cow health. Chemical information revealed with NIRS can be used to evaluate whether animal densities are compatible with animal health and welfare standards and can play a role in determining the carrying capacity of Mediterranean rangelands.

  15. Real-Time PCR in faecal samples of Triatoma infestans obtained by xenodiagnosis: proposal for an exogenous internal control.

    Science.gov (United States)

    Bravo, Nicolás; Muñoz, Catalina; Nazal, Nicolás; Saavedra, Miguel; Martínez, Gabriela; Araya, Eduardo; Apt, Werner; Zulantay, Inés

    2012-03-26

    The polymerase chain reaction (PCR) has proved to be a sensitive technique to detect Trypanosoma cruzi in the chronic phase of Chagas disease, which is characterized by low and fluctuating parasitemia. Another technique proposed for parasitological diagnosis in this phase of infection combines a microscopic search for motile trypomastigote forms in faecal samples (FS) obtained by xenodiagnosis (XD) with conventional PCR (XD-PCR). In this study we evaluate the use of human blood DNA as an exogenous internal control (EIC) for real time PCR (qPCR) combined with XD (XD-qPCR) using chromosome 12 (X12) detection. None of the FS-XD evaluated by qPCR amplified for X12. Nevertheless, all the EIC-FS-XD mixtures amplified for X12. We determined that X12 is useful as an EIC for XD-qPCR because we showed that the FS-XD does not contain human DNA after 30 or more days of XD incubation. This information is relevant for research on T. cruzi by XD-qPCR since it allows ruling out inhibition and false negative results due to DNA loss during the process of extraction and purification.

  16. Short communication prevalence of susceptibility to etravirine by genotype and phenotype in samples received for routine HIV type 1 resistance testing in the United States.

    Science.gov (United States)

    Picchio, Gaston; Vingerhoets, Johan; Tambuyzer, Lotke; Coakley, Eoin; Haddad, Mojgan; Witek, James

    2011-12-01

    Abstract The prevalence of susceptibility to etravirine was investigated among clinical samples submitted for routine clinical testing in the United States using two separate weighted genotypic scoring systems. The presence of etravirine mutations and susceptibility to etravirine by phenotype of clinical samples from HIV-1-infected patients, submitted to Monogram Biosciences for routine resistance testing between June 2008 and June 2009, were analyzed. Susceptibility by genotype was determined using the Monogram and Tibotec etravirine-weighted genotypic scoring systems, with scores of ≤3 and ≤2, respectively, indicating full susceptibility. Susceptibility by phenotype was determined using the PhenoSense HIV assay, with lower and higher clinical cut-offs of 2.9 and 10, respectively. The frequency of individual etravirine mutations and the impact of the K103N mutation on susceptibility to etravirine by genotype were also determined. Among the 5482 samples with ≥1 defined nonnucleoside reverse transcriptase inhibitor (NNRTI) mutations associated with resistance, 67% were classed as susceptible to etravirine by genotype by both scoring systems. Susceptibility to etravirine by phenotype was higher (76%). The proportion of first-generation NNRTI-resistant samples with (n=3598) and without (n=1884) K103N with susceptibility to etravirine by genotype was 77% and 49%, respectively. Among samples susceptible to first-generation NNRTIs (n=9458), >99% of samples were susceptible to etravirine by phenotype (FC <2.9); the remaining samples had FC ≥2.9-10. In summary, among samples submitted for routine clinical testing in the United States, a high proportion of samples with first-generation NNRTI resistance was susceptible to etravirine by genotype and phenotype. A higher proportion of NNRTI-resistant samples with K103N than without was susceptible to etravirine.

  17. The Neanderthal meal: a new perspective using faecal biomarkers.

    Directory of Open Access Journals (Sweden)

    Ainara Sistiaga

    Full Text Available Neanderthal dietary reconstructions have, to date, been based on indirect evidence and may underestimate the significance of plants as a food source. While zooarchaeological and stable isotope data have conveyed an image of Neanderthals as largely carnivorous, studies on dental calculus and scattered palaeobotanical evidence suggest some degree of contribution of plants to their diet. However, both views remain plausible and there is no categorical indication of an omnivorous diet. Here we present direct evidence of Neanderthal diet using faecal biomarkers, a valuable analytical tool for identifying dietary provenance. Our gas chromatography-mass spectrometry results from El Salt (Spain, a Middle Palaeolithic site dating to ca. 50,000 yr. BP, represents the oldest positive identification of human faecal matter. We show that Neanderthals, like anatomically modern humans, have a high rate of conversion of cholesterol to coprostanol related to the presence of required bacteria in their guts. Analysis of five sediment samples from different occupation floors suggests that Neanderthals predominantly consumed meat, as indicated by high coprostanol proportions, but also had significant plant intake, as shown by the presence of 5β-stigmastanol. This study highlights the applicability of the biomarker approach in Pleistocene contexts as a provider of direct palaeodietary information and supports the opportunity for further research into cholesterol metabolism throughout human evolution.

  18. The core faecal bacterial microbiome of Irish Thoroughbred racehorses.

    Science.gov (United States)

    O' Donnell, M M; Harris, H M B; Jeffery, I B; Claesson, M J; Younge, B; O' Toole, P W; Ross, R P

    2013-12-01

    In this study, we characterized the gut microbiota in six healthy Irish thoroughbred racehorses and showed it to be dominated by the phyla Firmicutes, Bacteroidetes, Proteobacteria, Verrucomicrobia, Actinobacteria, Euryarchaeota, Fibrobacteres and Spirochaetes. Moreover, all the horses harboured Clostridium, Fibrobacter, Faecalibacterium, Ruminococcus, Eubacterium, Oscillospira, Blautia Anaerotruncus, Coprococcus, Treponema and Lactobacillus spp. Notwithstanding the sample size, it was noteworthy that the core microbiota species assignments identified Fibrobacter succinogenes, Eubacterium coprostanoligenes, Eubacterium hallii, Eubacterium ruminantium, Oscillospira guillermondii, Sporobacter termiditis, Lactobacillus equicursoris, Treponema parvum and Treponema porcinum in all the horses. This is the first study of the faecal microbiota in the Irish thoroughbred racehorse, a significant competitor in the global bloodstock industry. The information gathered in this pilot study provides a foundation for veterinarians and other equine health-associated professionals to begin to analyse the microbiome of performance of racehorses. This study and subsequent work may lead to alternate dietary approaches aimed at minimizing the risk of microbiota-related dysbiosis in these performance animals. Although Irish thoroughbreds are used nationally and internationally as performance animals, very little is known about the core faecal microbiota of these animals. This is the first study to characterize the bacterial microbiota present in the Irish thoroughbred racehorse faeces and elucidate a core microbiome irrespective of diet, animal management and geographical location. © 2013 The Society for Applied Microbiology.

  19. Molecular characterization and antimicrobial resistance of faecal and urinary Escherichia coli isolated from dogs and humans in Italy

    Directory of Open Access Journals (Sweden)

    Clara Tramuta

    2014-03-01

    Full Text Available During this study, 109 faecal Escherichia coli samples isolated from 61 dogs and 48 humans were characterised according to phylogenetic group, extraintestinal virulence factors and antibiotic resistance. The isolates from dogs were predominantly distributed within phylogroup B1 (36%, while the majority of human strains belonged to phylogroup B2 (54%. The prevalence of cnf1, hlyA, papC and sfa virulence genes was significantly associated with the group B2. Canine isolates showed multidrug resistance (MDR more frequently than human strains. Since group B2 contains most of the strains that cause extraintestinal infections, all 46 B2 faecal strains were confronted against an addition population of 57 urinary E. coli strains belonging to the same phylogroup. The comparison shows that there was no significant difference in the occurrence of virulence factors or in the distribution of antibiotic resistance between faecal and urinary E. coli isolates fromd dogs. At the same time, a highly significant association was detected between multiple resistence and the source of the strains and between MDR and E. coli isolated from urine in human. This study highlighted similar features of E. coli isolated across sources and hosts. The data suggest a high prevalence of antibiotic resistance in faecal strains, which may represent a serious health risk since these strains can function as a reservoir for uropathogenic E. coli.

  20. Identification of Zoonotic Genotypes of Giardia duodenalis

    DEFF Research Database (Denmark)

    Sprong, H.; Cacciò, S.M.; van der Giessen, J.W.B

    2009-01-01

    Giardia duodenalis, originally regarded as a commensal organism, is the etiologic agent of giardiasis, a gastrointestinal disease of humans and animals. Giardiasis causes major public and veterinary health concerns worldwide. Transmission is either direct, through the faecal-oral route, or indirect......, through ingestion of contaminated water or food. Genetic characterization of G. duodenalis isolates has revealed the existence of seven groups (assemblages A to G) which differ in their host distribution. Assemblages A and B are found in humans and in many other mammals, but the role of animals......, mixtures of genotypes in individual isolates were repeatedly observed. Possible explanations are the uptake of genetically different Giardia cysts by a host, or subsequent infection of an already infected host, likely without overt symptoms, with a different Giardia species, which may cause disease. Other...

  1. Faecal incontinence in myotonic dystrophy

    OpenAIRE

    Abercrombie, J; Rogers, J; Swash, M

    1998-01-01

    Two siblings with myotonic dystrophy presented for treatment of faecal incontinence. The pathophysiology of this functional disorder is described with the results of anorectal manometry, EMG, and biopsy of smooth and striated muscle of the anorectal sphincters. Both medical and surgical management of the incontinence was unsatisfactory in the long term. Involvement of gastrointestinal musculature is a characteristic feature the disease.



  2. Estimating the numbers of malaria infections in blood samples using high-resolution genotyping data.

    Directory of Open Access Journals (Sweden)

    Amanda Ross

    Full Text Available People living in endemic areas often habour several malaria infections at once. High-resolution genotyping can distinguish between infections by detecting the presence of different alleles at a polymorphic locus. However the number of infections may not be accurately counted since parasites from multiple infections may carry the same allele. We use simulation to determine the circumstances under which the number of observed genotypes are likely to be substantially less than the number of infections present and investigate the performance of two methods for estimating the numbers of infections from high-resolution genotyping data. The simulations suggest that the problem is not substantial in most datasets: the disparity between the mean numbers of infections and of observed genotypes was small when there was 20 or more alleles, 20 or more blood samples, a mean number of infections of 6 or less and where the frequency of the most common allele was no greater than 20%. The issue of multiple infections carrying the same allele is unlikely to be a major component of the errors in PCR-based genotyping. Simulations also showed that, with heterogeneity in allele frequencies, the observed frequencies are not a good approximation of the true allele frequencies. The first method that we proposed to estimate the numbers of infections assumes that they are a good approximation and hence did poorly in the presence of heterogeneity. In contrast, the second method by Li et al estimates both the numbers of infections and the true allele frequencies simultaneously and produced accurate estimates of the mean number of infections.

  3. Influence of sampling depth and post-sampling analysis time on the ...

    African Journals Online (AJOL)

    Bacteriological analysis was carried out for samples taken at water depth and at 1, 6, 12 and 24 hours post-sampling. It was observed that the total and faecal coliform bacteria were significantly higher in the 3 m water depth samples than in the surface water samples (ANOVA, F = 59.41, 26.751, 9.82 (T.C); 46.41, 26.81, ...

  4. Applicability of Commercially Available ELISA Kits for the Quantification of Faecal Immunoreactive Corticosterone Metabolites in Mice

    DEFF Research Database (Denmark)

    Abelson, Klas S P; Kalliokoski, Otto; Teilmann, Anne Charlotte

    2016-01-01

    Background: Commercially available ELISA kits are popular among investigators that quantify faecal corticosterone or cortisol metabolites (FCM) for stress assessment in animals. However, in faeces, these assays mainly detect immunoreactive glucocorticoid metabolites. Since different assays contain......: The present study was designed to investigate corticosterone (CORT) in serum and FCM levels in faeces of laboratory mice, as quantified in four different ELISA kits (DRG EIA-4164, Demeditec DEV9922, Enzo ADI-900-097 and Cayman EIA kit 500655). Assay kits were chosen based on the origin of the antibody...... assays, in both groups of mice. In faecal samples, there was no consistent positive correlation between the levels detected in the four assays and the measured concentration of FCM also differed between assays. Conclusion: Whereas commercially available CORT ELISAs are frequently successfully used...

  5. Rescue of Fructose-Induced Metabolic Syndrome by Antibiotics or Faecal Transplantation in a Rat Model of Obesity.

    Science.gov (United States)

    Di Luccia, Blanda; Crescenzo, Raffaella; Mazzoli, Arianna; Cigliano, Luisa; Venditti, Paola; Walser, Jean-Claude; Widmer, Alex; Baccigalupi, Loredana; Ricca, Ezio; Iossa, Susanna

    2015-01-01

    A fructose-rich diet can induce metabolic syndrome, a combination of health disorders that increases the risk of diabetes and cardiovascular diseases. Diet is also known to alter the microbial composition of the gut, although it is not clear whether such alteration contributes to the development of metabolic syndrome. The aim of this work was to assess the possible link between the gut microbiota and the development of diet-induced metabolic syndrome in a rat model of obesity. Rats were fed either a standard or high-fructose diet. Groups of fructose-fed rats were treated with either antibiotics or faecal samples from control rats by oral gavage. Body composition, plasma metabolic parameters and markers of tissue oxidative stress were measured in all groups. A 16S DNA-sequencing approach was used to evaluate the bacterial composition of the gut of animals under different diets. The fructose-rich diet induced markers of metabolic syndrome, inflammation and oxidative stress, that were all significantly reduced when the animals were treated with antibiotic or faecal samples. The number of members of two bacterial genera, Coprococcus and Ruminococcus, was increased by the fructose-rich diet and reduced by both antibiotic and faecal treatments, pointing to a correlation between their abundance and the development of the metabolic syndrome. Our data indicate that in rats fed a fructose-rich diet the development of metabolic syndrome is directly correlated with variations of the gut content of specific bacterial taxa.

  6. Rescue of Fructose-Induced Metabolic Syndrome by Antibiotics or Faecal Transplantation in a Rat Model of Obesity.

    Directory of Open Access Journals (Sweden)

    Blanda Di Luccia

    Full Text Available A fructose-rich diet can induce metabolic syndrome, a combination of health disorders that increases the risk of diabetes and cardiovascular diseases. Diet is also known to alter the microbial composition of the gut, although it is not clear whether such alteration contributes to the development of metabolic syndrome. The aim of this work was to assess the possible link between the gut microbiota and the development of diet-induced metabolic syndrome in a rat model of obesity. Rats were fed either a standard or high-fructose diet. Groups of fructose-fed rats were treated with either antibiotics or faecal samples from control rats by oral gavage. Body composition, plasma metabolic parameters and markers of tissue oxidative stress were measured in all groups. A 16S DNA-sequencing approach was used to evaluate the bacterial composition of the gut of animals under different diets. The fructose-rich diet induced markers of metabolic syndrome, inflammation and oxidative stress, that were all significantly reduced when the animals were treated with antibiotic or faecal samples. The number of members of two bacterial genera, Coprococcus and Ruminococcus, was increased by the fructose-rich diet and reduced by both antibiotic and faecal treatments, pointing to a correlation between their abundance and the development of the metabolic syndrome. Our data indicate that in rats fed a fructose-rich diet the development of metabolic syndrome is directly correlated with variations of the gut content of specific bacterial taxa.

  7. SLIMS--a user-friendly sample operations and inventory management system for genotyping labs.

    Science.gov (United States)

    Van Rossum, Thea; Tripp, Ben; Daley, Denise

    2010-07-15

    We present the Sample-based Laboratory Information Management System (SLIMS), a powerful and user-friendly open source web application that provides all members of a laboratory with an interface to view, edit and create sample information. SLIMS aims to simplify common laboratory tasks with tools such as a user-friendly shopping cart for subjects, samples and containers that easily generates reports, shareable lists and plate designs for genotyping. Further key features include customizable data views, database change-logging and dynamically filled pre-formatted reports. Along with being feature-rich, SLIMS' power comes from being able to handle longitudinal data from multiple time-points and biological sources. This type of data is increasingly common from studies searching for susceptibility genes for common complex diseases that collect thousands of samples generating millions of genotypes and overwhelming amounts of data. LIMSs provide an efficient way to deal with this data while increasing accessibility and reducing laboratory errors; however, professional LIMS are often too costly to be practical. SLIMS gives labs a feasible alternative that is easily accessible, user-centrically designed and feature-rich. To facilitate system customization, and utilization for other groups, manuals have been written for users and developers. Documentation, source code and manuals are available at http://genapha.icapture.ubc.ca/SLIMS/index.jsp. SLIMS was developed using Java 1.6.0, JSPs, Hibernate 3.3.1.GA, DB2 and mySQL, Apache Tomcat 6.0.18, NetBeans IDE 6.5, Jasper Reports 3.5.1 and JasperSoft's iReport 3.5.1.

  8. Faecal shedding and strain diversity of Listeria monocytogenes in healthy ruminants and swine in Northern Spain

    Directory of Open Access Journals (Sweden)

    Hurtado Ana

    2009-01-01

    Full Text Available Abstract Background Listeria monocytogenes is among the most important foodborne bacterial pathogens due to the high mortality rate and severity of the infection. L. monocytogenes is a ubiquitous organism occasionally present in the intestinal tract of various animal species and faecal shedding by asymptomatically infected livestock poses a risk for contamination of farm environments and raw food at the pre-harvest stages. The aim of this study was to determine the prevalence and strain diversity of L. monocytogenes in healthy ruminants and swine herds. Results Faecal samples from 30 animals per herd were collected from 343 herds (120 sheep, 124 beef cattle, 82 dairy cattle and 17 swine in the Basque Country and screened in pools by an automated enzyme-linked fluorescent immunoassay (VIDAS® to estimate the prevalence of positive herds. Positive samples were subcultured onto the selective and differential agar ALOA and biochemically confirmed. L. monocytogenes was isolated from 46.3% of dairy cattle, 30.6% beef cattle and 14.2% sheep herds, but not from swine. Within-herd prevalence investigated by individually analysing 197 sheep and 221 cattle detected 1.5% of faecal shedders in sheep and 21.3% in cattle. Serotyping of 114 isolates identified complex 4b as the most prevalent (84.2%, followed by 1/2a (13.2%, and PFGE analysis of 68 isolates showed a highly diverse L. monocytogenes population in ruminant herds. Conclusion These results suggested that cattle represent a potentially important reservoir for L. monocytogenes in the Basque Country, and highlighted the complexity of pathogen control at the farm level.

  9. Detection and genotyping of group A rotaviruses isolated from sewage samples in Monastir, Tunisia between April 2007 and April 2010.

    Science.gov (United States)

    Hassine-Zaafrane, M; Kaplon, J; Ben Salem, I; Sdiri-Loulizi, K; Sakly, N; Pothier, P; Aouni, M; Ambert-Balay, K

    2015-11-01

    To ascertain the viral load, the distribution of G and P types of group A rotaviruses (RV-A) in sewage samples and to compare strains in clinical, animal and environmental samples. During our study from April 2007 to April 2010, 518 samples of raw and treated sewage were collected from two biological sewage treatment plants (STPs) located in the Monastir region, Tunisia. RV-A was detected by real-time RT-PCR in 375 (72·4%) sewage samples. According to the quantification results of RV-A, it appears that the viral load in raw and treated sewage of the two STPs was quite similar (P = 0·735). The genotyping of RV-A strains detected in sewage samples showed a great diversity with 10 G types and 8 P types. Most of them were described as common in humans, but we also detected genotypes commonly found in animals. All the genotypes detected in two previous studies performed in our laboratory on clinical and bovine samples were also found in environmental samples. However, some genotypes commonly found in animal were only found in sewage samples. The comparison of environmental, clinical and animal data suggests that STPs may convey not only human sewage but also animal wastes, both of them contaminated with numerous RV-A strains which are not efficiently eliminated by the sewage treatment process and may spread to surface waters. This work demonstrates the potential release of human and animal RV-A into water sources, representing a public health risk, by inducing gastroenteritis in population, but also by increasing the risk of zoonotic transmission and formation of reassortant viruses which could get a higher infectious potential. Our findings also suggest that monitoring of sewage may provide an additional tool to determine the epidemiology of RV-A circulating in a given community. © 2015 The Society for Applied Microbiology.

  10. Genotyping of human parvovirus B19 in clinical samples from Brazil and Paraguay using heteroduplex mobility assay, single-stranded conformation polymorphism and nucleotide sequencing

    Directory of Open Access Journals (Sweden)

    Marcos César Lima de Mendonça

    2011-06-01

    Full Text Available Heteroduplex mobility assay, single-stranded conformation polymorphism and nucleotide sequencing were utilised to genotype human parvovirus B19 samples from Brazil and Paraguay. Ninety-seven serum samples were collected from individuals presenting with abortion or erythema infectiosum, arthropathies, severe anaemia and transient aplastic crisis; two additional skin samples were collected by biopsy. After the procedure, all clinical samples were classified as genotype 1.

  11. Detection and genotyping of human papillomavirus in urine samples from unvaccinated male and female adolescents in Italy.

    Directory of Open Access Journals (Sweden)

    Silvia Bianchi

    Full Text Available The introduction of vaccination against Human Papillomavirus (HPV in adolescent girls in 2006 has focused virological surveillance on this age group. As few studies have evaluated HPV infections in young populations, further data are needed in order to improve and extend prophylactic policy and to monitor epidemiological changes. The present study aimed at evaluating overall and type-specific HPV prevalence in both female and male adolescents in Italy. HPV DNA detection and genotyping was performed on urine samples collected from 870 unvaccinated adolescents (369 females, 501 males, 11-18 years of age in five cities in Italy. Following DNA extraction by means of a commercial kit (NucliSENS(®-miniMAG(®, bioMérieux, the L1 gene fragment was PCR amplified and genotyped by restriction fragment length polymorphism analysis. HPV DNA was detected in 1.5% of all samples, and in 3% and 0.4% of samples from females and males, respectively. In approximately 70% of HPV DNA positive adolescents, the infection was due to a single genotype, with 88.9% of genotypes belonging to the HR-clade. The only two HPV-positive boys (14 and 18 years old had HPV-70 genotype. Only one of the 11 HPV-infected girls was in the 11-14 age-group. HPV prevalence was 4.2% in girls aged 15-18 years and 60% of infections were due to vaccine types HPV-16 or HPV-6/-11. This is one of the few studies, the first conducted in Italy, on HPV infection in adolescents. Urine testing is the easier way of detecting HPV infection in younger populations. Our data revealed a very low HPV prevalence, and no infections were observed in the 12-year-old vaccine target population. The majority of infections were seen in females aged 15-18 years. Overall, more than 50% and 30% of the potentially persistent HPV infections detected in this group could have been prevented by the quadrivalent and the bivalent vaccines, respectively.

  12. Detection and genotyping of human papillomavirus in urine samples from unvaccinated male and female adolescents in Italy.

    Science.gov (United States)

    Bianchi, Silvia; Frati, Elena Rosanna; Panatto, Donatella; Martinelli, Marianna; Amicizia, Daniela; Zotti, Carla Maria; Martinese, Morena; Bonanni, Paolo; Boccalini, Sara; Coppola, Rosa Cristina; Masia, Giuseppina; Meloni, Angelo; Castiglia, Paolo; Piana, Andrea; Gasparini, Roberto; Tanzi, Elisabetta

    2013-01-01

    The introduction of vaccination against Human Papillomavirus (HPV) in adolescent girls in 2006 has focused virological surveillance on this age group. As few studies have evaluated HPV infections in young populations, further data are needed in order to improve and extend prophylactic policy and to monitor epidemiological changes. The present study aimed at evaluating overall and type-specific HPV prevalence in both female and male adolescents in Italy. HPV DNA detection and genotyping was performed on urine samples collected from 870 unvaccinated adolescents (369 females, 501 males, 11-18 years of age) in five cities in Italy. Following DNA extraction by means of a commercial kit (NucliSENS(®)-miniMAG(®), bioMérieux), the L1 gene fragment was PCR amplified and genotyped by restriction fragment length polymorphism analysis. HPV DNA was detected in 1.5% of all samples, and in 3% and 0.4% of samples from females and males, respectively. In approximately 70% of HPV DNA positive adolescents, the infection was due to a single genotype, with 88.9% of genotypes belonging to the HR-clade. The only two HPV-positive boys (14 and 18 years old) had HPV-70 genotype. Only one of the 11 HPV-infected girls was in the 11-14 age-group. HPV prevalence was 4.2% in girls aged 15-18 years and 60% of infections were due to vaccine types HPV-16 or HPV-6/-11. This is one of the few studies, the first conducted in Italy, on HPV infection in adolescents. Urine testing is the easier way of detecting HPV infection in younger populations. Our data revealed a very low HPV prevalence, and no infections were observed in the 12-year-old vaccine target population. The majority of infections were seen in females aged 15-18 years. Overall, more than 50% and 30% of the potentially persistent HPV infections detected in this group could have been prevented by the quadrivalent and the bivalent vaccines, respectively.

  13. Simultaneous monitoring of faecal indicators and harmful algae using an in-situ autonomous sensor.

    Science.gov (United States)

    Yamahara, K M; Demir-Hilton, E; Preston, C M; Marin, R; Pargett, D; Roman, B; Jensen, S; Birch, J M; Boehm, A B; Scholin, C A

    2015-08-01

    Faecal indicator bacteria (FIB) and harmful algal blooms (HABs) threaten the health and the economy of coastal communities worldwide. Emerging automated sampling technologies combined with molecular analytical techniques could enable rapid detection of micro-organisms in-situ, thereby improving resource management and public health decision-making. We evaluated this concept using a robotic device, the Environmental Sample Processor (ESP). The ESP automates in-situ sample collection, nucleic acid extraction and molecular analyses. Here, the ESP measured and reported concentrations of FIB (Enterococcus spp.), a microbial source-tracking marker (human-specific Bacteriodales) and a HAB species (Psuedo-nitzschia spp.) over a 45-day deployment on the Santa Cruz Municipal Wharf (Santa Cruz, CA, USA). Both FIB and HABs were enumerated from single in-situ collected water samples. The in-situ qPCR efficiencies ranged from 86% to 105%, while the limit of quantifications during the deployment was 10 copies reaction(-1) . No differences were observed in the concentrations of enterococci, the human-specific marker in Bacteroidales spp., and P. australis between in-situ collected sample and traditional hand sampling methods (P > 0·05). Analytical results were Internet-accessible within hours of sample collection, demonstrating the feasibility of same-day public notification of current water quality conditions. This study presents the first report of in-situ qPCR enumeration of both faecal indicators and harmful algal species in coastal marine waters. We utilize a robotic device for in-situ quantification of enterococci, the human-specific marker in Bacteriodales and Pseudo-nitzschia spp. from the same water samples collected and processed in-situ. The results demonstrate that rapid, in-situ monitoring can be utilized to identify and quantify multiple health-relevant micro-organisms important in water quality monitoring and that this monitoring can be used to inform same

  14. Genotyping comparison of Mycobacterium leprae isolates by VNTR analysis from nasal samples in a Brazilian endemic region.

    Science.gov (United States)

    Lima, Luana Nepomueceno Costa; Frota, Cristiane Cunha; Suffys, Phillip Noel; Fontes, Amanda Nogueira Brum; Mota, Rosa Maria Salani; Almeida, Rosa Livia Freitas; Andrade Pontes, Maria Araci de; Gonçalves, Heitor de Sá; Kendall, Carl; Kerr, Ligia Regina Sansigolo

    2018-02-06

    This study analyzed the genetic diversity by MIRU-VNTR of Mycobacterium leprae isolates from nasal cavities and related to epidemiological and clinical data. The sample consisted of 48 newly diagnosed leprosy cases that tested positive for M. leprae PCR in nasal secretion (NS) attending to the National Reference Center of Dermatology Dona Libania (CDERM), Fortaleza, Brazil. Total DNA was extracted from NS of each patient and used for amplification of four M. leprae VNTR loci. Four clusters of M. leprae isolates were formed with identical genotypes. In the spatial analysis, 12 leprosy cases presented similar genotypes organized into 4 clusters. The most common genotypes in the current study was AC8b: 8, AC9: 7, AC8a: 8, GTA9: 10, which may represent a genotype of circulating strains most often in Ceará. A minimum set of four MIRU-VNTR loci was demonstrated to study the genetic diversity of M. leprae isolates from NS.

  15. Quantifying the sources of variability in equine faecal egg counts: implications for improving the utility of the method.

    Science.gov (United States)

    Denwood, M J; Love, S; Innocent, G T; Matthews, L; McKendrick, I J; Hillary, N; Smith, A; Reid, S W J

    2012-08-13

    The faecal egg count (FEC) is the most widely used means of quantifying the nematode burden of horses, and is frequently used in clinical practice to inform treatment and prevention. The statistical process underlying the FEC is complex, comprising a Poisson counting error process for each sample, compounded with an underlying continuous distribution of means between samples. Being able to quantify the sources of variability contributing to this distribution of means is a necessary step towards providing estimates of statistical power for future FEC and FECRT studies, and may help to improve the usefulness of the FEC technique by identifying and minimising unwanted sources of variability. Obtaining such estimates require a hierarchical statistical model coupled with repeated FEC observations from a single animal over a short period of time. Here, we use this approach to provide the first comparative estimate of multiple sources of within-horse FEC variability. The results demonstrate that a substantial proportion of the observed variation in FEC between horses occurs as a result of variation in FEC within an animal, with the major sources being aggregation of eggs within faeces and variation in egg concentration between faecal piles. The McMaster procedure itself is associated with a comparatively small coefficient of variation, and is therefore highly repeatable when a sufficiently large number of eggs are observed to reduce the error associated with the counting process. We conclude that the variation between samples taken from the same animal is substantial, but can be reduced through the use of larger homogenised faecal samples. Estimates are provided for the coefficient of variation (cv) associated with each within animal source of variability in observed FEC, allowing the usefulness of individual FEC to be quantified, and providing a basis for future FEC and FECRT studies. Copyright © 2012 Elsevier B.V. All rights reserved.

  16. Common genotypes of hepatitis B virus

    International Nuclear Information System (INIS)

    Idrees, M.; Khan, S.; Riazuddin, S.

    2004-01-01

    Objective: To find out the frequency of common genotypes of hepatitis-B virus (HBV). Subjects and Methods: HBV genotypes were determined in 112 HBV DNA positive sera by a simple and precise molecular genotyping system base on PCR using type-specific primers for the determination of genotypes of HBV A through H. Results: Four genotypes (A,B,C and D) out of total eight reported genotypes so far were identified. Genotypes A, B and C were predominant. HBV genotype C was the most predominant in this collection, appearing in 46 samples (41.7%). However, the genotypes of a total of 5 (4.46%) samples could not be determined with the present genotyping system. Mixed genotypes were seen in 8(7.14% HBV) isolates. Five of these were infected with genotypes A/D whereas two were with genotypes C/D. One patient was infected with 4 genotypes (A/B/C/D). Genotype A (68%) was predominant in Sindh genotype C was most predominant in North West Frontier Province (NWFP) (68.96) whereas genotype C and B were dominant in Punjab (39.65% and 25.86% respectively). Conclusion: All the four common genotypes of HBV found worldwide (A,B,C and D) were isolated. Genotype C is the predominant Genotypes B and C are predominant in Punjab and N.W.F.P. whereas genotype A is predominant in Sindh. (author)

  17. Pyrosequencing the Canine Faecal Microbiota: Breadth and Depth of Biodiversity

    Science.gov (United States)

    Hand, Daniel; Wallis, Corrin; Colyer, Alison; Penn, Charles W.

    2013-01-01

    Mammalian intestinal microbiota remain poorly understood despite decades of interest and investigation by culture-based and other long-established methodologies. Using high-throughput sequencing technology we now report a detailed analysis of canine faecal microbiota. The study group of animals comprised eleven healthy adult miniature Schnauzer dogs of mixed sex and age, some closely related and all housed in kennel and pen accommodation on the same premises with similar feeding and exercise regimes. DNA was extracted from faecal specimens and subjected to PCR amplification of 16S rDNA, followed by sequencing of the 5′ region that included variable regions V1 and V2. Barcoded amplicons were sequenced by Roche-454 FLX high-throughput pyrosequencing. Sequences were assigned to taxa using the Ribosomal Database Project Bayesian classifier and revealed dominance of Fusobacterium and Bacteroidetes phyla. Differences between animals in the proportions of different taxa, among 10,000 reads per animal, were clear and not supportive of the concept of a “core microbiota”. Despite this variability in prominent genera, littermates were shown to have a more similar faecal microbial composition than unrelated dogs. Diversity of the microbiota was also assessed by assignment of sequence reads into operational taxonomic units (OTUs) at the level of 97% sequence identity. The OTU data were then subjected to rarefaction analysis and determination of Chao1 richness estimates. The data indicated that faecal microbiota comprised possibly as many as 500 to 1500 OTUs. PMID:23382835

  18. Pyrosequencing the canine faecal microbiota: breadth and depth of biodiversity.

    Directory of Open Access Journals (Sweden)

    Daniel Hand

    Full Text Available Mammalian intestinal microbiota remain poorly understood despite decades of interest and investigation by culture-based and other long-established methodologies. Using high-throughput sequencing technology we now report a detailed analysis of canine faecal microbiota. The study group of animals comprised eleven healthy adult miniature Schnauzer dogs of mixed sex and age, some closely related and all housed in kennel and pen accommodation on the same premises with similar feeding and exercise regimes. DNA was extracted from faecal specimens and subjected to PCR amplification of 16S rDNA, followed by sequencing of the 5' region that included variable regions V1 and V2. Barcoded amplicons were sequenced by Roche-454 FLX high-throughput pyrosequencing. Sequences were assigned to taxa using the Ribosomal Database Project Bayesian classifier and revealed dominance of Fusobacterium and Bacteroidetes phyla. Differences between animals in the proportions of different taxa, among 10,000 reads per animal, were clear and not supportive of the concept of a "core microbiota". Despite this variability in prominent genera, littermates were shown to have a more similar faecal microbial composition than unrelated dogs. Diversity of the microbiota was also assessed by assignment of sequence reads into operational taxonomic units (OTUs at the level of 97% sequence identity. The OTU data were then subjected to rarefaction analysis and determination of Chao1 richness estimates. The data indicated that faecal microbiota comprised possibly as many as 500 to 1500 OTUs.

  19. Antimicrobial-resistant faecal organisms in algae products marketed as health supplements

    LENUS (Irish Health Repository)

    2017-09-01

    Dietary supplements are increasingly popular in Irish society. One of these is blue-green algae which is used with a variety health benefits in mind. A batch of Chlorella powder was found to be contaminated with Salmonella species in Ireland in 2015. This prompted additional testing of a total of 8 samples of three different products (Chlorella, Spirulina and Super Greens), for other faecal flora and antimicrobial resistance in any bacteria isolated. All 8 samples cultured enteric flora such as Enterococci, Enterobacteriaceae and Clostridium species. Antimicrobial susceptibility testing revealed one isolate with extended-spectrum β-lactamase (ESBL) activity and one with carbapenemase activity. Clinicians caring for vulnerable patients should be aware of the potential risk of exposure to antimicrobial resistant bacteria associated with these products

  20. Effects of Supplemental Mannanoligosaccharides on Growth Performance, Faecal Characteristics and Health in Dairy Calves

    Directory of Open Access Journals (Sweden)

    Cagdas Kara

    2015-11-01

    Full Text Available Twenty Holstein calves were used to investigate the effects of mannanoligosaccharides (MOS supplementation in the whole milk on growth performance, faecal score, faecal pH, selected faecal bacterial populations and health during the preweaning period. Healthy calves selected by clinical examination were allocated to one of the two groups (control [CG] and experimental [EG] at 5 days old. Each group consisted of 5 male and 5 female calves. Each calf in EG was supplemented with 7 g/d of a MOS product (Celmanax from 5 days to 56 days of age. MOS supplement was mixed with the whole milk once in the morning and administered to the calves in EG via nipple bottle, whereas the calves in CG were fed the whole milk without MOS. Calves were weaned at 56 days of age. The final body weight, average daily weight gain (ADG and average daily feed intake (ADFI were statistically similar (p>0.05 but were higher by 3.70%, 6.66%, and 10.97%, respectively, in MOS than in control calves. Feed efficiency (ADG/ADFI was also similar in two calves group. While faecal scores did not differ on day 5, 7, 14, 21, 28, 42, 49, and 56 between groups, EG had a higher faecal score (p = 0.05 than CG on day 35. Faecal concentration of Lactobacillus was lower (p0.05 in faecal concentrations of Bifidobacterium, Clostridium perfringens, and Escherichia coli were found between groups. Although there were no significant differences (p>0.05 in the incidence of diarrhoea, treatment days for diarrhoea and the costs associated with diarrhoea treatments between groups, collectively, the observed reductions in treatment days and the cost of diarrhoea treatments accompanying increases in final body weight, ADG and ADFI for EG may indicate potential benefit of MOS in treatment of diarrhoea.

  1. Faecal incontinence following radiotherapy for prostate cancer: A systematic review

    DEFF Research Database (Denmark)

    Maeda, Yasuko; Høyer, Morten; Lundby, Lilli

    2011-01-01

    BACKGROUND: Faecal incontinence (FI) after radiotherapy is a known phenomenon, but has received little attention to date. This article aimed to review current knowledge on faecal incontinence related to radiotherapy for prostate cancer. METHODS: PubMed was searched for English-language articles......-volume parameters and incidence is equivocal, although some studies suggest parameters confined to the lower rectum and/or anal canal may be of value to predict the extent of the injury and could be used as constraints in the dose planning process. CONCLUSIONS: Interpretation of data is limited due to lack of large...

  2. Transforming microbial genotyping: a robotic pipeline for genotyping bacterial strains.

    Directory of Open Access Journals (Sweden)

    Brian O'Farrell

    Full Text Available Microbial genotyping increasingly deals with large numbers of samples, and data are commonly evaluated by unstructured approaches, such as spread-sheets. The efficiency, reliability and throughput of genotyping would benefit from the automation of manual manipulations within the context of sophisticated data storage. We developed a medium- throughput genotyping pipeline for MultiLocus Sequence Typing (MLST of bacterial pathogens. This pipeline was implemented through a combination of four automated liquid handling systems, a Laboratory Information Management System (LIMS consisting of a variety of dedicated commercial operating systems and programs, including a Sample Management System, plus numerous Python scripts. All tubes and microwell racks were bar-coded and their locations and status were recorded in the LIMS. We also created a hierarchical set of items that could be used to represent bacterial species, their products and experiments. The LIMS allowed reliable, semi-automated, traceable bacterial genotyping from initial single colony isolation and sub-cultivation through DNA extraction and normalization to PCRs, sequencing and MLST sequence trace evaluation. We also describe robotic sequencing to facilitate cherrypicking of sequence dropouts. This pipeline is user-friendly, with a throughput of 96 strains within 10 working days at a total cost of 200,000 items were processed by two to three people. Our sophisticated automated pipeline can be implemented by a small microbiology group without extensive external support, and provides a general framework for semi-automated bacterial genotyping of large numbers of samples at low cost.

  3. NS3 protease resistance-associated substitutions in liver tissue and plasma samples from patients infected by hepatitis C virus genotype 1A or 1B.

    Science.gov (United States)

    Morsica, Giulia; Andolina, Andrea; Merli, Marco; Messina, Emanuela; Hasson, Hamid; Lazzarin, Adriano; Uberti-Foppa, Caterina; Bagaglio, Sabrina

    2017-08-01

    The presence of naturally occurring resistance-associated substitutions (RASs) in the HCV-protease domain has been poorly investigated in the liver, the main site of HCV replication. We evaluated the natural resistance of the virus to NS3 protease inhibitors in liver tissue and plasma samples taken from HCV-infected patients. RASs were investigated by means of viral population sequencing in liver tissue samples from 18 HCV-infected patients harbouring genotype 1a or genotype 1b; plasma samples from 12 of these patients were also available for virological investigation. A discordant genotype was found in two of the 12 patients (16.6%) who provided samples from both compartments. Sequence analysis of the NS3 protease domain showed the presence of RASs in four of the 18 liver tissue samples (22.2%), two of which showed cross-resistance to protease inhibitors in clinical use or phase 2-3 trials. The analysis of the 12 paired tissues and plasma samples excluded the presence of RASs in the plasma compartment. The dominance of discordant genotypes in the paired liver and plasma samples of some HCV-infected patients suggests mixed infection possibly leading to the selective advantage of different genotype in the two compartments. The presence of RASs at intra-hepatic level is not uncommon and may lead to the early emergence of cross-resistant strains.

  4. Identification of zoonotic genotypes of Giardia duodenalis.

    Directory of Open Access Journals (Sweden)

    Hein Sprong

    Full Text Available Giardia duodenalis, originally regarded as a commensal organism, is the etiologic agent of giardiasis, a gastrointestinal disease of humans and animals. Giardiasis causes major public and veterinary health concerns worldwide. Transmission is either direct, through the faecal-oral route, or indirect, through ingestion of contaminated water or food. Genetic characterization of G. duodenalis isolates has revealed the existence of seven groups (assemblages A to G which differ in their host distribution. Assemblages A and B are found in humans and in many other mammals, but the role of animals in the epidemiology of human infection is still unclear, despite the fact that the zoonotic potential of Giardia was recognised by the WHO some 30 years ago. Here, we performed an extensive genetic characterization of 978 human and 1440 animal isolates, which together comprise 3886 sequences from 4 genetic loci. The data were assembled into a molecular epidemiological database developed by a European network of public and veterinary health Institutions. Genotyping was performed at different levels of resolution (single and multiple loci on the same dataset. The zoonotic potential of both assemblages A and B is evident when studied at the level of assemblages, sub-assemblages, and even at each single locus. However, when genotypes are defined using a multi-locus sequence typing scheme, only 2 multi-locus genotypes (MLG of assemblage A and none of assemblage B appear to have a zoonotic potential. Surprisingly, mixtures of genotypes in individual isolates were repeatedly observed. Possible explanations are the uptake of genetically different Giardia cysts by a host, or subsequent infection of an already infected host, likely without overt symptoms, with a different Giardia species, which may cause disease. Other explanations for mixed genotypes, particularly for assemblage B, are substantial allelic sequence heterogeneity and/or genetic recombination. Although the

  5. Potential public health significance of faecal contamination and multidrug-resistant Escherichia coli and Salmonella serotypes in a lake in India.

    Science.gov (United States)

    Abhirosh, C; Sherin, V; Thomas, A P; Hatha, A A M; Mazumder, A

    2011-06-01

    To assess the prevalence of faecal coliform bacteria and multiple drug resistance among Escherichia coli and Salmonella serotypes from Vembanadu Lake. Systematic microbiological testing. Monthly collection of water samples were made from ten stations on the southern and northern parts of a salt water regulator constructed in Vembanadu Lake in order to prevent incursion of seawater during certain periods of the year. Density of faecal colifrom bacteria was estimated. E. coli and Salmonella were isolated and their different serotypes were identified. Antibiotic resistance analysis of E. coli and Salmonella serotypes was done and the MAR index of individual isolates was calculated. Density of faecal coliform bacteria ranged from mean MPN value 2900 -7100/100ml. Results showed multiple drug resistance pattern among the bacterial isolates. E. coli showed more than 50% resistance to amickacin, oxytetracycline, streptomycin, tetracycline and kanamycin while Salmonella showed high resistance to oxytetracycline, streptomycin, tetracycline and ampicillin. The MAR indexing of the isolates showed that they have originated from high risk source such as humans, poultry and dairy cows. The high density of faecal coliform bacteria and prevalence of multi drug resistant E. coli and Salmonella serotypes in the lake may pose severe public health risk through related water borne and food borne outbreaks. Copyright © 2011 The Royal Society for Public Health. Published by Elsevier Ltd. All rights reserved.

  6. Faecal nitrogen excretion as an approach to estimate forage intake of wethers.

    Science.gov (United States)

    Kozloski, G V; Oliveira, L; Poli, C H E C; Azevedo, E B; David, D B; Ribeiro Filho, H M N; Collet, S G

    2014-08-01

    Data from twenty-two digestibility trials were compiled to examine the relationship between faecal N concentration and organic matter (OM) digestibility (OMD), and between faecal N excretion and OM intake (OMI) by wethers fed tropical or temperate forages alone or with supplements. Data set was grouped by diet type as follows: only tropical grass (n = 204), only temperate grass (n = 160), tropical grass plus supplement (n = 216), temperate grass plus supplement (n = 48), tropical grass plus tropical legume (n = 60) and temperate grass with ruminal infusion of tannins (n = 16). Positive correlation between OMD and either total faecal N concentration (Nfc, % of OM) or metabolic faecal N concentration (Nmetfc, % of OM) was significant for most diet types. Exceptions were the diet that included a tropical legume, where both relationships were negative, and the diet that included tannin extract, where the correlation between OMD and Nfc was not significant. Pearson correlation and linear regressions between OM intake (OMI, g/day) and faecal N excretion (Nf, g/day) were significant for all diet types. When OMI was estimated from the OM faecal excretion and Nfc-based OMD values, the linear comparison between observed and estimated OMI values showed intercept different from 0 and slope different from 1. When OMI was estimated using the Nf-based linear regressions, the linear comparison between observed and estimated OMI values showed neither intercept different from 0 nor slope different from 1. Both linear comparisons showed similar R(2) values (i.e. 0.78 vs. 0.79). In conclusion, linear equations are suitable for directly estimating OM intake by wethers, fed only forage or forage plus supplements, from the amount of N excreted in faeces. The use of this approach in experiments with grazing wethers has the advantage of accounting for individual variations in diet selection and digestion processes and precludes the use of techniques to estimate forage

  7. One-step simultaneous detection of Ureaplasma parvum and genotypes SV1, SV3 and SV6 from clinical samples using PlexPCR technology.

    Science.gov (United States)

    Payne, M S; Furfaro, L L; Tucker, R; Tan, L Y; Mokany, E

    2017-08-01

    Ureaplasma spp. are associated with preterm birth. In recent times, it has become apparent that Ureaplasma parvum, but not Ureaplasma urealyticum, is of most relevance. We recently demonstrated this in Australian pregnant women and using high-resolution melt (HRM) PCR, further showed that U. parvum genotype SV6 was of particular significance. However, our assay was unable to identify multiple genotypes in the same sample, required a separate species-level qPCR for low titre samples and was not ideal for diagnostic laboratories due to the nature of HRM PCR result interpretation. Consequently, our current study developed a novel, one-step PlexPCR assay capable of detecting U. parvum and genotypes SV1, SV3 and SV6 in a single reaction directly from clinical samples. We then validated this using vaginal swab DNA from our Australian cohort of pregnant women. The PlexPCR was highly sensitive, detecting all targets to between 0.4 × 10 -5  ng DNA (SV3) and 0.4 × 10 -6  ng DNA (U. parvum, SV1 and SV6). Compared to our HRM PCR, the PlexPCR defined genotype distribution in all seven cases previously reported as 'mixed', and detected another eight cases where multiple genotypes (two) were present in samples previously reported as single genotypes using HRM PCR. Ureaplasma spp. have been associated with prematurity for decades, however, only a minority of studies have examined this beyond the genus level. In those that have, Ureaplasma parvum has been strongly associated with preterm birth. We recently demonstrated this in Australian women and further showed that U. parvum genotype SV6 was of particular significance. Our PlexPCR assay allows rapid detection and concurrent genotyping of U. parvum in clinical samples and may be of particular interest to obstetricians, particularly those caring for women at a high risk of preterm birth, and any other disease phenotypes where U. parvum is of interest. © 2017 The Authors. Letters in Applied Microbiology published by John

  8. Appraisal of the 14C-glycocholate acid test with special reference to the measurement of faecal 14C excretion

    International Nuclear Information System (INIS)

    Scarpello, J.H.B.; Sladen, G.E.

    1977-01-01

    The 14 C-glycocholate test, including the measurement of marker corrected faecal 14 C, has been assessed in the following groups of subjects: normal controls (18), patients with diarrhoea not attributable to altered bile acid metabolism (21), patients with diverticula of the small intestine (12), patients with previous resection of ileum and often proximal colon (34), and established ileostomists (10). Patients with diverticular disease had increased breath 14 CO 2 excretion, but normal faecal excretion of 14 C, and this test was more frequently abnormal than the Schilling test. Ileostomists excreted increased amounts of faecal 14 C, even when the ileum was intact and apparently normal. The pattern after resection was complex. Breath 14 C output was normal if the ileal resection was less than 25 cm in length, although some of these patients had increased faecal 14 C excretion if, in addition, at least 15 cm of proximal colon had been resected or by-passed. Longer ileal resections were associated with increased breath and/or faecal 14 C excretion, depending in part on the length of colon resected or by-passed and the 24 hour faecal volume. Fewer than half these patients had both increased breath and faecal excretion of isotope and faecal 14 C alone was occasionally normal with an ileal resection of 50 cm or more. The 14 C-glycocholate test was more frequently abnormal than the Schilling test in this group. The use of faecal marker correction had only a minor impact on the results. These data suggest that, in patients with ileal resection, faecal 14 C, like faecal weight, is determined by the extent of colonic resection as well as by the amount of ileum resected. (author)

  9. Laboratory Information Management Software for genotyping workflows: applications in high throughput crop genotyping

    Directory of Open Access Journals (Sweden)

    Prasanth VP

    2006-08-01

    Full Text Available Abstract Background With the advances in DNA sequencer-based technologies, it has become possible to automate several steps of the genotyping process leading to increased throughput. To efficiently handle the large amounts of genotypic data generated and help with quality control, there is a strong need for a software system that can help with the tracking of samples and capture and management of data at different steps of the process. Such systems, while serving to manage the workflow precisely, also encourage good laboratory practice by standardizing protocols, recording and annotating data from every step of the workflow. Results A laboratory information management system (LIMS has been designed and implemented at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT that meets the requirements of a moderately high throughput molecular genotyping facility. The application is designed as modules and is simple to learn and use. The application leads the user through each step of the process from starting an experiment to the storing of output data from the genotype detection step with auto-binning of alleles; thus ensuring that every DNA sample is handled in an identical manner and all the necessary data are captured. The application keeps track of DNA samples and generated data. Data entry into the system is through the use of forms for file uploads. The LIMS provides functions to trace back to the electrophoresis gel files or sample source for any genotypic data and for repeating experiments. The LIMS is being presently used for the capture of high throughput SSR (simple-sequence repeat genotyping data from the legume (chickpea, groundnut and pigeonpea and cereal (sorghum and millets crops of importance in the semi-arid tropics. Conclusion A laboratory information management system is available that has been found useful in the management of microsatellite genotype data in a moderately high throughput genotyping

  10. Nocturnal faecal soiling and anal masturbation.

    Science.gov (United States)

    Clark, A F; Tayler, P J; Bhate, S R

    1990-01-01

    Two cases of late onset faecal soiling as a result of anal masturbation in children who were neither mentally handicapped nor psychotic were studied. The role of soiling in aiding the young person and his family to avoid separating and maturing is highlighted. We suggest that the association of anal masturbation and resistant nocturnal soiling may be unrecognised. PMID:2270946

  11. Molecular identification and successful treatment of Chlamydophila psittaci (genotype B) in a clinically affected Congo African grey parrot (Psittacus erithacus erithacus)

    Science.gov (United States)

    Razmyar, J.; Rajabioun, M.; Zaeemi, M.; Afshari, A.

    2016-01-01

    Avian chlamydiosis is caused by Chlamydiophila psittaci with the highest infection rate in parrots (Psittacidae) and pigeons (Columbiformes). A two-year-old Congo African grey parrot was examined since the bird had shown clinical signs of anorexia, depression, diarrhea, and mild dyspnea and based on biochemical and hemathological analysis the bird was diagnosed as having anemia, leukocytosis, heterophilia, lymphopenia and monocytosis. With regards to clinical and paraclinical findings, the case was diagnosed to be carrying Chlamydiophila spp. In addition, choanal cleft and cloaca swabs were positive for Chlamydiophila spp. in a diagnostic polymerase chain reaction (PCR) (600 bp amplicon). Polymerase chain reaction products were typed by ompA gene-based PCR, using CTU/CTL primers (1050 bp amplicon). The PCR product sequence was compared with the sequences obtained from GenBank. The phylogenetic tree has revealed 100% identity with genotype B obtained from previous studies. The bird was hospitalized and treated with doxycycline regimen for 45 days, with a weekly sampling process to trace the presence of C. psittaci DNA in faecal and choanal swabs, this process continued to the point where the specimens turned negative after two weeks. Laboratory and radiology results were within normal limits after the treatment. Genotype B is predominantly isolated from Columbidae and there have not been any reports regarding the clinically affected African gray parrot with this genotype. Subsequently, to the best of our knowledge, this is the first report of chlamydiosis by genotype B on Congo African grey parrot. PMID:28224015

  12. Recent perspectives on the relations between faecal mutagenicity, genotoxicity and diet

    Directory of Open Access Journals (Sweden)

    Silvia eGratz

    2011-03-01

    Full Text Available DNA damage is an essential component of the genesis of colonic cancer. Gut microbial products and food components are thought to be principally responsible for the damage that initiates disease progression. Modified Ames tests and Comet assays have been developed for measuring mutagenicity and genotoxicity. Their relevance to oncogenesis remains to be confirmed, as does the relative importance of different mutagenic and genotoxic compounds present in faecal water and the bacteria involved in their metabolism. Dietary intervention studies provide clues to the likely risks of oncogenesis. High-protein diets lead to increases in N-nitroso compounds in faecal water and greater DNA damage as measured by the Comet assay, for example. Other dietary interventions, such as non-digestible carbohydrates and probiotics, may lead to lower faecal genotoxicity. In order to make recommendations to the general public, we must develop a better understanding of how genotoxic compounds are formed in the colon, how accurate the Ames and Comet assays are, and how diet affects genotoxicity.

  13. Factors affecting genotyping success in giant panda fecal samples

    Directory of Open Access Journals (Sweden)

    Ying Zhu

    2017-05-01

    Full Text Available Fecal samples play an important role in giant panda conservation studies. Optimal preservation conditions and choice of microsatellites for giant panda fecal samples have not been established. In this study, we evaluated the effect of four factors (namely, storage type (ethanol (EtOH, EtOH −20 °C, 2-step storage medium, DMSO/EDTA/Tris/salt buffer (DETs and frozen at −20 °C, storage time (one, three and six months, fragment length, and repeat motif of microsatellite loci on the success rate of microsatellite amplification, allelic dropout (ADO and false allele (FA rates from giant panda fecal samples. Amplification success and ADO rates differed between the storage types. Freezing was inferior to the other four storage methods based on the lowest average amplification success and the highest ADO rates (P < 0.05. The highest microsatellite amplification success was obtained from either EtOH or the 2-step storage medium at three storage time points. Storage time had a negative effect on the average amplification of microsatellites and samples stored in EtOH and the 2-step storage medium were more stable than the other three storage types. We only detected the effect of repeat motif on ADO and FA rates. The lower ADO and FA rates were obtained from tri- and tetra-nucleotide loci. We suggest that freezing should not be used for giant panda fecal preservation in microsatellite studies, and EtOH and the 2-step storage medium should be chosen on priority for long-term storage. We recommend candidate microsatellite loci with longer repeat motif to ensure greater genotyping success for giant panda fecal studies.

  14. Faecal shedding of canine parvovirus after modified-live vaccination in healthy adult dogs.

    Science.gov (United States)

    Freisl, M; Speck, S; Truyen, U; Reese, S; Proksch, A-L; Hartmann, K

    2017-01-01

    Since little is known about the persistence and faecal shedding of canine parvovirus (CPV) in dogs after modified-live vaccination, diagnostic tests for CPV can be difficult to interpret in the post-vaccination period. The primary aim of this study was to determine the incidence, duration and extent of CPV vaccine virus shedding in adult dogs and to investigate related factors, including the presence of protective antibodies, increase in anti-CPV antibody titres and development of any gastrointestinal side-effects. A secondary objective was to assess prevalence of CPV field virus shedding in clinically healthy dogs due to subclinical infections. One hundred adult, healthy privately owned dogs were vaccinated with a commercial CPV-2 modified-live vaccine (MLV). Faeces were tested for the presence of CPV DNA on days 0 (prior to vaccination), 3, 7, 14, 21 and 28 by quantitative real-time PCR. Pre- and post-vaccination serum titres were determined by haemagglutination inhibition on days 0, 7 and 28. Transient excretion of CPV DNA was detected in 2.0% of dogs before vaccination. About one quarter of dogs (23.0%) shed CPV DNA during the post-vaccination period, but field and vaccine virus differentiation by VP2 gene sequencing was only successful in few samples. Faecal CPV excretion occurred despite protective serum antibody titres. Post-vaccination CPV shedding was not related to adequate antibody response after vaccination or to the occurrence of gastrointestinal side-effects. Despite individual differences, CPV DNA was detectable for up to 28 days after vaccination, although the faecal CPV DNA load in these clinically healthy dogs was very low. Copyright © 2016 Elsevier Ltd. All rights reserved.

  15. Evaluation of sampling methods for the detection of Salmonella in broiler flocks

    DEFF Research Database (Denmark)

    Skov, Marianne N.; Carstensen, B.; Tornoe, N.

    1999-01-01

    The present study compares four different sampling methods potentially applicable to detection of Salmonella in broiler flocks, based on collection of faecal samples (i) by hand, 300 fresh faecal samples (ii) absorbed on five sheets of paper (iii) absorbed on five pairs of socks (elastic cotton...... horizontal or vertical) were found in the investigation. The results showed that the sock method (five pairs of socks) had a sensitivity comparable with the hand collection method (60 pools of five faecal samples); the paper collection method was inferior, as was the use of only one pair of socks, Estimation...... tubes pulled over the boots and termed 'socks') and (iv) by using only one pair of socks. Twenty-three broiler flocks were included in the investigation and 18 of these were found to be positive by at least one method. Seven serotypes of Salmonella with different patterns of transmission (mainly...

  16. Ano-rectal tuberculous granulomapresenting with faecal incontinence

    African Journals Online (AJOL)

    ... present a case of a 68-year old man with a huge mass in the ano-rectum with faecal incontinence, which was clinically diagnosed as an advanced carcinoma of the ano-rectum for which the biopsy was reported as tuberculosis. He improved with anti-tuberculosis treatment. Keywords: Ano-rectum, tuberculosis, cancer.

  17. High-throughput genotyping assay for the large-scale genetic characterization of Cryptosporidium parasites from human and bovine samples.

    Science.gov (United States)

    Abal-Fabeiro, J L; Maside, X; Llovo, J; Bello, X; Torres, M; Treviño, M; Moldes, L; Muñoz, A; Carracedo, A; Bartolomé, C

    2014-04-01

    The epidemiological study of human cryptosporidiosis requires the characterization of species and subtypes involved in human disease in large sample collections. Molecular genotyping is costly and time-consuming, making the implementation of low-cost, highly efficient technologies increasingly necessary. Here, we designed a protocol based on MALDI-TOF mass spectrometry for the high-throughput genotyping of a panel of 55 single nucleotide variants (SNVs) selected as markers for the identification of common gp60 subtypes of four Cryptosporidium species that infect humans. The method was applied to a panel of 608 human and 63 bovine isolates and the results were compared with control samples typed by Sanger sequencing. The method allowed the identification of species in 610 specimens (90·9%) and gp60 subtype in 605 (90·2%). It displayed excellent performance, with sensitivity and specificity values of 87·3 and 98·0%, respectively. Up to nine genotypes from four different Cryptosporidium species (C. hominis, C. parvum, C. meleagridis and C. felis) were detected in humans; the most common ones were C. hominis subtype Ib, and C. parvum IIa (61·3 and 28·3%, respectively). 96·5% of the bovine samples were typed as IIa. The method performs as well as the widely used Sanger sequencing and is more cost-effective and less time consuming.

  18. Male commuters in north and south England: risk factors for the presence of faecal bacteria on hands

    Directory of Open Access Journals (Sweden)

    Donachie Peter

    2011-01-01

    Full Text Available Abstract Background A previous study found that the prevalence of contamination with bacteria of faecal-origin on the hands of men differed across UK cities, with a general trend of increased contamination in northern cities. The aim of this study was to (1 confirm the north-south trend (2 identify causes for the trend. Methods Hand swabs from commuters (n = 308 at train stations in 4 cities were tested for the presence of faecal bacteria. Results The prevalence of hand contamination with faecal bacteria was again higher in cities in the north compared to the south (5% in London, 4% in Birmingham, 10% in Liverpool and 19% in Newcastle. Contamination risk decreased with age and better personal hygiene (self-reported. Soil contact and shaking hands increased contamination with faecal bacteria. However, in multivariable analysis, none of these factors fully explained the variation in contamination across cities. Conclusion The study confirmed the north-south differences in faecal contamination of hands without finding a clear cause for the trend. Faecal contamination of hands was associated with personal hygiene indicators suggesting that microbiological testing may contribute to evaluating hygiene promotion campaigns.

  19. Hepatitis E Virus (Genotype 3) in Slurry Samples from Swine Farming Activities in Italy.

    Science.gov (United States)

    La Rosa, G; Della Libera, S; Brambilla, M; Bisaglia, C; Pisani, G; Ciccaglione, A R; Bruni, R; Taffon, S; Equestre, M; Iaconelli, M

    2017-06-01

    Hepatitis E virus (HEV) is an emergent causative agent of acute hepatitis, transmitted by fecal-oral route. Infection with HEV is a global cause for morbidity and mortality throughout the world: it mainly causes large outbreaks in endemic areas and sporadic autochthonous cases in industrialized countries where HEV infections seem to be an emergent zoonotic disease. Infection of porcine livestock and its relationship with the human cases have been demonstrated. The present study describes an investigation on the prevalence and diversity of HEV in pig slurry in Italy. Slurry samples (24) were collected from ten farms located in North Italy during 2015 and analyzed for HEV, using four broad-range nested PCR assays targeting ORF1 (MTase), ORF2 (capsid) genes, and ORF2/3 regions. Overall, 18 samples (75%) were positive for HEV RNA, and characterized as genotype 3. Nine samples could be subtyped by ORF2 sequencing: Eight belonged to subtype 3f, while one sequence could not be characterized by blast analysis and phylogenetic analysis and may actually represent a new subtype. Furthermore, similarity of 99% was found between 3f Italian HEV sequences of human and swine origins. Real-Time PCR assay was also performed, in order to obtain quantitative data on positive samples. Two swine slurry samples were positive, containing 600 and 1000 UI per mL of sewage. The results of this study show that HEV strains belonging to zoonotic genotype 3 are widely present in swine excreta, and have high degree of identity with strains detected in autochthonous HEV cases. Improving swine farming operations safety and increasing operators' awareness of the zoonotic potential connected with the handling of swine effluents turn out to be key points in order to reduce the environmental and sanitary problem represented by the possible dissemination of HEV to water bodies.

  20. Cryptosporidium and Giardia in Danish organic pig farms: seasonal and age-related variation in prevalence, infection intensity and species/genotypes

    DEFF Research Database (Denmark)

    Petersen, Heidi Huus; Jianmin, Wang; Katakam, Kiran K.

    2015-01-01

    Although pigs are commonly infected with Cryptosporidium spp. and Giardia duodenalis, including potentially zoonotic species or genotypes, little is known about age-related infection levels, seasonal differences and genetic variation in naturally infected pigs raised in organic management systems....... Therefore, the current study was conducted to assess seasonal and age-related variations in prevalence and infection intensity of Cryptosporidium and Giardia, evaluate zoonotic potential and uncover correlations between species/genotypes, infection intensity and faecal consistency. Shedding of oocysts...... and cysts ((oo-) cysts) was monitored at quarterly intervals (September 2011 to June 2012) in piglets (n=152), starter pigs (n=234), fatteners (n=230) and sows (n=240) from three organic farms in Denmark. (Oo-) cysts were quantified by immunofluorescence microscopy; and 56/75 subsamples from Cryptosporidium...

  1. Survival and transport of faecal bacteria in agricultural soils

    DEFF Research Database (Denmark)

    Bech, Tina Bundgaard

    Today, there is yearly applied 34 million tonnes of animal waste to arable land in Denmark. This waste may contain pathogenic zoonotic bacteria and/or antibiotic resistant bacteria, and when applied to arable land there is a risk of contaminating groundwater, surface water, feeding animals or fresh...... produce. Prediction of faecal bacterial survival and transport in the soil environment will help minimize the risk of contamination, as best management practices can be adapted to this knowledge. The aim of this Ph.D. is to study factors influencing faecal bacteria survival and transport in soil...... – it is based on both field scale and lab scale experiments. The influence of application method and slurry properties has been tested on both survival and transport....

  2. Comparisons of Sampling Procedures and Time of Sampling for the Detection of Salmonella in Danish Infected Chicken Flocks Raised in Floor Systems

    Directory of Open Access Journals (Sweden)

    Madsen M

    2002-03-01

    Full Text Available Bacteriological follow-up samples were taken from 41 chicken (Gallus gallus flocks in floor systems, where Salmonella enterica (Salmonella had been detected either directly in bacteriological samples or indirectly by serological samples. Three types of follow-up samples were compared to each other within each flock: 1 5 pairs of socks, analysed as 5 samples, 2 2 pairs of socks, analysed as one sample, and 3 60 faecal samples, analysed as one pooled sample. Agreement between sampling methods was evaluated by the following statistical tests: 'Kappa', 'The adjusted rand', McNemar's test for marginal symmetry, Proportion of agreement P0, P+, P-, and Odds Ratio. The highest agreement was found between the 2 types of sock sampling, while the lowest agreement was found by comparing 60 faecal samples with 5 pairs of socks. Two pairs of socks analysed as one pool appeared to be just as effective in detecting S. enterica as the 60 faecal samples. In broiler flocks, 5 pairs of socks were used both in the routine samples taken at about 3 weeks of age for the establishment of infection of the flock, and as one of the follow-up samples taken shortly before slaughter age, which means that the only notable differences between the 2 sampling rounds were the age of the broilers and of their litter. S. enterica was detected more frequently in samples from broilers about 3 weeks old, than in similar samples taken from broilers a few days prior to slaughter at ca. 33–40 days of age.

  3. Effect of calcium from dairy and dietary supplements on faecal fat excretion: a meta-analysis of randomized controlled trials

    DEFF Research Database (Denmark)

    Christensen, R.; Lorenzen, Janne Kunchel; Svith, Carina Roholm

    2009-01-01

    Observational studies have found that dietary calcium intake is inversely related to body weight and body fat mass. One explanatory mechanism is that dietary calcium increases faecal fat excretion. To examine the effect of calcium from dietary supplements or dairy products on quantitative faecal...... fat excretion, we performed a systematic review with meta-analysis. We included randomized, controlled trials of calcium (supplements or dairy) in healthy subjects, where faecal fat excretion was measured. Meta-analyses used random-effects models with changes in faecal fat excreted expressed...

  4. A right whale pootree: classification trees of faecal hormones identify reproductive states in North Atlantic right whales (Eubalaena glacialis).

    Science.gov (United States)

    Corkeron, Peter; Rolland, Rosalind M; Hunt, Kathleen E; Kraus, Scott D

    2017-01-01

    Immunoassay of hormone metabolites extracted from faecal samples of free-ranging large whales can provide biologically relevant information on reproductive state and stress responses. North Atlantic right whales ( Eubalaena glacialis Müller 1776) are an ideal model for testing the conservation value of faecal metabolites. Almost all North Atlantic right whales are individually identified, most of the population is sighted each year, and systematic survey effort extends back to 1986. North Atlantic right whales number trees as an alternative method of analysing multiple-hormone data sets, building on univariate models that have previously been used to describe hormone profiles of individual North Atlantic right whales of known reproductive state. Our tree correctly classified the age class, sex and reproductive state of 83% of 112 faecal samples from known individual whales. Pregnant females, lactating females and both mature and immature males were classified reliably using our model. Non-reproductive [i.e. 'resting' (not pregnant and not lactating) and immature] females proved the most unreliable to distinguish. There were three individual males that, given their age, would traditionally be considered immature but that our tree classed as mature males, possibly calling for a re-evaluation of their reproductive status. Our analysis reiterates the importance of considering the reproductive state of whales when assessing the relationship between cortisol concentrations and stress. Overall, these results confirm findings from previous univariate statistical analyses, but with a more robust multivariate approach that may prove useful for the multiple-analyte data sets that are increasingly used by conservation physiologists.

  5. Appraisal of the /sup 14/C-glycocholate acid test with special reference to the measurement of faecal /sup 14/C excretion

    Energy Technology Data Exchange (ETDEWEB)

    Scarpello, J H.B.; Sladen, G E [Royal Hospital, Sheffield (UK). Academic Div. of Medicine

    1977-09-01

    The /sup 14/C-glycocholate test, including the measurement of marker corrected faecal /sup 14/C, has been assessed in the following groups of subjects: normal controls (18), patients with diarrhoea not attributable to altered bile acid metabolism (21), patients with diverticula of the small intestine (12), patients with previous resection of ileum and often proximal colon (34), and established ileostomists (10). Patients with diverticular disease had increased breath /sup 14/CO/sub 2/ excretion, but normal faecal excretion of /sup 14/C, and this test was more frequently abnormal than the Schilling test. Ileostomists excreted increased amounts of faecal /sup 14/C, even when the ileum was intact and apparently normal. The pattern after resection was complex. Breath /sup 14/C output was normal if the ileal resection was less than 25 cm in length, although some of these patients had increased faecal /sup 14/C excretion if, in addition, at least 15 cm of proximal colon had been resected or by-passed. Longer ileal resections were associated with increased breath and/or faecal /sup 14/C excretion, depending in part on the length of colon resected or by-passed and the 24 hour faecal volume. Fewer than half these patients had both increased breath and faecal excretion of isotope and faecal /sup 14/C alone was occasionally normal with an ileal resection of 50 cm or more. The /sup 14/C-glycocholate test was more frequently abnormal than the Schilling test in this group. The use of faecal marker correction had only a minor impact on the results. These data suggest that, in patients with ileal resection, faecal /sup 14/C, like faecal weight, is determined by the extent of colonic resection as well as by the amount of ileum resected.

  6. Steroid Biomarkers Revisited - Improved Source Identification of Faecal Remains in Archaeological Soil Material.

    Directory of Open Access Journals (Sweden)

    Katharina Prost

    Full Text Available Steroids are used as faecal markers in environmental and in archaeological studies, because they provide insights into ancient agricultural practices and the former presence of animals. Up to now, steroid analyses could only identify and distinguish between herbivore, pig, and human faecal matter and their residues in soils and sediments. We hypothesized that a finer differentiation between faeces of different livestock animals could be achieved when the analyses of several steroids is combined (Δ5-sterols, 5α-stanols, 5β-stanols, epi-5β-stanols, stanones, and bile acids. We therefore reviewed the existing literature on various faecal steroids from livestock and humans and analysed faeces from old livestock breed (cattle, horse, donkey, sheep, goat, goose, and pig and humans. Additionally, we performed steroid analyses on soil material of four different archaeological periods (sites located in the Lower Rhine Basin, Western Germany, dating to the Linearbandkeramik, Urnfield Period / Bronze Age, Iron Age, Roman Age with known or supposed faecal inputs. By means of already established and newly applied steroid ratios of the analysed faeces together with results from the literature, all considered livestock faeces, except sheep and cattle, could be distinguished on the basis of their steroid signatures. Most remarkably was the identification of horse faeces (via the ratio: epi-5β-stigmastanol: 5β-stigmastanol + epicoprostanol: coprostanol; together with the presence of chenodeoxycholic acid and a successful differentiation between goat (with chenodeoxycholic acid and sheep/cattle faeces (without chenodeoxycholic acid. The steroid analysis of archaeological soil material confirmed the supposed faecal inputs, even if these inputs had occurred several thousand years ago.

  7. New Insights into the Evolution of the Human Diet from Faecal Biomarker Analysis in Wild Chimpanzee and Gorilla Faeces.

    Directory of Open Access Journals (Sweden)

    Ainara Sistiaga

    Full Text Available Our understanding of early human diets is based on reconstructed biomechanics of hominin jaws, bone and teeth isotopic data, tooth wear patterns, lithic, taphonomic and zooarchaeological data, which do not provide information about the relative amounts of different types of foods that contributed most to early human diets. Faecal biomarkers are proving to be a valuable tool in identifying relative proportions of plant and animal tissues in Palaeolithic diets. A limiting factor in the application of the faecal biomarker approach is the striking absence of data related to the occurrence of faecal biomarkers in non-human primate faeces. In this study we explored the nature and proportions of sterols and stanols excreted by our closest living relatives. This investigation reports the first faecal biomarker data for wild chimpanzee (Pan troglodytes and mountain gorilla (Gorilla beringei. Our results suggest that the chemometric analysis of faecal biomarkers is a useful tool for distinguishing between NHP and human faecal matter, and hence, it could provide information for palaeodietary research and early human diets.

  8. New Insights into the Evolution of the Human Diet from Faecal Biomarker Analysis in Wild Chimpanzee and Gorilla Faeces.

    Science.gov (United States)

    Sistiaga, Ainara; Wrangham, Richard; Rothman, Jessica M; Summons, Roger E

    2015-01-01

    Our understanding of early human diets is based on reconstructed biomechanics of hominin jaws, bone and teeth isotopic data, tooth wear patterns, lithic, taphonomic and zooarchaeological data, which do not provide information about the relative amounts of different types of foods that contributed most to early human diets. Faecal biomarkers are proving to be a valuable tool in identifying relative proportions of plant and animal tissues in Palaeolithic diets. A limiting factor in the application of the faecal biomarker approach is the striking absence of data related to the occurrence of faecal biomarkers in non-human primate faeces. In this study we explored the nature and proportions of sterols and stanols excreted by our closest living relatives. This investigation reports the first faecal biomarker data for wild chimpanzee (Pan troglodytes) and mountain gorilla (Gorilla beringei). Our results suggest that the chemometric analysis of faecal biomarkers is a useful tool for distinguishing between NHP and human faecal matter, and hence, it could provide information for palaeodietary research and early human diets.

  9. Perianal injectable bulking agents as treatment for faecal incontinence in adults. (Update)

    DEFF Research Database (Denmark)

    Maeda, Yasuko; Laurberg, Søren; Norton, Christine

    2013-01-01

    BACKGROUND: Faecal incontinence is a complex and distressing condition with significant medical and social implications. Injection of perianal bulking agents has been used to treat the symptoms of passive faecal incontinence. However, various agents have been used without a standardised technique...... evaluation of outcomes and thus it is difficult to gauge whether the improvement in incontinence scores matched practical symptom improvements that mattered to the patients. AUTHORS' CONCLUSIONS: One large randomised controlled trial has shown that this form of treatment using dextranomer in stabilised...

  10. Indications for and outcome of primary repair compared with faecal diversion in the management of traumatic colon injury.

    Science.gov (United States)

    Fouda, E; Emile, S; Elfeki, H; Youssef, M; Ghanem, A; Fikry, A A; Elshobaky, A; Omar, W; Khafagy, W; Morshed, M

    2016-08-01

    Injuries of the colon are a serious sequel of abdominal trauma owing to the associated morbidity and mortality. This study aims to assess postoperative outcome and complications of faecal diversion and primary repair of colon injuries when applied according to established guidelines for the management of colon injuries. This retrospective study was conducted on 110 patients with colon injuries. Guided by estimation of risk factors, patients were managed either by primary repair alone, repair with proximal diversion or diversion alone. There were 102 (92.7%) male patients and 8 (7.3%) female patients of median age 38 years. Thirty-seven were managed by primary repair and 73 by faecal diversion. Colon injuries were caused by penetrating abdominal trauma in 65 and blunt trauma in 45 patients. Forty-three patients were in shock on admission, and were all managed by faecal diversion. Forty patients developed 84 complications after surgery. Primary repair had a significantly lower complication rate than faecal diversion (P = 0.037). Wound infection was the commonest complication. The overall mortality rate was 3.6%. Primary repair, when employed properly, resulted in a significantly lower complication rate than faecal diversion. Significant predictive factors associated with a higher complication rate were faecal diversion, severe faecal contamination, multiple colon injuries, an interval of more than 12 h after colon injury and shock. Colorectal Disease © 2016 The Association of Coloproctology of Great Britain and Ireland.

  11. Effect of high contents of dietary animal-derived protein or carbohydrates on canine faecal microbiota

    Directory of Open Access Journals (Sweden)

    Hang Ingrid

    2012-06-01

    Full Text Available Abstract Background Considerable evidence suggests that food impacts both the gastro-intestinal (GI function and the microbial ecology of the canine GI tract. The aim of this study was to evaluate the influence of high-carbohydrate (HC, high-protein (HP and dry commercial (DC diets on the canine colonic microbiota in Beagle dogs. Diets were allocated according to the Graeco-Latin square design. For this purpose, microbial DNA was isolated from faecal samples and separated by density gradient centrifugation, resulting in specific profiling based on the guanine-cytosine content (%G + C. In addition, 16 S rRNA gene amplicons were obtained from the most abundant %G + C peaks and analysed by sequence analysis, producing a total of 720 non-redundant sequences (240 sequences per diet. Results The DC diet sample showed high abundance of representatives of the orders Clostridiales, Lactobacillales, Coriobacteriales and Bacteroidales. Sequence diversity was highest for DC diet samples and included representatives of the orders Lactobacillales and Bacteroidales, which were not detected in samples from the HP and HC diets. These latter two diets also had reduced levels of representatives of the family Lachnospiraceae, specifically Clostridial cluster XIVa. The HC diet favoured representatives of the order Erysipelotrichales, more specifically the Clostridial cluster XVIII, while the HP diet favoured representatives of the order Fusobacteriales. Conclusions This study detected Coriobacteriales in dog faeces, possibly due to the non-selective nature of the %G + C profiling method used in combination with sequencing. Moreover, our work demonstrates that the effect of diet on faecal microbiota can be explained based on the metabolic properties of the detected microbial taxa.

  12. Environmental and genetic factors affecting faecal worm egg counts ...

    African Journals Online (AJOL)

    Environmental and genetic factors affecting faecal worm egg counts in Merinos divergently selected for reproduction. ... The fixed effect of birth year x sex interaction was significant, with rams showing higher mean values for FWEC than ewes ...

  13. Discovery of novel variants in genotyping arrays improves genotype retention and reduces ascertainment bias

    Directory of Open Access Journals (Sweden)

    Didion John P

    2012-01-01

    Full Text Available Abstract Background High-density genotyping arrays that measure hybridization of genomic DNA fragments to allele-specific oligonucleotide probes are widely used to genotype single nucleotide polymorphisms (SNPs in genetic studies, including human genome-wide association studies. Hybridization intensities are converted to genotype calls by clustering algorithms that assign each sample to a genotype class at each SNP. Data for SNP probes that do not conform to the expected pattern of clustering are often discarded, contributing to ascertainment bias and resulting in lost information - as much as 50% in a recent genome-wide association study in dogs. Results We identified atypical patterns of hybridization intensities that were highly reproducible and demonstrated that these patterns represent genetic variants that were not accounted for in the design of the array platform. We characterized variable intensity oligonucleotide (VINO probes that display such patterns and are found in all hybridization-based genotyping platforms, including those developed for human, dog, cattle, and mouse. When recognized and properly interpreted, VINOs recovered a substantial fraction of discarded probes and counteracted SNP ascertainment bias. We developed software (MouseDivGeno that identifies VINOs and improves the accuracy of genotype calling. MouseDivGeno produced highly concordant genotype calls when compared with other methods but it uniquely identified more than 786000 VINOs in 351 mouse samples. We used whole-genome sequence from 14 mouse strains to confirm the presence of novel variants explaining 28000 VINOs in those strains. We also identified VINOs in human HapMap 3 samples, many of which were specific to an African population. Incorporating VINOs in phylogenetic analyses substantially improved the accuracy of a Mus species tree and local haplotype assignment in laboratory mouse strains. Conclusion The problems of ascertainment bias and missing

  14. Genotyping of Coxiella burnetii from domestic ruminants in northern Spain

    Directory of Open Access Journals (Sweden)

    Astobiza Ianire

    2012-12-01

    Full Text Available Abstract Background Information on the genotypic diversity of Coxiella burnetii isolates from infected domestic ruminants in Spain is limited. The aim of this study was to identify the C. burnetii genotypes infecting livestock in Northern Spain and compare them to other European genotypes. A commercial real-time PCR targeting the IS1111a insertion element was used to detect the presence of C. burnetii DNA in domestic ruminants from Spain. Genotypes were determined by a 6-loci Multiple Locus Variable number tandem repeat analysis (MLVA panel and Multispacer Sequence Typing (MST. Results A total of 45 samples from 4 goat herds (placentas, N = 4, 12 dairy cattle herds (vaginal mucus, individual milk, bulk tank milk, aerosols, N = 20 and 5 sheep flocks (placenta, vaginal swabs, faeces, air samples, dust, N = 21 were included in the study. Samples from goats and sheep were obtained from herds which had suffered abortions suspected to be caused by C. burnetii, whereas cattle samples were obtained from animals with reproductive problems compatible with C. burnetii infection, or consisted of bulk tank milk (BTM samples from a Q fever surveillance programme. C. burnetii genotypes identified in ruminants from Spain were compared to those detected in other countries. Three MLVA genotypes were found in 4 goat farms, 7 MLVA genotypes were identified in 12 cattle herds and 4 MLVA genotypes were identified in 5 sheep flocks. Clustering of the MLVA genotypes using the minimum spanning tree method showed a high degree of genetic similarity between most MLVA genotypes. Overall 11 different MLVA genotypes were obtained corresponding to 4 different MST genotypes: MST genotype 13, identified in goat, sheep and cattle from Spain; MST genotype 18, only identified in goats; and, MST genotypes 8 and 20, identified in small ruminants and cattle, respectively. All these genotypes had been previously identified in animal and human clinical samples from several

  15. Baixa dosagem de óxido de cromo para estimativa da produção fecal em bovinos Low level of chromium oxide to estimate faecal output in cattle

    Directory of Open Access Journals (Sweden)

    Henrique Mendonça Nunes Ribeiro Filho

    2008-12-01

    214±31kg, receiving fresh Italian ryegrass (Lolium multiflorum Lam.. About 200g of concentrate with 5g kg-1 of Cr2O3 was daily rationed during 12 days, where 7 days were used for animal adaptation and 5 days for measurements. The total faecal output was collected and compared with faecal output estimated from grab samples, collected twice a day (8:00 am and 4:00 pm or at 2-hour intervals, from 8:00 am to 10:00 pm. The average faecal chrome concentration collected at 08:00 am and 04:00 pm (445mg kg-1 was similar with the average of samples collected at a 2-hour interval (447mg kg-1. The marker recovery rate (RR increased linearly, from approximately 40% to around 80%, with the faecal chrome concentration until approximately 250mg kg-1 OM. When the faecal chrome concentration was higher than 250mg kg-1 OM the RR was relatively constant, with values around 0.76. The faecal output was overestimated up to 35% when the RR was not considered. When the RR was used, faecal output estimative was similar to the total faecal output collected. The faecal output can be accurately estimated in cattle eating ryegrass using a low level of Cr2O3 incorporated into the concentrate ration concomitant with twice-a-day faecal grab samples collection.

  16. Detection and genotyping of human papillomavirus in self-obtained cervicovaginal samples by using the FTA cartridge: new possibilities for cervical cancer screening.

    Science.gov (United States)

    Lenselink, Charlotte H; de Bie, Roosmarie P; van Hamont, Dennis; Bakkers, Judith M J E; Quint, Wim G V; Massuger, Leon F A G; Bekkers, Ruud L M; Melchers, Willem J G

    2009-08-01

    This study assesses human papillomavirus (HPV) detection and genotyping in self-sampled genital smears applied to an indicating FTA elute cartridge (FTA cartridge). The study group consisted of 96 women, divided into two sample sets. All samples were analyzed by the HPV SPF(10)-Line Blot 25. Set 1 consisted of 45 women attending the gynecologist; all obtained a self-sampled cervicovaginal smear, which was applied to an FTA cartridge. HPV results were compared to a cervical smear (liquid based) taken by a trained physician. Set 2 consisted of 51 women who obtained a self-sampled cervicovaginal smear at home, which was applied to an FTA cartridge and to a liquid-based medium. DNA was obtained from the FTA cartridges by simple elution as well as extraction. Of all self-obtained samples of set 1, 62.2% tested HPV positive. The overall agreement between self- and physician-obtained samples was 93.3%, in favor of the self-obtained samples. In sample set 2, 25.5% tested HPV positive. The overall agreement for high-risk HPV presence between the FTA cartridge and liquid-based medium and between DNA elution and extraction was 100%. This study shows that HPV detection and genotyping in self-obtained cervicovaginal samples applied to an FTA cartridge is highly reliable. It shows a high level of overall agreement with HPV detection and genotyping in physician-obtained cervical smears and liquid-based self-samples. DNA can be obtained by simple elution and is therefore easy, cheap, and fast. Furthermore, the FTA cartridge is a convenient medium for collection and safe transport at ambient temperatures. Therefore, this method may contribute to a new way of cervical cancer screening.

  17. Studies to distinguish between human and animal faecal pollution ...

    African Journals Online (AJOL)

    In this study the application of F-RNA coliphages and faecal sterols to distinction between human and animal excreta has .... in a shaking water bath (LABOTEC) at 100 r·min-1. .... calibration standards that were plotted using Microsoft Excel.

  18. Psyllium husk fibre supplementation to soybean and coconut oil diets of humans: effect on fat digestibility and faecal fatty acid excretion.

    Science.gov (United States)

    Ganji, V; Kies, C V

    1994-08-01

    The effects of psyllium fibre supplementation to polyunsaturated fatty acid rich soybean oil and saturated fatty acid rich coconut oil diets on fat digestibility and faecal fatty acid excretion were investigated in healthy humans. The study consisted of four 7-day experimental periods. Participants consumed soybean oil (SO), soybean oil plus psyllium fibre (20 g/day) (SO+PF), coconut oil (CO) and coconut oil plus psyllium fibre (20 g/day) (CO+PF) diets. Laboratory diet provided 30% calories from fat (20% from test oils and 10% from basal diet), 15% calories from protein and 55% calories from carbohydrate. Fat digestibility was significantly lower and faecal fat excretion was significantly higher with SO+PF diet than SO diet and with CO+PF diet than CO diet. Faecal excretion of myristic and lauric acids was not affected by test diets. Percent faecal palmitic acid excretion was significantly higher during psyllium supplementation periods. Higher faecal linoleic acid excretion was observed with soybean oil diets compared with coconut oil diets. Increased faecal fat loss, decreased fat digestibility and increased faecal palmitic acid excretion with psyllium supplementation may partly explain the hypocholesterolaemic action of psyllium fibre.

  19. Impact of extensive antibiotic treatment on faecal carriage of antibiotic-resistant enterobacteria in children in a low resistance prevalence setting

    Science.gov (United States)

    Brandtzaeg, Petter; Høiby, E. Arne; Bohlin, Jon; Samuelsen, Ørjan; Steinbakk, Martin; Abrahamsen, Tore G.; Müller, Fredrik; Gammelsrud, Karianne Wiger

    2017-01-01

    We prospectively studied the consequences of extensive antibiotic treatment on faecal carriage of antibiotic-resistant enterobacteria in a cohort of children with cystic fibrosis (CF) and a cohort of children with cancer compared to healthy children with no or low antibiotic exposure. The study was conducted in Norway in a low resistance prevalence setting. Sixty longitudinally collected faecal samples from children with CF (n = 32), 88 samples from children with cancer (n = 45) and 127 samples from healthy children (n = 70) were examined. A direct MIC-gradient strip method was used to detect resistant Enterobacteriaceae by applying Etest strips directly onto agar-plates swabbed with faecal samples. Whole genome sequencing (WGS) data were analysed to identify resistance mechanisms in 28 multidrug-resistant Escherichia coli isolates. The prevalence of resistance to third-generation cephalosporins, gentamicin and ciprofloxacin was low in all the study groups. At inclusion the prevalence of ampicillin-resistant E. coli and trimethoprim-sulfamethoxazole-resistant E. coli in the CF group compared to healthy controls was 58.6% vs. 28.4% (p = 0.005) and 48.3% vs. 14.9% (p = 0.001), respectively, with a similar prevalence at the end of the study. The prevalence of resistant enterobacteria was not significantly different in the children with cancer compared to the healthy children, not even at the end of the study when the children with cancer had been treated with repeated courses of broad-spectrum antibiotics. Children with cancer were mainly treated with intravenous antibiotics, while the CF group mainly received peroral treatment. Our observations indicate that the mode of administration of antibiotics and the general level of antimicrobial resistance in the community may have an impact on emergence of resistance in intestinal enterobacteria during antibiotic treatment. The WGS analyses detected acquired resistance genes and/or chromosomal mutations that explained the

  20. The relationships between faecal worm egg count and subjectively ...

    African Journals Online (AJOL)

    Subjectively assessed wool and conformation traits form part of the selection objective in wool sheep enterprises. The present study investigated the genetic, phenotypic and environmental correlations for nematode resistance (using faecal worm egg count (FEC)) with subjectively assessed wool and conformation traits.

  1. Effects of levan-type fructan on growth performance, nutrient digestibility, diarrhoea scores, faecal shedding of total lactic acid bacteria and coliform bacteria, and faecal gas emission in weaning pigs.

    Science.gov (United States)

    Lei, Xin Jian; Kim, Yong Min; Park, Jae Hong; Baek, Dong Heon; Nyachoti, Charles Martin; Kim, In Ho

    2018-03-01

    The use of antibiotics as growth promoters in feed has been fully or partially banned in several countries. The objective of this study was to evaluate effects of levan-type fructan on growth performance, nutrient digestibility, faecal shedding of lactic acid bacteria and coliform bacteria, diarrhoea scores, and faecal gas emission in weaning pigs. A total of 144 weaning pigs [(Yorkshire × Landrace) × Duroc] were randomly allocated to four diets: corn-soybean meal-based diets supplemented with 0, 0.1, 0.5, or 1.0 g kg -1 levan-type fructan during this 42-day experiment. During days 0 to 21 and 0 to 42, average daily gain and average daily feed intake were linearly increased (P bacteria counts were linearly increased (P = 0.001). The results indicate that dietary supplementation with increasing levan-type fructan enhanced growth performance, improved nutrient digestibility, and increased faecal lactic acid bacteria counts in weaning pigs linearly. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

  2. Faecal shedding of antimicrobial-resistant Clostridium difficile strains by dogs.

    Science.gov (United States)

    Álvarez-Pérez, S; Blanco, J L; Peláez, T; Lanzarot, M P; Harmanus, C; Kuijper, E; García, M E

    2015-03-01

    To longitudinally assess the shedding of antimicrobial resistant Clostridium difficile strains by clinically healthy dogs raised at breeding facilities. 18 puppies from three different litters (#1, 2 and 3) were sampled weekly from parturition to day 20-55 postpartum. Faecal samples from the mothers of litters #2 and 3 were also available for analysis. Bacterial isolates were ribotyped, tested for in vitro antimicrobial susceptibility and further characterised. C. difficile was recovered from all sampled animals of litters #1 and 2, and a third of puppies from litter #3, but marked differences in C. difficile recovery were detected in different age groups (0-100%). Recovered PCR ribotypes included 056 (22 isolates), 010 (6 isolates), 078 and 213 (2 isolates each), and 009 and 020 (1 isolate each). Different ribotypes were shed by four individual animals. Regardless of their origin and ribotype, all isolates demonstrated full resistance to levofloxacin. Additionally, all but one isolate (belonging to ribotype 078) were resistant to ertapenem, and all ribotype 010 isolates displayed high-level resistance to clindamycin, clarithromycin and erythromycin. A single ribotype 078 isolate showed metronidazole heteroresistance. Healthy dogs can shed antimicrobial-resistant C. difficile strains. © 2014 British Small Animal Veterinary Association.

  3. Detection and genotyping of human papillomavirus in self-obtained cervicovaginal samples by using the FTA cartridge: new possibilities for cervical cancer screening.

    NARCIS (Netherlands)

    Lenselink, C.H.; Bie, R.P. de; Hamont, D. van; Bakkers, J.M.J.E.; Quint, W.G.V.; Massuger, L.F.A.G.; Bekkers, R.L.M.; Melchers, W.J.G.

    2009-01-01

    This study assesses human papillomavirus (HPV) detection and genotyping in self-sampled genital smears applied to an indicating FTA elute cartridge (FTA cartridge). The study group consisted of 96 women, divided into two sample sets. All samples were analyzed by the HPV SPF(10)-Line Blot 25. Set 1

  4. Quantification of Eimeria acervulina in faeces of broilers: Comparison of McMaster oocyst counts from 24 h faecal collections and single droppings to real-time PCR from cloacal swabs

    NARCIS (Netherlands)

    Velkers, F.C.; Blake, D.P.; Graat, E.A.M.; Vernooij, J.C.M.; Bouma, A.; de Jong, M.C.M; Stegeman, J.A.

    2010-01-01

    Coccidiosis is an economically important disease in chickens, caused by infection with Eimeria species parasites. Diagnosis of coccidiosis is frequently based on oocyst enumeration in pooled faecal samples or litter. In studies on infection dynamics and for monitoring in the field, samples from

  5. In vitro colonic metabolism of coffee and chlorogenic acid results in selective changes in human faecal microbiota growth.

    Science.gov (United States)

    Mills, Charlotte E; Tzounis, Xenofon; Oruna-Concha, Maria-Jose; Mottram, Don S; Gibson, Glenn R; Spencer, Jeremy P E

    2015-04-28

    Coffee is a relatively rich source of chlorogenic acids (CGA), which, as other polyphenols, have been postulated to exert preventive effects against CVD and type 2 diabetes. As a considerable proportion of ingested CGA reaches the large intestine, CGA may be capable of exerting beneficial effects in the large gut. Here, we utilise a stirred, anaerobic, pH-controlled, batch culture fermentation model of the distal region of the colon in order to investigate the impact of coffee and CGA on the growth of the human faecal microbiota. Incubation of coffee samples with the human faecal microbiota led to the rapid metabolism of CGA (4 h) and the production of dihydrocaffeic acid and dihydroferulic acid, while caffeine remained unmetabolised. The coffee with the highest levels of CGA (Pspp. relative to the control vessel at 10 h after exposure (Pspp. (PEubacterium rectale group (P<0·05). This selective metabolism and subsequent amplification of specific bacterial populations could be beneficial to host health.

  6. HPV genotype-specific concordance between EuroArray HPV, Anyplex II HPV28 and Linear Array HPV Genotyping test in Australian cervical samples

    Directory of Open Access Journals (Sweden)

    Alyssa M. Cornall

    2017-12-01

    Full Text Available Purpose: To compare human papillomavirus genotype-specific performance of two genotyping assays, Anyplex II HPV28 (Seegene and EuroArray HPV (EuroImmun, with Linear Array HPV (Roche. Methods: DNA extracted from clinican-collected cervical brush specimens in PreservCyt medium (Hologic, from 403 women undergoing management for detected cytological abnormalities, was tested on the three assays. Genotype-specific agreement were assessed by Cohen's kappa statistic and Fisher's z-test of significance between proportions. Results: Agreement between Linear Array and the other 2 assays was substantial to almost perfect (κ = 0.60 − 1.00 for most genotypes, and was almost perfect (κ = 0.81 – 0.98 for almost all high-risk genotypes. Linear Array overall detected most genotypes more frequently, however this was only statistically significant for HPV51 (EuroArray; p = 0.0497, HPV52 (Anyplex II; p = 0.039 and HPV61 (Anyplex II; p=0.047. EuroArray detected signficantly more HPV26 (p = 0.002 and Anyplex II detected more HPV42 (p = 0.035 than Linear Array. Each assay performed differently for HPV68 detection: EuroArray and LA were in moderate to substantial agreement with Anyplex II (κ = 0.46 and 0.62, respectively, but were in poor disagreement with each other (κ = −0.01. Conclusions: EuroArray and Anyplex II had similar sensitivity to Linear Array for most high-risk genotypes, with slightly lower sensitivity for HPV 51 or 52. Keywords: Human papillomavirus, Genotyping, Linear Array, Anyplex II, EuroArray, Cervix

  7. Performance of rats orogastrically dosed with faecal strains of ...

    African Journals Online (AJOL)

    Administrator

    strains of Lactobacillus acidophilus and challenged ... Albino rats (Rattus norvegicus) were orogastrically dosed with faecal strains of Lactobacillus .... Chang et al. (2001) reported a similar observation in piglets fed probiotic strain, Lactobacillus reuteri BSA 131. Francisco et al. (1995) had earlier reported that selected ...

  8. Faecal nitrogen of browser and mixed feeder game species during ...

    African Journals Online (AJOL)

    Faecal nitrogen of browser and mixed feeder game species during different seasons. ... A practical measure of assessing periods of potential nutritional stress of game species is needed in the management of ... AJOL African Journals Online.

  9. [Evaluation of hepatitis B virus genotyping EIA kit].

    Science.gov (United States)

    Tanaka, Yasuhito; Sugauchi, Fuminaka; Matsuuraa, Kentaro; Naganuma, Hatsue; Tatematsu, Kanako; Takagi, Kazumi; Hiramatsu, Kumiko; Kani, Satomi; Gotoh, Takaaki; Wakimoto, Yukio; Mizokami, Masashi

    2009-01-01

    Clinical significance of Hepatitis B virus(HBV) genotyping is increasingly recognized. The aim of this study was to evaluate reproducibility, accuracy, and sensitivity of an enzyme immunoassay (EIA) based HBV genotyping kit, which designed to discriminate between genotypes to A, B, C, or D by detecting genotype-specific epitopes in PreS2 region. Using the four genotypes panels, the EIA demonstrated complete inter and intra-assay genotyping reproducibility. Serum specimens had stable results after 8 days at 4 degrees C, or 10 cycles of freezing-thawing. In 91 samples that have been genotyped by DNA sequencing, 87(95.6%) were in complete accordance with EIA genotyping. Of examined 344 HBsAg-positive serum specimens, genotypes A, B, C and D were determined in 26 (7.6%), 62 (18.0%), 228 (66.3%), and 9 (2.6%) cases, respectively. Of 19 (5.5%) specimens unclassified by the EIA, 13 were found to have low titer of HBsAg concentration (< 3 IU/ml), and the other 5 had amino acid mutations or deletions within targeted PreS2 epitopes. The EIA allowed genotyping even in HBV DNA negative samples (96.2%). In conclusion, HBV genotype EIA is reliable, sensitive and easy assay for HBV genotyping. The assay would be useful for clinical use.

  10. HPV genotype-specific concordance between EuroArray HPV, Anyplex II HPV28 and Linear Array HPV Genotyping test in Australian cervical samples.

    Science.gov (United States)

    Cornall, Alyssa M; Poljak, Marin; Garland, Suzanne M; Phillips, Samuel; Machalek, Dorothy A; Tan, Jeffrey H; Quinn, Michael A; Tabrizi, Sepehr N

    2017-12-01

    To compare human papillomavirus genotype-specific performance of two genotyping assays, Anyplex II HPV28 (Seegene) and EuroArray HPV (EuroImmun), with Linear Array HPV (Roche). DNA extracted from clinican-collected cervical brush specimens in PreservCyt medium (Hologic), from 403 women undergoing management for detected cytological abnormalities, was tested on the three assays. Genotype-specific agreement were assessed by Cohen's kappa statistic and Fisher's z-test of significance between proportions. Agreement between Linear Array and the other 2 assays was substantial to almost perfect (κ = 0.60 - 1.00) for most genotypes, and was almost perfect (κ = 0.81 - 0.98) for almost all high-risk genotypes. Linear Array overall detected most genotypes more frequently, however this was only statistically significant for HPV51 (EuroArray; p = 0.0497), HPV52 (Anyplex II; p = 0.039) and HPV61 (Anyplex II; p=0.047). EuroArray detected signficantly more HPV26 (p = 0.002) and Anyplex II detected more HPV42 (p = 0.035) than Linear Array. Each assay performed differently for HPV68 detection: EuroArray and LA were in moderate to substantial agreement with Anyplex II (κ = 0.46 and 0.62, respectively), but were in poor disagreement with each other (κ = -0.01). EuroArray and Anyplex II had similar sensitivity to Linear Array for most high-risk genotypes, with slightly lower sensitivity for HPV 51 or 52. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

  11. Laboratory development and field testing of sentinel toys to assess environmental faecal exposure of young children in rural India.

    Science.gov (United States)

    Torondel, Belen; Gyekye-Aboagye, Yaw; Routray, Parimita; Boisson, Sophie; Schimdt, Wolf; Clasen, Thomas

    2015-06-01

    Sentinel toys are increasingly used as a method of assessing young children's exposure to faecal pathogens in households in low-income settings. However, there is no consensus on the suitability of different approaches. We evaluated three types of toy balls with different surfaces (plastic, rubber, urethane) in the laboratory to compare the uptake of faecal indicator bacteria (Escherichia coli) on their surface. We performed bacteria survival analysis under different environmental conditions and tested laboratory methods for bacteria removal and recovery. In a field study we distributed sterile urethane balls to children toys in sterile water, assayed for thermotolerant coliforms (TTC) and explored associations between the level of contamination and household characteristics. In the laboratory, urethane foam balls took up more indicator bacteria than the other balls. Bacteria recovery did not differ based on mechanic vs no agitation. Higher temperatures and moisture levels increased bacterial yield. In the field, the only factor associated with a decreased recovery of TTC from the balls was having a soil (unpaved) floor. Sentinel toys may be an effective tool for assessing young children's exposure to faecal pathogens. However, even using methods designed to increase bacterial recovery, limited sensitivity may require larger sample sizes. © The Author 2015. Published by Oxford University Press on behalf of Royal Society of Tropical Medicine and Hygiene. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  12. Existence of various human parvovirus B19 genotypes in Chinese plasma pools: genotype 1, genotype 3, putative intergenotypic recombinant variants and new genotypes.

    Science.gov (United States)

    Jia, Junting; Ma, Yuyuan; Zhao, Xiong; Huangfu, Chaoji; Zhong, Yadi; Fang, Chi; Fan, Rui; Lv, Maomin; Zhang, Jingang

    2016-09-17

    Human parvovirus B19 (B19V) is a frequent contaminant of blood and plasma-derived medicinal products. Three distinct genotypes of B19V have been identified. The distribution of the three B19V genotypes has been investigated in various regions or countries. However, in China, data on the existence of different B19V genotypes are limited. One hundred and eighteen B19V-DNA positive source plasma pool samples collected from three Chinese blood products manufacturers were analyzed. The subgenomic NS1/VP1u region junction of B19V was amplified by nested PCR. These amplified products were then cloned and subsequently sequenced. For genotyping, their phylogenetic inferences were constructed based on the NS1/VP1-unique region. Then putative recombination events were analyzed and identified. Phylogenetic analysis of 118 B19V sequences attributed 61.86 % to genotype 1a, 10.17 % to genotype 1b, and 17.80 % to genotype 3b. All the genotype 3b sequences obtained in this study grouped as a specific, closely related cluster with B19V strain D91.1. Four 1a/3b recombinants and 5 new atypical B19V variants with no recombination events were identified. There were at least 3 subtypes (1a, 1b and 3b) of B19V circulating in China. Furthermore, putative B19V 1a/3b recombinants and unclassified strains were identified as well. Such recombinant and unclassified strains may contribute to the genetic diversity of B19V and consequently complicate the B19V infection diagnosis and NAT screening. Further studies will be required to elucidate the biological significance of the recombinant and unclassified strains.

  13. Faecal cortisol metabolites in Bengal (Panthera tigris tigris) and Sumatran tigers (Panthera tigris sumatrae).

    Science.gov (United States)

    Narayan, Edward J; Parnell, Tempe; Clark, Giles; Martin-Vegue, Patrick; Mucci, Al; Hero, Jean-Marc

    2013-12-01

    The tiger (Panthera tigris) faces a great risk of extinction as its wild numbers have plummeted due to poaching and habitat destruction so ex-situ conservation programs are becoming ever more necessary. Reliable non-invasive biomarkers of the stress hormone (cortisol) are necessary for assessing the health and welfare of tigers in captivity. To our knowledge, non-invasive stress endocrinology methods have not been tested as widely in tigers. The first aim of this study was to describe and validate a faecal cortisol metabolite enzyme-immmunoassay (FCM EIA) for two tiger sub-species, the Bengal tiger (Panthera tigris tigris) and the Sumatran tiger (Panthera tigris sumatrae). Individual tigers (n=22) were studied in two large Zoos in Queensland, Australia (Dreamworld Theme Park and Australia Zoo). Fresh faecal samples (Zoos over a study period of 21 days. Biological validation was conducted separately by collecting feces 5 days before and 5 days after blood was taken from four male and five female tigers. Results showed that mean FCM levels increased by 138% and 285% in the male and female tigers within 1 day after bloods were taken, returning to baseline in 5 days. Laboratory validations of the FCM EIA were done using an extraction efficiency test and parallelism. Results showed >89% recovery of the cortisol standard that was added to tiger faecal extract. We also obtained parallel displacement of the serially diluted cortisol standard against serially diluted tiger faecal extract. Our second aim was to determine whether the FCM levels were significantly different between tiger sub-species and sex. Results showed no significant difference in mean FCM levels between the Bengal and Sumatran tiger sub-species. Mean levels of FCMs were significantly higher in females than in male tigers. Those male and female tigers with reported health issues during the study period expressed higher FCM levels than the reportedly healthy tigers. Interestingly, those tigers that took

  14. Efficacy of the nematode-trapping fungus Duddingtonia flagrans against three species of gastro-intestinal nematodes in laboratory faecal cultures from sheep and goats.

    Science.gov (United States)

    Waghorn, T S; Leathwick, D M; Chen, L-Y; Skipp, R A

    2003-12-30

    The ability of the nematode-killing fungus Duddingtonia flagrans to reduce number of infective larvae of three species of gastro-intestinal parasitic nematodes developing in dung was investigated in both goats and sheep. Groups of lambs and kids (12-20 weeks old) were given mono-specific infections of Haemonchus contortus, Ostertagia (Teladorsagia) circumcincta or Trichostrongylus colubriformis. Following patency of the infections (t1) faecal samples were collected for determination of faecal nematode egg count (FEC) and culture of parasite larvae. Groups of animals were then dosed on 2 consecutive days with one of the two dose rates of the fungus (250,000 or 500,000 spores/kg liveweight). One (t2) and 5 (t3) days after the second dose of fungus samples were again collected for FEC and culture. The number of larvae recovered from the faecal cultures at t1 and t3 were used as controls to assess the efficacy of the experimental treatment at t2. Average efficacy was 78% with group means ranging from 40 to 93%. Dose rate of fungus appeared to influence efficacy against O. circumcincta but not against H. contortus or T. colubriformis. Overall, there were no differences in the efficacy of the fungus against any of the parasite species or in either host animal. The results of this trial indicate the potential use of this fungus as a broad spectrum anti-parasite agent for use in both goats and sheep.

  15. Studies to distinguish between human and animal faecal pollution ...

    African Journals Online (AJOL)

    Human enteric viral infections are considered to be predominantly associated with human wastes, as opposed to animal wastes, and a distinction between these has benefits for water quality control and risk assessment. A variety of techniques have been described to distinguish between human and animal faecal pollution ...

  16. Performance of rats orogastrically dosed with faecal strains of ...

    African Journals Online (AJOL)

    Albino rats (Rattus norvegicus) were orogastrically dosed with faecal strains of Lactobacillus acidophilus and simultaneously infected with Escherichia coli, while the control was challenged with E. coli alone. The treatment was repeated the second day and post ingestion period of 18 days follow. It was observed that rats ...

  17. Evaluation of a method of assessing faecal loading on plain abdominal radiographs in children

    International Nuclear Information System (INIS)

    Leech, S.C.; Sullivan, P.B.; McHugh, K.

    1999-01-01

    Background. Childhood constipation is common and assessment is often difficult. Plain abdominal radiography is simple and commonly used to assess constipation. The role of radiography with the use of a simple scoring system has not been fully evaluated. Objective. To assess the reliability of scoring faecal loading on plain abdominal radiographs in children with intractable constipation. Materials and methods. Plain abdominal radiographs from 33 constipated and 67 control children were independently assessed by three observers on two separate occasions. A scoring system was devised with scores from 0 (no stool) to 5 (gross faecal loading with bowel dilatation) in three areas of the colon, giving a total score of 0-15. Results. There were significant differences between the scores of the constipated and control radiographs for each observer (P = 0.05). There was no intra-observer variation (P = 0.12-0.69), but significant inter-observer variation was demonstrated (P = 0.00). Conclusions. We have found this scoring system to be a clinically useful and a reproducible tool in assessing childhood constipation. Assessment of faecal loading is subjective and varies between observers, although one observer will consistently score faecal loading on the same radiograph on successive occasions. To limit exposure to ionising radiation, we recommend that radiography be reserved for the investigation of intractable constipation, and its accuracy is improved if all radiographs are scored by the same observer. (orig.)

  18. Conventional treatment of functional constipation has a positive impact on the behavioural difficulties in children with and without faecal incontinence

    DEFF Research Database (Denmark)

    Modin, Line; Jakobsen, Ida Skytte; Jakobsen, Marianne Skytte

    2016-01-01

    AIM: Constipation studies have only evaluated behavioural difficulties in children with faecal incontinence. This study evaluated changes in behavioural difficulties in childhood with functional constipation (FC) with and without faecal incontinence, based on treatment outcomes. METHODS: Children...... treatment of FC had a positive impact on behavioural difficulties in constipated children with and without faecal incontinence. This study highlights the importance of proactive detection and treatment of FC in paediatric patients....

  19. Establishment of a novel two-probe real-time PCR for simultaneously quantification of hepatitis B virus DNA and distinguishing genotype B from non-B genotypes.

    Science.gov (United States)

    Wang, Wei; Liang, Hongpin; Zeng, Yongbin; Lin, Jinpiao; Liu, Can; Jiang, Ling; Yang, Bin; Ou, Qishui

    2014-11-01

    Establishment of a simple, rapid and economical method for quantification and genotyping of hepatitis B virus (HBV) is of great importance for clinical diagnosis and treatment of chronic hepatitis B patients. We hereby aim to develop a novel two-probe real-time PCR for simultaneous quantification of HBV viral concentration and distinguishing genotype B from non-B genotypes. Conserved primers and TaqMan probes for genotype B and non-B genotypes were designed. The linear range, detection sensitivity, specificity and repeatability of the method were assessed. 539 serum samples from HBV-infected patients were assayed, and the results were compared with commercial HBV quantification and HBV genotyping kits. The detection sensitivity of the two-probe real-time PCR was 500IU/ml; the linear range was 10(3)-10(9)IU/ml, and the intra-assay CVs and inter-assay CVs were between 0.84% and 2.80%. No cross-reaction was observed between genotypes B and non-B. Of the 539 detected samples, 509 samples were HBV DNA positive. The results showed that 54.0% (275/509) of the samples were genotype B, 39.5% (201/509) were genotype non-B and 6.5% (33/509) were mixed genotype. The coincidence rate between the method and a commercial HBV DNA genotyping kit was 95.9% (488/509, kappa=0.923, PDNA qPCR kit were achieved. A novel two-probe real-time PCR method for simultaneous quantification of HBV viral concentration and distinguishing genotype B from non-B genotypes was established. The assay was sensitive, specific and reproducible which can be applied to areas prevalent with HBV genotypes B and C, especially in China. Copyright © 2014 Elsevier B.V. All rights reserved.

  20. Investigation of an Escherichia coli O145 outbreak in a child day-care centre - extensive sampling and characterization of eae- and stx1-positive E. coli yields epidemiological and socioeconomic insight

    Directory of Open Access Journals (Sweden)

    Bruheim Torkjel

    2011-09-01

    Full Text Available Abstract Background On October 29th 2009 the health authorities in the city of Trondheim, Norway were alerted about a case of Shiga toxin-positive E. coli (STEC O145 in a child with bloody diarrhoea attending a day-care centre. Symptomatic children in this day-care centre were sampled, thereby identifying three more cases. This initiated an outbreak investigation. Methods A case was defined as a child attending the day-care centre, in whom eae- and stx1- but not stx2-positive E. coli O145:H28 was diagnosed from a faecal sample, with multilocus variable number of tandem repeat analysis (MLVA profile identical to the index isolate. All 61 children, a staff of 14 in the day-care centre, and 74 close contacts submitted faecal samples. Staff and parents were interviewed about cases' exposure to foods and animals. Faecal samples from 31 ewes from a sheep herd to which the children were exposed were analyzed for E. coli O145. Results Sixteen cases were identified, from which nine presented diarrhoea but not haemolytic uremic syndrome (HUS. The attack rate was 0.26, and varied between age groups (0.13-0.40 and between the three day-care centre departments (0.20-0.50, and was significantly higher amongst the youngest children. Median duration of shedding was 20 days (0-71 days. Children were excluded from the day-care centre during shedding, requiring parents to take compassionate leave, estimated to be a minimum total of 406 days for all cases. Atypical enteropathogenic E. coli (aEPEC were detected among 14 children other than cases. These isolates were genotypically different from the outbreak strain. Children in the day-care centre were exposed to faecal pollution from a sheep herd, but E. coli O145 was not detected in the sheep. Conclusions We report an outbreak of stx1- and eae-positive STEC O145:H28 infection with mild symptoms among children in a day-care centre. Extensive sampling showed occurrence of the outbreak strain as well as other STEC and

  1. Comparing different post-mortem human samples as DNA sources for downstream genotyping and identification.

    Science.gov (United States)

    Calacal, Gayvelline C; Apaga, Dame Loveliness T; Salvador, Jazelyn M; Jimenez, Joseph Andrew D; Lagat, Ludivino J; Villacorta, Renato Pio F; Lim, Maria Cecilia F; Fortun, Raquel D R; Datar, Francisco A; De Ungria, Maria Corazon A

    2015-11-01

    The capability of DNA laboratories to perform genotyping procedures from post-mortem remains, including those that had undergone putrefaction, continues to be a challenge in the Philippines, a country characterized by very humid and warm conditions all year round. These environmental conditions accelerate the decomposition of human remains that were recovered after a disaster and those that were left abandoned after a crime. When considerable tissue decomposition of human remains has taken place, there is no other option but to extract DNA from bone and/or teeth samples. Routinely, femur shafts are obtained from recovered bodies for human identification because the calcium matrix protects the DNA contained in the osteocytes. In the Philippines, there is difficulty in collecting femur samples after natural disasters or even human-made disasters, because these events are usually characterized by a large number of fatalities. Identification of casualties is further delayed by limitation in human and material resources. Hence, it is imperative to test other types of biological samples that are easier to collect, transport, process and store. We analyzed DNA that were obtained from body fluid, bone marrow, muscle tissue, clavicle, femur, metatarsal, patella, rib and vertebral samples from five recently deceased untreated male cadavers and seven male human remains that were embalmed, buried for ∼ 1 month and then exhumed. The bodies had undergone different environmental conditions and were in various stages of putrefaction. A DNA extraction method utilizing a detergent-washing step followed by an organic procedure was used. The utility of bone marrow and vitreous fluid including bone marrow and vitreous fluid that was transferred on FTA(®) cards and subjected to autosomal STR and Y-STR DNA typing were also evaluated. DNA yield was measured and the presence or absence of PCR inhibitors in DNA extracts was assessed using Plexor(®)HY. All samples were amplified using

  2. Removal of faecal bacteria and nutrients from domestic wastewater ...

    African Journals Online (AJOL)

    The aim of this study was to evaluate the removal of faecal bacteria and nutrients from domestic wastewater, in surface flow wetlands vegetated with Echinochloa pyramidalis. Horizontal surface flow (HSF) wetlands were fed with primarily treated domestic wastewater at organic loading rates varying from 20.74 to 27.15 g ...

  3. Detection and Genotyping of Human Papillomavirus in Self-Obtained Cervicovaginal Samples by Using the FTA Cartridge: New Possibilities for Cervical Cancer Screening ▿

    Science.gov (United States)

    Lenselink, Charlotte H.; de Bie, Roosmarie P.; van Hamont, Dennis; Bakkers, Judith M. J. E.; Quint, Wim G. V.; Massuger, Leon F. A. G.; Bekkers, Ruud L. M.; Melchers, Willem J. G.

    2009-01-01

    This study assesses human papillomavirus (HPV) detection and genotyping in self-sampled genital smears applied to an indicating FTA elute cartridge (FTA cartridge). The study group consisted of 96 women, divided into two sample sets. All samples were analyzed by the HPV SPF10-Line Blot 25. Set 1 consisted of 45 women attending the gynecologist; all obtained a self-sampled cervicovaginal smear, which was applied to an FTA cartridge. HPV results were compared to a cervical smear (liquid based) taken by a trained physician. Set 2 consisted of 51 women who obtained a self-sampled cervicovaginal smear at home, which was applied to an FTA cartridge and to a liquid-based medium. DNA was obtained from the FTA cartridges by simple elution as well as extraction. Of all self-obtained samples of set 1, 62.2% tested HPV positive. The overall agreement between self- and physician-obtained samples was 93.3%, in favor of the self-obtained samples. In sample set 2, 25.5% tested HPV positive. The overall agreement for high-risk HPV presence between the FTA cartridge and liquid-based medium and between DNA elution and extraction was 100%. This study shows that HPV detection and genotyping in self-obtained cervicovaginal samples applied to an FTA cartridge is highly reliable. It shows a high level of overall agreement with HPV detection and genotyping in physician-obtained cervical smears and liquid-based self-samples. DNA can be obtained by simple elution and is therefore easy, cheap, and fast. Furthermore, the FTA cartridge is a convenient medium for collection and safe transport at ambient temperatures. Therefore, this method may contribute to a new way of cervical cancer screening. PMID:19553570

  4. [Detailed methodological recommendations for the treatment of Clostridium difficile-associated diarrhea with faecal transplantation].

    Science.gov (United States)

    Nagy, Gergely György; Várvölgyi, Csaba; Balogh, Zoltán; Orosi, Piroska; Paragh, György

    2013-01-06

    The incidence of Clostridium difficile associated enteral disease shows dramatic increase worldwide, with appallingly high treatment costs, mortality figures, recurrence rates and treatment refractoriness. It is not surprising, that there is significant interest in the development and introduction of alternative therapeutic strategies. Among these only stool transplantation (or faecal bacteriotherapy) is gaining international acceptance due to its excellent cure rate (≈92%), low recurrence rate (≈6%), safety and cost-effectiveness. Unfortunately faecal transplantation is not available for most patients, although based on promising international results, its introduction into the routine clinical practice is well justified and widely expected. The authors would like to facilitate this process, by presenting a detailed faecal transplantation protocol prepared in their Institution based on the available literature and clinical rationality. Officially accepted national methodological guidelines will need to be issued in the future, founded on the expert opinion of relevant professional societies and upcoming advances in this field.

  5. Evaluation of the Efficacy of the Mini Parasep SF Faecal Parasite ...

    African Journals Online (AJOL)

    Evaluation of the Efficacy of the Mini Parasep SF Faecal Parasite Concentrator; A New Technique against the Direct Smear and Formol Ether Concentration Technique for the Detection of Intestinal Parasites in Stool.

  6. Assessing the performance of multiplexed tandem PCR for the diagnosis of pathogenic genotypes of Theileria orientalis using pooled blood samples from cattle.

    Science.gov (United States)

    Gebrekidan, Hagos; Gasser, Robin B; Stevenson, Mark A; McGrath, Sean; Jabbar, Abdul

    2017-02-01

    Oriental theileriosis caused by multiple genotypes of Theileria orientalis is an important tick-borne disease of bovines. Here, we assessed the performance of an established multiplexed tandem PCR (MT-PCR) for the diagnosis of the two recognized, pathogenic genotypes (chitose and ikeda) of T. orientalis in cattle using pooled blood samples. We used a total of 265 cattle blood samples, which were divided into two groups according to previous MT-PCR results for individual samples. Samples in group 1 (n = 155) were from a herd with a relatively high prevalence of T. orientalis infection; and those in group 2 (n = 110) were from four herds with a low prevalence. For group 1, 31 and 15 batches of five- and ten-pooled samples (selected at random), respectively, were formed. For group 2, 22 and 11 batches of five- and ten-pooled samples (selected at random), respectively, were formed. DNAs from individual pooled samples in each batch and group were then tested by MT-PCR. For group 1, the apparent prevalences estimated using the 31 batches of five-pooled samples (97%) and 15 batches of ten-pooled samples (100%) were significantly higher compared with individual samples (75%). For group 2, higher apparent prevalences (9% and 36%) were also recorded for the 22 and 11 batches of pooled samples, respectively, compared with individual samples (7%). Overall, the average infection intensity recorded for the genotypes of chitose and ikeda were considerably lower in pooled compared with individual samples. The diagnostic specificities of MT-PCR were estimated at 95% and 94%, respectively, when batches of five- and ten-pooled samples were tested, and 94% for individual samples. The diagnostic sensitivity of this assay was estimated at 98% same for all individual, five- and ten-pooled samples. This study shows that screening batches of five- and ten-pooled blood samples from cattle herds are similar to those obtained for individual samples, and, importantly, that the reduced cost

  7. Faecal immunochemical tests to triage patients with lower abdominal symptoms for suspected colorectal cancer referrals in primary care: a systematic review and cost-effectiveness analysis.

    Science.gov (United States)

    Westwood, Marie; Corro Ramos, Isaac; Lang, Shona; Luyendijk, Marianne; Zaim, Remziye; Stirk, Lisa; Al, Maiwenn; Armstrong, Nigel; Kleijnen, Jos

    2017-05-01

    Colorectal cancer (CRC) is the third most common cancer in the UK. Presenting symptoms that can be associated with CRC usually have another explanation. Faecal immunochemical tests (FITs) detect blood that is not visible to the naked eye and may help to select patients who are likely to benefit from further investigation. To assess the effectiveness of FITs [OC-Sensor (Eiken Chemical Co./MAST Diagnostics, Tokyo, Japan), HM-JACKarc (Kyowa Medex/Alpha Laboratories Ltd, Tokyo, Japan), FOB Gold (Sentinel/Sysmex, Sentinel Diagnostics, Milan, Italy), RIDASCREEN Hb or RIDASCREEN Hb/Hp complex (R-Biopharm, Darmstadt, Germany)] for primary care triage of people with low-risk symptoms. Twenty-four resources were searched to March 2016. Review methods followed published guidelines. Summary estimates were calculated using a bivariate model or a random-effects logistic regression model. The cost-effectiveness analysis considered long-term costs and quality-adjusted life-years (QALYs) that were associated with different faecal occult blood tests and direct colonoscopy referral. Modelling comprised a diagnostic decision model, a Markov model for long-term costs and QALYs that were associated with CRC treatment and progression, and a Markov model for QALYs that were associated with no CRC. We included 10 studies. Using a single sample and 10 µg Hb/g faeces threshold, sensitivity estimates for OC-Sensor [92.1%, 95% confidence interval (CI) 86.9% to 95.3%] and HM-JACKarc (100%, 95% CI 71.5% to 100%) indicated that both may be useful to rule out CRC. Specificity estimates were 85.8% (95% CI 78.3% to 91.0%) and 76.6% (95% CI 72.6% to 80.3%). Triage using FITs could rule out CRC and avoid colonoscopy in approximately 75% of symptomatic patients. Data from our systematic review suggest that 22.5-93% of patients with a positive FIT and no CRC have other significant bowel pathologies. The results of the base-case analysis suggested minimal difference in QALYs between all of the

  8. Incidence of interval cancers in faecal immunochemical test colorectal screening programmes in Italy.

    Science.gov (United States)

    Giorgi Rossi, Paolo; Carretta, Elisa; Mangone, Lucia; Baracco, Susanna; Serraino, Diego; Zorzi, Manuel

    2018-03-01

    Objective In Italy, colorectal screening programmes using the faecal immunochemical test from ages 50 to 69 every two years have been in place since 2005. We aimed to measure the incidence of interval cancers in the two years after a negative faecal immunochemical test, and compare this with the pre-screening incidence of colorectal cancer. Methods Using data on colorectal cancers diagnosed in Italy from 2000 to 2008 collected by cancer registries in areas with active screening programmes, we identified cases that occurred within 24 months of negative screening tests. We used the number of tests with a negative result as a denominator, grouped by age and sex. Proportional incidence was calculated for the first and second year after screening. Results Among 579,176 and 226,738 persons with negative test results followed up at 12 and 24 months, respectively, we identified 100 interval cancers in the first year and 70 in the second year. The proportional incidence was 13% (95% confidence interval 10-15) and 23% (95% confidence interval 18-25), respectively. The estimate for the two-year incidence is 18%, which was slightly higher in females (22%; 95% confidence interval 17-26), and for proximal colon (22%; 95% confidence interval 16-28). Conclusion The incidence of interval cancers in the two years after a negative faecal immunochemical test in routine population-based colorectal cancer screening was less than one-fifth of the expected incidence. This is direct evidence that the faecal immunochemical test-based screening programme protocol has high sensitivity for cancers that will become symptomatic.

  9. Implementation of Cell Samples as Controls in National Proficiency Testing for Clopidogrel Therapy-Related CYP2C19 Genotyping in China: A Novel Approach.

    Directory of Open Access Journals (Sweden)

    Guigao Lin

    Full Text Available Laboratories are increasingly requested to perform CYP2C19 genetic testing when managing clopidogrel therapy, especially in patients with acute coronary syndrome undergoing percutaneous coronary intervention. To ensure high quality molecular testing and ascertain that the referring clinician has the correct information for CYP2C19 genotype-directed antiplatelet therapy, a proficiency testing scheme was set up to evaluate the laboratory performance for the entire testing process. Proficiency panels of 10 cell samples encompassing the common CYP2C19 genetic polymorphisms were distributed to 62 participating laboratories for routine molecular testing and the responses were analyzed for accuracy of genotyping and the reporting of results. Data including the number of samples tested, the accreditation/certification status, and test methodology of each individual laboratory were also reviewed. Fifty-seven of the 62 participants correctly identified the CYP2C19 variants in all samples. There were six genotyping errors, with a corresponding analytical sensitivity of 98.5% (333/338 challenges; 95% confidence interval: 96.5-99.5% and an analytic specificity of 99.6% (281/282; 95% confidence interval: 98.0-99.9%. Reports of the CYP2C19 genotyping results often lacked essential information. In conclusion, clinical laboratories demonstrated good analytical sensitivity and specificity; however, the pharmacogenetic testing community requires additional education regarding the correct reporting of CYP2C19 genetic test results.

  10. Assessing diet quality of African ungulates from faecal analyses: the effect of forage quality, intake and herbivore species

    Directory of Open Access Journals (Sweden)

    J.M. Wrench

    1997-08-01

    Full Text Available Faecal phosphorous and nitrogen can be used as indicators of the nutritive content of the veld. Dietary P concentrations can be predicted with reasonable accuracy from faecal P concentrations in faeces of caged impala rams using a simple linear regression model, Y = 0.393X (r2 = 0.97. This regression holds whether impala are grazing or browsing as well as for high and low levels of intake. The regression equation used in the prediction of dietary P in zebra, blue wildebeest and cattle, did not differ significantly from this simple regression and a combined regression equation could be formulated. A faecal P concentration of less than 2 g P/kg OM would appear to indicate a P deficiency in most species. The prediction of dietary N is influenced by the intake of phenolic compounds and different regression equations exist for grazers and browsers. For prediction of dietary N concentrations, both the concentration of N and P in the faeces should be taken into account. This multiple regression equation is applicable for grazing impala at all levels of intake. For impala utilising browse, a regression model with faecal Acid Detergent Insoluble Nitrogen (ADIN and Acid Detergent Lignin (ADL should be used to predict dietary N concentration. For grazers, a faecal N concentration of less than 14 g/kg DM would indicate a deficiency. Dietary digestibility can be predicted accurately in some species using faecal N, P and ADL concentrations. However, more work needs to be done to quantify their effects.

  11. Effect of ingredient particle sizes and dietary viscosity on digestion and faecal waste of striped catfish (Pangasianodon hypophthalmus)

    NARCIS (Netherlands)

    Tran, Tu; Hien, T.T.T.; Bosma, R.H.; Heinsbroek, L.T.N.; Verreth, J.A.J.; Schrama, J.W.

    2017-01-01

    The ingredients' particle size and dietary viscosity may alter digestion, performance and faecal waste management of fish. This study aimed to assess the effect of grinding screen sizes of feed ingredients and dietary viscosity on digestibility, faecal waste and performance of striped catfish

  12. Effect of ingredient particle sizes and dietary viscosity on digestion and faecal waste of striped catfish (Pangasianodon hypophthalmus)

    NARCIS (Netherlands)

    Tran, Tu; Hien, T.T.T.; Bosma, R.H.; Heinsbroek, L.T.N.; Verreth, J.A.J.; Schrama, J.W.

    2018-01-01

    The ingredients' particle size and dietary viscosity may alter digestion, performance and faecal waste management of fish. This study aimed to assess the effect of grinding screen sizes of feed ingredients and dietary viscosity on digestibility, faecal waste and performance of striped catfish

  13. Faecal near-IR spectroscopy to determine the nutritional value of diets consumed by beef cattle in east Mediterranean rangelands.

    Science.gov (United States)

    Landau, S Y; Dvash, L; Roudman, M; Muklada, H; Barkai, D; Yehuda, Y; Ungar, E D

    2016-02-01

    Rapid assessment of the nutritional quality of diets ingested by grazing animals is pivotal for successful cow-calf management in east Mediterranean rangelands, which receive unpredictable rainfall and are subject to hot-spells. Clipped vegetation samples are seldom representative of diets consumed, as cows locate and graze selectively. In contrast, faeces are easily sampled and their near-IR spectra contain information about nutrients and their utilization. However, a pre-requisite for successful faecal near-infrared reflectance spectroscopy (FNIRS) is that the calibration database encompass the spectral variability of samples to be analyzed. Using confined beef cows in Northern and Southern Israel, we calibrated prediction equations based on individual pairs of known dietary attributes and the NIR spectra of associated faeces (n=125). Diets were composed of fresh-cut green fodder of monocots (wheat and barley), dicots (safflower and garden pea) and natural pasture collected at various phenological states over 2 consecutive years, and, optionally, supplements of barley grain and dried poultry litter. A total of 48 additional pairs of faeces and diets sourced from cows fed six complete mixed rations covering a wide range of energy and CP concentrations. Precision (linearity of calibration, R2cal, and of cross-validation, R2cv) and accuracy (standard error of cross-validation, SEcv) were criteria for calibration quality. The calibrations for dietary ash, CP, NDF and in vitro dry matter digestibility yielded R2cal values >0.87, R2cv of 0.81 to 0.89 and SEcv values of 16, 13, 39 and 31 g/kg dry matter, respectively. Equations for nutrient intake were of low quality, with the exception of CP. Evaluation of FNIRS predictions was carried out with grazing animals supplemented or not with poultry litter, and implementation of the method in one herd over 2 years is presented. The potential usefulness of equations was also established by calculating the Mahalanobis (H

  14. Nutritionally-related blood metabolites and faecal egg counts in ...

    African Journals Online (AJOL)

    Nutritionally-related blood metabolites and faecal egg counts in indigenous Nguni goats of South Africa. ... It, therefore, is imperative to put measures in place to counteract the drop in any of these parameters, with season, if productivity of the indigenous goats is to be maintained. Further studies are required to determine the ...

  15. Genotyping of flavin-containing mono-oxygenase 3 (FMO3) gene by ...

    African Journals Online (AJOL)

    63.40%) of the 306 samples were genotyped using MAMA-PCR and 42 (13.72%) of the 306 samples were genotyped by both of PCR-RFLP and MAMA-PCR and genotyping data were validated by DNA sequencing. The results show that the ...

  16. Rapid ABO genotyping by high-speed droplet allele-specific PCR using crude samples.

    Science.gov (United States)

    Taira, Chiaki; Matsuda, Kazuyuki; Takeichi, Naoya; Furukawa, Satomi; Sugano, Mitsutoshi; Uehara, Takeshi; Okumura, Nobuo; Honda, Takayuki

    2018-01-01

    ABO genotyping has common tools for personal identification of forensic and transplantation field. We developed a new method based on a droplet allele-specific PCR (droplet-AS-PCR) that enabled rapid PCR amplification. We attempted rapid ABO genotyping using crude DNA isolated from dried blood and buccal cells. We designed allele-specific primers for three SNPs (at nucleotides 261, 526, and 803) in exons 6 and 7 of the ABO gene. We pretreated dried blood and buccal cells with proteinase K, and obtained crude DNAs without DNA purification. Droplet-AS-PCR allowed specific amplification of the SNPs at the three loci using crude DNA, with results similar to those for DNA extracted from fresh peripheral blood. The sensitivity of the methods was 5%-10%. The genotyping of extracted DNA and crude DNA were completed within 8 and 9 minutes, respectively. The genotypes determined by the droplet-AS-PCR method were always consistent with those obtained by direct sequencing. The droplet-AS-PCR method enabled rapid and specific amplification of three SNPs of the ABO gene from crude DNA treated with proteinase K. ABO genotyping by the droplet-AS-PCR has the potential to be applied to various fields including a forensic medicine and transplantation medical care. © 2017 Wiley Periodicals, Inc.

  17. Faecal calprotectin concentrations in apparently healthy children aged 0-12 years in urban Kampala, Uganda: a community-based survey

    Directory of Open Access Journals (Sweden)

    Grahnquist Lena

    2011-02-01

    Full Text Available Abstract Background Calprotectin is a calcium and zinc binding protein, abundant in neutrophils and is extremely stable in faeces. Faecal calprotectin is used as a non-specific marker for gastrointestinal inflammation. It has a good diagnostic precision to distinguish between irritable bowel syndrome and inflammatory bowel disease. Studies have established normal concentrations in healthy children; all these studies have been performed in high-income countries. The objective of this study was to determine the concentration of faecal calprotectin in apparently healthy children aged 0-12 years in urban Kampala, Uganda. Method We tested 302 apparently healthy children aged, age 0-12 years (162 female, 140 male in urban Kampala, Uganda. The children were recruited consecutively by door-to-door visits. Faecal calprotectin was analyzed using a quantitative enzyme-linked immunosorbent assay. Faeces were also tested for Helicobacter pylori (H. pylori antigen, for growth of enteropathogens and microscopy was performed to assess protozoa and helminths. A short standardized interview with socio-demographic information and medical history was obtained to assess health status of the children. Results In the different age groups the median faecal calprotectin concentrations were 249 mg/kg in 0 H. pylori or having other pathogens in the stool. Conclusion Concentrations of faecal calprotectin among healthy children, living in urban Ugandan, a low-income country, are comparable to those in healthy children living in high-income countries. In children older than 4 years, the faecal calprotectin concentration is low. In healthy infants faecal calprotectin is high. The suggested cut-off concentrations in the literature can be used in apparently healthy Ugandan children. This finding also shows that healthy children living under poor circumstances do not have a constant inflammation in the gut. We see an opportunity to use this relatively inexpensive test for

  18. Metabolomic profiling of faecal extracts from Cryptosporidium parvum infection in experimental mouse models.

    Directory of Open Access Journals (Sweden)

    Josephine S Y Ng Hublin

    Full Text Available Cryptosporidiosis is a gastrointestinal disease in humans and animals caused by infection with the protozoan parasite Cryptosporidium. In healthy individuals, the disease manifests mainly as acute self-limiting diarrhoea, but may be chronic and life threatening for those with compromised immune systems. Control and treatment of the disease is challenged by the lack of sensitive diagnostic tools and broad-spectrum chemotherapy. Metabolomics, or metabolite profiling, is an emerging field of study, which enables characterisation of the end products of regulatory processes in a biological system. Analysis of changes in metabolite patterns reflects changes in biochemical regulation, production and control, and may contribute to understanding the effects of Cryptosporidium infection in the host environment. In the present study, metabolomic analysis of faecal samples from experimentally infected mice was carried out to assess metabolite profiles pertaining to the infection. Gas-chromatography mass spectrometry (GC-MS carried out on faecal samples from a group of C. parvum infected mice and a group of uninfected control mice detected a mean total of 220 compounds. Multivariate analyses showed distinct differences between the profiles of C. parvum infected mice and uninfected control mice,identifying a total of 40 compounds, or metabolites that contributed most to the variance between the two groups. These metabolites consisted of amino acids (n = 17, carbohydrates (n = 8, lipids (n = 7, organic acids (n = 3 and other various metabolites (n = 5, which showed significant differences in levels of metabolite abundance between the infected and uninfected mice groups (p < 0.05. The metabolites detected in this study as well as the differences in abundance between the C. parvum infected and the uninfected control mice, highlights the effects of the infection on intestinal permeability and the fate of the metabolites as a result of nutrient scavenging by the

  19. Molecular genotyping of HCV infection in seropositive blood donor

    Science.gov (United States)

    Zarin, Siti Noraziah Abu; Ibrahim, Nazlina

    2013-11-01

    This study is to investigate the prevalence of hepatitis C virus infection in seropositive blood donor. RNA was extracted from 32 positive samples in National Blood Centre and Melaka Hospital. The core and NS5B sequences were obtained from 23 samples. Genotype 3a is most prevalent in this study followed by genotype 1a. Evidence of mixed-genotypes (3a and 1b) infections was found in 5 subjects.

  20. Evaluation of the Abbott Real Time HCV genotype II assay for Hepatitis C virus genotyping.

    Science.gov (United States)

    Sariguzel, Fatma Mutlu; Berk, Elife; Gokahmetoglu, Selma; Ercal, Baris Derya; Celik, Ilhami

    2015-01-01

    The determination of HCV genotypes and subtypes is very important for the selection of antiviral therapy and epidemiological studies. The aim of this study was to evaluate the performance of Abbott Real Time HCV Genotype II assay in HCV genotyping of HCV infected patients in Kayseri, Turkey. One hundred patients with chronic hepatitis C admitted to our hospital were evaluated between June 2012 and December 2012, HCV RNA levels were determined by the COBAS® AmpliPrep/COBAS® TaqMan® 48 HCV test. HCV genotyping was investigated by the Abbott Real Time HCV Genotype II assay. With the exception of genotype 1, subtypes of HCV genotypes could not be determined by Abbott assay. Sequencing analysis was used as the reference method. Genotypes 1, 2, 3 and 4 were observed in 70, 4, 2 and 24 of the 100 patients, respectively, by two methods. The concordance between the two systems to determine HCV major genotypes was 100%. Of 70 patients with genotype 1, 66 showed infection with subtype 1b and 4 with subtype 1a by Abbott Real Time HCV Genotype II assay. Using sequence analysis, 61 showed infection with subtype 1b and 9 with subtype 1a. In determining of HCV genotype 1 subtypes, the difference between the two methods was not statistically significant (P>0.05). HCV genotype 4 and 3 samples were found to be subtype 4d and 3a, respectively, by sequence analysis. There were four patients with genotype 2. Sequence analysis revealed that two of these patients had type 2a and the other two had type 2b. The Abbott Real Time HCV Genotype II assay yielded results consistent with sequence analysis. However, further optimization of the Abbott Real Time HCV Genotype II assay for subtype identification of HCV is required.

  1. Frequency of post-operative faecal incontinence in patients with closed and open internal anal sphincterotomy

    International Nuclear Information System (INIS)

    Ghayas, N.G.; Younus, S.M.; Mirani, A.J.; Ghayasuddin, M.

    2015-01-01

    Fissure in ano is one of the commonest benign and painful proctologic diseases causing considerable morbidity and reduction in quality of life. There are medical as well as surgical treatment options for anal fissure. The study was conducted to compare the frequency of postoperative faecal incontinence in patients with closed lateral internal anal sphincterotomy with von-greaves knife versus standard Parks operation (open method) for chronic anal fissure. Methods: This was a randomized controlled trial (RCT) was conducted at the Department of Surgery, KVSS, S.I.T.E. Hospital, Karachi, for a period of six months from 13th February to 12th August 2011. Ninety four consecutive patients having chronic anal fissure were assigned through blocked randomization to groups A and B, with 47 patients in each group. Closed lateral internal anal sphincterotomy (CLIAS) via von-greaves knife was carried out in patients of group-A whereas patients of group-B were subjected to open internal anal sphincterotomy (OIAS) also known as Parks procedure. Faecal incontinence was noted on the 5th post-operative day. Data was analysed using SPSS 16. Results: There were 81 (86.2%) males and 13 (13.8%) females with male to female ratio being 6:1. Mean age was 38.38 mp±14.56 years. Post-operative faecal incontinence in patients undergoing CLIAS was 4.3% while it was 21.3% in those undergoing OIAS with a p-value of 0.027. CLIAS with von-greaves knife is effective in reducing faecal incontinence on 5th postoperative day as compared to standard OIAS. Conclusion: CLIAS with von-greaves knife is effective in reducing faecal incontinence on 5th postoperative day as compared to OIAS (Park's procedure). Therefore, this technique may be used in future regularly to treat chronic anal fissure for prevention of this morbidity. (author)

  2. Impact of diets with a high content of greaves-meal protein or carbohydrates on faecal characteristics, volatile fatty acids and faecal calprotectin concentrations in healthy dogs

    NARCIS (Netherlands)

    Hang, I.; Heilmann, R.M.; Grützner, N.; Suchodolski, J.S.; Steiner, J.M.; Atroshi, F.; Sankari, S.; Kettunen, A.; Vos, de W.M.; Zentek, J.; Spillmann, T.

    2013-01-01

    BACKGROUND: Research suggests that dietary composition influences gastrointestinal function and bacteria-derived metabolic products in the dog colon. We previously reported that dietary composition impacts upon the faecal microbiota of healthy dogs. This study aims at evaluating the dietary

  3. Specificity of the Linear Array HPV Genotyping Test for detecting human papillomavirus genotype 52 (HPV-52)

    OpenAIRE

    Kocjan, Boštjan; Poljak, Mario; Oštrbenk, Anja

    2015-01-01

    Introduction: HPV-52 is one of the most frequent human papillomavirus (HPV) genotypes causing significant cervical pathology. The most widely used HPV genotyping assay, the Roche Linear Array HPV Genotyping Test (Linear Array), is unable to identify HPV- 52 status in samples containing HPV-33, HPV-35, and/or HPV-58. Methods: Linear Array HPV-52 analytical specificity was established by testing 100 specimens reactive with the Linear Array HPV- 33/35/52/58 cross-reactive probe, but not with the...

  4. Genetic relatedness of faecal coliforms and enterococci bacteria isolated from water and sediments of the Apies River, Gauteng, South Africa.

    Science.gov (United States)

    Ekwanzala, Mutshiene Deogratias; Abia, Akebe Luther King; Ubomba-Jaswa, Eunice; Keshri, Jitendra; Momba, Ndombo Benteke Maggy

    2017-12-01

    To date, the microbiological quality of river sediments and its impact on water resources are not included in the water quality monitoring assessment. Therefore, the aim of this study was to establish genetic relatedness between faecal coliforms and enterococci isolated from the river water and riverbed sediments of Apies River to better understand the genetic similarity of microorganisms between the sediment and water phases. Indicator bacteria were subjected to a molecular study, which consisted of PCR amplification and sequence analysis of the 16S rRNA and 23S rRNA gene using specific primers for faecal coliforms and enterococci, respectively. Results revealed that the Apies River had high faecal pollution levels with enterococci showing low to moderate correlation coefficient (r 2 values ranged from 0.2605 to 0.7499) compared to the faecal coliforms which showed zero to low correlation (r 2 values ranged from 0.0027 to 0.1407) indicating that enterococci may be better indicator than faecal coliforms for detecting faecal contamination in riverbed sediments. The phylogenetic tree of faecal coliforms revealed a 98% homology among their nucleotide sequences confirming the close genetic relatedness between river water and riverbed sediment isolates. The phylogenetic tree of the enterococci showed that Enterococcus faecalis and Enterococcus faecium are the predominant species found in both river water and riverbed sediments with bootstrap values of ≥99%. A high degree of genetic relatedness between sediment and water isolates indicated a possible common ancestry and transmission pathway. We recommend the microbial monitoring of riverbed sediments as it harbours more diverse microbial community and once resuspended may cause health and environmental problems.

  5. Molecular and phylogenetic characterization of Cryptosporidium and Giardia from pigs and cattle in Denmark

    DEFF Research Database (Denmark)

    Langkjær, Rikke Breinhold; Vigre, Håkan; Enemark, Heidi L.

    2007-01-01

    The genetic diversity of Cryptosporidium spp. and Giardia duodenalis from dairy cattle and pigs in Denmark was determined in the present study. Faecal samples from 1237 pigs and 1150 cattle originating from 50 sow herds and 50 dairy herds, respectively, were analysed for the presence of the two...... parasites by immunofluorescence microscopy. A large proportion of the (oo)cyst containing samples were selected for molecular characterization. Sequencing and phylogenetic analysis of the 18S rDNA locus and/or the HSP70 gene of 183 pig and 154 cattle isolates of Cryptosporidium revealed the presence of C....... suis, pig genotype II, C. parvum (cattle genotype), C. bovis, Cryptosporidium deer-like genotype and a novel C. suis-like genotype. For both cattle and pigs, a host age-related change in distribution of species/genotypes was observed. The zoonotic C. parvum (cattle genotype) was most prevalent in young...

  6. Combined quantification of faecal sterols, stanols, stanones and bile acids in soils and terrestrial sediments by gas chromatography-mass spectrometry.

    Science.gov (United States)

    Birk, Jago Jonathan; Dippold, Michaela; Wiesenberg, Guido L B; Glaser, Bruno

    2012-06-15

    Faeces incorporation can alter the concentration patterns of stanols, stanones, Δ(5)-sterols and bile acids in soils and terrestrial sediments. A joint quantification of these substances would give robust and specific information about the faecal input. Therefore, a method was developed for their purification and determination via gas chromatography-mass spectrometry (GC-MS) based on a total lipid extract (TLE) of soils and terrestrial sediments. Stanols, stanones, Δ(5)-steroles and bile acids were extracted by a single Soxhlet extraction yielding a TLE. The TLE was saponified with KOH in methanol. Sequential liquid-liquid extraction was applied to recover the biomarkers from the saponified extract and to separate the bile acids from the neutral stanoles, stanones and Δ(5)-steroles. The neutral fraction was directly purified using solid phase extraction (SPE) columns packed with 5% deactivated silica gel. The bile acids were methylated in dry HCl in methanol and purified on SPE columns packed with activated silica gel. A mixture of hexamethyldisilazane (HMDS), trimethylchlorosilane (TMCS) and pyridine was used to silylate the hydroxyl groups of the stanols and Δ(5)-sterols avoiding a silylation of the keto groups of the stanones in their enol-form. Silylation of the bile acids was carried out with N,O-bis(trimethylsilyl)trifluoroacetamide (BSTFA) containing N-trimethylsilylimidazole (TSIM). TLEs from a set of soils with different physico-chemical properties were used for method evaluation and for comparison of amounts of faecal biomarkers analysed with saponification and without saponification of the TLE. Therefore, a Regosol, a Podzol and a Ferralsol were sampled. To proof the applicability of the method for faecal biomarker analyses in archaeological soils and sediments, additional samples were taken from pre-Columbian Anthrosols in Amazonia and an Anthrosol from a site in central Europe settled since the Neolithic. The comparison of the amounts of steroids

  7. Liquid Chromatography/Mass Spectrometry Reveals the Effect of Lactobacillus Treatment on the Faecal Metabolite Profile of Rats with Chronic Renal Failure.

    Science.gov (United States)

    Wu, Bin; Jiang, Hongli; He, Quan; Wang, Meng; Xue, Jinhong; Liu, Hua; Shi, Kehui; Wei, Meng; Liang, Shanshan; Zhang, Liwen

    2017-01-01

    Chronic kidney disease is accompanied by changes in the gut microbiome and by an increase in the number of gut pathogenic bacteria. The aim of this study was to investigate the difference of the faecal metabolic profiles in rats with uremia, and to determine whether the altered metabolites in the rats with uremia can be restored by Lactobacillus. Thirty rats were randomly divided into 3 groups: sham, uremia and uremia + probiotic (UP) groups. The rats in uremia and UP groups were prepared through surgical renal mass 5/6 ablation. The rats in the UP group received Lactobacillus LB (1 ml, 109 CFU/ml) through gavage every day for 4 weeks. The rats were fed with a standard diet. Faecal samples were analysed through ultra performance liquid chromatography/mass spectrometry. Statistical analyses were performed using MetaboAnalyst and MATLAB. A total of 99, 324 and 177 significantly different ion peaks were selected between sham and uremia groups; sham and UP groups; and uremia and UP groups, respectively. In the 3 groups, 35 significantly altered metabolites were identified; of the 35 metabolites, 27 initially increased and then decreased; by contrast, 8 metabolites initially decreased and then increased. The 35 metabolites were subjected to pathway analysis in MetaboAnalyst. Faecal metabolites were significantly altered in rats with uremia; these changes were partially reversed by Lactobacillus. © 2016 S. Karger AG, Basel.

  8. Effects of inulin supplementation on selected faecal characteristics and health of neonatal Saanen kids sucking milk from their dams.

    Science.gov (United States)

    Kara, C; Orman, A; Gencoglu, H; Kovanlıkaya, A; Meral, Y; Cetin, I; Yıbar, A; Kasap, S; Turkmen, I; Deniz, G

    2012-12-01

    Fifty newborn Saanen kids were used to study the effects of inulin supplementation on faecal score, faecal pH, selected faecal bacterial population, BW, body temperature, haematological traits, selected health parameters and the incidence of diarrhoea. Kids were sorted by parity of their dams and multiple birth (twin or triplet) and assigned to one of the two groups (control: CG, and experimental: EG) at birth. Each group consisted of 25 kids. The groups were similar with regard to sex and birth weight. All kids were fed colostrum for the first 3 days after birth, and then the kids in EG were adapted to inulin supplementation by an increased dosage from day 4 to 7. Each kid in EG was supplemented with 0.2 g, 0.3 g, 0.4 g, 0.5 g and 0.6 g inulin on day 4, 5, 6, 7 and from day 8 to 28, respectively, whereas the kids in CG did not receive inulin. Faecal score and faecal bacterial population were not affected by inulin supplementation (P > 0.05). There were differences in faecal pH on day 14 (P = 0.01) and 28 (P 0.05) was detected between groups. No differences (P > 0.05) in BW and haematological traits were found between groups. Body temperature did not differ on day 14 and 21 (P > 0.05), whereas there was a difference in body temperature on day 28 (P = 0.01) between groups. The numbers of kids with pneumonia and kids treated for pneumonia and diarrhoea were similar for CG and EG. Kid losses during the study were the same for CG and EG. The incidence of diarrhoea was not affected by inulin supplementation (P > 0.05). Inulin supplemented to kids did not adversely affect faecal score. The effect of inulin on faecal pH was not consistent. The results of our study suggested that daily dose (0.6 g) of inulin might not be enough to observe effects of it. Our data will be useful to determine the dose and timing of inulin supplementation in future studies investigating the effects of inulin on the parameters associated with performance and health status in kids and other

  9. Characterisation by multilocus sequence and porA and flaA typing of Campylobacter jejuni isolated from samples of dog faeces collected in one city in New Zealand.

    Science.gov (United States)

    Mohan, V; Stevenson, M A; Marshall, J C; French, N P

    2017-07-01

    To investigate the prevalence of Campylobacter spp. and C. jejuni in dog faecal material collected from dog walkways in the city of Palmerston North, New Zealand, and to characterise the C. jejuni isolates by multilocus sequence typing (MLST) and porA and flaA antigen gene typing. A total of 355 fresh samples of dogs faeces were collected from bins provided for the disposal of dog faeces in 10 walkways in Palmerston North, New Zealand, between August 2008-July 2009. Presumptive Campylobacter colonies, cultured on modified charcoal cefoperazone deoxycholate plates, were screened for genus Campylobacter and C. jejuni by PCR. The C. jejuni isolates were subsequently characterised by MLST and porA and flaA typing, and C. jejuni sequence types (ST) were assigned. Of the 355 samples collected, 72 (20 (95% CI=16-25)%) were positive for Campylobacter spp. and 22 (6 (95% CI=4-9)%) were positive for C. jejuni. Of the 22 C. jejuni isolates, 19 were fully typed by MLST. Ten isolates were assigned to the clonal complex ST-45 and three to ST-52. The allelic combinations of ST-45/flaA 21/porA 44 (n=3), ST-45/flaA 22/porA 53 (n=3) and ST-52/ flaA 57/porA 905 (n=3) were most frequent. The successful isolation of C. jejuni from canine faecal samples collected from faecal bins provides evidence that Campylobacter spp. may survive outside the host for at least several hours despite requiring fastidious growth conditions in culture. The results show that dogs carry C. jejuni genotypes (ST-45, ST-50, ST-52 and ST-696) that have been reported in human clinical cases. Although these results do not provide any evidence either for the direction of infection or for dogs being a potential risk factor for human campylobacteriosis, dog owners are advised to practice good hygiene with respect to their pets to reduce potential exposure to infection.

  10. Plasma pharmacokinetics, faecal excretion and efficacy of pyrantel pamoate paste and granule formulations following per os administration in donkeys naturally infected with intestinal strongylidae.

    Science.gov (United States)

    Gokbulut, Cengiz; Aksit, Dilek; Smaldone, Giorgio; Mariani, Ugo; Veneziano, Vincenzo

    2014-09-15

    The plasma disposition, faecal excretion and efficacy of two formulations of pyrantel pamoate in donkeys were examined in a controlled trial. Three groups of seven donkeys received either no medication (control) or pyrantel paste or granule formulations at horse dosage of 20mg/kg B.W. (equals 6.94 mg/kg PYR base) of body weight. Heparinized blood and faecal samples were collected at various times between 1 and 144 h after treatment. The samples were analysed by high-performance liquid chromatography. The last detectable plasma concentration (tmax) of paste formulation was significantly earlier (36.00 h) compared with granule formulation (46.29 h). Although, there was no significant difference on terminal half lives (t1/2: 12.39 h vs. 14.86 h), tmax (14.86 h vs. 14.00) and MRT (24.80 h vs. 25.44 h) values; the Cmax (0.09 μg/ml) AUC (2.65 μgh/ml) values of paste formulation were significantly lower and smaller compared with those of granule formulation (0.21 μg/ml and 5.60 μgh/ml), respectively. The highest dry faecal concentrations were 710.46 μg/g and 537.21 μg/g and were determined at 48 h for both paste and granule formulation of PYR in donkeys, respectively. Pre-treatment EPG of 1104, 1061 and 1139 were observed for the control, PYR paste and PYR granule groups, respectively. Pre-treatment EPG were not significantly different (P>0.1) between groups. Post-treatment EPG for both PYR treatment groups were significantly different (P95% efficacy) until day 28. In all studied donkeys, coprocultures performed at day-3 revealed the presence of Cyathostomes, S. vulgaris. Faecal cultures performed on different days from C-group confirmed the presence of the same genera. Coprocultures from treated animals revealed the presence of few larvae of Cyathostomes. Copyright © 2014 Elsevier B.V. All rights reserved.

  11. Relative frequencies and significance of faecal coliforms as indicators related to water temperature.

    Science.gov (United States)

    Auban, E G; Ripolles, A A; Domarco, M J

    1983-01-01

    The faecal coliforms at different sites of a hypereutrophic lake near Valencia (Albufera) were identified and their relative amounts established along an annual cycle. Using lauryl tryptose broth at 35 degrees C, followed by incubation at 44.4 degrees C in 2% brilliant green bile, Escherichia coli and Klebsiella pneumoniae are practically the only coliforms present. A positive correlation was found between the water temperature and the relative amount of these two coliforms: K. pneumoniae predominates at high water temperatures, whereas E. coli shows preponderance during the cold period. The role of K. pneumoniae as the only faecal indicator under the circumstances described in the work is emphasized and discussed.

  12. Supervised pelvic floor muscle training versus attention-control massage treatment in patients with faecal incontinence

    DEFF Research Database (Denmark)

    Ussing, Anja; Dahn, Inge; Due, Ulla

    2017-01-01

    supplements is recommended as first-line treatment for faecal incontinence. Despite this, the effect of pelvic floor muscle training for faecal incontinence is unclear. No previous trials have investigated the efficacy of supervised pelvic floor muscle training in combination with conservative treatment...... treatment and conservative treatment. The primary outcome is participants' rating of symptom changes after 16 weeks of treatment using the Patient Global Impression of Improvement Scale. Secondary outcomes are the Vaizey Incontinence Score, the Fecal Incontinence Severity Index, the Fecal Incontinence...

  13. Toys and toilets: cross-sectional study using children's toys to evaluate environmental faecal contamination in rural Bangladeshi households with different sanitation facilities and practices.

    Science.gov (United States)

    Vujcic, Jelena; Ram, Pavani K; Hussain, Faruqe; Unicomb, Leanne; Gope, Partha Sarathi; Abedin, Jaynal; Mahmud, Zahid Hayat; Islam, M Sirajul; Luby, Stephen P

    2014-05-01

    To evaluate household faecal contamination using children's toys among 100 rural Bangladeshi households categorised as 'cleaner' (toilet that reliably separates faeces from the environment and no human faeces in/around living space) or 'less clean' (no toilet or toilet that does not reliably separate faeces from the environment and human faeces in/around living space). We distributed toy balls to each household and rinsed each study toy and a toy already owned by the household in 200 ml of Ringer's solution. We enumerated faecal coliforms and faecal streptococci from each rinse using membrane filtration methods. Study toys from 39 cleaner households had lower mean faecal coliform contamination than toys from 61 less clean households (2.4 log10 colony-forming units (CFU)/200 ml vs. 3.2 log10 CFU/200 ml, P = 0.03). However, wealth measures explained a portion of this relationship. Repeat measures were moderately variable [coefficient of variation (CV) = 6.5 between two toys in the household at the same time, CV = 37.6 between toys in the household at two different times 3-4 days apart]. Too few households owned a non-porous toy to compare groups without risk of bias. In rural Bangladesh, improved sanitation facilities and practices were associated with less environmental contamination. Whether this association is independent of household wealth and whether the difference in contamination improves child health merit further study. The variation found was typical for measures of environmental contamination, and requires large sample sizes to ascertain differences between groups with statistical significance. © 2014 John Wiley & Sons Ltd.

  14. Environmental sampling of Ceratonia siliqua (carob) trees in Spain reveals the presence of the rare Cryptococcus gattii genotype AFLP7/VGIV.

    Science.gov (United States)

    Linares, Carlos; Colom, María Francisca; Torreblanca, Marina; Esteban, Violeta; Romera, Álvaro; Hagen, Ferry

    2015-01-01

    Cryptococcus gattii is a pathogenic basidiomycetous yeast that is emerging in temperate climate zones worldwide. C. gattii has repetitively been isolated from numerous tree species. Ongoing environmental sampling and molecular characterization is essential to understand the presence of this primary pathogenic microorganism in the Mediterranean environment. To report the first isolation of the rare C. gattii genotype AFLP7/VGIV from the environment in Europe. Samples were collected from woody debris of carob trees (Ceratonia siliqua) and olive trees (Olea europaea) in El Perelló, Tarragona, Spain. Cryptococcus species were further characterized by using URA5-RFLP, MALDI-TOF, AFLP and MLST. The antifungal susceptibility profile to amphotericin B, 5-fluorocytosine, fluconazole, itraconazole, posaconazole and voriconazole was determined using Sensititre Yeast One and E-test. Cultures from one carob tree revealed the presence of ten Cryptococcus-like colonies. One colony was identified as C. gattii, and subsequent molecular characterization showed that it was an α mating-type that belonged to the rare genotype AFLP7/VGIV. Antifungal susceptibility testing showed values within the range of sensitivity described for other isolates of the same genotype and within the epidemiological cutoff values for this species. The isolation of the rare C. gattii genotype AFLP7/VGIV in Spain is the first report in the European environment, implying the possible presence in other regions of the Mediterranean area, and underlines that clinicians must be aware for C. gattii infections in healthy individuals. Copyright © 2014 Revista Iberoamericana de Micología. Published by Elsevier Espana. All rights reserved.

  15. Social, state-dependent and environmental modulation of faecal corticosteroid levels in free-ranging female spotted hyenas.

    Science.gov (United States)

    Goymann, W; East, M L; Wachter, B; Höner, O P; Möstl, E; Van't Hof, T J; Hofer, H

    2001-12-07

    Little is known about to what extent the sensitivity of the hypothalamic-pituitary-adrenal (HPA) axis may be state dependent and vary in the same species between environments. Here we tested whether the faecal corticosteroid concentrations of matrilineal adult female spotted hyenas are influenced by social and reproductive status in adjacent ecosystems and whether they vary between periods with and without social stress. Females in the Serengeti National Park frequently become socially subordinate intruders in other hyena territories by undertaking long-distance foraging trips to migratory herds, whereas in the Ngorongoro Crater they usually forage inside their own small territories on resident prey. The faecal corticosteroid concentrations in Serengeti females were significantly higher than in Ngorongoro females. Energy expenditure by lactation is exceptionally high in spotted hyenas and this may be reflected in their corticosteroid levels. The faecal corticosteroid levels in both populations were higher in lactating than in non-lactating females. During periods of social stability, faecal corticosteroid concentrations increased in non-lactating females but not in lactating females as social status declined. Lactating Serengeti females had significantly higher faecal corticosteroid concentrations during periods with acute severe social stress than during periods without, indicating that the HPA axis is sensitive to social stimuli even in lactating females. So far few studies have used non-invasive monitoring methods for assessing social stress in freeranging animals. This study demonstrates for the first time, to the authors' knowledge, that corticosteroid concentrations may differ between periods with and without social stress for a free-ranging female mammal and that the modulating effect of social status may depend on reproductive status.

  16. Near infrared spectrometry for faecal fat measurement: comparison with conventional gravimetric and titrimetric methods.

    Science.gov (United States)

    Benini, L; Caliari, S; Guidi, G C; Vaona, B; Talamini, G; Vantini, I; Scuro, L A

    1989-01-01

    This investigation was aimed at comparing a new method for measuring faecal fat excretion, carried out with a semi-automated instrument by using near infrared analysis (NIRA), with the traditional titrimetric (Van de Kamer) and gravimetric (Sobel) methods. Near infrared analysis faecal fat was assayed on the three day stool collection from 118 patients (68 chronic pancreatitis, 19 organic diseases of the gastrointestinal tract, 19 alcoholic liver disease, 12 functional gastrointestinal disorders). A strict linear correlation was found between NIRA and both the titrimetric (r = 0.928, p less than 0.0001) and the gravimetric (r = 0.971, p less than 0.0001) methods. On homogenised faeces, a mean coefficient of variation of 2.1 (SD 1.71)% was found. Before homogenisation (where a mean coefficient of variation of 7% was found) accurate results were obtained when the mean of five measurements was considered. In conclusion, the assay of faecal fat excretion by the near infrared reflessometry appears a simple, rapid and reliable method for measuring steatorrhoea. PMID:2583563

  17. Escherichia coli. A sanitary methodology for faecal water pollution tests

    International Nuclear Information System (INIS)

    Bonadonna, L.

    2001-01-01

    Among the traditional indictors of faecal water pollution, Escherichia coli has shown to fit better with the definition of indicator organism. Till now its recovery has been time-consuming and needs confirmation tests. In this report more rapid and direct methods, based on enzymatic reactions, are presented [it

  18. Quantifying the impact of storage procedures for faecal bacteriotherapy in the critically endangered New Zealand parrot, the kakapo (Strigops habroptilus).

    Science.gov (United States)

    Waite, David W; Deines, Peter; Taylor, Michael W

    2013-01-01

    The endemic New Zealand kakapo is classified as 'critically endangered' and, in an effort to prevent extinction and restore the kakapo population, intensive handling of rare kakapo chicks is often utilised to reduce mortality and improve health outcomes among juveniles. Due to concerns that hand-reared chicks may not receive a full bacterial complement in their gut in the absence of regurgitated food from their mother, conservation workers feed a suspension of frozen adult faeces to captive chicks. However, the efficacy of this practice is unknown, with no information about the viability of these bacteria, or whether certain bacterial taxa are selected for or against as a consequence of freezing. In this study we experimentally determined the effects of freezing and reanimation on bacterial cell viability and diversity, using a faecal sample obtained from a healthy adult kakapo. Freezing reduced the number of viable bacterial cells (estimated by colony-forming units, CFU) by 99.86%, although addition of a cryoprotectant prior to freezing resulted in recovery of bacterial cells equivalent to that of non-frozen controls. Bacterial taxonomic diversity was reduced by freezing, irrespective of the presence of a cryoprotectant. While this study did not address the efficacy of faecal supplementation per se, the obtained data do suggest that faecal bacteriotherapy using frozen faeces (with a cryoprotectant) from healthy adult birds warrants further consideration as a conservation strategy for intensively managed species. © 2013 Wiley Periodicals, Inc.

  19. Lycopene, Lutein and Zeaxanthin May Reduce Faecal Blood, Mucus and Pus but not Abdominal Pain in Individuals with Ulcerative Colitis.

    Science.gov (United States)

    Głąbska, Dominika; Guzek, Dominika; Zakrzewska, Paulina; Włodarek, Dariusz; Lech, Gustaw

    2016-09-30

    The main symptom of ulcerative colitis is diarrhoea, which is often accompanied by painful tenesmus and faecal blood and mucus. It sometimes co-occurs with abdominal pain, fever, feeling of fatigue, loss of appetite and weight loss. Some dietary factors have been indicated as important in the treatment of ulcerative colitis. The aim of the study was to analyse the association between retinoid intake (total vitamin A, retinol, β-carotene, α-carotene, β-cryptoxanthin, lycopene, lutein and zeaxanthin) and ulcerative colitis symptoms (abdominal pain, faecal blood, faecal mucus, faecal pus) in individuals with ulcerative colitis in remission. Assessment of diet was based on self-reported data from each patient's dietary records taken over a period of three typical, random days (2 weekdays and 1 day of the weekend). A total of 56 individuals with ulcerative colitis in remission (19 males and 37 females) were recruited for the study. One in every four individuals with ulcerative colitis in remission was characterised as having inadequate vitamin A intake. Higher lycopene, lutein and zeaxanthin intakes in individuals with ulcerative colitis in remission were associated with lower faecal blood, mucus and pus but not with lower incidence of abdominal pain. Higher carotene intake in individuals with ulcerative colitis in remission may contribute to higher incidence of faecal mucus. Optimising intake of specific retinoids may enhance disease control in individuals with ulcerative colitis. Prospective studies, including patient reported and objective outcomes, are required to confirm this.

  20. Frequency, severity and risk factors for urinary and faecal incontinence at 4 years postpartum: a prospective cohort.

    Science.gov (United States)

    Gartland, D; MacArthur, C; Woolhouse, H; McDonald, E; Brown, S J

    2016-06-01

    To investigate frequency, severity and risk factors for urinary incontinence and faecal incontinence 4 years after a first birth. Prospective pregnancy cohort study. Melbourne, Australia. A total of 1011 nulliparous women recruited in early pregnancy. Participants were followed up at 32 weeks of gestation; then at 3, 6, 9 and 12 months and 4 years postpartum. Frequency and severity of urinary and faecal incontinence. At 4 years, 29.6% of women reported urinary incontinence and 7.1% reported faecal incontinence. Compared with women having only spontaneous vaginal births, women who delivered exclusively by caesarean section were less likely to have urinary incontinence at 4 years postpartum (adjusted odds ratio 0.4, 95% confidence interval 0.3-0.6). Women who reported urinary incontinence before or during the index pregnancy, and those experiencing symptoms in the first year postpartum had increased odds of incontinence at 4 years, with the highest odds (6-12 times higher) among women who had previously reported moderate or severe symptoms. The odds of reporting faecal incontinence at 4 years were two to six times higher for women experiencing symptoms in pregnancy, and around four to eight times higher for those with symptoms in the first year postpartum. Urinary and faecal incontinence are prevalent conditions 4 years after a first birth. Women reporting urinary or faecal incontinence during pregnancy had markedly higher odds of reporting symptoms at 4 years postpartum, suggesting a need for further investigation and elucidation of aetiological pathways involving nonbirth-related risk factors. Moderate/severe incontinence prevalent 4 years after first birth in population cohort. Prior symptoms are biggest predictor. © 2015 Royal College of Obstetricians and Gynaecologists.

  1. Faecal S100A12 as a non-invasive marker distinguishing inflammatory bowel disease from irritable bowel syndrome

    NARCIS (Netherlands)

    Kaiser, T; Langhorst, J; Wittkowski, H; Becker, K; Friedrich, A W; Rueffer, A; Dobos, G J; Roth, J; Foell, D

    2007-01-01

    OBJECTIVE: S100A12 is a pro-inflammatory protein that is secreted by granulocytes. S100A12 serum levels increase during inflammatory bowel disease (IBD). We performed the first study analysing faecal S100A12 in adults with signs of intestinal inflammation. METHODS: Faecal S100A12 was determined by

  2. A diet high in fat and meat but low in dietary fibre increases the genotoxic potential of 'faecal water'

    DEFF Research Database (Denmark)

    Rieger, Martin A.; Parlesak, Alexandr; Pool-Zobel, Beatrice

    1999-01-01

    To determine the effects of different diets on the genotoxicity of human faecal water, a diet rich in fat, meat and sugar but poor in vegetables and free of wholemeal products (diet 1) was consumed by seven healthy volunteers over a period of 12 days. One week after the end of this period......, the volunteers started to consume a diet enriched with vegetables and wholemeal products but poor in fat and meat (diet 2) over a second period of 12 days. The genotoxic effect of faecal waters obtained after both diets was assessed with the single cell gel electrophoresis (Comet assay) using the human colon...... and purine bases revealed no differences after pretreatment with both types of faecal water. The results indicate that diets high in fat and meat but low in dietary fibre increase the genotoxicity of faecal water to colonic cells and may contribute to an enhanced risk of colorectal cancer....

  3. Faecal consistency and risk factors for diarrhoea and constipation in cats in UK rehoming shelters.

    Science.gov (United States)

    German, Allison C; Cunliffe, Nigel A; Morgan, Kenton L

    2017-01-01

    Objectives The aim of the study was to describe faecal consistency, prevalence and risk factors for diarrhoea and constipation in a rescue cat population. Methods Faecal samples in litter trays from a stratified random sample of cats in pens at 25 UK rehoming centres were scored for consistency in two discrete time periods, summer and winter. A six-point scale was used, with diarrhoea ⩽3, severe diarrhoea ⩽2 and constipation as 6. The effect on faecal consistency of age, number of cats per pen and season was investigated using multivariable hierarchical logistic regression with centre and pen as random effects. Intraclass correlation coefficients were used to estimate the effect of pen and centre. Results Overall, 11.9% (95% confidence interval [CI]:10.4-13.7) of cats had diarrhoea, 2.4% (95% CI 1.6-3.7) had severe diarrhoea and 5.6% (95% CI 4.2-7.5) were constipated. The prevalence of diarrhoea (median 11.0%, interquartile range [IQR] 5.0-14.5%) and constipation (median 4.2%, IQR 1.8-5.9) varied at the centre level. Diarrhoea was associated with being a kitten (odds ratio [OR] 2.54, 95% CI 1.45-4.46; P = 0.001) and being in a multi-cat pen (OR 1.24, 95% CI 1.04-1.48; P = 0.02) but not with season (OR 0.99, 95% CI 0.55-1.77; P = 0.96). Severe diarrhoea was associated with senior cats (OR 4.66, 95% CI 1.25-17.44; P = 0.02). Constipation was associated with increasing age (OR 1.01; 95% CI 1.00-1.01; P = 0.02) and winter (OR 0.43, 95% CI 0.21-0.89; P = 0.02). Both diarrhoea and constipation showed moderate correlation with pens within a centre. Conclusions and relevance From IQRs, we suggest acceptable levels for diarrhoea and constipation of 11% and 4%, respectively, targets of 5% and 2%, and intervention at 15% and 6%. Increasing age was associated with decreased risk of diarrhoea and increased risk of constipation. However, severe diarrhoea was associated with being a senior cat. Season (winter) was a risk factor for constipation; multi-cat pens were a risk

  4. Genetic parameters and relationships of faecal worm egg count with ...

    African Journals Online (AJOL)

    The costs of internal parasite control and treatment are potentially very high in grazing sheep. Faecal worm egg count (FEC) has been suggested as a suitable criterion for selection for resistance to nematode infestation in livestock. Genetic parameter estimates for FEC and its relationship with wool traits were assessed in ...

  5. Hepatitis E Virus Genotype 3 in Sewage and Genotype 1 in Acute Hepatitis Cases, Israel

    Science.gov (United States)

    Ram, Daniela; Manor, Yossi; Gozlan, Yael; Schwartz, Eli; Ben-Ari, Ziv; Mendelson, Ella; Mor, Orna

    2016-01-01

    Hepatitis E virus (HEV) is an emerging infectious agent in developed countries. HEV genotypes 1 (G1) and 3 (G3) have been identified in environmental and clinical samples in Europe. In Israel, the overall prevalence of anti-HEV IgG antibodies was found to be 10.6%; however, reports of HEV infection are scarce. In this study, the presence of HEV in Israel was investigated using 169 sewage samples from 32 treatment facilities and 49 samples from acute hepatitis patients, all collected between 2013 and 2015. Fourteen sewage samples, from Haifa (11/18 samples), Tel Aviv (2/29 samples), and Beer Sheva (1/17 samples), regions with good sanitary conditions and middle-high socioeconomic populations, were HEV positive. Among the patient samples, 6.1% (3/49) were HEV positive, all returning travelers from India. Genotype analysis revealed G1 HEV in patients and G3 HEV sequences in sewage. Evidence that HEV could be establishing itself in our region may justify more active surveillance to monitor its spread. PMID:27246446

  6. Are carnivore digestive separation mechanisms revealed on structure-rich diets?: Faecal inconsistency in dogs (Canis familiaris) fed day old chicks

    NARCIS (Netherlands)

    Cuyper, De Annelies; Clauss, M.; Hesta, Myriam; Cools, An; Bosch, G.; Hendriks, W.H.; Janssens, Geert P.J.

    2018-01-01

    Pronounced variations in faecal consistency have been described anecdotally for some carnivore species fed a structure-rich diet. Typically two faecal consistencies are distinguished, namely hard and firm versus liquid and viscous faeces. It is possible that a separation mechanism is operating in

  7. Haematology and faecal parasitic load of West African Dwarf goats ...

    African Journals Online (AJOL)

    Haematology and faecal parasitic load of West African Dwarf goats fed Panicum maximum supplemented with wheat offal. ... Total White Blood Cell (TWBC), L and N. There was an increased post-trial hematological over pre-trial hematological parameters for PCV, N and M while a decrease was observed for L in animals ...

  8. Lycopene, Lutein and Zeaxanthin May Reduce Faecal Blood, Mucus and Pus but not Abdominal Pain in Individuals with Ulcerative Colitis

    Science.gov (United States)

    Głąbska, Dominika; Guzek, Dominika; Zakrzewska, Paulina; Włodarek, Dariusz; Lech, Gustaw

    2016-01-01

    Background: The main symptom of ulcerative colitis is diarrhoea, which is often accompanied by painful tenesmus and faecal blood and mucus. It sometimes co-occurs with abdominal pain, fever, feeling of fatigue, loss of appetite and weight loss. Some dietary factors have been indicated as important in the treatment of ulcerative colitis. The aim of the study was to analyse the association between retinoid intake (total vitamin A, retinol, β-carotene, α-carotene, β-cryptoxanthin, lycopene, lutein and zeaxanthin) and ulcerative colitis symptoms (abdominal pain, faecal blood, faecal mucus, faecal pus) in individuals with ulcerative colitis in remission. Methods: Assessment of diet was based on self-reported data from each patient’s dietary records taken over a period of three typical, random days (2 weekdays and 1 day of the weekend). Results: A total of 56 individuals with ulcerative colitis in remission (19 males and 37 females) were recruited for the study. One in every four individuals with ulcerative colitis in remission was characterised as having inadequate vitamin A intake. Higher lycopene, lutein and zeaxanthin intakes in individuals with ulcerative colitis in remission were associated with lower faecal blood, mucus and pus but not with lower incidence of abdominal pain. Higher carotene intake in individuals with ulcerative colitis in remission may contribute to higher incidence of faecal mucus. Conclusions: Optimising intake of specific retinoids may enhance disease control in individuals with ulcerative colitis. Prospective studies, including patient reported and objective outcomes, are required to confirm this. PMID:27706028

  9. Evaluation of a cost effective in-house method for HIV-1 drug resistance genotyping using plasma samples.

    Directory of Open Access Journals (Sweden)

    Devidas N Chaturbhuj

    Full Text Available OBJECTIVES: Validation of a cost effective in-house method for HIV-1 drug resistance genotyping using plasma samples. DESIGN: The validation includes the establishment of analytical performance characteristics such as accuracy, reproducibility, precision and sensitivity. METHODS: The accuracy was assessed by comparing 26 paired Virological Quality Assessment (VQA proficiency testing panel sequences generated by in-house and ViroSeq Genotyping System 2.0 (Celera Diagnostics, US as a gold standard. The reproducibility and precision were carried out on five samples with five replicates representing multiple HIV-1 subtypes (A, B, C and resistance patterns. The amplification sensitivity was evaluated on HIV-1 positive plasma samples (n = 88 with known viral loads ranges from 1000-1.8 million RNA copies/ml. RESULTS: Comparison of the nucleotide sequences generated by ViroSeq and in-house method showed 99.41±0.46 and 99.68±0.35% mean nucleotide and amino acid identity respectively. Out of 135 Stanford HIVdb listed HIV-1 drug resistance mutations, partial discordance was observed at 15 positions and complete discordance was absent. The reproducibility and precision study showed high nucleotide sequence identities i.e. 99.88±0.10 and 99.82±0.20 respectively. The in-house method showed 100% analytical sensitivity on the samples with HIV-1 viral load >1000 RNA copies/ml. The cost of running the in-house method is only 50% of that for ViroSeq method (112$ vs 300$, thus making it cost effective. CONCLUSIONS: The validated cost effective in-house method may be used to collect surveillance data on the emergence and transmission of HIV-1 drug resistance in resource limited countries. Moreover, the wide applications of a cost effective and validated in-house method for HIV-1 drug resistance testing will facilitate the decision making for the appropriate management of HIV infected patients.

  10. Evaluation of antibiotic resistance analysis and ribotyping for identification of faecal pollution sources in an urban watershed.

    Science.gov (United States)

    Moore, D F; Harwood, V J; Ferguson, D M; Lukasik, J; Hannah, P; Getrich, M; Brownell, M

    2005-01-01

    The accuracy of ribotyping and antibiotic resistance analysis (ARA) for prediction of sources of faecal bacterial pollution in an urban southern California watershed was determined using blinded proficiency samples. Antibiotic resistance patterns and HindIII ribotypes of Escherichia coli (n = 997), and antibiotic resistance patterns of Enterococcus spp. (n = 3657) were used to construct libraries from sewage samples and from faeces of seagulls, dogs, cats, horses and humans within the watershed. The three libraries were analysed to determine the accuracy of host source prediction. The internal accuracy of the libraries (average rate of correct classification, ARCC) with six source categories was 44% for E. coli ARA, 69% for E. coli ribotyping and 48% for Enterococcus ARA. Each library's predictive ability towards isolates that were not part of the library was determined using a blinded proficiency panel of 97 E. coli and 99 Enterococcus isolates. Twenty-eight per cent (by ARA) and 27% (by ribotyping) of the E. coli proficiency isolates were assigned to the correct source category. Sixteen per cent were assigned to the same source category by both methods, and 6% were assigned to the correct category. Addition of 2480 E. coli isolates to the ARA library did not improve the ARCC or proficiency accuracy. In contrast, 45% of Enterococcus proficiency isolates were correctly identified by ARA. None of the methods performed well enough on the proficiency panel to be judged ready for application to environmental samples. Most microbial source tracking (MST) studies published have demonstrated library accuracy solely by the internal ARCC measurement. Low rates of correct classification for E. coli proficiency isolates compared with the ARCCs of the libraries indicate that testing of bacteria from samples that are not represented in the library, such as blinded proficiency samples, is necessary to accurately measure predictive ability. The library-based MST methods used in

  11. Phenotypic and genotypic profiling of antimicrobial resistance in enteric Escherichia coli communities isolated from finisher pigs in Australia.

    Science.gov (United States)

    Smith, M G; Jordan, D; Gibson, J S; Cobbold, R N; Chapman, T A; Abraham, S; Trott, D J

    2016-10-01

    To assess herd-to-herd variation in antimicrobial resistance phenotypes and associated antimicrobial resistance genes (ARGs) in faecal commensal Escherichia coli communities isolated from Australian slaughter-age pigs. Hydrophobic grid-membrane filtration (HGMF) was used to screen populations of E. coli isolated from faecal samples obtained from pigs prior to or at slaughter. Multiplex PCRs were applied to the pooled DNA extracted from the samples to identify specific ARGs. Pooled faecal samples from 30 finishers, from 72 different Australian pig farms, produced 5003 isolates for screening. HGMF techniques and image analysis were used to confirm E. coli resistance phenotypes to four antimicrobial agents (ampicillin, gentamicin, florfenicol and ceftiofur) using selective agars. Multiplex PCRs were performed on DNA from pooled samples for 35 ARGs associated with seven chemical classes. The prevalence of E. coli isolates showing no resistance to any of the drugs was 50.2% (95% confidence interval (CI) 41.8-58.6%). Ceftiofur resistance was very low (1.8%; CI 0.8-3.9%) and no ARGs associated with 3rd-generation cephalosporin resistance were detected. By contrast, ampicillin (29.4%, CI 22.8-37.0%), florfenicol (24.3%, CI 17.8-32.3%) and gentamicin (CI 17.5%, 10.7-27.2%) resistance prevalence varied greatly between farms and associated ARGs were common. The most common combined resistance phenotype was ampicillin-florfenicol. The use of registered antimicrobials in Australian pigs leads to the enteric commensal populations acquiring associated ARGs. However, despite a high intensity of sampling, ARGs imparting resistance to the critically important 3rd-generation cephalosporins were not detected. © 2016 Australian Veterinary Association.

  12. Lactic Acid Fermentation, Urea and Lime Addition: Promising Faecal Sludge Sanitizing Methods for Emergency Sanitation.

    Science.gov (United States)

    Anderson, Catherine; Malambo, Dennis Hanjalika; Perez, Maria Eliette Gonzalez; Nobela, Happiness Ngwanamoseka; de Pooter, Lobke; Spit, Jan; Hooijmans, Christine Maria; de Vossenberg, Jack van; Greya, Wilson; Thole, Bernard; van Lier, Jules B; Brdjanovic, Damir

    2015-10-29

    In this research, three faecal sludge sanitizing methods-lactic acid fermentation, urea treatment and lime treatment-were studied for application in emergency situations. These methods were investigated by undertaking small scale field trials with pit latrine sludge in Blantyre, Malawi. Hydrated lime was able to reduce the E. coli count in the sludge to below the detectable limit within 1 h applying a pH > 11 (using a dosage from 7% to 17% w/w, depending faecal sludge alkalinity), urea treatment required about 4 days using 2.5% wet weight urea addition, and lactic acid fermentation needed approximately 1 week after being dosed with 10% wet weight molasses (2 g (glucose/fructose)/kg) and 10% wet weight pre-culture (99.8% pasteurised whole milk and 0.02% fermented milk drink containing Lactobacillus casei Shirota). Based on Malawian prices, the cost of sanitizing 1 m³ of faecal sludge was estimated to be €32 for lactic acid fermentation, €20 for urea treatment and €12 for hydrated lime treatment.

  13. Experimental study of faecal continence and colostomy irrigation.

    Science.gov (United States)

    O'Bichere, A; Sibbons, P; Doré, C; Green, C; Phillips, R K

    2000-07-01

    Colostomy irrigation is a useful method of achieving faecal continence in selected conditions, but remains largely underutilized because it is time consuming. This study investigated the effect of modifying irrigation technique (route, infusion regimen and pharmacological manipulation) on colonic emptying time in a porcine model. An end-colostomy and caecostomy were fashioned in six pigs. Twenty markers were introduced into the caecum immediately before colonic irrigation. Irrigation route (antegrade or retrograde), infusion regimen (tap water, polyethylene glycol (PEG), 1.5 per cent glycine) and pharmacological agent (glyceryl trinitrate (GTN) 0.25 mg/kg, diltiazem 3.9 mg/kg, bisacodyl 0.25 mg/kg) were assigned to each animal at random. Colonic transit was assessed by quantifying cumulative expelled markers (CEM) and stool every hour for 12 h. Mean CEM at 6 h for bisacodyl, GTN and diltiazem were 18.17, 12.17 and zero respectively; all pairwise differences in means were significant (P irrigation. PEG and glycine enhance emptying similar to bisacodyl and GTN solution. These findings show promise for improved faecal continence by colostomy irrigation and may justify construction of a Malone conduit at the time of colostomy in selected patients who wish to irrigate. Presented in part to the British Society of Gastroenterology in Glasgow, UK, March 1999, and published in abstract form as Gut 1999; 44(Suppl 1): A135

  14. Mediterranean diet and faecal microbiota: a transversal study.

    Science.gov (United States)

    Gutiérrez-Díaz, I; Fernández-Navarro, T; Sánchez, B; Margolles, A; González, S

    2016-05-18

    Despite the existing evidence on the impact of olive oil and red wine on the intestinal microbiota, the effect of the global Mediterranean Diet (MD) has not been sufficiently studied. We explored the association between the adherence to a Mediterranean dietary pattern, and its components, with faecal microbiota in a cohort of adults with non-declared pathology. This transversal study involved 31 adults without a previous diagnosis of cancer, autoimmune or digestive diseases. Based on the data obtained by means of an annual food frequency questionnaire (FFQ), and the information existing in the literature, a Mediterranean Diet Score (MDS) was calculated. Dietary fibre was obtained from Marlett et al. tables and Phenol-Explorer Database was used for phenolic compounds intake. Quantification of microbial groups was performed by Ion Torrent 16S rRNA gene-based analysis and quantification of short-chain fatty acids (SCFAs) was performed using gas chromatography-mass spectrometry (MS). MDS was associated with a higher abundance of Bacteroidetes (p = 0.001), Prevotellacea (p = 0.002) and Prevotella (p = 0.003) and a lower concentration of Firmicutes (p = 0.003) and Lachnospiraceae (p = 0.045). Also, in subjects with MDS ≥ 4, higher concentrations of faecal propionate (p = 0.034) and butyrate (p = 0.018) were detected. These results confirm the complexity of the diet-microbiota interrelationship.

  15. Reducing fluxes of faecal indicator compliance parameters to bathing waters from diffuse agricultural sources: The Brighouse Bay study, Scotland

    International Nuclear Information System (INIS)

    Kay, D.; Aitken, M.; Crowther, J.; Dickson, I.; Edwards, A.C.; Francis, C.; Hopkins, M.; Jeffrey, W.; Kay, C.; McDonald, A.T.; McDonald, D.; Stapleton, C.M.; Watkins, J.; Wilkinson, J.; Wyer, M.D.

    2007-01-01

    The European Water Framework Directive requires the integrated management of point and diffuse pollution to achieve 'good' water quality in 'protected areas'. These include bathing waters, which are regulated using faecal indicator organisms as compliance parameters. Thus, for the first time, European regulators are faced with the control of faecal indicator fluxes from agricultural sources where these impact on bathing water compliance locations. Concurrently, reforms to the European Union (EU) Common Agricultural Policy offer scope for supporting on-farm measures producing environmental benefits through the new 'single farm payments' and the concept of 'cross-compliance'. This paper reports the first UK study involving remedial measures, principally stream bank fencing, designed to reduce faecal indicator fluxes at the catchment scale. Considerable reduction in faecal indicator flux was observed, but this was insufficient to ensure bathing water compliance with either Directive 76/160/EEC standards or new health-evidence-based criteria proposed by WHO and the European Commission. - Diffuse microbiological pollution from farming activities can be reduced by protected riparian zones

  16. Genotyping of samples from German patients with ocular, cerebral and systemic toxoplasmosis reveals a predominance of Toxoplasma gondii type II.

    Science.gov (United States)

    Herrmann, Daland C; Maksimov, Pavlo; Hotop, Andrea; Groß, Uwe; Däubener, Walter; Liesenfeld, Oliver; Pleyer, Uwe; Conraths, Franz J; Schares, Gereon

    2014-10-01

    Toxoplasmosis is an important zoonosis transmitted from animals to humans world-wide. In order to determine Toxoplasma gondii genotypes in individuals living in Germany and to compare findings with those in animals, we analysed nine independent and unlinked genetic markers (nSAG2, SAG3, BTUB, GRA6, c22-8, c29-2, L358, PK1 and Apico) by PCR-RFLP in 83 archived T. gondii-positive DNA samples from patients with ocular toxoplasmosis (n=35), toxoplasmic encephalitis (n=32), systemic toxoplasmosis after bone-marrow transplantation (n=15) and congenital toxoplasmosis (n=1). In 46 of these 83 samples the presence of T. gondii DNA was confirmed by conventional end-point PCR. Among these, 17 T. gondii-positive samples were typed at all nine loci. The majority (15/17, 88.2%) of these samples were of T. gondii type II (i.e., including both, the Apico type II and Apico type I variants). In addition, in one sample a T. gondii type II/type III allele combination and in another sample a T. gondii genotype displaying type III alleles at all markers was observed. In the remaining 11 samples, in which T. gondii could only be partially typed, exclusively type II (n=10) or type III (n=1) alleles were observed. Results of the present study suggest that the majority of patients in Germany are infected with type II T. gondii regardless of the clinical manifestation of toxoplasmosis. This finding is in accord with the predominance of type II T. gondii in oocysts isolated from cats and in tissues of other intermediate hosts in Germany. Copyright © 2014 Elsevier GmbH. All rights reserved.

  17. Implementation of immunochemical faecal occult blood test in general practice

    DEFF Research Database (Denmark)

    Juul, Jakob Søgaard; Bro, Flemming; Hornung, Nete

    2016-01-01

    anvendelsen af immunochemical faecal occult blood test (iFOBT) i almen praksis. iFOBT detekterer humant globin i fæces og indikerer gastrointestinal blødning. Studiet udgør en del af et ph.d.-studie, der bidrager med ny viden til at optimere udredningen af patienter med tarmkræft. Der er et stort behov...

  18. Old beagle dogs have lower faecal concentrations of some fermentation products and lower peripheral lymphocyte counts than young adult beagles.

    Science.gov (United States)

    Gomes, Márcia de Oliveira Sampaio; Beraldo, Mariana Casteleti; Putarov, Thaila Cristina; Brunetto, Márcio Antônio; Zaine, Leandro; Glória, Maria Beatriz Abreu; Carciofi, Aulus Cavalieri

    2011-10-01

    The effects of age on microbiota composition, gut fermentation end-product formation and peripheral lymphocyte numbers were compared between old and young adult Beagle dogs fed four kibble diets differing in yeast cell wall contents. The experiment had a double 4 × 4 Latin square design, one with four mature dogs (4 years old) and the other with four old dogs (10 years old), with four replicates (diets) per dog. In each period a 15 d adaptation period preceded a 5 d total collection of faeces for the digestibility trial. On day 21, fresh faecal samples were collected for the determination of bacterial enumeration, pH, biogenic amine and short-chain fatty acid. Flow cytometry was used for immunophenotypic evaluation. Dogs were fed four kibble diets with similar composition with 0, 0.15, 0.30 and 0.45 % of yeast cell wall (as-fed), respectively. Data were evaluated using general linear models of Statistical Analysis Systems statistical software (P 0.15). Faecal concentrations of butyrate, histamine, agmatine and spermine were lower (P ≤ 0.05) and faecal pH was higher (P = 0.03) in older dogs than in mature adult dogs, suggesting an alteration in bacterial metabolic activity, or in the rate of intestinal absorption of these compounds. Concentrations of T-lymphocytes, T-cytotoxic lymphocytes and B-lymphocytes were also lower (P ≤ 0.01) in older dogs than in mature adult dogs. The study confirmed alterations in peripheral lymphocytes and revealed a reduced concentration of some fermentation end products in the colon of old dogs.

  19. A multiplex PCR-based method to identify strongylid parasite larvae recovered from ovine faecal cultures and/or pasture samples.

    Science.gov (United States)

    Bisset, S A; Knight, J S; Bouchet, C L G

    2014-02-24

    A multiplex PCR-based method was developed to overcome the limitations of microscopic examination as a means of identifying individual infective larvae from the wide range of strongylid parasite species commonly encountered in sheep in mixed sheep-cattle grazing situations in New Zealand. The strategy employed targets unique species-specific sequence markers in the second internal transcribed spacer (ITS-2) region of ribosomal DNA of the nematodes and utilises individual larval lysates as reaction templates. The basic assay involves two sets of reactions designed to target the ten strongylid species most often encountered in ovine faecal cultures under New Zealand conditions (viz. Haemonchus contortus, Teladorsagia circumcincta, Trichostrongylus axei, Trichostrongylus colubriformis, Trichostrongylus vitrinus, Cooperia curticei, Cooperia oncophora, Nematodirus spathiger, Chabertia ovina, and Oesophagostomum venulosum). Five species-specific primers, together with a pair of "generic" (conserved) primers, are used in each of the reactions. Two products are generally amplified, one by the generic primer pair regardless of species (providing a positive PCR control) and the other (whose size is indicative of the species present) by the appropriate species-specific primer in combination with one or other of the generic primers. If necessary, any larvae not identified by these reactions can subsequently be tested using primers designed specifically to detect those species less frequently encountered in ovine faecal cultures (viz. Ostertagia ostertagi, Ostertagia leptospicularis, Cooperia punctata, Nematodirus filicollis, and Bunostomum trigonocephalum). Results of assays undertaken on >5500 nematode larvae cultured from lambs on 16 different farms distributed throughout New Zealand indicated that positive identifications were initially obtained for 92.8% of them, while a further 4.4% of reactions gave a generic but no visible specific product and 2.8% gave no discernible

  20. Revision of the SNPforID 34-plex forensic ancestry test: Assay enhancements, standard reference sample genotypes and extended population studies.

    Science.gov (United States)

    Fondevila, M; Phillips, C; Santos, C; Freire Aradas, A; Vallone, P M; Butler, J M; Lareu, M V; Carracedo, A

    2013-01-01

    A revision of an established 34 SNP forensic ancestry test has been made by swapping the under-performing rs727811 component SNP with the highly informative rs3827760 that shows a near-fixed East Asian specific allele. We collated SNP variability data for the revised SNP set in 66 reference populations from 1000 Genomes and HGDP-CEPH panels and used this as reference data to analyse four U.S. populations showing a range of admixture patterns. The U.S. Hispanics sample in particular displayed heterogeneous values of co-ancestry between European, Native American and African contributors, likely to reflect in part, the way this disparate group is defined using cultural as well as population genetic parameters. The genotyping of over 700 U.S. population samples also provided the opportunity to thoroughly gauge peak mobility variation and peak height ratios observed from routine use of the single base extension chemistry of the 34-plex test. Finally, the genotyping of the widely used DNA profiling Standard Reference Material samples plus other control DNAs completes the audit of the 34-plex assay to allow forensic practitioners to apply this test more readily in their own laboratories. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

  1. Metagenomic analysis of faecal microbiome as a tool towards targeted non-invasive biomarkers for colorectal cancer

    DEFF Research Database (Denmark)

    Yu, Jun; Feng, Qiang; Wong, Sunny Hei

    2017-01-01

    known associations of Fusobacterium nucleatum and Peptostreptococcus stomatis with CRC, we found significant associations with several species, including Parvimonas micra and Solobacterium moorei. We identified 20 microbial gene markers that differentiated CRC and control microbiomes, and validated 4...... in the independent Chinese cohort with AUC=0.84 and OR of 23. These genes were enriched in early-stage (I-II) patient microbiomes, highlighting the potential for using faecal metagenomic biomarkers for early diagnosis of CRC. CONCLUSIONS: We present the first metagenomic profiling study of CRC faecal microbiomes...

  2. High prevalence of Hepatitis C virus genotype 6 in Vietnam.

    Science.gov (United States)

    Pham, Duc Anh; Leuangwutiwong, Pornsawan; Jittmittraphap, Akanitt; Luplertlop, Nattanej; Bach, Hoa Khanh; Akkarathamrongsin, Srunthron; Theamboonlers, Apiradee; Poovorawan, Yong

    2009-01-01

    This study aimed to update the prevalence of the various Hepatitis C virus genotypes in Vietnamese blood donors. One hundred and three HCV antibody-positive plasma samples were collected from blood donors at the National Institute of Hematology and Blood Transfusion, Hanoi, Vietnam. All specimens were subjected to RT-PCR of the 5' untranslated region (UTR) to confirm the presence of HCV RNA. The core and NS5B regions of thh positive samples were subsequently amplified by RT-PCR followed by direct sequencing and phylogenetic analysis. Seventy out of 103 samples (68.0%) were RNA positive. Core and NS5B were successfully amplified and sequences were obtained for 70 and 65 samples, respectively. Phylogenetic analysis revealed that genotype 6a was the most predominant among Vietnamese blood donors with a prevalence of 37.1% (26/70), followed by genotype 1a at 30.0% (21/70) and genotype 1b at 17.1% (12/70). The prevalence of two other genotype 6 variants, 6e and 61 was 8.6% and 1.4%, respectively. Further analysis of recent studies showed that the geographic distribution of genotype 6 covered mainly southern China and the mainland of Southeast Asia including Vietnam, Laos, Thailand, and Myanmar. The GenBank accession numbers for the sequences reported in this study are FJ768772-FJ768906.

  3. Gram-negative bacteria account for main differences between faecal microbiota from patients with ulcerative colitis and healthy controls

    DEFF Research Database (Denmark)

    Vigsnæs, Louise Kristine; Brynskov, J.; Steenholdt, C.

    2012-01-01

    process of the gut mucosa. The aim of this study was to investigate the faecal microbiota in patients either with UC in remission (n=6) or with active disease (n=6), and in healthy controls (n=6). The composition of Gram-negative bacteria and Gram-positive bacteria was examined. Antigenic structures...... of Gram-negative bacteria such as lipopolysaccharides have been related to the inflammatory responses and pathogenesis of inflammatory bowel disease. Dice cluster analysis and principal component analysis of faecal microbiota profiles obtained by denaturing gradient gel electrophoresis and quantitative...... PCR, respectively, revealed that the composition of faecal bacteria from UC patients with active disease differed from the healthy controls and that this difference should be ascribed to Gram-negative bacteria. The analysis did not show any clear grouping of UC patients in remission. Even...

  4. Molecular genotyping of ABO blood groups in some population groups from India.

    Science.gov (United States)

    Ray, Sabita; Gorakshakar, Ajit C; Vasantha, K; Nadkarni, Anita; Italia, Yazdi; Ghosh, Kanjaksha

    2014-01-01

    Indian population is characterized by the presence of various castes and tribal groups. Various genetic polymorphisms have been used to differentiate among these groups. Amongst these, the ABO blood group system has been extensively studied. There is no information on molecular genotyping of ABO blood groups from India. Therefore, the main objective of this study was to characterize the common A, B and O alleles by molecular analysis in some Indian population groups. One hundred samples from the mixed population from Mumbai, 101 samples from the Dhodia tribe and 100 samples from the Parsi community were included in this study. Initially, the samples were phenotyped by standard serologic techniques. PCR followed by single strand conformational polymorphsim (SSCP) was used for molecular ABO genotyping. Samples showing atypical SSCP patterns were further analysed by DNA sequencing to characterize rare alleles. Seven common ABO alleles with 19 different genotypes were found in the mixed population. The Dhodias showed 12 different ABO genotypes and the Parsis revealed 15 different ABO genotypes with six common ABO alleles identified in each of them. Two rare alleles were also identified. This study reports the distribution of molecular genotypes of ABO alleles among some population groups from India. Considering the extremely heterogeneous nature of the Indian population, in terms of various genotype markers like blood groups, red cell enzymes, etc., many more ABO alleles are likely to be encountered.

  5. Integrated analysis of water quality parameters for cost-effective faecal pollution management in river catchments.

    Science.gov (United States)

    Nnane, Daniel Ekane; Ebdon, James Edward; Taylor, Huw David

    2011-03-01

    In many parts of the world, microbial contamination of surface waters used for drinking, recreation, and shellfishery remains a pervasive risk to human health, especially in Less Economically Developed Countries (LEDC). However, the capacity to provide effective management strategies to break the waterborne route to human infection is often thwarted by our inability to identify the source of microbial contamination. Microbial Source Tracking (MST) has potential to improve water quality management in complex river catchments that are either routinely, or intermittently contaminated by faecal material from one or more sources, by attributing faecal loads to their human or non-human sources, and thereby supporting more rational approaches to microbial risk assessment. The River Ouse catchment in southeast England (U.K.) was used as a model with which to investigate the integration and application of a novel and simple MST approach to monitor microbial water quality over one calendar year, thereby encompassing a range of meteorological conditions. A key objective of the work was to develop simple low-cost protocols that could be easily replicated. Bacteriophages (viruses) capable of infecting a human specific strain of Bacteroides GB-124, and their correlation with presumptive Escherichia coli, were used to distinguish sources of faecal pollution. The results reported here suggest that in this river catchment the principal source of faecal pollution in most instances was non-human in origin. During storm events, presumptive E. coli and presumptive intestinal enterococci levels were 1.1-1.2 logs higher than during dry weather conditions, and levels of the faecal indicator organisms (FIOs) were closely associated with increased turbidity levels (presumptive E. coli and turbidity, r = 0.43). Spatio-temporal variation in microbial water quality parameters was accounted for by three principal components (67.6%). Cluster Analysis, reduced the fourteen monitoring sites to six

  6. Patterns of faecal nematode egg shedding after treatment of sheep with a long-acting formulation of moxidectin.

    Science.gov (United States)

    Crilly, James Patrick; Jennings, Amy; Sargison, Neil

    2015-09-15

    Much of the current information on the effects of long-acting anthelmintics on nematode populations derives either from research farms or mathematical models. A survey was performed with the aim of establishing how moxidectin is currently being used on sheep farms in the south-east of Scotland. A study was undertaken on a subsection of the surveyed farms to examine the effects of long-acting moxidectin treatments in both spring and autumn on faecal nematode egg output. The survey showed that whole flock treatments of injectable 2% moxidectin were used to control sheep scab on 21% of farms. Injectable 2% moxidectin and oral moxidectin were used to control the periparturient rise in faecal nematode egg shedding by ewes on 13% and 55% of farms respectively. The effects of injectable 2% moxidectin treatment on faecal nematode egg shedding post-treatment in both the autumn and spring were investigated by faecal nematode egg counts at the time of treatment and at 2-weekly interval thereafter on eight and six farms in the autumn and spring, respectively. Faecal egg shedding recommenced at 8 weeks (autumn) and 4 weeks (spring) post-treatment. Counts increased to a peak and then declined. The mean (95% confidence interval) peak counts post-treatment were 2.8 (0.6, 5.1), 3.6 (1.7, 5.5) and 53.5 (25.1, 82.0) eggs per gram (EPG) for autumn-treated ewes, autumn-treated lambs and spring-treated ewes respectively. The spring treated sheep showed a statistically significantly earlier return to faecal egg shedding (p=0.0125, p=0.0342) compared to both other groups, statistically significantly higher peak in egg counts than the autumn treated sheep (pegg counts (p=0.0148). There was no statistically significant difference in the timing of the peak FECs between autumn and spring (p=0.211). The FECs of all groups of sheep treated with an injectable long-acting formulation of moxidectin became positive earlier than would be expected from the period of persistence given on the datasheet

  7. Population-based V3 genotypic tropism assay: a retrospective analysis using screening samples from the A4001029 and MOTIVATE studies.

    Science.gov (United States)

    McGovern, Rachel A; Thielen, Alexander; Mo, Theresa; Dong, Winnie; Woods, Conan K; Chapman, Douglass; Lewis, Marilyn; James, Ian; Heera, Jayvant; Valdez, Hernan; Harrigan, P Richard

    2010-10-23

    The MOTIVATE-1 and 2 studies compared maraviroc (MVC) along with optimized background therapy (OBT) vs. placebo along with OBT in treatment-experienced patients screened as having R5-HIV (original Monogram Trofile). A subset screened with non-R5 HIV were treated with MVC or placebo along with OBT in a sister safety trial, A4001029. This analysis retrospectively examined the performance of population-based sequence analysis of HIV-1 env V3-loop to predict coreceptor tropism. Triplicate V3-loop sequences were generated using stored screening plasma samples and data was processed using custom software ('ReCall'), blinded to clinical response. Tropism was inferred using geno2pheno ('g2p'; 5% false positive rate). Primary outcomes were viral load changes after starting maraviroc; and concordance with prior screening Trofile results. Genotype and Trofile results were available for 1164 individuals with virological outcome data (N = 169 non-R5 by Trofile). Compared with Trofile, V3 genotyping had a specificity of 92.6% and a sensitivity of 67.4% for detecting non-R5 virus. However, when compared with clinical outcome, virological responses were consistently similar between Trofile and V3 genotype at weeks 8 and 24 following the initiation of therapy for patients categorized as R5. Despite differences in sensitivity for predicting non-R5 HIV, week 8 and 24 week virological responses were similar in this treatment-experienced population. These findings suggest the potential utility of V3 genotyping as an accessible assay to select patients who may benefit from maraviroc treatment. Optimization of the predictive tropism algorithm may lead to further improvement in the clinical utility of HIV genotypic tropism assays.

  8. Effects of age, sex, lactation and social dominance on faecal egg count patterns of gastrointestinal nematodes in farmed eland (Taurotragus oryx).

    Science.gov (United States)

    Vadlejch, J; Kotrba, R; Čadková, Z; Růžičková, A; Langrová, I

    2015-10-01

    The eland is a large African antelope that can be bred in a temperate climate, under similar conditions and production systems as cattle. However, knowledge of parasites in farmed elands outside the area of their native habitat is still limited, and information concerning factors that influence these parasites is lacking. Therefore, faecal samples from an entire herd of elands, including calves and adult females and males, were examined monthly over a one year period. Almost 84% of the animals were found to be positive for gastrointestinal nematodes. Strongyle-type eggs were most frequently detected (prevalence 75%), followed by Capillaria sp., Nematodirus sp. and Trichuris sp. eggs. Following culturing eggs to infective larvae, Teladorsagia sp., Trichostrongylus sp., Nematodirus sp., Cooperia sp. and Oesophagostomum sp. were identified. Following necropsy of two calves that died during the study one abomasal nematode (Teladorsagia circumcincta), five small intestinal nematode species (Nematodirus helvetianus, N. spathiger, Cooperia oncophora, C. curticei and Capillaria bovis) and two large intestinal nematodes (Oesophagostomum venulosum and Trichuris ovis) were recovered. From these findings, it is evident that the eland harbours nematodes that are typical for domestic cattle and small ruminants. Morphological and morphometric analyses of recovered nematodes revealed that these parasites do not require any special morphological adaptation to establish infection in elands. The faecal output of strongyle-type and Nematodirus sp. eggs was seasonal, with the highest egg production taking place during spring and summer. Calves had higher faecal egg counts (for all the monitored nematode species) than adults did. Lactation in females was significantly (Pnematode egg shedding. Social dominance also affected faecal egg count patterns. The lower the hierarchical position among adults (regardless of sex), the higher the risk of nematode infection. This effect was evident

  9. Effects of cattle manure on erosion rates and runoff water pollution by faecal coliforms.

    Science.gov (United States)

    Ramos, M C; Quinton, J N; Tyrrel, S F

    2006-01-01

    The large quantities of slurry and manure that are produced annually in many areas in which cattle are raised could be an important source of organic matter and nutrients for agriculture. However, the benefits of waste recycling may be partially offset by the risk of water pollution associated with runoff from the fields to which slurry or manure has been applied. In this paper, the effects of cattle manure application on soil erosion rates and runoff and on surface water pollution by faecal coliforms are analysed. Rainfall simulations at a rate of 70 mm h(-1) were conducted in a sandy loam soil packed into soil flumes (2.5m long x 1m wide) at a bulk density of 1400 kg m(-3), with and without cattle slurry manure applied on the surface. For each simulation, sediment and runoff rates were analysed and in those simulations with applied slurry, presumptive faecal coliform (PFC) concentrations in the runoff were evaluated. The application of slurry on the soil surface appeared to have a protective effect on the soils, reducing soil detachment by up to 70% but increasing runoff volume by up to 30%. This practice implies an important source of pollution for surface waters especially if rainfall takes place within a short period after application. The concentrations of micro-organisms (presumptive faecal coliforms (PFCs)) found in water runoff ranged from 1.9 x 10(4) to 1.1 x 10(6) PFC 100mL(-1), depending on the initial concentration in the slurry, and they were particularly high during the first phases of the rainfall event. The result indicates a strong relationship between the faecal coliforms transported by runoff and the organic matter in the sediment.

  10. Adaptation of Escherichia coli traversing from the faecal environment to the urinary tract.

    Science.gov (United States)

    Nielsen, Karen L; Stegger, Marc; Godfrey, Paul A; Feldgarden, Michael; Andersen, Paal S; Frimodt-Møller, Niels

    2016-12-01

    The majority of extraintestinal pathogenic Escherichia coli (ExPEC) causing urinary tract infections (UTI) are found in the patient's own gut flora, but only limited knowledge is available on the potential adaptation that may occur in the bacteria in order to traverse the perineum and successfully infect the urinary tract. Here, matching pairs of faecal and UTI isolates from 42 patients were compared pairwise using in-depth whole-genome sequencing to investigate whether genetic changes were evident for successful colonization in these two different environments. The identified non-synonymous mutations (0-12 substitutions in each pair) were primarily associated to genes encoding virulence factors and nutrient metabolism; and indications of parallel evolution were observed in genes encoding the major phase-variable protein antigen 43, a toxin/antitoxin locus and haemolysin B. No differences in virulence potential were observed in a mouse UTI model for five matching faecal and UTI isolates with or without mutations in antigen 43 and haemolysin B. Variations in plasmid content were observed in only four of the 42 pairs. Although, we observed mutations in known UTI virulence genes for a few pairs, the majority showed no detectable differences with respect to mutations or mobilome when compared to their faecal counterpart. The results show that UPECs are successful in colonizing both the bladder and gut without adaptation. Copyright © 2016 Elsevier GmbH. All rights reserved.

  11. Early detection of Haemonchus contortus infection in sheep using three different faecal occult blood tests

    Directory of Open Access Journals (Sweden)

    A.V. Rodríguez

    2015-07-01

    Full Text Available Haemonchus contortus is a blood-sucking parasite causing the presence of faecal occult blood (FOB. The objective was to study three different FOB tests in order to have a new indicator of H. contortus infection in sheep that could be included in the genetic evaluation system as an alternative selection criterion to faecal worm egg count (FEC. A total of 29 Corriedale lambs were experimentally infected with 10.000 larvae of H. contortus. Stool samples were recorded for FEC and FOB tests (Hexagon, Hematest® and Multistix®, blood for packed cell volume (PCV, haemoglobin, white and red blood cell count (RBC, and FAMACHA© for scoring anaemia. At the end of the experiment lambs were slaughtered to worm burden count. Field infection was achieved in 309 Merino lambs under natural parasite challenge. FEC data were normalized through logarithmic transformation (LnFEC. Pearson correlation was estimated to examine the relationship between all traits. The three tests were able to detect the presence of FOB at day 11. FEC, PCV and RBC decreased to sub-normal values from day 18. FAMACHA© score 3 was considered to be indicative of anaemia. Most of the correlations were of high magnitude, with the exception of Multistix® test that was moderately correlated with haematological parameters, LnFEC and FEC. In field infection, most samples were negative to FOB tests and the correlations were lower than those calculated under experimental infection. In conclusion, FOB tests were able to detect haemonchosis earlier than FEC under high experimental parasite challenge. However, they were not able to detect FOB under natural mixed parasite challenge. FAMACHA© and PCV demonstrated to be good indicators of Haemonchosis, having moderate to high correlations with FEC.

  12. Incidence of Echinococcus granulosus in Domestic Dogs in Palestine as Revealed by Copro-PCR

    Science.gov (United States)

    Al-Jawabreh, Amer; Dumaidi, Kamal; Ereqat, Suheir; Nasereddin, Abedelmajeed; Al-Jawabreh, Hanan; Azmi, Kifaya; Al-Laham, Nahed; Abdeen, Ziad

    2015-01-01

    Hydatidosis or echinococcosisis considered a neglected zoonotic disease despite its high burden in the livestock industry and the high risk of infection by humans in endemic areas. In a cross-sectional study we estimated the copro-Incidence and also genotyped Echinococcus granulosus isolates from domestic dogs using polymerase chain reaction (PCR). Medical archives in nine major hospitals in Palestine were reviewed to determine incidence of E. granulosus infection detected in humans during surgery. Faecal samples were collected from 93 domestic dogs in three districts with the highest number of human cases: Al-Khalil (Hebron), Tubas and Jenin. Genomic DNA was extracted from dog faecal samples and amplified by PCR targeting the repeat DNA sequence (EgG1 Hae III) followed by sequencing of five positive samples. Genotyping was determined by sequencing and BLAST searching of mitochondrial cytochrome c oxidase subunit (CO1). The incidence of E. granulosus infection detected in humans at surgery was 1.2 per 100,000 in the West Bank and 1.0 per 100,000 in Gaza Strip. Seventeen of 93 domestic dogs (18%) were positive, based upon comparison with the Echinococcus DNA control. The five sequenced samples were confirmed to be E. granulosus. Successfully genotyped sample belonged to E.granulosus sensu stricto (formerly G1-G3 complex, sheep strain). For domestic dogs, age group (13-24 months) and sex were identified as two risk factors for contracting E. granulosus. The study identified the high incidence of E. granulosus sensu stricto in dogs in Palestine. PMID:26181591

  13. Incidence of Echinococcus granulosus in Domestic Dogs in Palestine as Revealed by Copro-PCR.

    Directory of Open Access Journals (Sweden)

    Amer Al-Jawabreh

    Full Text Available Hydatidosis or echinococcosisis considered a neglected zoonotic disease despite its high burden in the livestock industry and the high risk of infection by humans in endemic areas. In a cross-sectional study we estimated the copro-Incidence and also genotyped Echinococcus granulosus isolates from domestic dogs using polymerase chain reaction (PCR. Medical archives in nine major hospitals in Palestine were reviewed to determine incidence of E. granulosus infection detected in humans during surgery. Faecal samples were collected from 93 domestic dogs in three districts with the highest number of human cases: Al-Khalil (Hebron, Tubas and Jenin. Genomic DNA was extracted from dog faecal samples and amplified by PCR targeting the repeat DNA sequence (EgG1 Hae III followed by sequencing of five positive samples. Genotyping was determined by sequencing and BLAST searching of mitochondrial cytochrome c oxidase subunit (CO1. The incidence of E. granulosus infection detected in humans at surgery was 1.2 per 100,000 in the West Bank and 1.0 per 100,000 in Gaza Strip. Seventeen of 93 domestic dogs (18% were positive, based upon comparison with the Echinococcus DNA control. The five sequenced samples were confirmed to be E. granulosus. Successfully genotyped sample belonged to E.granulosus sensu stricto (formerly G1-G3 complex, sheep strain. For domestic dogs, age group (13-24 months and sex were identified as two risk factors for contracting E. granulosus. The study identified the high incidence of E. granulosus sensu stricto in dogs in Palestine.

  14. Faecal short chain fatty acids in healthy subjects participating in a randomised controlled trial examining a soluble highly viscous polysaccharide versus control.

    Science.gov (United States)

    Reimer, R A; Pelletier, X; Carabin, I G; Lyon, M R; Gahler, R J; Wood, S

    2012-08-01

    Short chain fatty acids (SCFA) are produced by the bacterial fermentation of dietary fibre and have been linked with intestinal health. The present study examined faecal SCFA concentrations in subjects consuming a novel soluble highly viscous polysaccharide (HVP) or control for 3 weeks. A total of 54 healthy adults participated in a randomised, double-blind, placebo-controlled study. Subjects were randomised to consume HVP or control (skim milk powder). A dose of 5 g day(-1) was consumed in the first week, followed by 10 g day(-1) in the second and third weeks (n = 27 per group). The primary outcome was SCFA concentrations in faecal samples collected at baseline (visit 1, V1), at 1 week (V2) and at 3 week (V3). The reduction in faecal acetate from V1 to V3 in control subjects was not observed in subjects consuming HVP. There were no differences in propionate, butyrate, valerate or caproate concentrations. There was a significant treatment effect (P = 0.03) for total SCFA, with higher concentrations observed in subjects consuming HVP versus control. HVP is a viscous functional fibre that may influence gut microbial fermentation. Further work is warranted to examine the fermentative properties of HVP and possible links with appetite regulation and reduced serum low-density lipoprotein cholesterol concentrations. © 2012 The Authors. Journal of Human Nutrition and Dietetics © 2012 The British Dietetic Association Ltd.

  15. Association between the porcine Escherichia coli F18 receptor genotype and phenotype and susceptibility to colonisation and postweaning diarrhoea caused by E-coli O138 : F18

    DEFF Research Database (Denmark)

    Frydendahl, K.; Jensen, Tim Kåre; Andersen, Jens Strodl

    2003-01-01

    Porcine postweaning Escherichia coli enteritis is a cause of significant morbidity and mortality in pigs worldwide, and effective prevention remains an unsolved problem. This study examined the correlation between susceptibility of pigs to experimental infection with an E. coli F18 strain...... and the porcine intestinal F18 receptor genotypes. Thirty-one pigs classified as either belonging to the susceptible or the resistant genotype were inoculated with cultures of an E. coli 0138:F18 isolated from a pig with postweaning diarrhoea. Susceptibility to colonisation and diarrhoea was assessed by clinical...... and heterozygotic susceptible pigs. Faecal shedding of the challenge strain correlated with the genetic receptor profile. Twenty pigs examined immunohistochemically revealed focal to extensive small intestinal mucosal colonisation by E. coli O138:F18 in nine of 10 susceptible and three of 10 resistant pigs. Results...

  16. Rotavirus genotype shifts among Swedish children and adults-Application of a real-time PCR genotyping.

    Science.gov (United States)

    Andersson, Maria; Lindh, Magnus

    2017-11-01

    It is well known that human rotavirus group A is the most important cause of severe diarrhoea in infants and young children. Less is known about rotavirus infections in other age groups, and about how rotavirus genotypes change over time in different age groups. Develop a real-time PCR to easily genotype rotavirus strains in order to monitor the pattern of circulating genotypes. In this study, rotavirus strains in clinical samples from children and adults in Western Sweden during 2010-2014 were retrospectively genotyped by using specific amplification of VP 4 and VP 7 genes with a new developed real-rime PCR. A genotype was identified in 97% of 775 rotavirus strains. G1P[8] was the most common genotype representing 34.9%, followed by G2P[4] (28.3%), G9P[8] (11.5%), G3P[8] (8.1%), and G4P[8] (7.9%) The genotype distribution changed over time, from predominance of G1P[8] in 2010-2012 to predominance of G2P[4] in 2013-2014. There were also age-related differences, with G1P[8] being the most common genotype in children under 2 years (47.6%), and G2P[4] the most common in those over 70 years of age (46.1%.). The shift to G2P[4] in 2013-2014 was associated with a change in the age distribution, with a greater number of rotavirus positive cases in elderly than in children. By using a new real-time PCR method for genotyping we found that genotype distribution was age related and changed over time with a decreasing proportion of G1P[8]. Copyright © 2017. Published by Elsevier B.V.

  17. Copromicroscopic and molecular investigations on intestinal parasites in kenneled dogs.

    Science.gov (United States)

    Simonato, Giulia; Frangipane di Regalbono, Antonio; Cassini, Rudi; Traversa, Donato; Beraldo, Paola; Tessarin, Cinzia; Pietrobelli, Mario

    2015-05-01

    Intestinal parasites are common in dogs worldwide, and their importance has recently increased for a renewed awareness on the public health relevance that some of them have. In this study, the prevalence of helminths and protozoa was evaluated by microscopy in 318 canine faecal samples collected from eight rescue shelters in the North-eastern Italy; 285 of them were also submitted to the molecular characterization of Giardia duodenalis and Cryptosporidium spp. isolates. An analysis was performed to evaluate the prevalence rates in relation to canine individual data, shelter provenance and anthelmintic treatments. Overall, 52.5% (167/318) of faecal samples were positive for at least one parasite. Trichuris vulpis showed the highest overall prevalence rate (29.2%), followed by G. duodenalis (15.1%), Toxocara canis (9.7%), ancylostomatids (8.2%) and Cystoisospora (5.7%). The prevalence of G. duodenalis, evaluated by real-time PCR, was 57.9% (165/285), and 79 isolates were characterized by nested PCR on the β-giardin gene. The assemblages found were mainly the host-specific genotypes C and D, while only one assemblage was identified as the human-specific genotype B1. Isolates of Cryptosporidium spp., recorded in 3/285 (1.1%) stool samples, were Cryptosporidium parvum based on the characterization of the Cryptosporidium oocyst wall protein (COWP) gene. Although the results describe a relatively limited risk of dog-originating zoonoses, there is the need to improve the quality of shelter practices towards better health managements for safe pet-adoption campaigns and a minimization of the environmental faecal pollution with canine intestinal parasites.

  18. Genotyping of F-RNA coliphages isolated from wastewater and river ...

    African Journals Online (AJOL)

    Faecal contamination of water sources can only be managed if the sources of pollution are identified and thus tools to distinguish between human and animal faecal sources are needed. Male-specific F-RNA coliphages have been classified into four sero-groups and evidence has been presented that two of these ...

  19. SNPMClust: Bivariate Gaussian Genotype Clustering and Calling for Illumina Microarrays

    Directory of Open Access Journals (Sweden)

    Stephen W. Erickson

    2016-07-01

    Full Text Available SNPMClust is an R package for genotype clustering and calling with Illumina microarrays. It was originally developed for studies using the GoldenGate custom genotyping platform but can be used with other Illumina platforms, including Infinium BeadChip. The algorithm first rescales the fluorescent signal intensity data, adds empirically derived pseudo-data to minor allele genotype clusters, then uses the package mclust for bivariate Gaussian model fitting. We compared the accuracy and sensitivity of SNPMClust to that of GenCall, Illumina's proprietary algorithm, on a data set of 94 whole-genome amplified buccal (cheek swab DNA samples. These samples were genotyped on a custom panel which included 1064 SNPs for which the true genotype was known with high confidence. SNPMClust produced uniformly lower false call rates over a wide range of overall call rates.

  20. South Asian Ethnicity, Socioeconomic Status, and Psychological Mediators of Faecal Occult Blood Colorectal Screening Participation: A Prospective Test of a Process Model

    OpenAIRE

    Orbell, Sheina; Szczepura, Ala; Weller, David; Gumber, Anil; Hagger, Martin

    2017-01-01

    Objective: Although ethnicity and socio-economic status (SES) correlate with health inequality, efforts to explain variance in health behavior attributable to these factors are limited by difficulties in population sampling. We used ethnicity identification software to test effects of psychological beliefs about screening as mediators of ethnicity and SES on faecal occult blood colorectal screening behavior in a no-cost health care context. Method: N=1678 adults aged 50-67 years of whom 28 % ...

  1. Spontaneous scrotal faecal fistula in a neonate: report of a case ...

    African Journals Online (AJOL)

    A 21 day old boy with spontaneous scrotal faecal fistula following a neglected strangulated right inguinal hernia is reported. He had necrotizing fasciitis of the right scrotum with sparing of the testis. He successfully had debridement, herniotomy and bowel resection with end-to-end anastomosis. This is a rare occurrence in ...

  2. RT-PCR for detection of all seven genotypes of Lyssavirus genus.

    Science.gov (United States)

    Vázquez-Morón, S; Avellón, A; Echevarría, J E

    2006-08-01

    The Lyssavirus genus includes seven species or genotypes named 1-7. Rabies genotypes correlate with geographical distribution and specific hosts. Co-circulation of different lyssaviruses, imported cases, and the presence of unknown viruses, such as Aravan, Khujand, Irkut and West Caucasian Bat Virus, make it necessary to use generic methods able to detect all lyssaviruses. Primer sequences were chosen from conserved regions in all genotypes in order to optimise a generic RT-PCR. Serial dilutions of 12 RNA extracts from all seven Lyssavirus genotypes were examined to compare the sensitivity of the RT-PCR standardised in this study with a published RT-PCR optimised for EBLV1 detection and capable of amplifying RNA from all seven lyssaviruses. All seven genotypes were detected by both RT-PCRs, however, the sensitivity was higher with the new version of the test. Twenty samples submitted for rabies diagnosis were tested by the new RT-PCR. Eight out of 20 samples from six dogs, one horse and one bat were found positive, in agreement with immunofluorescence results. Seven samples from terrestrial mammals were genotype 1 and one from a bat was genotype 5. In conclusion, this method can be used to complement immunofluorescence for the diagnosis of rabies, enabling the detection of unexpected lyssaviruses during rabies surveillance.

  3. SaFaRI: sacral nerve stimulation versus the FENIX magnetic sphincter augmentation for adult faecal incontinence: a randomised investigation.

    Science.gov (United States)

    Williams, Annabelle E; Croft, Julie; Napp, Vicky; Corrigan, Neil; Brown, Julia M; Hulme, Claire; Brown, Steven R; Lodge, Jen; Protheroe, David; Jayne, David G

    2016-02-01

    Faecal incontinence is a physically, psychologically and socially disabling condition. NICE guidance (2007) recommends surgical intervention, including sacral nerve stimulation (SNS), after failed conservative therapies. The FENIX magnetic sphincter augmentation (MSA) device is a novel continence device consisting of a flexible band of interlinked titanium beads with magnetic cores that is placed around the anal canal to augment anal sphincter tone through passive attraction of the beads. Preliminary studies suggest the FENIX MSA is safe, but efficacy data is limited. Rigorous evaluation is required prior to widespread adoption. The SaFaRI trial is a National Institute of Health Research (NIHR) Health Technology Assessment (HTA)-funded UK multi-site, parallel group, randomised controlled, unblinded trial that will investigate the use of the FENIX MSA, as compared to SNS, for adult faecal incontinence resistant to conservative management. Twenty sites across the UK, experienced in the treatment of faecal incontinence, will recruit 350 patients randomised equally to receive either SNS or FENIX MSA. Participants will be followed-up at 2 weeks post-surgery and at 6, 12 and 18 months post-randomisation. The primary endpoint is success, as defined by device in use and ≥50 % improvement in the Cleveland Clinic Incontinence Score (CCIS) at 18 months post-randomisation. Secondary endpoints include complications, quality of life and cost effectiveness. SaFaRI will rigorously evaluate a new technology for faecal incontinence, the FENIX™ MSA, allowing its safe and controlled introduction into current clinical practice. These results will inform the future surgical management of adult faecal incontinence.

  4. Distribution of Hepatitis C Virus Genotypes in the South Marmara Region

    Directory of Open Access Journals (Sweden)

    Harun Agca

    2014-03-01

    Full Text Available Aim: Hepatitis C virus (HCV is an important caustive agent of hepatitis, cirrhosis and hepatocellular carcinoma both in our country and the world. Prognosis and response to treatment is related with the genotype of HCV which has six genotypes and over a hundred quasispecies. Knowing the HCV genotype is also important for epidemiological data. In this study we aimed to investigate the HCV genotypes of samples sent to Uludag University Hospital Microbiology Laboratory which is the reference centre in the South Marmara Region. Material and Method: This study was done retrospectively to analyse the HCV patients%u2019 sera sent to our laboratory between July 2010and December 2012 for HCV genotyping. Artus HCV QS-RGQ PCR kit (Qiagene,Hilden, Germany was used in Rotor-Gene Q (Qiagene, Hilden Germany for detection of HCV RNA. HCV RNA positive samples of patients%u2019 sera were were used for genotyping by the Linear Array HCV genotyping test (Roche, NJ, USA.Results: 214 (92.6 % of total 231 patients included in the study were genotype 1, one (0.4 % was genotype 2, nine (3.9 % were genotype 3 and, seven (3.4 % were found genotype 4. Three of genotype 3 patients were of foreign nationality, two were born abroad and one of the genotype 4 patients were born abroad. Discussion: Concordant with our country data the most frequent genotype was 1, genotype 2 was seen in patients especially related with foreign countries and genotype 4 was seen rare. The importance of genotype 1, which is seen more frequent in our country and region is; resistance to antiviral treatment and prolonged treatment duration in chronic hepatitis C patients.

  5. Earlier stages of colorectal cancer detected with immunochemical faecal occult blood tests

    NARCIS (Netherlands)

    van Rossum, L. G. M.; van Rijn, A. F.; van Munster, I. P.; Jansen, J. B. M. J.; Fockens, P.; Laheij, R. J. F.; Dekker, E.

    2009-01-01

    Background: The aim of colorectal cancer screening is to improve prognosis by the detection of early cancer and precursor stages. We compared the stage distribution of asymptomatic colorectal cancer patients detected by a positive immunochemical or guaiac-based faecal occult blood test (FOBT) with

  6. Calcium intake and the associations with faecal fat and energy excretion, and lipid profile in a free-living population

    DEFF Research Database (Denmark)

    Kjølbæk, Louise; Lorenzen, Janne Kunchel; Larsen, Lesli Hingstrup

    2017-01-01

    registration (days 1–7), a 5-d faeces collection (days 3–7), a 2-d urine collection (days 5–7), and anthropometric measurements and a fasting blood sample (day 8) were collected. Analyses showed that dietary Ca intake (g/10 MJ per d) was positively associated with excretion of faecal fat (P = 0·004) and energy......·96, −0·28) mmol/l, P food products in a habitual diet was associated with reduced total CHOL and LDL-CHOL concentrations, which may lower...

  7. Age and microenvironment outweigh genetic influence on the Zucker rat microbiome.

    Directory of Open Access Journals (Sweden)

    Hannah Lees

    Full Text Available Animal models are invaluable tools which allow us to investigate the microbiome-host dialogue. However, experimental design introduces biases in the data that we collect, also potentially leading to biased conclusions. With obesity at pandemic levels animal models of this disease have been developed; we investigated the role of experimental design on one such rodent model. We used 454 pyrosequencing to profile the faecal bacteria of obese (n = 6 and lean (homozygous n = 6; heterozygous n = 6 Zucker rats over a 10 week period, maintained in mixed-genotype cages, to further understand the relationships between the composition of the intestinal bacteria and age, obesity progression, genetic background and cage environment. Phylogenetic and taxon-based univariate and multivariate analyses (non-metric multidimensional scaling, principal component analysis showed that age was the most significant source of variation in the composition of the faecal microbiota. Second to this, cage environment was found to clearly impact the composition of the faecal microbiota, with samples from animals from within the same cage showing high community structure concordance, but large differences seen between cages. Importantly, the genetically induced obese phenotype was not found to impact the faecal bacterial profiles. These findings demonstrate that the age and local environmental cage variables were driving the composition of the faecal bacteria and were more deterministically important than the host genotype. These findings have major implications for understanding the significance of functional metagenomic data in experimental studies and beg the question; what is being measured in animal experiments in which different strains are housed separately, nature or nurture?

  8. Demographics of cattle positive for Mycobacterium avium subspecies paratuberculosis by faecal culture, from submissions to the Cork Regional Veterinary Laboratory

    Science.gov (United States)

    2009-01-01

    The demography of bovine infections caused by Mycobacterium avium subspecies paratuberculosis (MAP) in Ireland is poorly defined. The objective of this study was to describe the demographics of cattle positive to MAP on faecal culture, based on submissions to the Cork Regional Veterinary Laboratory (Cork RVL) from 1994 to 2006. The study focused on all available faecal samples from adult cattle with non-responsive chronic diarrhoea that were submitted by private veterinary practitioners to Cork RVL for MAP culture. For each MAP-positive by faecal culture animal, data were collated from Cork RVL and Cattle Movement Monitoring Scheme (CMMS) records. Johne's disease (JD) was confirmed in 110 animals from 86 herds by the Cork RVL between 1994 and 2006, with a rate of positive cases between 15% and 18% over last four years of the study. Two breeds (Holstein/Friesian or Limousin) made up 78% of submissions. Movements were assessed for the 57 study animals with available movement information, 90% died within one year of the test and 26% tested positive in the herd they were born into. The study provides preliminary information about movement trends and demographics of animals with MAP positive submissions. Although the study area is restricted, it includes the most intensive (and economically-important) dairy region in Ireland. The demographics of JD infection from the study area are in agreement with international reports. Further work is required to determine demographic trends, incidence and prevalence of JD throughout Ireland. It is hoped this work may contribute to the development of a surveillance strategy for MAP by regional veterinary laboratories. PMID:21851736

  9. Identification of Coxiella burnetii genotypes in Croatia using multi-locus VNTR analysis.

    Science.gov (United States)

    Račić, Ivana; Spičić, Silvio; Galov, Ana; Duvnjak, Sanja; Zdelar-Tuk, Maja; Vujnović, Anja; Habrun, Boris; Cvetnić, Zeljko

    2014-10-10

    Although Q fever affects humans and animals in Croatia, we are unaware of genotyping studies of Croatian strains of the causative pathogen Coxiella burnetii, which would greatly assist monitoring and control efforts. Here 3261 human and animal samples were screened for C. burnetii DNA by conventional PCR, and 335 (10.3%) were positive. Of these positive samples, 82 were genotyped at 17 loci using the relatively new method of multi-locus variable number tandem repeat analysis (MLVA). We identified 13 C. burnetii genotypes not previously reported anywhere in the world. Two of these 13 genotypes are typical of the continental part of Croatia and share more similarity with genotypes outside Croatia than with genotypes within the country. The remaining 11 novel genotypes are typical of the coastal part of Croatia and show more similarity to one another than to genotypes outside the country. Our findings shed new light on the phylogeny of C. burnetii strains and may help establish MLVA as a standard technique for Coxiella genotyping. Copyright © 2014 Elsevier B.V. All rights reserved.

  10. Dietary carbohydrate source influences molecular fingerprints of the rat faecal microbiota

    DEFF Research Database (Denmark)

    Licht, Tine Rask; Hansen, Max; Poulsen, Morten

    2006-01-01

    Background: A study was designed to elucidate effects of selected carbohydrates on composition and activity of the intestinal microbiota. Five groups of eight rats were fed a western type diet containing cornstarch (reference group), sucrose, potato starch, inulin (a long-chained fructan) or olig......Background: A study was designed to elucidate effects of selected carbohydrates on composition and activity of the intestinal microbiota. Five groups of eight rats were fed a western type diet containing cornstarch (reference group), sucrose, potato starch, inulin (a long-chained fructan...... of coliform bacteria in faeces. In the inulin and oligofructose groups, higher levels of butyrate and propionate, respectively, were measured. Principal Component Analysis of profiles of the faecal microbiota obtained by Denaturing Gradient Gel Electrophoresis (DGGE) of PCR amplified bacterial 16S rRNA genes...... and are not expected to reach the large intestine, the DGGE band patterns obtained indicated that these carbohydrates indeed affected the composition of bacteria in the large gut. Also the two fructans resulted in completely different molecular fingerprints of the faecal microbiota, indicating that even though...

  11. Effect of yoghurt containing Bifidobacterium lactis Bb12® on faecal excretion of secretory immunoglobulin A and human beta-defensin 2 in healthy adult volunteers

    Directory of Open Access Journals (Sweden)

    Kabeerdoss Jayakanthan

    2011-12-01

    Full Text Available Abstract Background Probiotics are used to provide health benefits. The present study tested the effect of a probiotic yoghurt on faecal output of beta-defensin and immunoglobulin A in a group of young healthy women eating a defined diet. Findings 26 women aged 18-21 (median 19 years residing in a hostel were given 200 ml normal yoghurt every day for a week, followed by probiotic yoghurt containing Bifidobacterium lactis Bb12® (109 in 200 ml for three weeks, followed again by normal yoghurt for four weeks. Stool samples were collected at 0, 4 and 8 weeks and assayed for immunoglobulin A and human beta-defensin-2 by ELISA. All participants tolerated both normal and probiotic yoghurt well. Human beta-defensin-2 levels in faeces were not altered during the course of the study. On the other hand, compared to the basal sample, faecal IgA increased during probiotic feeding (P = 0.0184 and returned to normal after cessation of probiotic yoghurt intake. Conclusions Bifidobacterium lactis Bb12® increased secretory IgA output in faeces. This property may explain the ability of probiotics to prevent gastrointestinal and lower respiratory tract infections.

  12. Chlamydia trachomatis Genotypes and the Swedish New Variant among Urogenital Chlamydia trachomatis Strains in Finland

    Directory of Open Access Journals (Sweden)

    Suvi Niemi

    2011-01-01

    Full Text Available Our aims were to genotype Chlamydia trachomatis strains present in urogenital samples and to investigate the occurrence of the Swedish new variant of C. trachomatis in Finland. We genotyped 160 C. trachomatis positive samples with ompA real-time PCR and analyzed 495 samples for the new variant. The three most prevalent genotypes were E (40%, F (28%, and G (13%. Only two specimens containing bacteria with the variant plasmid were detected. It seems that in Finland the percentage of infections due to genotypes F and G has slightly increased during the last 20 years. Genotypes E and G appear to be more common, and genotypes J/Ja and I/Ia appear to be less common in Europe than in the USA. Although the genotype E was the most common genotype among C. trachomatis strains, the new variant was rarely found in Finland.

  13. PCR-based identification of eight Lactobacillus species and 18 hr-HPV genotypes in fixed cervical samples of South African women at risk of HIV and BV.

    NARCIS (Netherlands)

    Dols, J.A.M.; Reid, G.; Kort, R.; Schuren, F.H.J.; Tempelman, H.; Bontekoe, T.R.; Korporaal, H.; van der Veer, E.M.; Smit, P.W,; Boon, M.E.

    2012-01-01

    Vaginal lactobacilli assessed by PCR-based microarray and PCR-based genotyping of HPV in South African women at risk for HIV and BV. Vaginal lactobacilli can be defined by microarray techniques in fixed cervical samples of South African women. Cervical brush samples suspended in the coagulant

  14. PCR-based identification of eight lactobacillus species and 18 hr-HPV genotypes in fixed cervical samples of south african women at risk of HIV and BV

    NARCIS (Netherlands)

    Dols, J.A.M.; Reid, G.; Kort, R.; Schuren, F.H.J.; Tempelman, H.; Bontekoe, T.R.; Korporaal, H.; Veer, E.M. van der; Smit, P.W.; Boon, M.E.

    2012-01-01

    Vaginal lactobacilli assessed by PCR-based microarray and PCR-based genotyping of HPV in South African women at risk for HIV and BV. Vaginal lactobacilli can be defined by microarray techniques in fixed cervical samples of South African women. Cervical brush samples suspended in the coagulant

  15. Genotypic characterization of Echinococcus granulosus in Iranian goats

    Directory of Open Access Journals (Sweden)

    Mohammad Reza Youssefi

    2013-10-01

    Full Text Available Objective: To isolate and characterize the genotype of Echinococcus granulosus (E. granulosus from goats in Mazandaran Province, Northern Iran. Methods: A total of 120 goats were screened from abattoirs of Mazandaran Province, Northern Iran. Forty out of 120 samples were infected with cystic echinococcosis and 29 out of 40 infected samples were fertile hydatid cysts (containing protoscolices which were collected from the livers and lungs of infected goats. DNA samples were extracted from the protoscolices and characterized by mitochondrial DNA sequencing of part of the mitochondrial cytochrome C oxidase subunit 1 gene. Results: Sequences analysis of nine fertile hydatid cysts indicated that all isolated samples were infected with the G1 sheep strain and two sequences were belonged to G1 4 and G1c microvarients of the G1 genotype. Conclusions: The results showed that goats act as alternative intermediate hosts for sheep strain. G1 genotype seems to be the main route of transmission and it should be considered in further studies.

  16. Immunochemical faecal occult blood test for colorectal cancer screening: a systematic review.

    Science.gov (United States)

    Syful Azlie, M F; Hassan, M R; Junainah, S; Rugayah, B

    2015-02-01

    A systematic review on the effectiveness and costeffectiveness of Immunochemical faecal occult IFOBT for CRC screening was carried out. A total of 450 relevant titles were identified, 41 abstracts were screened and 18 articles were included in the results. There was fair level of retrievable evidence to suggest that the sensitivity and specificity of IFOBT varies with the cut-off point of haemoglobin, whereas the diagnostic accuracy performance was influenced by high temperature and haemoglobin stability. A screening programme using IFOBT can be effective for prevention of advanced CRC and reduced mortality. There was also evidence to suggest that IFOBT is cost-effective in comparison with no screening, whereby a two-day faecal collection method was found to be costeffective as a means of screening for CRC. Based on the review, quantitative IFOBT method can be used in Malaysia as a screening test for CRC. The use of fully automated IFOBT assay would be highly desirable.

  17. Adaptation of Escherichia coli traversing from the faecal environment to the urinary tract

    DEFF Research Database (Denmark)

    Nielsen, Karen L.; Stegger, Marc; Godfrey, Paul A.

    2016-01-01

    The majority of extraintestinal pathogenic Escherichia coli (ExPEC) causing urinary tract infections (UTI) are found in the patient’s own gut flora, but only limited knowledge is available on the potential adaptation that may occur in the bacteria in order to traverse the perineum and successfully...... infect the urinary tract. Here, matching pairs of faecal and UTI isolates from 42 patients were compared pairwise using in-depth whole-genome sequencing to investigate whether genetic changes were evident for successful colonization in these two different environments. The identified non...... in virulence potential were observed in a mouse UTI model for five matching faecal and UTI isolates with or without mutations in antigen 43 and haemolysin B. Variations in plasmid content were observed in only four of the 42 pairs. Although, we observed mutations in known UTI virulence genes for a few pairs...

  18. Faecal-wood biomass co-combustion and ash composition analysis.

    Science.gov (United States)

    Somorin, Tosin Onabanjo; Kolios, Athanasios J; Parker, Alison; McAdam, Ewan; Williams, Leon; Tyrrel, Sean

    2017-09-01

    Fuel blending is a widely used approach in biomass combustion, particularly for feedstocks with low calorific value and high moisture content. In on-site sanitation technologies, fuel blending is proposed as a pre-treatment requirement to reduce moisture levels and improve the physiochemical properties of raw faeces prior to drying. This study investigates the co-combustion performance of wood dust: raw human faeces blends at varying air-to-fuel ratios in a bench-scale combustor test rig. It concludes with ash composition analyses and discusses their potential application and related problems. The study shows that a 50:50 wood dust (WD): raw human faeces (FC) can reduce moisture levels in raw human faeces by ∼40% prior to drying. The minimum acceptable blend for treating moist faeces without prior drying at a combustion air flow rate of 14-18 L/min is 30:70 WD: FC. For self-sustained ignition and flame propagation, the minimum combustion temperature required for conversion of the fuel to ash is ∼400 °C. The most abundant elements in faecal ash are potassium and calcium, while elements such as nickel, aluminium and iron are in trace quantities. This suggests the potential use of faecal ash as a soil conditioner, but increases the tendency for fly ash formation and sintering problems.

  19. Captive-bred neotropical birds diagnosed with Cryptosporidium Avian genotype III.

    Science.gov (United States)

    Silva Novaes, Ricardo; Pires, Marcus Sandes; Sudré, Adriana Pittella; Bergamo do Bomfim, Teresa Cristina

    2018-02-01

    Currently, there are only three valid species of Cryptosporidium infecting avian hosts, namely, Cryptosporidium meleagridis, Cryptosporidium baileyi, Cryptosporidium galli and Cryptosporidium avium in addition to 12 genotypes of unknown species status. The objectives of this study were to microscopically diagnose the presence of Cryptosporidium in birds from a commercial aviary located in Rio de Janeiro, Brazil; genotypically characterize species and/or genotypes of genus Cryptosporidum; and conduct sequencing and phylogenetic analyses to compare the obtained DNA sequences with those deposited in GenBank. A total of 85 fecal samples were collected from wild captive-bred birds: 48 of family Psittacidae and 37 of family Ramphastidae. Initially, a search for the presence of Cryptosporidium sp. oocysts was conducted using the centrifugal-flotation in saturated sugar solution technique, after that, the collected samples were analyzed microscopically. Cryptosporidium infections were only detected in 24.32% of samples belonging to the family Ramphastidae. DNA was extracted from positive samples and molecular diagnostics was applied targeting the 18S rRNA gene, followed by sequencing and phylogenetic analysis. The Cryptosporidium Avian genotype III was diagnosed in this study more closely related to the gastric species. This is the first record of Cryptosporidium Avian genotype III in order Piciformes and family Ramphastidae, where three host species (Ramphastus toco, Ramphastus tucanus, and Pteroglossus bailloni) were positive for the etiologic agent. Based on the molecular data obtained, these wild birds raised in captivity do not represent a source of human cryptosporidiosis, considering that Cryptosporidium Avian genotype III does not constitute a zoonosis. Copyright © 2017. Published by Elsevier B.V.

  20. Simulation of the fate of faecal bacteria in estuarine and coastal waters based on a fractionated sediment transport model

    Science.gov (United States)

    Yang, Chen; Liu, Ying

    2017-08-01

    A two-dimensional depth-integrated numerical model is refined in this paper to simulate the hydrodynamics, graded sediment transport process and the fate of faecal bacteria in estuarine and coastal waters. The sediment mixture is divided into several fractions according to the grain size. A bed evolution model is adopted to simulate the processes of the bed elevation change and sediment grain size sorting. The faecal bacteria transport equation includes enhanced source and sink terms to represent bacterial kinetic transformation and disappearance or reappearance due to sediment deposition or re-suspension. A novel partition ratio and dynamic decay rates of faecal bacteria are adopted in the numerical model. The model has been applied to the turbid water environment in the Bristol Channel and Severn estuary, UK. The predictions by the present model are compared with field data and those by non-fractionated model.

  1. Two-temperature LATE-PCR endpoint genotyping

    Directory of Open Access Journals (Sweden)

    Reis Arthur H

    2006-12-01

    Full Text Available Abstract Background In conventional PCR, total amplicon yield becomes independent of starting template number as amplification reaches plateau and varies significantly among replicate reactions. This paper describes a strategy for reconfiguring PCR so that the signal intensity of a single fluorescent detection probe after PCR thermal cycling reflects genomic composition. The resulting method corrects for product yield variations among replicate amplification reactions, permits resolution of homozygous and heterozygous genotypes based on endpoint fluorescence signal intensities, and readily identifies imbalanced allele ratios equivalent to those arising from gene/chromosomal duplications. Furthermore, the use of only a single colored probe for genotyping enhances the multiplex detection capacity of the assay. Results Two-Temperature LATE-PCR endpoint genotyping combines Linear-After-The-Exponential (LATE-PCR (an advanced form of asymmetric PCR that efficiently generates single-stranded DNA and mismatch-tolerant probes capable of detecting allele-specific targets at high temperature and total single-stranded amplicons at a lower temperature in the same reaction. The method is demonstrated here for genotyping single-nucleotide alleles of the human HEXA gene responsible for Tay-Sachs disease and for genotyping SNP alleles near the human p53 tumor suppressor gene. In each case, the final probe signals were normalized against total single-stranded DNA generated in the same reaction. Normalization reduces the coefficient of variation among replicates from 17.22% to as little as 2.78% and permits endpoint genotyping with >99.7% accuracy. These assays are robust because they are consistent over a wide range of input DNA concentrations and give the same results regardless of how many cycles of linear amplification have elapsed. The method is also sufficiently powerful to distinguish between samples with a 1:1 ratio of two alleles from samples comprised of

  2. High density FTA plates serve as efficient long-term sample storage for HLA genotyping.

    Science.gov (United States)

    Lange, V; Arndt, K; Schwarzelt, C; Boehme, I; Giani, A S; Schmidt, A H; Ehninger, G; Wassmuth, R

    2014-02-01

    Storage of dried blood spots (DBS) on high-density FTA(®) plates could constitute an appealing alternative to frozen storage. However, it remains controversial whether DBS are suitable for high-resolution sequencing of human leukocyte antigen (HLA) alleles. Therefore, we extracted DNA from DBS that had been stored for up to 4 years, using six different methods. We identified those extraction methods that recovered sufficient high-quality DNA for reliable high-resolution HLA sequencing. Further, we confirmed that frozen whole blood samples that had been stored for several years can be transferred to filter paper without compromising HLA genotyping upon extraction. Concluding, DNA derived from high-density FTA(®) plates is suitable for high-resolution HLA sequencing, provided that appropriate extraction protocols are employed. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  3. Helicobacter pylori in Vegetables and Salads: Genotyping and Antimicrobial Resistance Properties

    Directory of Open Access Journals (Sweden)

    Emad Yahaghi

    2014-01-01

    Full Text Available From a clinical and epidemiological perspective, it is important to know which genotypes and antibiotic resistance patterns are present in H. pylori strains isolated from salads and vegetables. Therefore, the present investigation was carried out to find this purpose. Three hundred eighty washed and unwashed vegetable samples and fifty commercial and traditional salad samples were collected from Isfahan, Iran. Samples were cultured and those found positive for H. pylori were analyzed using PCR. Antimicrobial susceptibility testing was performed using disk diffusion method. Seven out of 50 (14% salad and 52 out of 380 (13.68% vegetable samples harbored H. pylori. In addition, leek, lettuce, and cabbage were the most commonly contaminated samples (30%. The most prevalent virulence genes were oipA (86.44% and cagA (57.625. VacA s1a (37.28% and iceA1 (47.45% were the most prevalent genotypes. Forty different genotypic combinations were recognized. S1a/cagA+/iceA1/oipA+ (33.89%, s1a/cagA+/iceA2/oipA (30.50%, and m1a/cagA+/iceA1/oipA+ (28.81% were the most prevalent combined genotypes. Bacterial strains had the highest levels of resistance against metronidazole (77.96%, amoxicillin (67.79%, and ampicillin (61.01%. High similarity in the genotyping pattern of H. pylori among vegetable and salad samples and human specimens suggests that vegetable and salads may be the sources of the bacteria.

  4. Glycoprotein B genotyping in congenital/perinatal Cytomegalovirus infection in symptomatic infants.

    Science.gov (United States)

    Gandhoke, Inderjeet; Hussain, S Akhtar; Pasha, S T; Chauhan, L S; Khare, Shashi

    2013-07-01

    Molecular epidemiological studies on circulating strains of CMV in cogenital/perinatal infections have not been done earlier in this region. To study the glycoprotein B genotypes in babies with symptomatic congenital/perinatal CMV infection and to assess the possible influence of genotype on the outcome of the infection. Clinical samples (blood and urine) of symptomatic babies are sent to the Virology Department of NCDC, Delhi for the diagnosis of congenital infections. 375 clinical samples of infants (newborn - 6 months old) were included for the study. Serum samples were subjected to ELISA for detection of IgM antibodies against CMV. DNA isolation and amplification of CMV genomic DNA targeting gB gene fragment by nested PCR, was carried out in the samples. The amplified fragment including the cleavage site was subjected to RFLP using restriction enzymes Rsal and Hinf1. They were also verified by sequencing using Big Dye Terminator chemistry. 75 samples out of 375 tested were confirmed positive for CMV infection by serology and PCR. Both RFLP and sequencing of gB gene fragment showed that gB 1, 2 and 3 genotypes were in circulation. gB 3 was the most prevalent genotype in symptomatic infants. Hepatosplenomegaly was the most common feature in gB-3 genotype of CMV. gB2 congenital CMV infection was more commonly associated with long term sequelae.

  5. Percutaneous tibial nerve stimulation vs sacral nerve stimulation for faecal incontinence: a comparative case-matched study.

    Science.gov (United States)

    Al Asari, S; Meurette, G; Mantoo, S; Kubis, C; Wyart, V; Lehur, P-A

    2014-11-01

    The study assessed the initial experience with posterior tibial nerve stimulation (PTNS) for faecal incontinence and compared it with sacral nerve stimulation (SNS) performed in a single centre during the same timespan. A retrospective review of a prospectively collected database was conducted at the colorectal unit, University Hospital, Nantes, France, from May 2009 to December 2010. Seventy-eight patients diagnosed with chronic severe faecal incontinence underwent neurostimulation including PTNS in 21 and SNS in 57. The main outcome measures were faecal incontinence (Wexner score) and quality of life (Fecal Incontinence Quality of Life, FIQL) scores in a short-term follow-up. No significant differences were observed in patients' characteristics. Of 57 patients having SNS, 18 (32%) failed peripheral nerve evaluation and 39 (68%) received a permanent implant. Two (5%) developed a wound infection. No adverse effects were recorded in the PTNS group. There was no significant difference in the mean Wexner and FIQL scores between patients having PTNS and SNS at 6 (P = 0.39 and 0.09) and 12 months (P = 0.79 and 0.37). A 50% or more improvement in Wexner score was seen at 6 and 12 months in 47% and 30% of PTNS patients and in 50% and 58% of SNS patients with no significant difference between the groups. Posterior tibial nerve stimulation is a valid method of treating faecal incontinence in the short term when conservative treatment has failed. It is easier, simpler, cheaper and less invasive than SNS with a similar short-term outcome. Colorectal Disease © 2014 The Association of Coloproctology of Great Britain and Ireland.

  6. New perspectives to the enterotoxigenic E. coli F4 porcine infection model: Susceptibility genotypes in relation to performance, diarrhoea and bacterial shedding.

    Science.gov (United States)

    Roubos-van den Hil, Petra J; Litjens, Ralph; Oudshoorn, Anna-Katharina; Resink, Jan Willem; Smits, Coen H M

    2017-04-01

    Enterotoxigenic E. coli (ETEC), causing post-weaning diarrhoea, is a major problem in weaned piglets. Individual animal responses to ETEC infection show high variability in animal experiments. Two studies were designed to optimize the ETEC F4ac infection model in piglets by combining the genotype susceptibility with performance, diarrhoea incidence and bacterial shedding. The studies were performed with respectively 120 and 80 male piglets that were tested for susceptibility or resistance towards ETEC O149:F4ac by a DNA marker based test. Three different genotypes were observed; resistant (RR), susceptible heterozygote (RS) and susceptible homozygote (SS). Piglets, were orally infected with an inoculum suspension (containing 1.5E8 CFU/ml ETEC F4ac) at day 0, 1 and 2 of the study. Performance, diarrhoea incidence and bacterial shedding were followed for 21days. In the first week after challenge a difference in average daily gain was observed between resistant and susceptible piglets in both studies. For the complete study period no significant differences were observed. Diarrhoea incidence was significantly higher in susceptible pigs compared to the resistant pigs in the first week after challenge. Bacterial shedding was much higher in the susceptible pigs and ETEC excretion lasted longer. ETEC was hardly detected in the faecal material of the resistant pigs. In conclusion, susceptible pigs showed higher diarrhoea incidence and higher numbers of faecal ETEC shedding in the first week after challenge compared to resistant pigs. The DNA marker based test can be used to select pigs that are susceptible for ETEC for inclusion in ETEC infection model, resulting in less animals needed to perform infection studies. Copyright © 2016 Elsevier B.V. All rights reserved.

  7. Human papillomavirus genotype distribution in Madrid and correlation with cytological data.

    Science.gov (United States)

    Martín, Paloma; Kilany, Linah; García, Diego; López-García, Ana M; Martín-Azaña, Ma José; Abraira, Victor; Bellas, Carmen

    2011-11-15

    Cervical cancer is the second most common cancer in women worldwide. Infection with certain human papillomavirus (HPV) genotypes is the most important risk factor associated with cervical cancer. This study analysed the distribution of type-specific HPV infection among women with normal and abnormal cytology, to assess the potential benefit of prophylaxis with anti-HPV vaccines. Cervical samples of 2,461 women (median age 34 years; range 15-75) from the centre of Spain were tested for HPV DNA. These included 1,656 samples with normal cytology (NC), 336 with atypical squamous cells of undetermined significance (ASCUS), 387 low-grade squamous intraepithelial lesions (LSILs), and 82 high-grade squamous intraepithelial lesions (HSILs). HPV detection and genotyping were performed by PCR using 5'-biotinylated MY09/11 consensus primers, and reverse dot blot hybridisation. HPV infection was detected in 1,062 women (43.2%). Out of these, 334 (31%) samples had normal cytology and 728 (69%) showed some cytological abnormality: 284 (27%) ASCUS, 365 (34%) LSILs, and 79 (8%) HSILs. The most common genotype found was HPV 16 (28%) with the following distribution: 21% in NC samples, 31% in ASCUS, 26% in LSILs, and 51% in HSILs. HPV 53 was the second most frequent (16%): 16% in NC, 16% in ASCUS, 19% in LSILs, and 5% in HSILs. The third genotype was HPV 31 (12%): 10% in NC, 11% in ASCUS, 14% in LSILs, and 11% in HSILs. Co-infections were found in 366 samples (34%). In 25%, 36%, 45% and 20% of samples with NC, ASCUS, LSIL and HSIL, respectively, more than one genotype was found. HPV 16 was the most frequent genotype in our area, followed by HPV 53 and 31, with a low prevalence of HPV 18 even in HSILs. The frequency of genotypes 16, 52 and 58 increased significantly from ASCUS to HSILs. Although a vaccine against HPV 16 and 18 could theoretically prevent approximately 50% of HSILs, genotypes not covered by the vaccine are frequent in our population. Knowledge of the epidemiological

  8. Human papillomavirus genotype distribution in Madrid and correlation with cytological data

    Directory of Open Access Journals (Sweden)

    Martín Paloma

    2011-11-01

    Full Text Available Abstract Background Cervical cancer is the second most common cancer in women worldwide. Infection with certain human papillomavirus (HPV genotypes is the most important risk factor associated with cervical cancer. This study analysed the distribution of type-specific HPV infection among women with normal and abnormal cytology, to assess the potential benefit of prophylaxis with anti-HPV vaccines. Methods Cervical samples of 2,461 women (median age 34 years; range 15-75 from the centre of Spain were tested for HPV DNA. These included 1,656 samples with normal cytology (NC, 336 with atypical squamous cells of undetermined significance (ASCUS, 387 low-grade squamous intraepithelial lesions (LSILs, and 82 high-grade squamous intraepithelial lesions (HSILs. HPV detection and genotyping were performed by PCR using 5'-biotinylated MY09/11 consensus primers, and reverse dot blot hybridisation. Results HPV infection was detected in 1,062 women (43.2%. Out of these, 334 (31% samples had normal cytology and 728 (69% showed some cytological abnormality: 284 (27% ASCUS, 365 (34% LSILs, and 79 (8% HSILs. The most common genotype found was HPV 16 (28% with the following distribution: 21% in NC samples, 31% in ASCUS, 26% in LSILs, and 51% in HSILs. HPV 53 was the second most frequent (16%: 16% in NC, 16% in ASCUS, 19% in LSILs, and 5% in HSILs. The third genotype was HPV 31 (12%: 10% in NC, 11% in ASCUS, 14% in LSILs, and 11% in HSILs. Co-infections were found in 366 samples (34%. In 25%, 36%, 45% and 20% of samples with NC, ASCUS, LSIL and HSIL, respectively, more than one genotype was found. Conclusions HPV 16 was the most frequent genotype in our area, followed by HPV 53 and 31, with a low prevalence of HPV 18 even in HSILs. The frequency of genotypes 16, 52 and 58 increased significantly from ASCUS to HSILs. Although a vaccine against HPV 16 and 18 could theoretically prevent approximately 50% of HSILs, genotypes not covered by the vaccine are frequent in

  9. Identification of novel Coxiella burnetii genotypes from Ethiopian ticks.

    Directory of Open Access Journals (Sweden)

    Kinga M Sulyok

    Full Text Available BACKGROUND: Coxiella burnetii, the etiologic agent of Q fever, is a highly infectious zoonotic bacterium. Genetic information about the strains of this worldwide distributed agent circulating on the African continent is limited. The aim of the present study was the genetic characterization of C. burnetii DNA samples detected in ticks collected from Ethiopian cattle and their comparison with other genotypes found previously in other parts of the world. METHODOLOGY/PRINCIPAL FINDINGS: A total of 296 tick samples were screened by real-time PCR targeting the IS1111 region of C. burnetii genome and from the 32 positive samples, 8 cases with sufficient C. burnetii DNA load (Amblyomma cohaerens, n = 6; A. variegatum, n = 2 were characterized by multispacer sequence typing (MST and multiple-locus variable-number tandem repeat analysis (MLVA. One novel sequence type (ST, the proposed ST52, was identified by MST. The MLVA-6 discriminated the proposed ST52 into two newly identified MLVA genotypes: type 24 or AH was detected in both Amblyomma species while type 26 or AI was found only in A. cohaerens. CONCLUSIONS/SIGNIFICANCE: Both the MST and MLVA genotypes of the present work are closely related to previously described genotypes found primarily in cattle samples from different parts of the globe. This finding is congruent with the source hosts of the analyzed Ethiopian ticks, as these were also collected from cattle. The present study provides genotype information of C. burnetii from this seldom studied East-African region as well as further evidence for the presumed host-specific adaptation of this agent.

  10. Genotyping of Leptospira directly in urine samples of cattle demonstrates a diversity of species and strains in Brazil.

    Science.gov (United States)

    Hamond, C; Pestana, C P; Medeiros, M A; Lilenbaum, W

    2016-01-01

    The aim of this study was to identify Leptospira in urine samples of cattle by direct sequencing of the secY gene. The validity of this approach was assessed using ten Leptospira strains obtained from cattle in Brazil and 77 DNA samples previously extracted from cattle urine, that were positive by PCR for the genus-specific lipL32 gene of Leptospira. Direct sequencing identified 24 (31·1%) interpretable secY sequences and these were identical to those obtained from direct DNA sequencing of the urine samples from which they were recovered. Phylogenetic analyses identified four species: L. interrogans, L. borgpetersenii, L. noguchii, and L. santarosai with the most prevalent genotypes being associated with L. borgpetersenii. While direct sequencing cannot, as yet, replace culturing of leptospires, it is a valid additional tool for epidemiological studies. An unexpected finding from this study was the genetic diversity of Leptospira infecting Brazilian cattle.

  11. Effect of chito-oligosaccharides over human faecal microbiota during fermentation in batch cultures.

    Science.gov (United States)

    Mateos-Aparicio, Inmaculada; Mengíbar, Marian; Heras, Angeles

    2016-02-10

    Chitosan with high number of deacetylated units, its reacetylated derivative and COS obtained through an enzymatic treatment with chitosanase were tested in pH controlled batch cultures to investigate the ability of the human faecal microbiota to utilise them. Chitosan derivatives with high number of deacetylated units decreased the bacterial populations: Bifidobacterium spp., Eubacterium rectale/Clostridium coccoides, C. Histolyticum and Bacteroides/Prevotella. On the other hand, chitosan derivatives with high content of acetylated residues maintained the tested bacterial groups and could increase Lactobacillus/Enterococcus. Regarding short chain fatty acids (SCFA), only low Mw COS increased the production in similar levels than fructo-oligossacharides (FOS). The acetylated chitosans and their COS do not appear as potential prebiotics but did not affect negatively the faecal microbiota, while derivatives with high number of deacetylated units could induce a colonic microbiota imbalance. Copyright © 2015 Elsevier Ltd. All rights reserved.

  12. Generic Modelling of Faecal Indicator Organism Concentrations in the UK

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    Carl M. Stapleton

    2011-06-01

    Full Text Available To meet European Water Framework Directive requirements, data are needed on faecal indicator organism (FIO concentrations in rivers to enable the more heavily polluted to be targeted for remedial action. Due to the paucity of FIO data for the UK, especially under high-flow hydrograph event conditions, there is an urgent need by the policy community for generic models that can accurately predict FIO concentrations, thus informing integrated catchment management programmes. This paper reports the development of regression models to predict base- and high-flow faecal coliform (FC and enterococci (EN concentrations for 153 monitoring points across 14 UK catchments, using land cover, population (human and livestock density and other variables that may affect FIO source strength, transport and die-off. Statistically significant models were developed for both FC and EN, with greater explained variance achieved in the high-flow models. Both land cover and, in particular, population variables are significant predictors of FIO concentrations, with r2 maxima for EN of 0.571 and 0.624, respectively. It is argued that the resulting models can be applied, with confidence, to other UK catchments, both to predict FIO concentrations in unmonitored watercourses and evaluate the likely impact of different land use/stocking level and human population change scenarios.

  13. Human papillomavirus genotyping by multiplex pyrosequencing in ...

    Indian Academy of Sciences (India)

    PRAKASH KUMAR G

    malignant cervical samples ... low- and high-risk HPV genotypes without identifying ... Since these samples were not from “healthy .... major capsid protein, any variation in its coding sequence is .... worldwide: a meta-analysis; Br. J. Cancer 88 63–73.

  14. High prevalence of Human Parechovirus (HPeV) genotypes in the Amsterdam region and the identification of specific HPeV variants by direct genotyping of stool samples

    NARCIS (Netherlands)

    Benschop, K.; Thomas, X.; Serpenti, C.; Molenkamp, R.; Wolthers, K.

    2008-01-01

    Human Parechoviruses (HPeV) are widespread pathogens belonging to the Picornavirus family. Six genotypes are known which have predominantly been isolated from children. Data on prevalence of HPeV genotypes are generally based on cell culture, which may underestimate the prevalence of certain HPeV

  15. Modelling anaerobic digestion of concentrated black water and faecal matter in accumulation system

    NARCIS (Netherlands)

    Elmitwalli, T.; Zeeman, G.; Otterpohl, R.

    2011-01-01

    A dynamic mathematical model based on anaerobic digestion model no. 1 (ADM1) was developed for accumulation (AC) system treating concentrated black water and faecal matter at different temperatures. The AC system was investigated for the treatment of waste(water) produced from the following systems:

  16. Heterogeneity and compartmentalization of Pneumocystis carinii f. sp. hominis genotypes in autopsy lungs

    DEFF Research Database (Denmark)

    Helweg-Larsen, J; Lundgren, Bettina; Lundgren, Jens Dilling

    2001-01-01

    The extent and importance of genotype heterogeneity of Pneumocystis carinii f. sp. hominis within lungs have not previously been investigated. Two hundred forty PCR clones obtained from respiratory specimens and lung segments from three patients with fatal P. carinii pneumonia were investigated....... Not all genotypes present in the lungs at autopsy were detected in the diagnostic respiratory samples. Compartmentalization of specific ITS and mtLSU rRNA sequence types was observed in different lung segments. In conclusion, the interpretation of genotype data and in particular ITS sequence types...... in the assessment of epidemiological questions should be cautious since genotyping done on respiratory samples cannot a priori be assumed to represent all genotypes present within the lung....

  17. Thermophilic Campylobacter spp. in turkey samples: evaluation of two automated enzyme immunoassays and conventional microbiological techniques

    DEFF Research Database (Denmark)

    Borck, Birgitte; Stryhn, H.; Ersboll, A.K.

    2002-01-01

    Aims: To determine the sensitivity and specificity of two automated enzyme immunoassays (EIA), EiaFoss and Minividas, and a conventional microbiological culture technique for detecting thermophilic Campylobacter spp. in turkey samples. Methods and Results: A total of 286 samples (faecal, meat...

  18. Distribution of hepatitis C virus genotypes among injecting drug users in Lebanon

    Directory of Open Access Journals (Sweden)

    Shamra Sarah

    2010-05-01

    Full Text Available Abstract Background The aim of this study is to determine the prevalence of anti-HCV among injecting drug users (IDUs in Lebanon, to establish the current prevalence of HCV genotypes in this population and to determine whether demographic characteristics and behavioral variables differ between participants who were HCV-RNA positive and those who were HCV-RNA negative or between the different genotypes. Participants were recruited using respondent-driven sampling method. The blood samples were collected as dried blood spots and then eluted to be tested for HCV, HBV and HIV by ELISA. Anti-HCV positive samples were subjected to RNA extraction followed by qualitative detection and genotyping. Results Among 106 IDUs, 56 (52.8% were anti-HCV-positive. The two groups did not differ in terms of age, marital status, and nationality. As for the behavioral variable, there was a trend of increased risky behaviors among the HCV-RNA positive group as compared to the HCV-RNA negative group but none of the variables reached statistical significance. Half (50% of the 56 anti-HCV-positive were HCV-RNA positive. Genotype 3 was the predominant one (57.1% followed by genotype 1 (21% and genotype 4 (18%. Conclusions The predominance of genotype 3 seems to be the predominant genotype among IDUs in Lebanon, a situation similar to that among IDUs in Western Europe. This study provides a base-line against possible future radical epidemiological variant that might occur in IDUs.

  19. Faecal microbiota of healthy adults in south India: Comparison of a tribal & a rural population

    Directory of Open Access Journals (Sweden)

    Balamurugan Ramadass

    2017-01-01

    Interpretation & conclusions: Phylum Firmicutes and genus Clostridium constituted the bulk of the faecal microbiota, while significant differences in composition between the groups were probably due to differences in diet and lifestyle.

  20. Discrepancy between Hepatitis C Virus Genotypes and NS4-Based Serotypes: Association with Their Subgenomic Sequences

    Directory of Open Access Journals (Sweden)

    Nan Nwe Win

    2017-01-01

    Full Text Available Determination of hepatitis C virus (HCV genotypes plays an important role in the direct-acting agent era. Discrepancies between HCV genotyping and serotyping assays are occasionally observed. Eighteen samples with discrepant results between genotyping and serotyping methods were analyzed. HCV serotyping and genotyping were based on the HCV nonstructural 4 (NS4 region and 5′-untranslated region (5′-UTR, respectively. HCV core and NS4 regions were chosen to be sequenced and were compared with the genotyping and serotyping results. Deep sequencing was also performed for the corresponding HCV NS4 regions. Seventeen out of 18 discrepant samples could be sequenced by the Sanger method. Both HCV core and NS4 sequences were concordant with that of genotyping in the 5′-UTR in all 17 samples. In cloning analysis of the HCV NS4 region, there were several amino acid variations, but each sequence was much closer to the peptide with the same genotype. Deep sequencing revealed that minor clones with different subgenotypes existed in two of the 17 samples. Genotyping by genome amplification showed high consistency, while several false reactions were detected by serotyping. The deep sequencing method also provides accurate genotyping results and may be useful for analyzing discrepant cases. HCV genotyping should be correctly determined before antiviral treatment.

  1. Exhausted implanted pulse generator in sacral nerve stimulation for faecal incontinence: What next in daily practice for patients?

    Science.gov (United States)

    Duchalais, Emilie; Meurette, Guillaume; Perrot, Bastien; Wyart, Vincent; Kubis, Caroline; Lehur, Paul-Antoine

    2016-02-01

    The efficacy of sacral nerve stimulation in faecal incontinence relies on an implanted pulse generator known to have a limited lifespan. The long-term use of sacral nerve stimulation raises concerns about the true lifespan of generators. The aim of the study was to assess the lifespan of sacral nerve stimulation implanted pulse generators in daily practice, and the outcome of exhausted generator replacement, in faecal incontinent patients. Faecal incontinent patients with pulse generators (Medtronic Interstim™ or InterstimII™) implanted in a single centre from 2001 to 2014 were prospectively followed up. Generator lifespan was measured according to the Kaplan-Meier method. Patients with a generator explanted/turned off before exhaustion were excluded. Morbidity of exhausted generator replacement and the outcome (Cleveland Clinic Florida Faecal Incontinence (CCF-FI) and Faecal Incontinence Quality of Life (FIQL) scores) were recorded. Of 135 patients with an implanted pulse generator, 112 (InterstimII 66) were included. Mean follow-up was 4.9 ± 2.8 years. The generator reached exhaustion in 29 (26%) cases. Overall median lifespan of an implanted pulse generator was approximately 9 years (95% CI 8-9.2). Interstim and InterstimII 25th percentile lifespan was 7.2 (CI 6.4-8.3) and 5 (CI 4-not reached) years, respectively. After exhaustion, generators were replaced, left in place or explanted in 23, 2 and 4 patients, respectively. Generator replacement was virtually uneventful. CCF-FI/FIQL scores remained unchanged after generator replacement (CCF-FI 8 ± 2 vs 7 ± 3; FIQL 3 ± 0.6 vs 3 ± 0.5; p = ns). In this study, the implanted pulse generator observed median lifespan was 9 years. After exhaustion, generators were safely and efficiently replaced. The study also gives insight into long-term needs and costs of sacral nerve stimulation (SNS) therapy.

  2. Faecal incontinence after chemoradiotherapy in anal cancer survivors: Long-term results of a national cohort

    International Nuclear Information System (INIS)

    Bentzen, Anne Gry; Guren, Marianne G.; Vonen, Barthold; Wanderås, Eva H.; Frykholm, Gunilla; Wilsgaard, Tom; Dahl, Olav; Balteskard, Lise

    2013-01-01

    Purpose: To examine the prevalence and severity of faecal incontinence amongst anal cancer survivors after chemoradiotherapy. Material and methods: Anal cancer survivors from a complete, unselected, national cohort, minimum 2-years follow-up, were invited to a cross-sectional study. The St. Mark’s incontinence score was used to evaluate occurrence and degree of faecal incontinence the last four weeks. The results were compared to age- and sex-matched volunteers from the general population. Results: Of 199 invited survivors and 1211volunteers, 66% and 21%, respectively, signed informed consent. The survivors had significantly higher St. Mark’s score than the volunteers (mean 9.7 vs. 1.1, p < 0.001). Incontinence of stool of any degree was reported by 43% vs. 5% (OR 4.0, CI 2.73–6.01), and urgency was reported by 64% vs. 6% (OR 6.6, CI 4.38–9.90) of the survivors and volunteers, respectively. Only 29% of those with leakage of liquid stool used constipating drugs. Survivors of locally advanced tumours had a higher incontinence score (p < 0.01). Conclusions: Moderate to severe faecal incontinence is common amongst anal cancer survivors. Post-treatment follow-up should include the evaluation of continence, and incontinent survivors should be offered better symptom management and multidisciplinary approach if simple measures are insufficient

  3. Comparison of cobas HCV GT against Versant HCV Genotype 2.0 (LiPA) with confirmation by Sanger sequencing.

    Science.gov (United States)

    Yusrina, Falah; Chua, Cui Wen; Lee, Chun Kiat; Chiu, Lily; Png, Tracy Si-Yu; Khoo, Mui Joo; Yan, Gabriel; Lee, Guan Huei; Yan, Benedict; Lee, Hong Kai

    2018-05-01

    Correct identification of infecting hepatitis C virus (HCV) genotype is helpful for targeted antiviral therapy. Here, we compared the HCV genotyping performance of the cobas HCV GT assay against the Versant HCV Genotype 2.0 (LiPA) assay, using 97 archived serum samples. In the event of discrepant or indeterminate results produced by either assay, the core and NS5B regions were sequenced. Of the 97 samples tested by the cobas, 25 (26%) were deemed indeterminate. Sequencing analyses confirmed 21 (84%) of the 25 samples as genotype 6 viruses with either subtype 6m, 6n, 6v, 6xa, or unknown subtype. Of the 97 samples tested by the LiPA, thirteen (13%) were deemed indeterminate. Seven (7%) were assigned with genotype 1, with unavailable/inconclusive results from the core region of the LiPA. Notably, the 7 samples were later found to be either genotype 3 or 6 by sequencing analyses. Moreover, 1 sample by the LiPA was assigned as genotypes 4 (cobas: indeterminate) but were later found to be genotype 3 by sequencing analyses, highlighting its limitation in assigning the correct genotype. The cobas showed similar or slightly higher accuracy (100%; 95% CI 94-100%) compared to the LiPA (99%; 95% CI 92-100%). Twenty-six percent of the 97 samples tested by the cobas had indeterminate results, mainly due to its limitation in identifying genotype 6 other than subtypes 6a and 6b. This presents a significant assay limitation in Southeast Asia, where genotype 6 infection is highly prevalent. Copyright © 2018 Elsevier B.V. All rights reserved.

  4. Validation of the DNATyper™15 PCR Genotyping System for Forensic Application

    Directory of Open Access Journals (Sweden)

    Jian Ye

    2015-01-01

    Full Text Available We describe the optimization and validation of the DNATyper™15 multiplex polymerase chain reaction (PCR genotyping system for autosomal short tandem repeat (STR amplification at 14 autosomal loci (D6S1043, D21S11, D7S820, CSF1PO, D2S1338, D3S1358, D13S317, D8S1179, D16S539, Penta E, D5S818, vWA, D18S51, and FGA and  amelogenin, a sex-determining locus. Several DNATyper™15 assay variables were optimized, including hot start Taq polymerase concentration, Taq polymerase activation time, magnesium concentration, primer concentration, annealing temperature, reaction volume, and cycle number. The performance of the assay was validated with respect to species specificity, sensitivity to template concentration, stability, accuracy, influence of the DNA extraction methods, and the ability to genotype the mixture samples. The performance of the DNATyper™15 system on casework samples was compared with that of two widely used STR amplification kits, Identifiler™ (Applied Biosystems, Carlsbad, CA, USA and PowerPlex 16 ® (Promega, Madison, WI, USA. The conditions for PCR-based DNATyper™15 genotyping were optimized. Contamination from forensically relevant nonhuman DNA was not found to impact genotyping results, and full profiles were generated for all the reactions containing ≥ 0.125 ng of DNA template. No significant difference in performance was observed even after the DNATyper™15 assay components were subjected to 20 freeze-thaw cycles. The performances of DNATyper™15, Identifiler™, and PowerPlex 16 ® were comparable in terms of sensitivity and the ability to genotype the mixed samples and case-type samples, with the assays giving the same genotyping results for all the shared loci. The DNA extraction methods did not affect the performance of any of the systems. Our results demonstrate that the DNATyper™15 system is suitable for genotyping in both forensic DNA database work and case-type samples.

  5. Reset of a critically disturbed microbial ecosystem: faecal transplant in recurrent Clostridium difficile infection

    NARCIS (Netherlands)

    Fuentes, Susana; van Nood, Els; Tims, Sebastian; Heikamp-de Jong, Ineke; ter Braak, Cajo J. F.; Keller, Josbert J.; Zoetendal, Erwin G.; de Vos, Willem M.

    2014-01-01

    Recurrent Clostridium difficile infection (CDI) can be effectively treated by infusion of a healthy donor faeces suspension. However, it is unclear what factors determine treatment efficacy. By using a phylogenetic microarray platform, we assessed composition, diversity and dynamics of faecal

  6. Filter Paper-based Nucleic Acid Storage in High-throughput Solid Tumor Genotyping.

    Science.gov (United States)

    Stachler, Matthew; Jia, Yonghui; Sharaf, Nematullah; Wade, Jacqueline; Longtine, Janina; Garcia, Elizabeth; Sholl, Lynette M

    2015-01-01

    Molecular testing of tumors from formalin-fixed paraffin-embedded (FFPE) tissue blocks is central to clinical practice; however, it requires histology support and increases test turnaround time. Prospective fresh frozen tissue collection requires special handling, additional storage space, and may not be feasible for small specimens. Filter paper-based collection of tumor DNA reduces the need for histology support, requires little storage space, and preserves high-quality nucleic acid. We investigated the performance of tumor smears on filter paper in solid tumor genotyping, as compared with paired FFPE samples. Whatman FTA Micro Card (FTA preps) smears were prepared from 21 fresh tumor samples. A corresponding cytology smear was used to assess tumor cellularity and necrosis. DNA was isolated from FTA preps and FFPE core samples using automated methods and quantified using SYBR green dsDNA detection. Samples were genotyped for 471 mutations on a mass spectrophotometry-based platform (Sequenom). DNA concentrations from FTA preps and FFPE correlated for untreated carcinomas but not for mesenchymal tumors (Spearman σ=0.39 and σ=-0.1, respectively). Average DNA concentrations were lower from FTA preps as compared with FFPE, but DNA quality was higher with less fragmentation. Seventy-six percent of FTA preps and 86% of FFPE samples generated adequate DNA for genotyping. FTA preps tended to perform poorly for collection of DNA from pretreated carcinomas and mesenchymal neoplasms. Of the 16 paired DNA samples that were genotyped, 15 (94%) gave entirely concordant results. Filter paper-based sample preservation is a feasible alternative to FFPE for use in automated, high-throughput genotyping of carcinomas.

  7. Dientamoeba fragilis is more prevalent than Giardia duodenalis in children and adults attending a day care centre in Central Italy

    Directory of Open Access Journals (Sweden)

    Crotti D.

    2005-06-01

    Full Text Available Giardia duodenalis is a well recognised enteropathogen, while Dientamoeba fragilis is rarely detected and consequently it is not recognised as an important human pathogen. In 2002-2003, a survey has been carried out on enteroparasites in faecal samples of outpatients attending a day care centre in the town of Perugia (Central Italy. To improve the detection level, at least three samples from each patient were collected at different days and within two hours from defecation. The coproparasitological examination has been carried out by direct microscopic examination, faecal concentration, and Giemsa and modified Ziehl-Nielsen stainings of faecal smears. The genotypes of Giardia duodenalis isolates were determined by PCR of the β-giardin gene. Of 1,989 enrolled people (966 children, 1,023 adults, 165 persons (8.3%; 153 adults, 15.0%; 12 children, 1.2%, were positive for parasites, but only 112 adults (73.2% of those infected and eight children (66.7% of those infected harboured D. fragilis and G. duodenalis. Both the Assemblages A and B were detected in 18 G. duodenalis isolates examined at the β-giardin gene. The higher prevalence of D. fragilis infections than that of G. duodenalis is probably related to the method used, a procedure, which is rarely followed in laboratories for the diagnosis of enteric parasites. These epidemiological data suggest that when faecal samples are examined after a period of time and without Giemsa staining, most D. fragilis infections goes undetected.

  8. Genotyping of Trypanosoma cruzi Sublineage in Human Samples from a North-East Argentina Area by Hybridization with DNA Probes and Specific Polymerase Chain Reaction (PCR)

    Science.gov (United States)

    Diez, Cristina; Lorenz, Virginia; Ortiz, Silvia; Gonzalez, Verónica; Racca, Andrea; Bontempi, Iván; Manattini, Silvia; Solari, Aldo; Marcipar, Iván

    2010-01-01

    We have evaluated blood samples of chronic and congenital Trypanosoma cruzi-infected patients from the city of Reconquista located in the northeast of Argentina where no information was previously obtained about the genotype of infecting parasites. Fourteen samples of congenital and 19 chronical patients were analyzed by hybridization with DNA probes of minicircle hypervariable regions (mHVR). In congenital patients, 50% had single infections with TcIId, 7% single infections with TcIIe, 29% mixed infections with TcIId/e, and 7% had mixed infections with TcIId/b and 7% TcIId/b, respectively. In Chronical patients, 52% had single infections with TcIId, 11% single infections with TcIIe, 26% had mixed infections with TcIId/e, and 11% had non-identified genotypes. With these samples, we evaluated the minicircle lineage-specific polymerase chain reaction assay (MLS-PCR), which involves a nested PCR to HVR minicircle sequences and we found a correlation with hybridization probes of 96.4% for TcIId and 54.8% for TcIIe. PMID:20064998

  9. Loss of deuterium in faecal solids and by sequestration in reindeer: effect on doubly labelled water studies

    Directory of Open Access Journals (Sweden)

    Geir Gotaas

    2000-03-01

    Full Text Available An underlying assumption when estimating total energy expenditure (TEE using doubly labelled water (DLW is that the injected isotopes (lsO and 2H leave the body only in the form of CO, and H20. However, both isotopes have additional routes of loss. We quantified the loss of 2H (i attached to faecal solids and (ii by sequestration into newly synthesised fat in reindeer (Rangifer tarandus tarandus. Estimates of the errors caused by these processes were applied to data from DLW studies with reindeer in summer and in winter. Given the net rate of faecal dry matter output and lipid synthesis in the present study, ignoring both sources of error caused the TEE of reindeer to be underestimated by approximately 5% in winter and approximately 9% in summer. The separate effect of each source of error was evaluated in summer. If ignored, loss of 2H through sequestration alone caused TEE to be underestimated by approximately 3.7%. Similarly, if ignored, loss of 2H attached to faecal solids alone caused TEE to be underestimated by approximately 5.9%.

  10. Detection of Giardia intestinalis in water samples collected from natural water reservoirs and wells in northern and north-eastern Poland using LAMP, real-time PCR and nested PCR.

    Science.gov (United States)

    Lass, Anna; Szostakowska, Beata; Korzeniewski, Krzysztof; Karanis, Panagiotis

    2017-10-01

    Giardia intestinalis is a protozoan parasite, transmitted to humans and animals by the faecal-oral route, mainly through contaminated water and food. Knowledge about the distribution of this parasite in surface water in Poland is fragmentary and incomplete. Accordingly, 36 environmental water samples taken from surface water reservoirs and wells were collected in Pomerania and Warmia-Masuria provinces, Poland. The 50 L samples were filtered and subsequently analysed with three molecular detection methods: loop-mediated isothermal amplification (LAMP), real-time polymerase chain reaction (real-time PCR) and nested PCR. Of the samples examined, Giardia DNA was found in 15 (42%) samples with the use of LAMP; in 12 (33%) of these samples, Giardia DNA from this parasite was also detected using real-time PCR; and in 9 (25%) using nested PCR. Sequencing of selected positive samples confirmed that the PCR products were fragments of the Giardia intestinalis small subunit rRNA gene. Genotyping using multiplex real-time PCR indicated the presence of assemblages A and B, with the latter predominating. The results indicate that surface water in Poland, as well as water taken from surface wells, may be a source of Giardia strains which are potentially pathogenic for humans. It was also demonstrated that LAMP assay is more sensitive than the other two molecular assays.

  11. High Risk Human Papilloma Virus Genotypes in Kurdistan Region in Patients with Vaginal Discharge.

    Science.gov (United States)

    Hussein, Nawfal R; Balatay, Amer A; Assafi, Mahde S; AlMufty, Tamara Abdulezel

    2016-01-01

    The human papilloma virus (HPV) is considered as the major risk factor for the development of cervical cancer. This virus is of different genotypes and generally can be classified into high and low risk types. To determine the rate of high risk HPV genotypes in women with vaginal discharge and lower abdominal pain in Kurdistan region, Iraq. Cervical swabs were taken from 104 women. DNA was extracted and the polymerase chain reaction (PCR) technique was used to determine the presence of high risk genotypes. It was found that 13/104 (12.5%) of the samples were positive for high risk HPV genotypes. Amongst those who were positive, 4/13 (30.7%) were typed as genotype 16 and 7/13 (53.8%) showed mixed genotyping. On the other hand, genotypes 53 and 56 were found in only one sample each. High risk HPV genotypes are not uncommon and further community based study is needed to determine the prevalence of HPV and its genotypes and plan for prevention of infection.

  12. A synbiotic mixture of scGOS/lcFOS and Bifidobacterium breve M-16V increases faecal Bifidobacterium in healthy young children.

    Science.gov (United States)

    Kosuwon, P; Lao-Araya, M; Uthaisangsook, S; Lay, C; Bindels, J; Knol, J; Chatchatee, P

    2018-04-10

    Little is known about the impact of nutrition on toddler gut microbiota. The plasticity of the toddler gut microbiota indicates that nutritional modulation beyond infancy could potentially impact its maturation. The objective of this study was to determine the effect of consuming Young Child Formula (YCF) supplemented with short chain galactooligosaccharides and long chain fructooligosaccharides (scGOS/lcFOS, ratio 9:1) and Bifidobacterium breve M-16V on the development of the faecal microbiota in healthy toddlers. A cohort of 129 Thai children aged 1-3 years were included in a randomised controlled clinical study. The children were assigned to receive either YCF with 0.95 g/100 ml of scGOS/lcFOS and 1.8×10 7 cfu/g of B. breve M-16V (Active-YCF) or Control-YCF for 12 weeks. The composition and metabolic activity of the faecal microbiota, and the level of secretory immunoglobulin A were determined in the stool samples. The consumption of Active-YCF increased the proportion of Bifidobacterium (mean 27.3% at baseline to 33.3%, at week 12, P=0.012) with a difference in change from baseline at week 12 between the Active and Control of 7.48% (P=0.030). The consumption of Active-YCF was accompanied with a more acidic intestinal milieu compared to the Control-YCF. The pH value decreased statistically significantly in the Active-YCF group from a median of 7.05 at baseline to 6.79 at week 12 (Pbreve M-16V positively influences the development of the faecal microbiota in healthy toddlers by supporting higher levels of Bifidobacterium. The synbiotic supplementation is also accompanied with a more acidic intestinal milieu and softer stools.

  13. Water potential changes in faecal matter and Escherichia coli survival.

    Science.gov (United States)

    Garfield, L M; Walker, M J

    2008-10-01

    This study investigated the influence of a range of evaporation rates (2.0, 5.3 and 7.4 mm day(-1)) on degradation of E. coli (ATCC Strain 25922) inoculated in canine faeces. Experiments were carried out in an environmental chamber and a first order exponential decay function (Chick's Law) was used to estimate degradation rates. We estimated die-off coefficients using linear regression. Die-off rates were -0.07, -0.22 and -0.23 h(-1), respectively, for evaporation rates of 2.0, 5.3 and 7.4 mm day(-1) (P = 0.000+, for each model). Nearly complete die-off was found within 15-60 h (7.4-2.0 mm day(-1) evaporation rates), which corresponds with a water potential of approximately -22.4 MPa. This study indicates that canine faeces need not be desiccated to achieve complete loss of indicator organisms. Water potential, which is a combination of osmotic and matric potential, is a key stress that increases as evaporation removes water from the faecal matrix and increases concentration of the remaining faecal solution. Evaporation may remove populations of indicator organisms in faeces relatively quickly, even though faeces are not completely dehydrated. This research may be used as the foundation for studies more closely resembling real-world evaporation conditions including diurnal fluctuations, rewetting and freezing.

  14. Spatial distribution of Legionella pneumophila MLVA-genotypes in a drinking water system.

    Science.gov (United States)

    Rodríguez-Martínez, Sarah; Sharaby, Yehonatan; Pecellín, Marina; Brettar, Ingrid; Höfle, Manfred; Halpern, Malka

    2015-06-15

    Bacteria of the genus Legionella cause water-based infections, resulting in severe pneumonia. To improve our knowledge about Legionella spp. ecology, its prevalence and its relationships with environmental factors were studied. Seasonal samples were taken from both water and biofilm at seven sampling points of a small drinking water distribution system in Israel. Representative isolates were obtained from each sample and identified to the species level. Legionella pneumophila was further determined to the serotype and genotype level. High resolution genotyping of L. pneumophila isolates was achieved by Multiple-Locus Variable number of tandem repeat Analysis (MLVA). Within the studied water system, Legionella plate counts were higher in summer and highly variable even between adjacent sampling points. Legionella was present in six out of the seven selected sampling points, with counts ranging from 1.0 × 10(1) to 5.8 × 10(3) cfu/l. Water counts were significantly higher in points where Legionella was present in biofilms. The main fraction of the isolated Legionella was L. pneumophila serogroup 1. Serogroup 3 and Legionella sainthelensis were also isolated. Legionella counts were positively correlated with heterotrophic plate counts at 37 °C and negatively correlated with chlorine. Five MLVA-genotypes of L. pneumophila were identified at different buildings of the sampled area. The presence of a specific genotype, "MLVA-genotype 4", consistently co-occurred with high Legionella counts and seemed to "trigger" high Legionella counts in cold water. Our hypothesis is that both the presence of L. pneumophila in biofilm and the presence of specific genotypes, may indicate and/or even lead to high Legionella concentration in water. This observation deserves further studies in a broad range of drinking water systems to assess its potential for general use in drinking water monitoring and management. Copyright © 2015 Elsevier Ltd. All rights reserved.

  15. vacA Genotype Status of Helicobacter pylori Isolated from Foods with Animal Origin

    Directory of Open Access Journals (Sweden)

    Elnaz Saeidi

    2016-01-01

    Full Text Available According to controversial theories and results of studies, foods with animal origins play an important role in the transmission of H. pylori to human. The aim of this study was to determine the distribution of vacA genotypes of H. pylori, isolated from milk and meat samples of cow, sheep, goat, camel, and buffalo. Eight hundred and twenty raw milk and meat samples were collected from various parts of Iran. Samples were cultured and those found positive for H. pylori were analyzed for the presence of various genotypes of vacA gene. Out of 420 milk and 400 meat samples, 92 (21.90% and 105 (26.25% were positive for H. pylori, respectively. The most commonly detected genotypes in the vacA gene were s1a (86.80%, m1a (79.18%, s1b (69.54%, and m1b (63.45% and detected combined genotypes were mostly m1as1a (68.52%, m1as1b (60.40%, m1bs1b (55.83%, and m1bs1a (53.29%. High presence of bacteria in the milk and meat samples of sheep represents that sheep may be the natural host of H. pylori. High presence of H. pylori strains in milk and meat samples similar to vacA genotypes in human being suggests that milk and meat samples could be the sources of bacteria for human.

  16. vacA Genotype Status of Helicobacter pylori Isolated from Foods with Animal Origin.

    Science.gov (United States)

    Saeidi, Elnaz; Sheikhshahrokh, Amirhossein

    2016-01-01

    According to controversial theories and results of studies, foods with animal origins play an important role in the transmission of H. pylori to human. The aim of this study was to determine the distribution of vacA genotypes of H. pylori, isolated from milk and meat samples of cow, sheep, goat, camel, and buffalo. Eight hundred and twenty raw milk and meat samples were collected from various parts of Iran. Samples were cultured and those found positive for H. pylori were analyzed for the presence of various genotypes of vacA gene. Out of 420 milk and 400 meat samples, 92 (21.90%) and 105 (26.25%) were positive for H. pylori, respectively. The most commonly detected genotypes in the vacA gene were s1a (86.80%), m1a (79.18%), s1b (69.54%), and m1b (63.45%) and detected combined genotypes were mostly m1as1a (68.52%), m1as1b (60.40%), m1bs1b (55.83%), and m1bs1a (53.29%). High presence of bacteria in the milk and meat samples of sheep represents that sheep may be the natural host of H. pylori. High presence of H. pylori strains in milk and meat samples similar to vacA genotypes in human being suggests that milk and meat samples could be the sources of bacteria for human.

  17. Monitoring stress in captive and free-ranging African wild dogs (Lycaon pictus) using faecal glucocorticoid metabolites.

    Science.gov (United States)

    Van der Weyde, L K; Martin, G B; Paris, M C J

    2016-01-15

    An understanding of stress physiology is important for species management because high levels of stress can hamper reproduction and affect an individual's ability to cope with threats to their survival, such as disease and human-wildlife conflict. A commonly used indicator of stress, faecal concentrations of cortisol metabolites (FCM), can be used to assess the impact of social, biological and environmental factors. Measurements of FCM are particularly valuable for endangered species that are logistically challenging to study and where non-invasive techniques are preferred. As the second most endangered canid in Africa, the African wild dog (Lycaon pictus) has been the focus of considerable conservation research, yet there is still little understanding of factors associated with stress, in either captive or free-ranging populations. The present study therefore aimed to determine whether stress levels differ between captive and free-ranging populations, and to detect social, biological and environmental factors that are stressful in these populations. Faecal samples were collected from 20 captive and 62 free-ranging animals. Within free-ranging populations, the sexes differed significantly, but there was no effect of social status, age or breeding period for either sex. Captive females had higher FCM concentrations than free-ranging females. In captive populations, FCM concentrations differed among zoos and with reproductive status in females, but were not related to age class or group-housing structure. In conclusion, FCM is a useful indicator of stress and should be considered an integrative aspect of management, for both in situ and ex situ African wild dog populations. Copyright © 2015 Elsevier Inc. All rights reserved.

  18. A European database of Fusarium graminearum and F. culmorum trichothecene genotypes

    Directory of Open Access Journals (Sweden)

    Matias ePasquali

    2016-04-01

    Full Text Available Fusarium species, particularly Fusarium graminearum and F. culmorum, are the main cause of trichothecene type B contamination in cereals. Data on the distribution of Fusarium trichothecene genotypes in cereals in Europe are scattered in time and space. Furthermore, a common core set of related variables (sampling method, host cultivar, previous crop, etc. that would allow more effective analysis of factors influencing the spatial and temporal population distribution, is lacking. Consequently, based on the available data, it is difficult to identify factors influencing chemotype distribution and spread at the European level. Here we describe the results of a collaborative integrated work which aims 1 to characterize the trichothecene genotypes of strains from three Fusarium species, collected over the period 2000-2013, and 2 to enhance the standardization of epidemiological data collection.Information on host plant, country of origin, sampling location, year of sampling and previous crop of 1147 F. graminearum, 479 F. culmorum and 3 F. cortaderiae strains obtained from 17 European countries was compiled and a map of trichothecene type B genotype distribution was plotted for each species. All information on the strains was collected in a freely accessible and updatable database (www.catalogueeu.luxmcc.lu, which will serve as a starting point for epidemiological analysis of potential spatial and temporal trichothecene genotype shifts in Europe.The analysis of the currently available European dataset showed that in F. graminearum, the predominant genotype was 15-acetyldeoxynivalenol (15-ADON (82.9%, followed by 3-acetyldeoxynivalenol (3-ADON (13.6% and nivalenol (NIV (3.5%. In F. culmorum, the prevalent genotype was 3-ADON (59.9%, while the NIV genotype accounted for the remaining 40.1%. Both geographical and temporal patterns of trichothecene genotypes distribution were identified.

  19. Neutralizing antibodies in patients with chronic hepatitis C, genotype 1, against a panel of genotype 1 culture viruses

    DEFF Research Database (Denmark)

    Pedersen, Jannie; Jensen, Tanja B; Carlsen, Thomas H R

    2013-01-01

    , infection treated with pegylated interferon-α and ribavirin. Thirty-nine patients with chronic hepatitis C, genotype 1a or 1b, with either sustained virologic response (n = 23) or non-sustained virologic response (n = 16) were enrolled. Samples taken prior to treatment were tested for their ability...... to neutralize 6 different HCV genotype 1 cell culture recombinants (1a: H77/JFH1, TN/JFH1, DH6/JFH1; 1b: J4/JFH1, DH1/JFH1, DH5/JFH1). The results were expressed as the highest dilution yielding 50% neutralization (NAb50-titer). We observed no genotype or subtype specific differences in NAb50-titers between......The correlation of neutralizing antibodies to treatment outcome in patients with chronic hepatitis C virus (HCV) infection has not been established. The aim of this study was to determine whether neutralizing antibodies could be used as an outcome predictor in patients with chronic HCV, genotype 1...

  20. The use of geoinformatic data and spatial analysis to predict faecal pollution during extreme precipitation events

    Science.gov (United States)

    Ward, Ray; Purnell, Sarah; Ebdon, James; Nnane, Daniel; Taylor, Huw

    2013-04-01

    The Water Framework Directive (WFD) regulates surface water quality standards in the European Union (EU). The Directive call for the identification and management of point and diffuse sources of pollution and requires the establishment of a 'programme of measures' for identified river basin districts, in order to achieve a "good status" by 2015. The hygienic quality of water is normally monitored using faecal indicator organisms (FIO), such as Escherichia coli, which indicate a potential risk to public health from human waterborne pathogens. Environmental factors influence the transmission of these pathogens and indicator organisms, and statistically significant relationships have been found between rainfall and outbreaks of waterborne disease. Climate change has been predicted to lead to an increase in severe weather events in many parts of Europe, including an increase in the frequency of extreme rainfall events. This in turn is likely to lead to an increase in incidents of human waterborne disease in Europe, unless measures are taken to predict and mitigate for such events. This study investigates a variety of environmental factors that influence the concentration of FIO in surface waters receiving faecal contamination from a variety of sources. Levels of FIO, including Escherichia coli, intestinal enterococci, somatic coliphage and GB124 (a human-specific microbial source tracking marker), were monitored in the Sussex Ouse catchment in Southeast England over a period of 26 months. These data were combined with geoinformatic environmental data within a GIS to map faecal contamination within the river. Previously, precipitation and soil erosion have been identified as major factors that can influence the concentration of these faecal markers, and studies have shown that slope, soil type and vegetation influence both the mechanisms and the rate by which erosion occurs in river catchments. Of the environmental variables studied, extreme precipitation was found to

  1. Improved Ancestry Estimation for both Genotyping and Sequencing Data using Projection Procrustes Analysis and Genotype Imputation

    Science.gov (United States)

    Wang, Chaolong; Zhan, Xiaowei; Liang, Liming; Abecasis, Gonçalo R.; Lin, Xihong

    2015-01-01

    Accurate estimation of individual ancestry is important in genetic association studies, especially when a large number of samples are collected from multiple sources. However, existing approaches developed for genome-wide SNP data do not work well with modest amounts of genetic data, such as in targeted sequencing or exome chip genotyping experiments. We propose a statistical framework to estimate individual ancestry in a principal component ancestry map generated by a reference set of individuals. This framework extends and improves upon our previous method for estimating ancestry using low-coverage sequence reads (LASER 1.0) to analyze either genotyping or sequencing data. In particular, we introduce a projection Procrustes analysis approach that uses high-dimensional principal components to estimate ancestry in a low-dimensional reference space. Using extensive simulations and empirical data examples, we show that our new method (LASER 2.0), combined with genotype imputation on the reference individuals, can substantially outperform LASER 1.0 in estimating fine-scale genetic ancestry. Specifically, LASER 2.0 can accurately estimate fine-scale ancestry within Europe using either exome chip genotypes or targeted sequencing data with off-target coverage as low as 0.05×. Under the framework of LASER 2.0, we can estimate individual ancestry in a shared reference space for samples assayed at different loci or by different techniques. Therefore, our ancestry estimation method will accelerate discovery in disease association studies not only by helping model ancestry within individual studies but also by facilitating combined analysis of genetic data from multiple sources. PMID:26027497

  2. Genotypic Diversity of Escherichia coli in the Water and Soil of Tropical Watersheds in Hawaii ▿

    Science.gov (United States)

    Goto, Dustin K.; Yan, Tao

    2011-01-01

    High levels of Escherichia coli were frequently detected in tropical soils in Hawaii, which present important environmental sources of E. coli to water bodies. This study systematically examined E. coli isolates from water and soil of several watersheds in Hawaii and observed high overall genotypic diversity (35.5% unique genotypes). In the Manoa watershed, fewer than 9.3% of the observed E. coli genotypes in water and 6.6% in soil were shared between different sampling sites, suggesting the lack of dominant fecal sources in the watershed. High temporal variability of E. coli genotypes in soil was also observed, which suggests a dynamic E. coli population corresponding with the frequently observed high concentrations in tropical soils. When E. coli genotypes detected from the same sampling events were compared, limited sharing between the soil and water samples was observed in the majority of comparisons (73.5%). However, several comparisons reported up to 33.3% overlap of E. coli genotypes between soil and water, illustrating the potential for soil-water interactions under favorable environmental conditions. In addition, genotype accumulation curves for E. coli from water and soil indicated that the sampling efforts in the Manoa watershed could not exhaust the overall genotypic diversity. Comparisons of E. coli genotypes from other watersheds on Oahu, Hawaii, identified no apparent grouping according to sampling locations. The results of the present study demonstrate the complexity of using E. coli as a fecal indicator bacterium in tropical watersheds and highlight the need to differentiate environmental sources of E. coli from fecal sources in water quality monitoring. PMID:21515724

  3. Nephele: genotyping via complete composition vectors and MapReduce

    Directory of Open Access Journals (Sweden)

    Mardis Scott

    2011-08-01

    Full Text Available Abstract Background Current sequencing technology makes it practical to sequence many samples of a given organism, raising new challenges for the processing and interpretation of large genomics data sets with associated metadata. Traditional computational phylogenetic methods are ideal for studying the evolution of gene/protein families and using those to infer the evolution of an organism, but are less than ideal for the study of the whole organism mainly due to the presence of insertions/deletions/rearrangements. These methods provide the researcher with the ability to group a set of samples into distinct genotypic groups based on sequence similarity, which can then be associated with metadata, such as host information, pathogenicity, and time or location of occurrence. Genotyping is critical to understanding, at a genomic level, the origin and spread of infectious diseases. Increasingly, genotyping is coming into use for disease surveillance activities, as well as for microbial forensics. The classic genotyping approach has been based on phylogenetic analysis, starting with a multiple sequence alignment. Genotypes are then established by expert examination of phylogenetic trees. However, these traditional single-processor methods are suboptimal for rapidly growing sequence datasets being generated by next-generation DNA sequencing machines, because they increase in computational complexity quickly with the number of sequences. Results Nephele is a suite of tools that uses the complete composition vector algorithm to represent each sequence in the dataset as a vector derived from its constituent k-mers by passing the need for multiple sequence alignment, and affinity propagation clustering to group the sequences into genotypes based on a distance measure over the vectors. Our methods produce results that correlate well with expert-defined clades or genotypes, at a fraction of the computational cost of traditional phylogenetic methods run on

  4. Immunochemical faecal occult blood tests have superior stability and analytical performance characteristics over guaiac-based tests in a controlled in vitro study.

    LENUS (Irish Health Repository)

    Lee, Chun Seng

    2011-06-01

    The aims of this study were (1) to determine the measurement accuracy of a widely used guaiac faecal occult blood test (gFOBT) compared with an immunochemical faecal occult blood test (iFOBT) during in vitro studies, including their analytical stability over time at ambient temperature and at 4°C; and (2) to compare analytical imprecision and other characteristics between two commercially available iFOBT methods.

  5. Distribution of Porphyromonas gingivalis fimA genotypes in primary endodontic infections.

    Science.gov (United States)

    Rôças, Isabela N; Siqueira, José F

    2010-03-01

    Long fimbriae (FimA) are important virulence factors of Porphyromonas gingivalis. Based on the diversity of the fimA gene, this species is classified into 6 genotypes. This study surveyed samples from primary endodontic infections for the presence of these P. gingivalis fimA variants. Genomic DNA isolated from samples taken from 25 root canals of teeth with chronic apical periodontitis and 25 aspirates from acute apical abscess was used as template in polymerase chain reaction (PCR) assays directed toward the detection of the different P. gingivalis fimA genotypes. Porphyromonas gingivalis was detected by a 16S rRNA gene-based PCR in 36% of the total number of cases sampled (44% of chronic apical periodontitis and 28% of abscess aspirates). In cases of chronic apical periodontitis, P. gingivalis variant type IV was the most prevalent (24%), followed by types I (20%), II (16%), and III (8%). In acute abscess samples, variant type II was the most prevalent (12%), followed by types III and IV (8% of each) and type I (4%). Combinations of up to 3 different genotypes were detected in a few cases. No single fimA genotype variant or combination thereof was significantly associated with symptoms. Overall, fimA types IV (16%), II (14%), and I (12%) were the most prevalent. Findings demonstrated that different P. gingivalis fimA genotypes can be present in primary endodontic infections. Copyright 2010 Mosby, Inc. All rights reserved.

  6. Pelvic floor muscle lesions at endoanal MR imaging in female patients with faecal incontinence

    NARCIS (Netherlands)

    Terra, Maaike P.; Beets-Tan, Regina G. H.; Vervoorn, Inge; Deutekom, Marije; Wasser, Martin N. J. M.; Witkamp, Theo D.; Dobben, Annette C.; Baeten, Cor G. M. I.; Bossuyt, Patrick M. M.; Stoker, Jaap

    2008-01-01

    To evaluate the frequency and spectrum of lesions of different pelvic floor muscles at endoanal MRI in women with severe faecal incontinence and to study their relation with incontinence severity and manometric findings. In 105 women MRI examinations were evaluated for internal anal sphincter (IAS),

  7. Climate and land-use change impact on faecal indicator bacteria in a temperate maritime catchment (the River Conwy, Wales)

    Science.gov (United States)

    Bussi, Gianbattista; Whitehead, Paul G.; Thomas, Amy R. C.; Masante, Dario; Jones, Laurence; Jack Cosby, B.; Emmett, Bridget A.; Malham, Shelagh K.; Prudhomme, Christel; Prosser, Havard

    2017-10-01

    Water-borne pathogen contamination from untreated sewage effluent and runoff from farms is a serious threat to the use of river water for drinking and commercial purposes, such as downstream estuarine shellfish industries. In this study, the impact of climate change and land-use change on the presence of faecal indicator bacteria in freshwater was evaluated, through the use of a recently-developed catchment-scale pathogen model. The River Conwy in Wales has been used as a case-study, because of the large presence of livestock in the catchment and the importance of the shellfish harvesting activities in its estuary. The INCA-Pathogens catchment model has been calibrated through the use of a Monte-Carlo-based technique, based on faecal indicator bacteria measurements, and then driven by an ensemble of climate projections obtained from the HadRM3-PPE model (Future Flow Climate) plus four land-use scenarios (current land use, managed ecosystem, abandonment and agricultural intensification). The results show that climate change is not expected to have a very large impact on average river flow, although it might alter its seasonality. The abundance of faecal indicator bacteria is expected to decrease in response to climate change, especially during the summer months, due to reduced precipitation, causing reduced runoff, and increased temperature, which enhances the bacterial die-off processes. Land-use change can also have a potentially large impact on pathogens. The "managed ecosystems" scenario proposed in this study can cause a reduction of 15% in average water faecal indicator bacteria and up to 30% in the 90th percentile of water faecal indicator bacteria, mainly due to the conversion of pasture land into grassland and the expansion of forest land. This study provides an example of how to assess the impacts of human interventions on the landscape, and what may be the extent of their effects, for other catchments where the human use of the natural resources in the

  8. `Assessment of Hybrid White Yam (Discorea Rotundata) Genotypes ...

    African Journals Online (AJOL)

    Ako-Isu had black colour while the remaining amala samples had varying shades of grey colouration. Though all the elubo samples from the experimental yam genotypes were found to be usable in amala preparation, only the amala sample made from TDr 89/02677 compared favourably (especially in the handfeel sensory ...

  9. First time identification of Acanthamoeba genotypes in the cornea samples of wild birds; Is Acanthamoeba keratitis making the predatory birds a target?

    Science.gov (United States)

    Karakavuk, Muhammet; Aykur, Mehmet; Şahar, Esra Atalay; Karakuş, Mehmet; Aldemir, Duygu; Döndüren, Ömer; Özdemir, Hüseyin Gökhan; Can, Hüseyin; Gürüz, Adnan Yüksel; Dağcı, Hande; Döşkaya, Mert

    2017-12-01

    Acanthamoeba is a free-living amoeba which can be isolated from environment and among others well known as an opportunist protozoan parasite causing infections in humans and animals. Eyes are extremely important for the wild birds and losing sight ability due to Acanthamoeba can be dangerous. The studies on Acanthamoeba infection in wild birds is very few in world and Turkey therefore we aimed to screen deceased wild birds found in İzmir and Manisa provinces located in western Turkey using PCR and non-nutrition agar (NNA) plate method. Cornea samples were obtained from 18 deceased wild birds. During the external examination, signs of keratitis were observed in two Eurasian sparrowhawks (Accipiter nisus). All of the corneal samples were analyzed by two PCR methods and NNA plate. According to results, the Acanthamoeba positivity in corneal samples was 16.6% and 5.5% by PCR and plate method, respectively. According to sequencing data, two of isolates belonged to genotype T5 and one was genotype T4. In conclusion, Acanthamoeba infection was detected in wild bird cornea samples with/without keratitis for the first time in the world. The result of this study also show that Acanthamoeba can be a cause of keratitis in wild birds of Turkey and thus these predator birds can be a target of other wild animals due to loss of sight ability. In terms of public health, these results show the importance of wild birds as a source of Acanthamoeba infection in nature. Copyright © 2017 Elsevier Inc. All rights reserved.

  10. Genotyping of vacA alleles of Helicobacter pylori strains recovered ...

    African Journals Online (AJOL)

    Genotyping of vacA alleles of Helicobacter pylori strains recovered from some Iranian food items. ... Tropical Journal of Pharmaceutical Research ... Conclusion: The presence of similar genotypes in H. pylori strains of foods and those of human clinical samples suggest that contaminated foods may be the source of bacteria ...

  11. Comparison of Three Different Commercial Kits for the Human Papilloma Virus Genotyping.

    Science.gov (United States)

    Lim, Yong Kwan; Choi, Jee-Hye; Park, Serah; Kweon, Oh Joo; Park, Ae Ja

    2016-11-01

    High-risk type human papilloma virus (HPV) is the most important cause of cervical cancer. Recently, real-time polymerase chain reaction and reverse blot hybridization assay-based HPV DNA genotyping kits are developed. So, we compared the performances of different three HPV genotyping kits using different analytical principles and methods. Two hundred positive and 100 negative cervical swab specimens were used. DNA was extracted and all samples were tested by the MolecuTech REBA HPV-ID, Anyplex II HPV28 Detection, and HPVDNAChip. Direct sequencing was performed as a reference method for confirming high-risk HPV genotypes 16, 18, 45, 52, and 58. Although high-level agreement results were observed in negative samples, three kits showed decreased interassay agreement as screening setting in positive samples. Comparing the genotyping results, three assays showed acceptable sensitivity and specificity for the detection of HPV 16 and 18. Otherwise, various sensitivities showed in the detection of HPV 45, 52, and 58. The three assays had dissimilar performance of HPV screening capacity and exhibited moderate level of concordance in HPV genotyping. These discrepant results were unavoidable due to difference in type-specific analytical sensitivity and lack of standardization; therefore, we suggested that the efforts to standardization of HPV genotyping kits and adjusting analytical sensitivity would be important for the best clinical performance. © 2016 Wiley Periodicals, Inc.

  12. Porphyromonas gingivalis Fim-A genotype distribution among Colombians

    Science.gov (United States)

    Jaramillo, Adriana; Parra, Beatriz; Botero, Javier Enrique; Contreras, Adolfo

    2015-01-01

    Introduction: Porphyromonas gingivalis is associated with periodontitis and exhibit a wide array of virulence factors, including fimbriae which is encoded by the FimA gene representing six known genotypes. Objetive: To identify FimA genotypes of P. gingivalis in subjects from Cali-Colombia, including the co-infection with Aggregatibacter actinomycetemcomitans, Treponema denticola, and Tannerella forsythia. Methods: Subgingival samples were collected from 151 people exhibiting diverse periodontal condition. The occurrence of P. gingivalis, FimA genotypes and other bacteria was determined by PCR. Results: P. gingivalis was positive in 85 patients. Genotype FimA II was more prevalent without reach significant differences among study groups (54.3%), FimA IV was also prevalent in gingivitis (13.0%). A high correlation (p= 0.000) was found among P. gingivalis, T. denticola, and T. forsythia co-infection. The FimA II genotype correlated with concomitant detection of T. denticola and T. forsythia. Conclusions: Porphyromonas gingivalis was high even in the healthy group at the study population. A trend toward a greater frequency of FimA II genotype in patients with moderate and severe periodontitis was determined. The FimA II genotype was also associated with increased pocket depth, greater loss of attachment level, and patients co-infected with T. denticola and T. forsythia. PMID:26600627

  13. High-throughput single nucleotide polymorphism genotyping using nanofluidic Dynamic Arrays

    Directory of Open Access Journals (Sweden)

    Crenshaw Andrew

    2009-01-01

    Full Text Available Abstract Background Single nucleotide polymorphisms (SNPs have emerged as the genetic marker of choice for mapping disease loci and candidate gene association studies, because of their high density and relatively even distribution in the human genomes. There is a need for systems allowing medium multiplexing (ten to hundreds of SNPs with high throughput, which can efficiently and cost-effectively generate genotypes for a very large sample set (thousands of individuals. Methods that are flexible, fast, accurate and cost-effective are urgently needed. This is also important for those who work on high throughput genotyping in non-model systems where off-the-shelf assays are not available and a flexible platform is needed. Results We demonstrate the use of a nanofluidic Integrated Fluidic Circuit (IFC - based genotyping system for medium-throughput multiplexing known as the Dynamic Array, by genotyping 994 individual human DNA samples on 47 different SNP assays, using nanoliter volumes of reagents. Call rates of greater than 99.5% and call accuracies of greater than 99.8% were achieved from our study, which demonstrates that this is a formidable genotyping platform. The experimental set up is very simple, with a time-to-result for each sample of about 3 hours. Conclusion Our results demonstrate that the Dynamic Array is an excellent genotyping system for medium-throughput multiplexing (30-300 SNPs, which is simple to use and combines rapid throughput with excellent call rates, high concordance and low cost. The exceptional call rates and call accuracy obtained may be of particular interest to those working on validation and replication of genome- wide- association (GWA studies.

  14. THE USE OF MULTIPLE DISPLACEMENT AMPLIFICATION TO INCREASE THE DETECTION AND GENOTYPING OF TRYPANOSOMA SPECIES SAMPLES IMMOBILISED ON FTA FILTERS

    Science.gov (United States)

    MORRISON, LIAM J.; McCORMACK, GILLIAN; SWEENEY, LINDSAY; LIKEUFACK, ANNE C. L.; TRUC, PHILIPPE; TURNER, C. MICHAEL; TAIT, ANDY; MacLEOD, ANNETTE

    2007-01-01

    Whole genome amplification methods are a recently developed tool for amplifying DNA from limited template. We report its application in trypanosome infections, characterised by low parasitaemias. Multiple Displacement Amplification (MDA) amplifies DNA with a simple in vitro step, and was evaluated on mouse blood samples on FTA filter cards with known numbers of Trypanosoma brucei parasites. The data showed a twenty-fold increase in the number of PCRs possible per sample, using primers diagnostic for the multi-copy ribosomal ITS region or 177 bp repeats, and a twenty-fold increase in sensitivity over nested PCR against a single copy microsatellite. Using MDA for microsatellite genotyping caused allele dropout at low DNA concentrations, which was overcome by pooling multiple MDA reactions. The validity of using MDA was established with samples from Human African Trypanosomiasis patients. The use of MDA allows maximal use of finite DNA samples and may prove a valuable tool in studies where multiple reactions are necessary, such as population genetic analyses. PMID:17556624

  15. Performance of the digene LQ, RH and PS HPVs genotyping systems on clinical samples and comparison with HC2 and PCR-based Linear Array.

    Science.gov (United States)

    Godínez, Jose M; Tous, Sara; Baixeras, Nuria; Moreno-Crespi, Judith; Alejo, María; Lejeune, Marylène; Bravo, Ignacio G; Bosch, F Xavier; de Sanjosé, Silvia

    2011-11-18

    Certain Human Papillomaviruses (HPVs) are the infectious agents involved in cervical cancer development. Detection of HPVs DNA is part of the cervical cancer screening protocols and HPVs genotyping has been proposed for its inclusion in these preventive programs. The aim of this study was to evaluate three novel genotyping tests, namely Qiagen LQ, RH and PS, in clinical samples with and without abnormalities. For this, 305 cervical samples were processed and the results of the evaluated techniques were compared with those obtained in the HPVs diagnostic process in our lab, by using HC2 and Linear Array (LA) technologies. The concordances and kappa statistics (k) for each technique compared with HC2 were 98.69% (k = 0.94) for LQ, 98.03% (k = 0.91) for RH and 91.80% (k = 0.82) for PS. There was a very good agreement in HPVs type-specific concordance for the most prevalent types HPV16 (kappa range = 0.83-0.90), HPV18 (k.r.= 0.74-0.80) and HPV45 (k.r.= 0.82-0.90). The three tests showed an overall good concordance for HPVs detection when compared with HR-HC2 system. LQ and RH rendered lower detection rate for multiple infections than LA genotyping. However, our understanding of the clinical significance of multiple HPVs infections is still incomplete and therefore the relevance of the lower ability to detect multiple infections needs to be evaluated.

  16. Performance of the digene LQ, RH and PS HPVs genotyping systems on clinical samples and comparison with HC2 and PCR-based Linear Array

    Directory of Open Access Journals (Sweden)

    Godínez Jose M

    2011-11-01

    Full Text Available Abstract Background Certain Human Papillomaviruses (HPVs are the infectious agents involved in cervical cancer development. Detection of HPVs DNA is part of the cervical cancer screening protocols and HPVs genotyping has been proposed for its inclusion in these preventive programs. The aim of this study was to evaluate three novel genotyping tests, namely Qiagen LQ, RH and PS, in clinical samples with and without abnormalities. For this, 305 cervical samples were processed and the results of the evaluated techniques were compared with those obtained in the HPVs diagnostic process in our lab, by using HC2 and Linear Array (LA technologies. Results The concordances and kappa statistics (k for each technique compared with HC2 were 98.69% (k = 0.94 for LQ, 98.03% (k = 0.91 for RH and 91.80% (k = 0.82 for PS. There was a very good agreement in HPVs type-specific concordance for the most prevalent types HPV16 (kappa range = 0.83-0.90, HPV18 (k.r.= 0.74-0.80 and HPV45 (k.r.= 0.82-0.90. Conclusions The three tests showed an overall good concordance for HPVs detection when compared with HR-HC2 system. LQ and RH rendered lower detection rate for multiple infections than LA genotyping. However, our understanding of the clinical significance of multiple HPVs infections is still incomplete and therefore the relevance of the lower ability to detect multiple infections needs to be evaluated.

  17. Faecal microbiota transplantation: Where did it start? What have studies taught us? Where is it going?

    Directory of Open Access Journals (Sweden)

    Ryan M Chanyi

    2017-05-01

    Full Text Available The composition and activity of microorganisms in the gut, the microbiome, is emerging as an important factor to consider with regard to the treatment of many diseases. Dysbiosis of the normal community has been implicated in inflammatory bowel disease, Crohn’s disease, diabetes and, most notoriously, Clostridium difficile infection. In Canada, the leading treatment strategy for recalcitrant C. difficile infection is to receive faecal material which by nature is filled with microorganisms and their metabolites, from a healthy individual, known as a faecal microbiota transplantation. This influx of bacteria into the gut helps to restore the microbiota to a healthy state, preventing C. difficile from causing further disease. Much of what is known with respect to the microbiota and faecal microbiota transplantation comes from animal studies simulating the human disease. Although these models allow researchers to perform studies that would be difficult in humans, they do not always recapitulate the human microbiome. This makes the translation of these results to humans somewhat questionable. The purpose of this review is to analyse these animal models and discuss the advantages and the disadvantages of them in relation to human translation. By understanding some of the limitation of animal models, we will be better able to design and perform experiments of most relevance to human applications.

  18. Distribution of HCV genotypes among different exposure categories in Brazil

    Directory of Open Access Journals (Sweden)

    Oliveira M.L.A.

    1999-01-01

    Full Text Available Hepatitis C virus (HCV infection is widespread and responsible for more than 60% of chronic hepatitis cases. HCV presents a genetic variability which has led to viral classification into at least 6 genotypes and a series of subtypes. These variants present characteristic geographical distribution, but their association with different responses to treatment with interferon and severity of disease still remains controversial. The aim of this study was to investigate the patterns of distribution of HCV genotypes among different exposure categories in Brazil. Two hundred and fifty anti-HCV positive samples were submitted to HCV-RNA detection by RT-PCR and their genotype was determined by restriction fragment length polymorphism (RFLP analysis. In addition, the genotype/subtype of 60 samples was also determined by a reverse hybridization assay. HCV 1 was the most prevalent (72.0%, followed by type 3 (25.3%, HCV 2 (2.0% and HCV 4 (0.7%. The HCV genotype distribution varied among the different exposure categories, with HCV 1 being more frequent among blood donors, hemophiliacs and hemodialysis patients. A high frequency of HCV 3 was observed in cirrhotic patients, blood donors from the South of Brazil and injecting drug users (IDUs. The general distribution of the HCV genotype in Brazil is similar to that in other regions of the world.

  19. Prevalence of α-thalassaemia genotypes in pregnant women in northern Thailand

    Science.gov (United States)

    Pharephan, Somphon; Sirivatanapa, Pannee; Makonkawkeyoon, Sanit; Tuntiwechapikul, Wirote; Makonkawkeyoon, Luksana

    2016-01-01

    Background & objectives: Alpha-thalassaemias are genetic disorders with high prevalence in northern Thailand. However, common genotypes and current data on the prevalence of α-thalassaemias have not been reported in this region. Therefore, the objective of the present study was to determine the prevalence of α-thalassaemia genotypes in pregnant women in northern Thailand. Methods: Genomic DNA was extracted from blood samples of pregnant women who came to Maharaj Nakorn Chiang Mai University Hospital during July 2009 to 2010. The common deletion and point mutation genotypes of α-thalassaemia were evaluated by gap- polymerase chain reaction (PCR) and PCR with restriction fragment length polymorphism (RFLP). Results: Genotypes of 638 pregnant women were: 409 samples (64.11%) being normal subjects (αα/αα) and 229 samples (35.89%) with α-thalassaemias. These 229 samples could be classified into deletional HbH disease (--SEA/-α3.7) for 18 samples (2.82%); heterozygous α0-thalassaemia --SEA type (--SEA/αα)) for 78 (12.23%); heterozygous α+-thalassaemia - α3.7 type (-α3.7/αα) for 99 (15.52%); homozygous α+-thalassaemia - α3.7 type (-α3.7/- α3.7) for five (0.78%); heterozygous α+-thalassaemia - α4.2 type (-α4.2/αα) for two (0.31%); and heterozygous HbCS (αCSα/αα) for 27 (4.23%) cases. Interpretation & conclusions: The prevalence of α-thalassaemias in pregnant women in northern Thailand was high. This finding supports the implementation of the prevention and control of this common genetic disorder by screening for α-thalassaemia genotypes. PMID:27241645

  20. The potential for disinfection of separated faecal matter by urea and by peracetic acid for hygienic nutrient recycling.

    Science.gov (United States)

    Vinnerås, B; Holmqvist, A; Bagge, E; Albihn, A; Jönsson, H

    2003-09-01

    No efficient, reliable, and scale independent disinfection methods for toilet waste are available today for safe recycling of plant nutrients. Therefore, two chemical treatment methods, addition of urea or of PAA (a quaternary mixture of 15% peracetic acid, 15% hydrogen peroxide and 30% acetic acid), were evaluated for disinfection of faecal matter.Degradation of the added urea resulted in 30 g of ammonia nitrogen per kilogram of treated matter and a pH increase to approximately 9.3. This produced an efficient disinfection of E. coli, Enterococcus spp., and Salmonella spp. within 3 weeks (>6log(10) reduction) and a reduction of the chemical resistant Salmonella typhimurium 28b phage, corresponding to a decimal reduction within 7.5 days. No viable Ascaris suum eggs were found after 50 days of treatment. No reduction of spore forming Clostridia spp. was observed. Urea treatment proved to be efficient for disinfection of source separated faecal matter in a scale independent method used for safe recycling of nutrients found in the faecal matter.PAA reduced all of the above indicator organisms within 12 h after application. For this faecal material, with a dry matter content of approximately 10%, an addition of 0.5-1% of PAA (active substance, corresponding to 3.3-6.7% of the Proxitane 15 used) was required before no viable organisms were found in the material. However, this was not tested for the A. suum. No viable spore-forming bacteria or phages were detected. A high rate of bacteria regrowth occurred at 0.15% dosage and 5 days of treatment. PAA is an efficient alternative for disinfection of separated faeces if a rapid treatment is needed.

  1. Distribution of Human papilloma virus genotypes in cervical cancer tissues

    Directory of Open Access Journals (Sweden)

    Stamenković M.

    2014-01-01

    Full Text Available Cervical cancer incidence and mortality rates in Serbia are among the highest in Europe and data on Human papilloma virus (HPV type distribution are scarce. The aim of this study was to determine the prevalence of HPV types in archival specimens of cervical cancer tissues of women in the Serbian population. A total of 45 paraffin-embedded tissue samples of cervical carcinoma were used in this study. The procedure included deparaffinization of tissue samples, DNA extraction, PCR, gel electrophoresis and HPV genotyping by direct sequencing. HPV was detected in 32 samples (71%. Genotyping revealed the presence of 6 high-risk HPV types 16, 18, 33, 45, 53 and 58, where HPV type 16 was the most prevalent type (73.7%. The results of this study and further studies will provide more detailed information about HPV genotype distribution and may contribute to the formulation of national guidelines for the prevention of cervical cancer. [175073

  2. Evaluation of Soybean and Cowpea Genotypes for Phosphorus Use Efficiency

    Energy Technology Data Exchange (ETDEWEB)

    Kumaga, F. K.; Ofori, K.; Adiku, S. K.; Kugblenu, Y. O.; Asante, W.; Seidu, H. [College of Agriculture and Consumer Sciences, University of Ghana, Legon, Accra (Ghana); Adu-Gyamfi, J. J. [Soil and Water Management and Crop Nutrition Laboratory, International Atomic Energy Agency, Vienna (Austria)

    2013-11-15

    Initial screening of one hundred and fifty-two (152) and fifty (50) genotypes of soybean and cowpea, respectively, were conducted at the early growth stage to evaluate root traits associated with phosphorus (P) efficiency. Fifty soybean genotypes were subsequently selected and evaluated on a tropical low P soil (Lixisol) for growth and yield under low and adequate P availability. Plants were sampled at twelve and thirty days after sowing and at maturity. Six cowpea genotypes were also selected and evaluated in pots filled with Alfisol under low, moderate and high P availability. Plants were sampled at forty days and assessed for shoot yield and nodulation under low P availability. Using Principal Component Analysis (PCA), Phosphorus Efficiency Index (PEI) was used to determine P efficiency of soybean and cowpea genotypes. A wide variation in root traits for soybean and cowpea at the early growth stage was found, and allometric analysis showed a significant correlation between the root and shoot parameters at this stage. The study provided an opportunity to compare root traits of newly developed cowpea genotypes (early maturing, medium maturing, dual purpose and Striga resistant lines) with older released cultivars. There were significant differences in root length among the groups. In general, dual purpose, Striga resistant and medium/early maturing genotypes showed the longest roots while the older varieties showed the least total root length. Field and pot results also showed differential growth of soybean and cowpea with low P availability. Further, PCA of the results indicated that soybean genotypes could be grouped into three distinct P efficiency categories. Retaining the PC and the relative weight for each genotype in combination with yield potential under high P, four categories of responsiveness to P were obtained. Cowpea genotypes were grouped into three P efficiency categories and two categories of responsiveness to P. The study also found genetic

  3. An interview study analysing patients' experiences and perceptions of non-laxative or full-laxative preparation with faecal tagging prior to CT colonography

    International Nuclear Information System (INIS)

    Ghanouni, A.; Smith, S.G.; Halligan, S.; Taylor, S.A.; Plumb, A.; Boone, D.; Wagner, C. von

    2013-01-01

    Aim: To compare patients' experiences of either non- or full-laxative bowel preparation with additional faecal tagging and subsequent computed tomographic (CT) colonography using in-depth interviews to elicit detailed responses. Materials and methods: Patients who received CT colonography after non- (n = 9) or full-laxative (n = 9) preparation participated in a semi-structured telephone interview at least 2 days after the investigation. Full-laxative preparation consisted of magnesium citrate and sodium picosulphate administered at home (or polyethylene glycol, if contraindicated), followed by hospital-based faecal tagging with iohexol. Non-laxative preparation was home-based barium sulphate for faecal tagging. Interviews were transcribed and thematically analysed to identify recurrent themes on patients' perceptions and experiences. Results: Experiences of full-laxative preparation were usually negative and characterized by pre-test diarrhoea that caused significant interference with daily routine. Post-test flatus was common. Non-laxative preparation was well-tolerated; patients reported no or minimal changes to bowel habit and rapid return to daily routine. Patients reported worry and uncertainty about the purpose of faecal tagging. For iohexol, this also added burden from waiting before testing. Conclusion: Patients' responses supported previous findings that non-laxative preparation is more acceptable than full-laxative preparation but both can be improved. Faecal tagging used in combination with laxative preparation is poorly understood, adding burden and worry. Home-based non-laxative preparation is also poorly understood and patients require better information on the purpose and mechanism in order to give fully informed consent. This may also optimize adherence to instructions. Allowing home-based self-administration of all types of preparation would prevent waiting before testing

  4. Identifying the Genotypes of Hepatitis B Virus (HBV) with DNA Origami Label.

    Science.gov (United States)

    Liu, Ke; Pan, Dun; Wen, Yanqin; Zhang, Honglu; Chao, Jie; Wang, Lihua; Song, Shiping; Fan, Chunhai; Shi, Yongyong

    2018-02-01

    The hepatitis B virus (HBV) genotyping may profoundly affect the accurate diagnosis and antiviral treatment of viral hepatitis. Existing genotyping methods such as serological, immunological, or molecular testing are still suffered from substandard specificity and low sensitivity in laboratory or clinical application. In a previous study, a set of high-efficiency hybridizable DNA origami-based shape ID probes to target the templates through which genetic variation could be determined in an ultrahigh resolution of atomic force microscopy (AFM) nanomechanical imaging are established. Here, as a further confirmatory research to explore the sensitivity and applicability of this assay, differentially predesigned DNA origami shape ID probes are also developed for precisely HBV genotyping. Through the specific identification of visualized DNA origami nanostructure with clinical HBV DNA samples, the genetic variation information of genotypes can be directly identified under AFM. As a proof-of-concept, five genotype B and six genotype C are detected in 11 HBV-infected patients' blood DNA samples of Han Chinese population in the single-blinded test. The AFM image-based DNA origami shape ID genotyping approach shows high specificity and sensitivity, which could be promising for virus infection diagnosis and precision medicine in the future. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. Effect of faecal soiling on skatole and androstenone occurrence in organic entire male pigs

    DEFF Research Database (Denmark)

    Thomsen, Rikke; Edwards, Sandra; Jensen, Bent Borg

    2015-01-01

    Production of entire male pigs could be a future strategy for organic pig production. However, production of entire males leads to increased risk of carcasses with elevated boar taint levels. It is hypothesized that skatole levels in pig meat are affected by faecal soiling and that organic housing...

  6. Supervised pelvic floor muscle training versus attention-control massage treatment in patients with faecal incontinence: Statistical analysis plan for a randomised controlled trial.

    Science.gov (United States)

    Ussing, Anja; Dahn, Inge; Due, Ulla; Sørensen, Michael; Petersen, Janne; Bandholm, Thomas

    2017-12-01

    Faecal incontinence affects approximately 8-9% of the adult population. The condition is surrounded by taboo; it can have a devastating impact on quality of life and lead to major limitations in daily life. Pelvic floor muscle training in combination with information and fibre supplements is recommended as first-line treatment for faecal incontinence. Despite this, the effect of pelvic floor muscle training for faecal incontinence is unclear. No previous trials have investigated the efficacy of supervised pelvic floor muscle training in combination with conservative treatment and compared this to an attention-control massage treatment including conservative treatment. The aim of this trial is to investigate if 16 weeks of supervised pelvic floor muscle training in combination with conservative treatment is superior to attention-control massage treatment and conservative treatment in patients with faecal incontinence. Randomised, controlled, superiority trial with two parallel arms. 100 participants with faecal incontinence will be randomised to either (1) individually supervised pelvic floor muscle training and conservative treatment or (2) attention-control massage treatment and conservative treatment. The primary outcome is participants' rating of symptom changes after 16 weeks of treatment using the Patient Global Impression of Improvement Scale. Secondary outcomes are the Vaizey Incontinence Score, the Fecal Incontinence Severity Index, the Fecal Incontinence Quality of Life Scale, a 14-day bowel diary, anorectal manometry and rectal capacity measurements. Follow-up assessment at 36 months will be conducted. This paper describes and discusses the rationale, the methods and in particular the statistical analysis plan of this trial.

  7. High prevalence of Beijing and EAI4-VNM genotypes among M. tuberculosis isolates in northern Vietnam: sampling effect, rural and urban disparities.

    Directory of Open Access Journals (Sweden)

    Van Anh Thi Nguyen

    Full Text Available A total of 221 isolates of M. tuberculosis were sampled from hospitals and the general population in the northern plain of Vietnam, one of the most populated region of the country. Genotypic composition and diversity were characterized, and we investigated how they are affected by sampling (hospital vs. general population, correcting for potential confounding effects (location, age and gender of the patients. Spoligotyping and 12 MIRU-VNTR typing were used as first line. Then 15 MIRU-VNTR standard set was used, making 21 MIRU-VNTR typing for the clustered isolates. Result showed that 8 lineages and 13 sub-lineages were circulating in the region. The most predominant lineages were Beijing (38.5% and EAI (38.5%. Others appeared with small proportions H (1.4%, LAM (1.8%, T (8.1%, X (0.9%, MANU (2.3%, and Zero (0.4%. Higher clustering rate was found in the hospital samples (17.9% in urban and 19.2% in rural areas compared to the population ones (0%. The typical Vietnamese EAI4-VNM sub-lineage of EAI lineage accounted for 67% of EAI strains and was associated with older ages. Beijing genotypes were associated with younger, urban population and were characterized by high clustering rates. These characteristics strongly suggest that Beijing strains are invading the population, replacing the local EAI-VNM4, thus predicting a more serious tuberculosis situation in the future in the absence of more effective control strategies.

  8. Digestive physiology of captive giant anteaters (Myrmecophaga tridactyla): determinants of faecal dry matter content.

    Science.gov (United States)

    Gull, J M; Stahl, M; Osmann, C; Ortmann, S; Kreuzer, M; Hatt, J-M; Clauss, M

    2015-06-01

    Giant anteaters (Myrmecophaga tridactyla) are specialized insectivores and consume mainly ants and termites in the wild. In captivity, giant anteaters are either fed a complete diet, or a combination of a domestic carnivore diet with leaf eater pellets, or a traditional gruel-type diet. Soft faeces are a frequently encountered problem with this type of feeding. In the present study, we analysed diet and faeces composition, calculated digestibility and measured mean retention time on various diets in eight giant anteaters (total of n = 64 experiments). The results suggest that the digestive physiology of giant anteaters is similar to that of domestic dogs and cats in terms of nutrient digestibility and digesta retention. When testing correlations between faecal dry matter content and other variables, no relationship with dietary crude fibre content or mean digesta retention time could be detected. However, acid insoluble ash intake was significantly and positively correlated with faecal dry matter content. The amount of acid insoluble ash excreted with the faeces was higher than that ingested with the diet offered, indicating that the giant anteaters ingested soil from their enclosure of up to 93 g per day. This finding is consistent with observation of faeces of wild giant anteaters that contain soil or sand most likely due to indiscriminate feeding. It also corresponds to reports that indigestible materials such as peat, soil, chitin or cellulose contribute to a firmer faecal consistency in various carnivore species. Therefore, offering giant anteaters the opportunity to voluntarily ingest soil from their enclosure might be beneficial. Journal of Animal Physiology and Animal Nutrition © 2014 Blackwell Verlag GmbH.

  9. Seasonal evolution of faecal egg output by gastrointestinal worms in goats on communal farms in eastern Namibia

    Directory of Open Access Journals (Sweden)

    F.F. Kumba

    2003-11-01

    Full Text Available As a more detailed continuation of a previous study, faecal samples for worm egg counts were collected per rectum from ten marked adult animals in selected flocks of goats, in each of six villages evenly spread out in the communal farming district of Okakarara in eastern Namibia. The study was conducted on a monthly basis from August 1999 to July 2000. Average faecal worm egg counts (FECs were highest during the warm-wet season, much lower during the cold-dry months and moderate during the hot-dry season. Least square means of FECs were 2 140, 430 and 653 per gram of faeces for the three seasons, respectively. Seasonal variation in egg counts was significant (P < 0.0001. Gastrointestinal strongyles, and to a lesser extent Strongyloides species, were the predominant parasite groups identified in goats. Kidding rates peaked in the cold-dry season and mortality rates in the hot-dry season. Results of this study suggest that gastrointestinal parasitism may be a problem that accentuates the effect of poor nutrition on small ruminants during the season of food shortages in the east of Namibia and that the use of FECs per se to assess the severity of gastrointestinal parasitic infection in goats followed by chemoprophylactic strategic and / or tactical treatment, may not be the best approach to addressing the worm problem under resource-poor conditions. The use of the FAMACHA(c system that identifies severely affected animals for treatment is technically a better option for communal farmers.

  10. A vegan or vegetarian diet substantially alters the human colonic faecal microbiota.

    Science.gov (United States)

    Zimmer, J; Lange, B; Frick, J-S; Sauer, H; Zimmermann, K; Schwiertz, A; Rusch, K; Klosterhalfen, S; Enck, P

    2012-01-01

    Consisting of ≈10(14) microbial cells, the intestinal microbiota represents the largest and the most complex microbial community inhabiting the human body. However, the influence of regular diets on the microbiota is widely unknown. We examined faecal samples of vegetarians (n=144), vegans (n=105) and an equal number of control subjects consuming ordinary omnivorous diet who were matched for age and gender. We used classical bacteriological isolation, identification and enumeration of the main anaerobic and aerobic bacterial genera and computed absolute and relative numbers that were compared between groups. Total counts of Bacteroides spp., Bifidobacterium spp., Escherichia coli and Enterobacteriaceae spp. were significantly lower (P=0.001, P=0.002, P=0.006 and P=0.008, respectively) in vegan samples than in controls, whereas others (E. coli biovars, Klebsiella spp., Enterobacter spp., other Enterobacteriaceae, Enterococcus spp., Lactobacillus spp., Citrobacter spp. and Clostridium spp.) were not. Subjects on a vegetarian diet ranked between vegans and controls. The total microbial count did not differ between the groups. In addition, subjects on a vegan or vegetarian diet showed significantly (P=0.0001) lower stool pH than did controls, and stool pH and counts of E. coli and Enterobacteriaceae were significantly correlated across all subgroups. Maintaining a strict vegan or vegetarian diet results in a significant shift in the microbiota while total cell numbers remain unaltered.

  11. Genotyping of Single Nucleotide Polymorphisms in DNA Isolated from Serum Using Sequenom MassARRAY Technology.

    Directory of Open Access Journals (Sweden)

    Tess V Clendenen

    Full Text Available Large epidemiologic studies have the potential to make valuable contributions to the assessment of gene-environment interactions because they prospectively collected detailed exposure data. Some of these studies, however, have only serum or plasma samples as a low quantity source of DNA.We examined whether DNA isolated from serum can be used to reliably and accurately genotype single nucleotide polymorphisms (SNPs using Sequenom multiplex SNP genotyping technology. We genotyped 81 SNPs using samples from 158 participants in the NYU Women's Health Study. Each participant had DNA from serum and at least one paired DNA sample isolated from a high quality source of DNA, i.e. clots and/or cell precipitates, for comparison.We observed that 60 of the 81 SNPs (74% had high call frequencies (≥95% using DNA from serum, only slightly lower than the 85% of SNPs with high call frequencies in DNA from clots or cell precipitates. Of the 57 SNPs with high call frequencies for serum, clot, and cell precipitate DNA, 54 (95% had highly concordant (>98% genotype calls across all three sample types. High purity was not a critical factor to successful genotyping.Our results suggest that this multiplex SNP genotyping method can be used reliably on DNA from serum in large-scale epidemiologic studies.

  12. Detection of the pandemic norovirus variant GII.4 Sydney 2012 in Rio Branco, state of Acre, northern Brazil

    Directory of Open Access Journals (Sweden)

    Luciana Damascena da Silva

    2013-12-01

    Full Text Available Noroviruses (NoVs are important cause of gastroenteritis in humans worldwide. Genotype GII.4 is responsible for the majority of outbreaks reported to date. This study describes, for the first time in Brazil, the circulation of NoV GII.4 variant Sydney 2012 in faecal samples collected from children aged less than or equal to eight years in Rio Branco, state of Acre, northern Brazil, during July-September 2012.

  13. Age-specific prevalence of HPV genotypes in cervical cytology samples with equivocal or low-grade lesions

    Science.gov (United States)

    Brismar-Wendel, S; Froberg, M; Hjerpe, A; Andersson, S; Johansson, B

    2009-01-01

    Background: To define the spectrum of human papillomavirus (HPV) types and establish an age limit for triage HPV testing in atypical squamous cells of undetermined significance (ASCUS) and low-grade squamous intraepithelial lesion (LSIL). Materials and methods: 343 liquid-based cytological samples from the population-based screening programme with minor abnormalities were subjected to HPV genotyping (Linear Array, Roche, Basel, Switzerland). Results: High-risk human papillomavirus (HR-HPV) was found in 71% of LSIL and 49% of ASCUS cases (Page-dependent in LSIL (P=0.01), with decreasing prevalence until the age of 50 years, followed by a slight increase. Human papillomavirus type 16 was the most common HR-HPV, found in 23% of HPV-positive women. Human papillomavirus type 18 was the sixth most common, found in 9.9% (Page-dependent quadratic trend was observed for multiple infections (P=0.01) with a trough at about 42 years. The most common HR-HPV types to show a coinfection with HPV16 (clade 9) were HPV39 (28%), 45 (38%), and 59 (46%), belonging to HPV18 clade 7. The frequency of low-risk (LR) vs probable HR and HR-HPV also followed an age-dependent quadratic trend. Conclusions: After the age of 25 years, HR-HPV prevalence is similar in LSIL and ASCUS cases, motivating a low age limit for triage HPV testing. Multiple infections and LR/HR-HPV dominance are age-dependent. Genotyping in longitudinal design is needed to elucidate the importance of multiple infections in cancer progression and in cross-protection from vaccination. PMID:19623178

  14. Detection and genotyping of enteroviruses in cerebrospinal fluid in patients in Victoria, Australia, 2007-2013.

    Science.gov (United States)

    Papadakis, Georgina; Chibo, Doris; Druce, Julian; Catton, Michael; Birch, Chris

    2014-09-01

    Genotyping by VP1 fragment polymerase chain reaction (PCR) and nucleic acid sequencing to detect enterovirus (EV) genotypes was performed directly on 729 EV PCR positive cerebrospinal fluid (CSF) samples collected between 2007 and 2012 from Victorian hospital inpatients. The overall genotype identification rate from CSF-positive material was 43%. The four most common genotypes identified were Echovirus 6 (24%), Echovirus 30 (17%), Echovirus 25 (10%), and Coxsackievirus A9 (10%), together comprising 61% of all EVs typed. The seasonal distribution of all EVs identified followed the recognized pattern of mainly summer epidemics. Three of the four predominant genotypes were present in each of the 6 years in which the study was conducted, with 20 other EV genotypes also detected, often in only a single year. Genotyping of EVs directly in CSF is faster, simpler and more sensitive than traditional virus neutralization assays performed on EV positive samples. © 2014 Wiley Periodicals, Inc.

  15. The genetic diversity of hepatitis A genotype I in Bulgaria.

    Science.gov (United States)

    Cella, Eleonora; Golkocheva-Markova, Elitsa N; Trandeva-Bankova, Diljana; Gregori, Giulia; Bruni, Roberto; Taffon, Stefania; Equestre, Michele; Costantino, Angela; Spoto, Silvia; Curtis, Melissa; Ciccaglione, Anna Rita; Ciccozzi, Massimo; Angeletti, Silvia

    2018-01-01

    The purpose of this study was to analyze sequences of hepatitis A virus (HAV) Ia and Ib genotypes from Bulgarian patients to investigate the molecular epidemiology of HAV genotype I during the years 2012 to 2014. Around 105 serum samples were collected by the Department of Virology of the National Center of Infectious and Parasitic Diseases in Bulgaria. The sequenced region encompassed the VP1/2A region of HAV genome. The sequences obtained from the samples were 103. For the phylogenetic analyses, 5 datasets were built to investigate the viral gene in/out flow among distinct HAV subpopulations in different geographic areas and to build a Bayesian dated tree, Bayesian phylogenetic and migration pattern analyses were performed. HAV Ib Bulgarian sequences mostly grouped into a single clade. This indicates that the Bulgarian epidemic is partially compartmentalized. It originated from a limited number of viruses and then spread through fecal-oral local transmission. HAV Ia Bulgarian sequences were intermixed with European sequences, suggesting that an Ia epidemic is not restricted to Bulgaria but can affect other European countries. The time-scaled phylogeny reconstruction showed the root of the tree dating in 2008 for genotype Ib and in 1999 for genotype Ia with a second epidemic entrance in 2003. The Bayesian skyline plot for genotype Ib showed a slow but continuous growth, sustained by fecal-oral route transmission. For genotype Ia, there was an exponential growth followed by a plateau, which suggests better infection control. Bidirectional viral flow for Ib genotype, involving different Bulgarian areas, was observed, whereas a unidirectional flow from Sofia to Ihtiman for genotype Ia was highlighted, suggesting the fecal-oral transmission route for Ia. Copyright © 2017 The Authors. Published by Wolters Kluwer Health, Inc. All rights reserved.

  16. Raw meat based diet influences faecal microbiome and end products of fermentation in healthy dogs.

    Science.gov (United States)

    Sandri, Misa; Dal Monego, Simeone; Conte, Giuseppe; Sgorlon, Sandy; Stefanon, Bruno

    2017-02-28

    Dietary intervention studies are required to deeper understand the variability of gut microbial ecosystem in healthy dogs under different feeding conditions and to improve diet formulations. The aim of the study was to investigate in dogs the influence of a raw based diet supplemented with vegetable foods on faecal microbiome in comparison with extruded food. Eight healthy adult Boxer dogs were recruited and randomly divided in two experimental blocks of 4 individuals. Dogs were regularly fed a commercial extruded diet (RD) and starting from the beginning of the trial, one group received the raw based diet (MD) and the other group continued to be fed with the RD diet (CD) for a fortnight. After 14 days, the two groups were inverted, the CD group shifted to the MD and the MD shifted to the CD, for the next 14 days. Faeces were collected at the beginning of the study (T0), after 14 days (T14) before the change of diet and at the end of experimental period (T28) for DNA extraction and analysis of metagenome by sequencing 16SrRNA V3 and V4 regions, short chain fatty acids (SCFA), lactate and faecal score. A decreased proportion of Lactobacillus, Paralactobacillus (P diet significantly (P diet composition modifies faecal microbial composition and end products of fermentation. The administration of MD diet promoted a more balanced growth of bacterial communities and a positive change in the readouts of healthy gut functions in comparison to RD diet.

  17. The effects of feeding resistant starch on apparent total tract macronutrient digestibility, faecal characteristics and faecal fermentative end-products in healthy adult dogs.

    Science.gov (United States)

    Beloshapka, Alison N; Alexander, Lucille G; Buff, Preston R; Swanson, Kelly S

    2014-01-01

    The benefits of whole grain consumption have been studied in human subjects, but little research exists on their effects in dogs. The objective of the present study was to test the effects of resistant starch (RS) in the diet of healthy adult dogs. Twelve adult Miniature Schnauzer dogs (eight males, four females; mean age: 3·3 (1·6) years; mean body weight: 8·4 (1·2) kg; mean body condition score: D/ideal) were randomly allotted to one of three treatment groups, which consisted of different amounts of RS supplied in a biscuit format. Dogs received either 0, 10 or 20 g biscuits per d (estimated to be 0, 2·5 or 5 g RS per d) that were fed within their daily energetic allowance. A balanced Latin square design was used, with each treatment period lasting 21 d (days 0-17 adaptation; days 18-21 fresh and total faecal collection). All dogs were fed the same diet to maintain body weight throughout the study. Dogs fed 5 g RS per d had lower (P = 0·03) fat digestibility than dogs fed 0 gRS per d, but DM, organic matter and crude protein digestibilities were not affected. Faecal fermentative end-products, including SCFA and branched-chain fatty acids, ammonia, phenols and indoles, and microbial populations were not affected. The minor changes observed in the present study suggest the RS doses provided to the dogs were too low. Further work is required to assess the dose of RS required to affect gut health.

  18. Genetic patterns in forest antelope populations in the Udzungwa Mountains, Tanzania, as inferred from non-invasive sampling

    DEFF Research Database (Denmark)

    Bowkett, Andrew E.; Jones, Trevor; Rovero, Francesco

    2015-01-01

    As for many tropical regions, the evolutionary and demographic status of antelope populations in the Udzungwa Mountains, Tanzania, are poorly resolved. We employed genetic information from 618 faecal samples to assess the status of forest antelope species in terms of their distribution, intraspec...... except the endangered C. spadix. Overall, our results demonstrate the value of non-invasive genetic sampling in studying the distribution and evolution of rarely observed species.......As for many tropical regions, the evolutionary and demographic status of antelope populations in the Udzungwa Mountains, Tanzania, are poorly resolved. We employed genetic information from 618 faecal samples to assess the status of forest antelope species in terms of their distribution......, intraspecific diversity and population subdivision within the Udzungwa landscape. Most species were detected in the majority of forest fragments, except for Philantomba monticola. Phylogenetic analyses were consistent with traditional taxonomy with the exception of Cephalophus harveyi which was paraphyletic...

  19. The potential beneficial role of faecal microbiota transplantation in diseases other than Clostridium difficile infection

    NARCIS (Netherlands)

    Singh, R.; Nieuwdorp, M.; ten Berge, I. J. M.; Bemelman, F. J.; Geerlings, S. E.

    2014-01-01

    This review gives an outline of the indications for faecal microbiota transplantation (FMT) for diseases other than Clostridium difficile (C. difficile) infection. The remarkable efficacy of FMT against C. difficile infection has already been demonstrated. The use of FMT for other diseases, such as

  20. A comparison of faecal analysis with backtracking to determine the diet composition and species preference of the black rhinoceros (Diceros bicornis minor)

    OpenAIRE

    Lieverloo, van, R.J.; Schuiling, B.F.; Boer, de, W.F.; Lent, P.C.; Jong, de, C.B.; Brown, D.; Prins, H.H.T.

    2009-01-01

    The diet of black rhinoceros (Diceros bicornis minor) was studied using backtracking and faecal analysis in South Africa. Both methods yielded different results, with a large bias for dominant species. Results of backtracking showed that the rhinos browsed on 80 plant species. Grasses comprised 4.5% of the diet in the faecal analysis, but were not recorded during the backtracking. The backtracking method, along with a measure of forage availability, was used to identify two groups of plant sp...

  1. Does the Internet provide patients or clinicians with useful information regarding faecal incontinence? An observational study.

    Science.gov (United States)

    Leo, C A; Murphy, J; Hodgkinson, J D; Vaizey, C J; Maeda, Y

    2018-01-01

    The Internet has become an important platform for information communication. This study aim to investigate the utility of social media and search engines to disseminate faecal incontinence information. We looked into Social media platforms and search engines. There was not a direct patient recruitment and any available information from patients was already on public domain at the time of search. A quantitative analysis of types and volumes of information regarding faecal incontinence was made. Twelve valid pages were identified on Facebook: 5 (41%) pages were advertising commercial incontinence products, 4 (33%) pages were dedicated to patients support groups and 3 (25%) pages provided healthcare information. Also we found 192 Facebook posts. On Twitter, 2890 tweets were found of which 51% tweets provided healthcare information; 675 (45%) were sent by healthcare professionals to patients, 530 tweets (35.3%) were between healthcare professionals, 201 tweets (13.4%) were from medical journals or scientific books and 103 tweets (7%) were from hospitals or clinics with information about events and meetings. The second commonest type of tweets was advertising commercial incontinence products 27%. Patients tweeted to exchange information and advice between themselves (20.5%). In contrast, search engines as Google/Yahoo/Bing had a higher proportion of healthcare information (over 70%). Internet appears to have potential to be a useful platform for patients to learn about faecal incontinence and share information; however, given one lack of focus of available data, patients may struggle to identify valid and useful information.

  2. Importance of the fat content within the cheese-matrix for blood lipid profile, faecal fat excretion, and gut microbiome in growing pigs

    DEFF Research Database (Denmark)

    Thorning, Tanja K.; Raben, Anne; Bendsen, Nathalie T.

    2016-01-01

    and energy excretion and gut microbiome in pigs. A 14-d run-in period was followed by 14-d interventions with macronutrient-matched diets. Fasting total cholesterol and HDL-cholesterol after 14 days were higher in REG compared with BUT, but only tended to be higher in RED. Compared with BUT, REG and RED had......Cheese and butter have been shown to affect blood lipids differently. This parallel-arm, randomised, controlled study in 36 crossbred growing sows compared the effect of diets with either regular-fat cheese (REG), reduced-fat cheese + butter (RED) or butter (BUT) on blood lipids, faecal fat...... higher faecal fat excretion. Faecal energy excretion was only higher in REG, and this correlated with a lower microbiome Firmicutes-to-Bacteroidetes ratio. In conclusion, dairy fat consumed as cheese or butter caused different metabolic effects. Differences between reduced-fat cheese+butter and butter...

  3. Simultaneous Delorme's procedure and inter-sphinteric prosthetic implant for the treatment of rectal prolapse and faecal incontinence: preliminary experience and literature review.

    Science.gov (United States)

    Cavazzoni, Emanuel; Rosati, Emanuele; Zavagno, Valentina; Graziosi, Luigina; Donini, Annibale

    2015-02-01

    Rectal prolapse is a distressing condition affecting mostly elderly patients and females. Delorme's procedure is frequently performed since it offers good results and is burdened by a particularly low morbidity. Faecal Incontinence is associated with prolapse in a large percentage of patients, due to the sphincter damage caused by the prolapsed rectum through the anal canal. Prolapse resection is often ineffective in treating incontinence, and further specific procedures are frequently required. At present, no data are available on combined Delorme's procedure with the implant of Bulking Agents for the simultaneous treatment of rectal prolapse and faecal incontinence. Three patients affected by complete external rectal prolapse underwent simultaneous Delorme's procedure with application of six polyacrylonitrile prosthetic cylinders in the inter-sphinteric space (Gate Keeper™, THD, Correggio Italy). Follow up was at 3,6 and 12 months. Gate Keeper procedure required a short operative time; no morbidity or complications were experienced. Prolapse was successfully treated in all patients and the mean Vaizey's incontinence score value dropped from pre-operative 19.3 to 9.3 after 3 months. All patients experienced a reduction of incontinence episodes and an improvement in daily activities and lifestyle. Gate Keeper implant is feasible and safe when associated to surgical procedures like Delorme's prolapse resection. Preliminary results are positive even if a study with a larger numbers of patients is needed to confirm the efficacy. A simultaneous treatment of faecal incontinence should be always considered when performing surgery for rectal prolapse. The present manuscript describes a simultaneous combination of two surgical techniques to treat rectal prolapse and faecal incontinence. To date, there are no published data on a similar approach. The paper underlies the importance of treating faecal incontinence when performing surgery for rectal prolapse. Copyright

  4. First record of Giardia assemblage D infection in farmed raccoon dogs (Nyctereutes procyonoides

    Directory of Open Access Journals (Sweden)

    Piotr Solarczyk

    2016-09-01

    Full Text Available The presence of Giardia genotypes was investigated in 18 raccoon dogs ( Nyctereutes procyonoides and 80 red foxes ( Vulpes vulpes on one farm. To demonstrate Giardia cysts, fresh and trichrome stained smears were microscopically screened. Two molecular markers were used for Giardia genotyping: a fragment of the beta-giardin gene and a fragment of the glutamate dehydrogenase gene. All faecal samples obtained from red foxes were negative. Giardia cysts were identified only in 2 of the 18 raccoon dogs. The result of genotyping and phylogenetic analysis showed that the G. duodenalis from both raccoon dogs belonged to the D assemblage. This finding of a new animal reservoir of G. duodenalis canids-specific genotypes is important in order to eliminate the risk of infecting other animals bred for fur. Further molecular analyses of Giardia isolates in raccoon dogs are required. The present study represents the first contribution to knowledge of G. duodenalis genotypes in raccoon dogs.

  5. Sample preparation for avian and porcine influenza virus cDNA amplification simplified: Boilign vs. conventional RNA extraction

    International Nuclear Information System (INIS)

    Fereidouni, S.R.; Starick, E.; Ziller, M.; Harder, T.C.; Unger, H.; Hamilton, K.; Globig, A.

    2016-01-01

    Full text: RNA extraction and purification is a fundamental step that allows for highly sensitive amplification of specific RNA targets in PCR applications. However, commercial extraction kits that are broadly used because of their robustness and high yield of purified RNA are expensive and labor-intensive. In this study, boiling in distilled water or a commerical lysis buffer of different sample matrices containing avian or porcine influenza viruses was tested as an alternative. Real-time PCR (RTaPCR) for nucleoprotein gene fragment was used as read out. Results were compared with freshly extracted RNA by use of a commercial extraction kit. Different batches of virus containing material materials, including diluted virus positive allontoic fluid or cell culture supernatnat, and avian faecal, cloacal or oropharyngeal swab samples were used in this study. Simple boiling of samples without any additional purification steps can be used as an alternative RNA preparation method to detect influenza A virus nucleoprotein RNA in oropharyngeal swab samples, allantoic fluid or cell-culture supernatant. The boiling method is not applicable for sample matrices containing faecal material. (author)

  6. Concept and design of a genome-wide association genotyping array tailored for transplantation-specific studies

    DEFF Research Database (Denmark)

    Li, Yun R.; van Setten, Jessica; Verma, Shefali S.

    2015-01-01

    genome-wide genotyping array, the 'TxArray', comprising approximately 782,000 markers with tailored content for deeper capture of variants across HLA, KIR, pharmacogenomic, and metabolic loci important in transplantation. To test concordance and genotyping quality, we genotyped 85 HapMap samples...

  7. Breed traceability of buffalo meat using microsatellite genotyping technique.

    Science.gov (United States)

    Kannur, Bheemashankar H; Fairoze, Md Nadeem; Girish, P S; Karabasanavar, Nagappa; Rudresh, B H

    2017-02-01

    Although buffalo has emerged as a major meat producing animal in Asia, major research on breed traceability has so far been focused on cattle (beef). This research gap on buffalo breed traceability has impelled development and validation of buffalo breed traceability using a set of eight microsatellite (STR) markers in seven Indian buffalo breeds (Bhadawari, Jaffaarabadi, Murrah, Mehsana, Nagpuri, Pandharpuri and Surti). Probability of sharing same profile by two individuals at a specific locus was computed considering different STR numbers, allele pooling in breed and population. Match probabilities per breed were considered and six most polymorphic loci were genotyped. Out of eight microsatellite markers studied, markers CSSMO47, DRB3 and CSSM060 were found most polymorphic. Developed technique was validated with known and unknown, blood and meat samples; wherein, samples were genetically traced in 24 out of 25 samples tested. Results of this study showed potential applications of the methodology and encourage other researchers to address the problem of buffalo traceability so as to create a world-wide archive of breed specific genotypes. This work is the first report of breed traceability of buffalo meat utilizing microsatellite genotyping technique.

  8. Validation of an enzyme-immunoassay for the non-invasive monitoring of faecal testosterone metabolites in male cheetahs (Acinonyx jubatus).

    Science.gov (United States)

    Pribbenow, Susanne; Wachter, Bettina; Ludwig, Carsten; Weigold, Annika; Dehnhard, Martin

    2016-03-01

    In mammals, the sex hormone testosterone is the major endocrine variable to objectify testicular activity and thus reproductive function in males. Testosterone is involved in the development and function of male reproductive physiology and sex-related behaviour. The development of a reliable androgen enzyme-immunoassay (EIA) to monitor faecal testosterone metabolites (fTM) is a powerful tool to non-invasively assess the gonadal status of males. We validated an epiandrosterone EIA for male cheetahs by performing a testosterone radiometabolism study followed by high-performance liquid chromatography (HPLC) analyses and excluding possible cross-reactivities with androgenic metabolites not derived from testosterone metabolism. The physiological and biological relevance of the epiandrosterone EIA was validated by demonstrating (1) a significant increase in fTM concentrations within one day in response to a testosterone injection, (2) a significant increase in fTM concentrations within one day in response to a gonadotropin-releasing hormone (GnRH) injection, which failed following a placebo injection, and (3) significant differences in fTM concentrations between adult male and adult female cheetahs and between adult and juvenile male cheetahs of a free-ranging population. Finally, we demonstrated stability of fTM concentrations measured in faecal samples exposed to ambient temperatures up to 72h. Our results clearly demonstrate that the epiandrosterone EIA is a reliable non-invasive method to monitor testicular activity in male cheetahs. Copyright © 2016 Elsevier Inc. All rights reserved.

  9. Saponin profile of green asparagus genotypes.

    Science.gov (United States)

    Vázquez-Castilla, Sara; Jaramillo-Carmona, Sara; Fuentes-Alventosa, Jose María; Jiménez-Araujo, Ana; Rodríguez-Arcos, Rocío; Cermeño-Sacristán, Pedro; Espejo-Calvo, Juan Antonio; Guillén-Bejarano, Rafael

    2013-11-20

    The main goal of this study was to determine the saponin profiles of different "triguero" asparagus genotypes and to compare them to green asparagus commercial hybrids. The samples consisted of 31 commercial hybrids and 58 genotypes from the Huétor-Tájar (HT) population variety ("triguero"). The saponin analysis by high-performance liquid chromatography-mass spectrometry allowed for the determination of 12 saponins derived from a furostan-type steroidal genin, 4 of which had never been described in the edible part of asparagus. The saponin profile of "triguero" asparagus was a combination of these new saponins and protodioscin. Although protodioscin was the major saponin found in commercial hybrids, some of these 12 saponins were detected as major components in some of the commercial hybrids. The total contents of saponins described in some of these HT genotypes reach values as high as 10-100 times higher than those found in commercial hybrids.

  10. Effect of oral diclofenac intake on faecal calprotectin.

    Science.gov (United States)

    Rendek, Zlatica; Falk, Magnus; Grodzinsky, Ewa; Wahlin, Karl; Kechagias, Stergios; Svernlöv, Rikard; Hjortswang, Henrik

    2016-01-01

    NSAIDs are a known source of increased faecal calprotectin (FC) levels. Currently, there is a lack of knowledge about how long it takes for an increased FC level to return to normal after NSAID intake. The aim was to investigate how oral diclofenac intake affects FC levels and assess how long it takes for an increased FC level to return to normal after oral diclofenac intake. Thirty healthy volunteers received diclofenac 50 mg three times daily for 14 days. Participants provided a stool sample on Days 0, 2, 4, 7, 14 during intake and Days 17, 21, 28 after discontinuation. FC levels were then followed at 7-day intervals until normalization. During diclofenac intake, eight participants (27%) had FC levels exceeding the upper limit of normal (median, 76 μg/g; range, 60-958 μg/g), corresponding to 8.3% of measurements. FC was not constantly increased and became normal in most participants during diclofenac intake. FC levels were on average significantly higher during intake (M = 9.5, interquartile range (IQR) = 13.4) than on baseline (M = 7.5, IQR = 0.0), p = 0.003. After discontinuation, two participants had increased FC on Days 17 and 21, respectively. No significant differences in FC levels were found between baseline and measurements after discontinuation. Two weeks after discontinuation, all participants had normal FC levels. Short-term oral diclofenac intake is associated with increased FC levels. However, the likelihood of an increased test result is low. Our results suggest that 2 weeks of diclofenac withdrawal is sufficient to get an uninfluenced FC test result.

  11. Efficacy of β-mannanase supplementation to corn-soya bean meal-based diets on growth performance, nutrient digestibility, blood urea nitrogen, faecal coliform and lactic acid bacteria and faecal noxious gas emission in growing pigs.

    Science.gov (United States)

    Upadhaya, Santi Devi; Park, Jae Won; Lee, Jae Hwan; Kim, In Ho

    2016-01-01

    A study was conducted to determine the efficacy of β-mannanase supplementation to a diet based on corn and soya bean meal (SBM) on growth performance, nutrient digestibility, blood urea nitrogen (BUN), faecal coliforms and lactic acid bacteria, and noxious gas emission in growing pigs. A total of 140 pigs [(Landrace × Yorkshire) × Duroc; average body weight 25 ± 3 kg] were randomly allotted to a 2 × 2 factorial arrangement with dietary treatments consisting of hulled or dehulled SBM without or with supplementation of 400 U β-mannanase/kg. During the 6 weeks of experimental feeding, β-mannanase supplementation had no effect on body weight gain, feed intake and gain:feed (G:F) ratio. Compared with dehulled SBM, feeding hulled SBM caused an increased feed intake of pigs in the entire trial (p = 0.05). The G:F ratio was improved in pigs receiving dehulled SBM (p < 0.05). Dietary treatments did not influence the total tract digestibility of dry matter, nitrogen and gross energy. Enzyme supplementation reduced (p < 0.05) the population of faecal coliforms and tended to reduce the NH3 concentration after 24 h of fermentation in a closed box containing faecal slurry. Feeding hulled SBM tended to reduce NH3 emission on days 3 and 5 of fermentation. In conclusion, mannanase supplementation had no influence on growth performance and nutrient digestibility but showed a positive effect on reducing coliform population and tended to reduce NH3 emission. Dehulled SBM increased G:F ratio and hulled SBM tended to reduce NH3 emission.

  12. [The artificial sphincter: therapy for faecal incontinence].

    Science.gov (United States)

    Baumgartner, U

    2012-08-01

    Faecal incontinence (FI) challenges a patient's professional, social and sexual life. Often the patient becomes depressive and socially isolated. If able to break open for therapy the patient should receive as first line a conservative treatment (like dietary measures, pelvic re-education, biofeedback, bulking agents, irrigation). When is the time to implant an artificial anal sphincter? If conservative therapy fails as well as surgical options (like a sphincteroplasty - if indicated a reconstruction of the pelvic floor if insufficient, or a sacral nerve stimulation) an ultimo surgical procedure should be offered to appropriate and compliant patients: an artificial anal sphincter. Worldwide, there are two established devices on the market: the artificial bowel sphincter® (ABS) from A. M. S. (Minnetonka, MN, USA) and the soft anal band® from A. M. I. (Feldkirch, Austria). How to implant the artificial anal sphincter? Both devices consist of a silicon cuff which can be filled with fluid. Under absolute aseptic conditions this cuff is placed in the lithotomy position by perianal incisions around the anal canal below the pelvic floor. A silicon tube connects the anal cuff with a reservoir (containing fluid) which is placed either behind the pubis bone in front of the bladder (ABS) or below the costal arch (anal band). With a pump placed in the scrotum/labia (ABS) or by pressing the balloon (anal band) in both types operated by the patient the fluid is shifted forth and back between the anal cuff and the reservoir closing or opening the anal canal. Both systems are placed completely subcutaneously. Both devices improve significantly the anal continence. Both systems have a high rate of reoperations. However, the causes for the redos are different. The ABS is associated with high infection and anal penetration rates of the cuff leading to an explantation rate to up to 60 % of the implants. This kind of complication seems to be much lower with the anal band. The major

  13. Inappropriate use of the faecal occult blood test in a university hospital in the Netherlands

    NARCIS (Netherlands)

    van Rijn, Anne F.; Stroobants, An K.; Deutekom, Marije; Lauppe, Corinne; Sturk, Auguste; Bossuyt, Patrick M. M.; Fockens, Paul; Dekker, Evelien

    2012-01-01

    Objectives Although all international guidelines state that there is no indication to perform a faecal occult blood test (FOBT) in symptomatic patients, we believe the test is frequently used as a diagnostic test. The objective of this study was to investigate whether the current guidelines for FOBT

  14. Dynamic variable selection in SNP genotype autocalling from APEX microarray data

    Directory of Open Access Journals (Sweden)

    Zamar Ruben H

    2006-11-01

    Full Text Available Abstract Background Single nucleotide polymorphisms (SNPs are DNA sequence variations, occurring when a single nucleotide – adenine (A, thymine (T, cytosine (C or guanine (G – is altered. Arguably, SNPs account for more than 90% of human genetic variation. Our laboratory has developed a highly redundant SNP genotyping assay consisting of multiple probes with signals from multiple channels for a single SNP, based on arrayed primer extension (APEX. This mini-sequencing method is a powerful combination of a highly parallel microarray with distinctive Sanger-based dideoxy terminator sequencing chemistry. Using this microarray platform, our current genotype calling system (known as SNP Chart is capable of calling single SNP genotypes by manual inspection of the APEX data, which is time-consuming and exposed to user subjectivity bias. Results Using a set of 32 Coriell DNA samples plus three negative PCR controls as a training data set, we have developed a fully-automated genotyping algorithm based on simple linear discriminant analysis (LDA using dynamic variable selection. The algorithm combines separate analyses based on the multiple probe sets to give a final posterior probability for each candidate genotype. We have tested our algorithm on a completely independent data set of 270 DNA samples, with validated genotypes, from patients admitted to the intensive care unit (ICU of St. Paul's Hospital (plus one negative PCR control sample. Our method achieves a concordance rate of 98.9% with a 99.6% call rate for a set of 96 SNPs. By adjusting the threshold value for the final posterior probability of the called genotype, the call rate reduces to 94.9% with a higher concordance rate of 99.6%. We also reversed the two independent data sets in their training and testing roles, achieving a concordance rate up to 99.8%. Conclusion The strength of this APEX chemistry-based platform is its unique redundancy having multiple probes for a single SNP. Our

  15. Genotyping-By-Sequencing for Plant Genetic Diversity Analysis: A Lab Guide for SNP Genotyping

    Directory of Open Access Journals (Sweden)

    Gregory W. Peterson

    2014-10-01

    Full Text Available Genotyping-by-sequencing (GBS has recently emerged as a promising genomic approach for exploring plant genetic diversity on a genome-wide scale. However, many uncertainties and challenges remain in the application of GBS, particularly in non-model species. Here, we present a GBS protocol we developed and use for plant genetic diversity analysis. It uses two restriction enzymes to reduce genome complexity, applies Illumina multiplexing indexes for barcoding and has a custom bioinformatics pipeline for genotyping. This genetic diversity-focused GBS (gd-GBS protocol can serve as an easy-to-follow lab guide to assist a researcher through every step of a GBS application with five main components: sample preparation, library assembly, sequencing, SNP calling and diversity analysis. Specifically, in this presentation, we provide a brief overview of the GBS approach, describe the gd-GBS procedures, illustrate it with an application to analyze genetic diversity in 20 flax (Linum usitatissimum L. accessions and discuss related issues in GBS application. Following these lab bench procedures and using the custom bioinformatics pipeline, one could generate genome-wide SNP genotype data for a conventional genetic diversity analysis of a non-model plant species.

  16. A Non-Invasive Strategy for Neonatal Alloimmune Thrombocytopenia Diagnosis: Newborn Platelet Genotyping with Buccal Swabs

    Directory of Open Access Journals (Sweden)

    Gérald Bertrand

    2016-07-01

    Full Text Available Neonatal alloimmune thrombocytopenia results from the maternal immune response against fetal-specific antigens inherited from the father. The diagnosis is ascertained only when the maternal alloantibody and the offending antigen present in the newborn are identified. Up until now most laboratories perform DNA extraction for neonatal genotyping from newborn blood samplings. In order to avoid such an invasive procedure, two protocols of DNA extraction from buccal swabs were developed: a manual protocol using the QIAamp mini blood kit (Qiagen, and an automated procedure with the MagNA Pure Compact instrument (Roche. Both EDTA-blood and buccal swabs from thrombocytopenic newborns were genotyped manually (14 samples, automatically (15 samples or both manually and automatically (two samples. Human Platelet Antigen (HPA genotyping was performed using the BeadChip assay (BioArray, Immucor. Concordant genotypings were obtained for all samples except for one swab with the manual method. The automated DNA extraction from newborn buccal swabs with the MagNA Pure Compact instrument was chosen as the first-line strategy, with a significant gain of time in processing buccal swabs.

  17. ABO Blood Group Genotyping by Real-time PCR in Kazakh Population

    Directory of Open Access Journals (Sweden)

    Pavel Tarlykov

    2014-12-01

    Full Text Available Introduction. ABO blood group genotyping is a new technology in hematology that helps prevent adverse transfusion reactions in patients. Identification of antigens on the surface of red blood cells is based on serology; however, genotyping employs a different strategy and is aimed directly at genes that determine the surface proteins. ABO blood group genotyping by real-time PCR has several crucial advantages over other PCR-based techniques, such as high rapidity and reliability of analysis. The purpose of this study was to examine nucleotide substitutions differences by blood types using a PCR-based method on Kazakh blood donors.Methods. The study was approved by the Ethics Committee of the National Center for Biotechnology. Venous blood samples from 369 healthy Kazakh blood donors, whose blood types had been determined by serological methods, were collected after obtaining informed consent. The phenotypes of the samples included blood group A (n = 99, B (n = 93, O (n = 132, and AB (n = 45. Genomic DNA was extracted using a salting-out method. PCR products of ABO gene were sequenced on an ABI 3730xl DNA analyzer (Applied Biosystems. The resulting nucleotide sequences were compared and aligned against reference sequence NM_020469.2. Real-time PCR analysis was performed on CFX96 Touch™ Real-Time PCR Detection System (BioRad.Results. Direct sequencing of ABO gene in 369 samples revealed that the vast majority of nucleotide substitutions that change the ABO phenotype were limited to exons 6 and 7 of the ABO gene at positions 261, 467, 657, 796, 803, 930 and 1,060. However, genotyping of only three of them (261, 796 and 803 resulted in identification of major ABO genotypes in the Kazakh population. As a result, TaqMan probe based real-time PCR assay for the specific detection of genotypes 261, 796 and 803 was developed. The assay did not take into account several other mutations that may affect the determination of blood group, because they have a

  18. Prototheca zopfii genotypes isolated from cow barns and bovine mastitis in Japan.

    Science.gov (United States)

    Osumi, Takafumi; Kishimoto, Yuji; Kano, Rui; Maruyama, Haruhiko; Onozaki, Masanobu; Makimura, Koichi; Ito, Takaaki; Matsubara, Kiyoshi; Hasegawa, Atsuhiko

    2008-10-15

    This study is the first investigation on Japanese isolates of Prototheca zopfii from bovine mastitis and the cow-barn surroundings by molecular characterization to clarify routes of infection for bovine protothecal mastitis. We performed isolation of Prototheca from cow-barn surroundings (drinking water, sewage and feces) and milk samples from cases of bovine mastitis. Genotypes of the 32 isolates of P. zopfii from cow-barn surroundings and 67 isolates from mastitis were analyzed by genotype-specific PCR assays and restriction fragment length polymorphism (RFLP) assays. All mastitis isolates were identified as P. zopfii genotype 2. Conversely, 29 isolates from cow-barn surroundings were identified as P. zopfii genotypes 1 and 3 isolates as genotype 2, respectively. Given these results, both genotypes of P. zopfii could exist in cow-barn surroundings, but no sites were identified as frequent sources of P. zopfii genotype 2. P. zopfii isolates should thus be further explored with regard to genotype to clarify the reservoir of etiological agents in bovine Prototheca mastitis.

  19. A comparison of in vitro tests and a faecal egg count reduction test in detecting anthelmintic resistance in horse strongyles

    DEFF Research Database (Denmark)

    Craven, J.; Bjørn, H.; Barnes, E.H.

    1999-01-01

    This study reports a comparison between faecal egg count reduction test (FECRT), egg hatch assay (EHA) and larval development assay (LDA) for detecting anthelmintic resistance in equine strongyles. Resistance to benzimidazoles was demonstrated in 33 of 42 (79%) farms tested by FECRT and in 32 (62......%) of the 52 farms tested by EHA. As the reference strain used was not fully susceptible to benzimidazoles it was not possible to determine the level of resistance by LDA. Pyrantel resistance was indicated on three of 15 farms by faecal egg count reduction. Resistance was also indicated by LDA for one...

  20. Rotavirus Genotypes in Sewage Treatment Plants and in Children Hospitalized with Acute Diarrhea in Italy in 2010 and 2011

    Science.gov (United States)

    Ruggeri, Franco M.; Bonomo, Paolo; Ianiro, Giovanni; Battistone, Andrea; Delogu, Roberto; Germinario, Cinzia; Chironna, Maria; Triassi, Maria; Campagnuolo, Rosalba; Cicala, Antonella; Giammanco, Giovanni M.; Castiglia, Paolo; Serra, Caterina; Gaggioli, Andrea

    2014-01-01

    Although the molecular surveillance network RotaNet-Italy provides useful nationwide data on rotaviruses causing severe acute gastroenteritis in children in Italy, scarce information is available on rotavirus circulation in the general Italian population, including adults with mild or asymptomatic infection. We investigated the genotypes of rotaviruses present in urban wastewaters and compared them with those of viral strains from clinical pediatric cases. During 2010 and 2011, 285 sewage samples from 4 Italian cities were tested by reverse transcription-PCRs (RT-PCRs) specific for rotavirus VP7 and VP4 genes. Rotavirus was detected in 172 (60.4%) samples, 26 of which contained multiple rotavirus G (VP7 gene) genotypes, for a total of 198 G types. Thirty-two samples also contained multiple P (VP4 gene) genotypes, yielding 204 P types in 172 samples. Genotype G1 accounted for 65.6% of rotaviruses typed, followed by genotypes G2 (20.2%), G9 (7.6%), G4 (4.6%), G6 (1.0%), G3 (0.5%), and G26 (0.5%). VP4 genotype P[8] accounted for 75.0% of strains, genotype P[4] accounted for 23.0% of strains, and the uncommon genotypes P[6], P[9], P[14], and P[19] accounted for 2.0% of strains altogether. These rotavirus genotypes were also found in pediatric patients hospitalized in the same areas and years but in different proportions. Specifically, genotypes G2, G9, and P[4] were more prevalent in sewage samples than among samples from patients, which suggests either a larger circulation of the latter strains through the general population not requiring medical care or their greater survival in wastewaters. A high level of nucleotide identity in the G1, G2, and G6 VP7 sequences was observed between strains from the environment and those from patients. PMID:25344240

  1. Modeling of Faecal Contamination in Water from Catchment to Shellfish Growing Area

    OpenAIRE

    Bougeard, Morgane; Le Saux, Jean-claude; Perenne, Nicolas; Le Guyader, Soizick; Pommepuy, Monique

    2009-01-01

    During rainstorms, watersheds can introduce large amounts of faecal pollution into the rivers and sea, leading to shellfish contamination. In this study, we assessed Escherichia coli fluxes from a catchment, and their impact on estuarine water quality, using two assembled models. For the catchment, the agro-hydrological model SWAT was implemented integrating land uses, soil, topography, rainfall and other climatic data on Daoulas watershed (France). Initially, the SWAT model was calibrated an...

  2. Effects of DNA mass on multiple displacement whole genome amplification and genotyping performance

    Directory of Open Access Journals (Sweden)

    Haque Kashif A

    2005-09-01

    Full Text Available Abstract Background Whole genome amplification (WGA promises to eliminate practical molecular genetic analysis limitations associated with genomic DNA (gDNA quantity. We evaluated the performance of multiple displacement amplification (MDA WGA using gDNA extracted from lymphoblastoid cell lines (N = 27 with a range of starting gDNA input of 1–200 ng into the WGA reaction. Yield and composition analysis of whole genome amplified DNA (wgaDNA was performed using three DNA quantification methods (OD, PicoGreen® and RT-PCR. Two panels of N = 15 STR (using the AmpFlSTR® Identifiler® panel and N = 49 SNP (TaqMan® genotyping assays were performed on each gDNA and wgaDNA sample in duplicate. gDNA and wgaDNA masses of 1, 4 and 20 ng were used in the SNP assays to evaluate the effects of DNA mass on SNP genotyping assay performance. A total of N = 6,880 STR and N = 56,448 SNP genotype attempts provided adequate power to detect differences in STR and SNP genotyping performance between gDNA and wgaDNA, and among wgaDNA produced from a range of gDNA templates inputs. Results The proportion of double-stranded wgaDNA and human-specific PCR amplifiable wgaDNA increased with increased gDNA input into the WGA reaction. Increased amounts of gDNA input into the WGA reaction improved wgaDNA genotyping performance. Genotype completion or genotype concordance rates of wgaDNA produced from all gDNA input levels were observed to be reduced compared to gDNA, although the reduction was not always statistically significant. Reduced wgaDNA genotyping performance was primarily due to the increased variance of allelic amplification, resulting in loss of heterozygosity or increased undetermined genotypes. MDA WGA produces wgaDNA from no template control samples; such samples exhibited substantial false-positive genotyping rates. Conclusion The amount of gDNA input into the MDA WGA reaction is a critical determinant of genotyping performance of wgaDNA. At least 10 ng of

  3. Jerusalem artichoke and chicory inulin in bakery products affect faecal microbiota of healthy volunteers.

    Science.gov (United States)

    Kleessen, Brigitta; Schwarz, Sandra; Boehm, Anke; Fuhrmann, H; Richter, A; Henle, T; Krueger, Monika

    2007-09-01

    A study was conducted to test the effects of Jerusalem artichoke inulin (JA) or chicory inulin (CH) in snack bars on composition of faecal microbiota, concentration of faecal SCFA, bowel habit and gastrointestinal symptoms. Forty-five volunteers participated in a double-blind, randomized, placebo-controlled, parallel-group study. At the end of a 7 d run-in period, subjects were randomly assigned to three groups of fifteen subjects each, consuming either snack bars with CH or JA, or snack bars without fructans (placebo); for 7 d (adaptation period), they ingested one snack bar per day (7.7 g fructan/d) and continued for 14 d with two snack bars per day. The composition of the microbiota was monitored weekly. The consumption of CH or JA increased counts of bifidobacteria (+1.2 log10 in 21 d) and reduced Bacteroides/Prevotella in number and the Clostridium histolyticum/C. lituseburense group in frequency at the end of intervention (P bakery products stimulates the growth of bifidobacteria and may contribute to the suppression of potential pathogenic bacteria.

  4. Genotyping of Kell, Duffy, Kidd and RHD in patients with b Thalassemia

    Directory of Open Access Journals (Sweden)

    Castilho Lilian

    2000-01-01

    Full Text Available Determination of Rh, Kell, Duffy and Kidd phenotypes in addition to ABO is used to prevent the alloimmunization to red blood cells (RBCs antigens and as part of the antibody identification process in patients with beta Thalassemia. However, phenotyping in these patients can be time consuming and difficult to interpret. In these situations, it would be valuable to have an alternative to hemagglutination tests to determine the patient's antigen profile. We used PCR-RFLP to genotype such patients. DNA was prepared from 50 patients with beta Thalassemia who had been phenotyped by routine hemagglutination, and tested for Kell, Kidd, Duffy/GATA mutation by PCR-RFLP. RHD/non-D was analysed by PCR product size associated to RHD gene sequence in intron 4 and exon 10/3'UTR. The genotyping assays were performed without knowledge of phenotype results. For RHD/non-D, 47 were RhD+ and RHD+/RHCE+, and 3 were RhD- and RHD-/RHCE+. For Kell, 48 kk were K2K2 and 2 Kk were K1K2. For Duffy, of 44 samples that had normal GATA box, 8 Fy(a+b- were FYA/FYA, 15 Fy(a+b+ were FYB/FYB, and 19 Fy(a+b+ were FYA/FYB; of the other 4 samples 3 were FYA/FYB and heterozygous GATA mutation, and 1 Fy(a-b- was FYB/FYB, homozygous GATA mutation. Two samples phenotyped as Fy(a+b- that had normal GATA , presented the 265T/298A mutations and two samples phenotyped as Fy(a-b+ were genotyped was FYA/FYB.. For Kidd , 15 Jk(a+b were JKA/JKA, 12 Jk(a-b+ were JKB/JKB, and 20 Jk(a+b+ were JKA/JKB. Three samples phenotyped as JK(a+b+ were genotyped as JKB/JKB. Genotype is more accurate than phenotype for determination of blood groups in polytransfused patients with betaThalassemia. Genotyping in these patients can be helpful to select antigen-negative RBCs for transfusion.

  5. VacA and cagA genotypes of Helicobacter pylori isolated from raw meat in Isfahan province, Iran.

    Science.gov (United States)

    Gilani, Ali; Razavilar, Vadood; Rokni, Nordahr; Rahimi, Ebrahim

    2017-01-01

    Foods with animal origins play a substantial role in the transmission of Helicobacter pylori . The present investigation was carried out to study the vacA and cagA genotypes status of H. pylori isolated from various types of meat samples. Two hundred and twenty meat samples were collected and cultured. H. pylori -positive strains were analyzed for the presence of vacA and cagA genotypes. Eleven out of 220 (5.00%) samples were positive for H. pylori . Findings were confirmed by nested PCR. Prevalence of H. pylori in the meat samples of slaughterhouses and butcheries were 72.20% and 27.70%, respectively. The most commonly detected genotypes in the meat samples of slaughterhouses and butcheries were vacA m1a (66.66%) and vacA s1a (37.50%), respectively. The S1am1a was the most commonly detected genotype. Meat sampled from butcheries had the higher prevalence of H. pylori and its genotypes than those of slaughterhouses ( p meat samples could be the potential sources of virulent strains of H. pylori . Application of sanitary measures in the storage, transportation and sale of meat is essential for reducing the levels of H. pylori cross contamination.

  6. A Multiplex PCR for the Simultaneous Detection and Genotyping of the Echinococcus granulosus Complex

    Science.gov (United States)

    Boubaker, Ghalia; Macchiaroli, Natalia; Prada, Laura; Cucher, Marcela A.; Rosenzvit, Mara C.; Ziadinov, Iskender; Deplazes, Peter; Saarma, Urmas; Babba, Hamouda; Gottstein, Bruno; Spiliotis, Markus

    2013-01-01

    Echinococcus granulosus is characterized by high intra-specific variability (genotypes G1–G10) and according to the new molecular phylogeny of the genus Echinococcus, the E. granulosus complex has been divided into E. granulosus sensu stricto (G1–G3), E. equinus (G4), E. ortleppi (G5), and E. canadensis (G6–G10). The molecular characterization of E. granulosus isolates is fundamental to understand the spatio-temporal epidemiology of this complex in many endemic areas with the simultaneous occurrence of different Echinococcus species and genotypes. To simplify the genotyping of the E. granulosus complex we developed a single-tube multiplex PCR (mPCR) allowing three levels of discrimination: (i) Echinococcus genus, (ii) E. granulosus complex in common, and (iii) the specific genotype within the E. granulosus complex. The methodology was established with known DNA samples of the different strains/genotypes, confirmed on 42 already genotyped samples (Spain: 22 and Bulgaria: 20) and then successfully applied on 153 unknown samples (Tunisia: 114, Algeria: 26 and Argentina: 13). The sensitivity threshold of the mPCR was found to be 5 ng Echinoccoccus DNA in a mixture of up to 1 µg of foreign DNA and the specificity was 100% when template DNA from closely related members of the genus Taenia was used. Additionally to DNA samples, the mPCR can be carried out directly on boiled hydatid fluid or on alkaline-lysed frozen or fixed protoscoleces, thus avoiding classical DNA extractions. However, when using Echinococcus eggs obtained from fecal samples of infected dogs, the sensitivity of the mPCR was low (Echinococcus genus. PMID:23350011

  7. A multiplex PCR for the simultaneous detection and genotyping of the Echinococcus granulosus complex.

    Science.gov (United States)

    Boubaker, Ghalia; Macchiaroli, Natalia; Prada, Laura; Cucher, Marcela A; Rosenzvit, Mara C; Ziadinov, Iskender; Deplazes, Peter; Saarma, Urmas; Babba, Hamouda; Gottstein, Bruno; Spiliotis, Markus

    2013-01-01

    Echinococcus granulosus is characterized by high intra-specific variability (genotypes G1-G10) and according to the new molecular phylogeny of the genus Echinococcus, the E. granulosus complex has been divided into E. granulosus sensu stricto (G1-G3), E. equinus (G4), E. ortleppi (G5), and E. canadensis (G6-G10). The molecular characterization of E. granulosus isolates is fundamental to understand the spatio-temporal epidemiology of this complex in many endemic areas with the simultaneous occurrence of different Echinococcus species and genotypes. To simplify the genotyping of the E. granulosus complex we developed a single-tube multiplex PCR (mPCR) allowing three levels of discrimination: (i) Echinococcus genus, (ii) E. granulosus complex in common, and (iii) the specific genotype within the E. granulosus complex. The methodology was established with known DNA samples of the different strains/genotypes, confirmed on 42 already genotyped samples (Spain: 22 and Bulgaria: 20) and then successfully applied on 153 unknown samples (Tunisia: 114, Algeria: 26 and Argentina: 13). The sensitivity threshold of the mPCR was found to be 5 ng Echinoccoccus DNA in a mixture of up to 1 µg of foreign DNA and the specificity was 100% when template DNA from closely related members of the genus Taenia was used. Additionally to DNA samples, the mPCR can be carried out directly on boiled hydatid fluid or on alkaline-lysed frozen or fixed protoscoleces, thus avoiding classical DNA extractions. However, when using Echinococcus eggs obtained from fecal samples of infected dogs, the sensitivity of the mPCR was low (Echinococcus genus.

  8. Detection and genotyping of human papilloma virus in cervical cancer specimens from Saudi patients.

    Science.gov (United States)

    Al-Badawi, Ismail A; Al-Suwaine, Abdulrahman; Al-Aker, Murad; Asaad, Lina; Alaidan, Alwaleed; Tulbah, Asma; Fe Bohol, Marie; Munkarah, Adnan R

    2011-07-01

    To determine the rates and types of human papilloma virus (HPV) infection in cervical cancer specimens from Saudi patients. One hundred specimens were randomly selected and retrieved from the achieved samples stored in the pathology department accessioned under the diagnosis of cervical cancer and carcinoma in situ between the years 1997 and 2007. Human papilloma virus in the clinical samples was detected using polymerase chain reaction amplification methods. Two primer systems are commonly used: the MY09-MY11 primers and the GP5+-GP6+ that amplify a wide range of HPV genotypes. Human papilloma virus isolates were genotyped using DNA sequencing and reverse line blot hybridization assay to identify the high-risk HPV genotypes. Ninety cases fulfilled the diagnostic criteria and were analyzed. The rate of HPV genotype detection among cervical cancer samples was 95.5%. The most common HPV genotype detected by both methods was HPV-16 (63.4%), followed by HPV-18 (11.1%), HPV-45 (4.5%), HPV-33 (3.3%), and HPV-31, HPV-52, HPV-53, HPV-58, HPV-59, and HPV-66 with 2.2% prevalence rate each. Prevalence of HPV genotypes among patients with cervical cancer in Saudi Arabia is comparable to the international rates. The use of the reverse line blot hybridization assay genotyping method could be useful for classifying oncogenic HPV-positive women. It is relatively inexpensive and reliable and can be performed in routine practice or epidemiological study compared with the available standard commercial kits.

  9. Genetic characterization of Toxoplasma gondii from Brazilian wildlife revealed abundant new genotypes.

    Science.gov (United States)

    Vitaliano, S N; Soares, H S; Minervino, A H H; Santos, A L Q; Werther, K; Marvulo, M F V; Siqueira, D B; Pena, H F J; Soares, R M; Su, C; Gennari, S M

    2014-12-01

    This study aimed to isolate and genotype T. gondii from Brazilian wildlife. For this purpose, 226 samples were submitted to mice bioassay and screened by PCR based on 18S rRNA sequences. A total of 15 T. gondii isolates were obtained, including samples from four armadillos (three Dasypus novemcinctus, one Euphractus sexcinctus), three collared anteaters (Tamandua tetradactyla), three whited-lipped peccaries (Tayassu pecari), one spotted paca (Cuniculus paca), one oncilla (Leopardus tigrinus), one hoary fox (Pseudalopex vetulus), one lineated woodpecker (Dryocopus lineatus) and one maned wolf (Chrysocyon brachyurus). DNA from the isolates, originated from mice bioassay, and from the tissues of the wild animal, designated as "primary samples", were genotyped by PCR-restriction fragment length polymorphism (PCR/RFLP), using 12 genetic markers (SAG1, SAG2, alt.SAG2, SAG3, BTUB, GRA6, c22-8, c29-2, L258, PK1, CS3 and Apico). A total of 17 genotypes were identified, with 13 identified for the first time and four already reported in published literature. Results herein obtained corroborate previous studies in Brazil, confirming high diversity and revealing unique genotypes in this region. Given most of genotypes here identified are different from previous studies in domestic animals, future studies on T. gondii from wildlife is of interest to understand population genetics and structure of this parasite.

  10. Crossbreeding of large white and Nsukka local pigs: Genotype and ...

    African Journals Online (AJOL)

    5-Blood samples from 80 pigs of 4 genotypes - the Nsukka local (Lo), the exotic Large White (LW), the one-way F1 (LW x Lo) and the F2 crosses belonging to 5 age groups, were analyzed, to determine the mean values of the haematological parameters in the genotypes and different age groups and to check if and how the ...

  11. Prevalence of nematode infection and faecal egg counts in free-range laying hens: relations to housing and husbandry.

    Science.gov (United States)

    Sherwin, C M; Nasr, M A F; Gale, E; Petek, M; Stafford, K; Turp, M; Coles, G C

    2013-01-01

    1. Faecal samples from 19 commercial, 65 week old free-range egg laying flocks were examined to assess the prevalence and number of parasitic nematode eggs. Data were collected to characterise the housing, husbandry, behaviour and welfare of the flocks to examine possible relationships with the egg counts. 2. Eggs of at least one genus of nematode were present in the faeces of all 19 flocks. Heterakis eggs were detected in 17 (89%) flocks, Ascaridia in 16 (84%), Trichostrongylus in 9 (47%), and Syngamus in 6 (32%). Faecal egg counts (FEC) were greatest for Ascaridia and Heterakis. 3. For each nematode genus, there was no significant difference in FEC between organic (N = 9) and non-organic (N = 10) flocks, or between static (N = 8) and mobile (N = 11) flocks. 4. FEC were correlated with a range of housing, husbandry and management practices which varied between the nematode genus and included depth of the litter, percentage of hens using the range, and number of dead hens. Statistical analysis indicated relationships with FEC that included light intensity above the feeder, indoor and outdoor stocking density, fearfulness in the shed and on the range, distance to the nearest shelter, and swollen toes. 5. None of the FEC for any of the genera was correlated with weekly egg production or cumulative mortality. 6. Although nematode FEC were highly prevalent among the flocks, the overall lack of relation to other welfare and production measures suggests that these infections were not severe.

  12. Coral host transcriptomic states are correlated with Symbiodinium genotypes

    KAUST Repository

    DeSalvo, Michael K.

    2010-03-01

    A mutualistic relationship between reef-building corals and endosymbiotic dinoflagellates (Symbiodinium spp.) forms the basis for the existence of coral reefs. Genotyping tools for Symbiodinium spp. have added a new level of complexity to studies concerning cnidarian growth, nutrient acquisition, and stress. For example, the response of the coral holobiont to thermal stress is connected to the host-Symbiodinium genotypic combination, as different partnerships can have different bleaching susceptibilities. In this study, we monitored Symbiodinium physiological parameters and profiled the coral host transcriptional responses in acclimated, thermally stressed, and recovered fragments of the coral Montastraea faveolata using a custom cDNA gene expression microarray. Interestingly, gene expression was more similar among samples with the same Symbiodinium content rather than the same experimental condition. In order to discount for host-genotypic effects, we sampled fragments from a single colony of M. faveolata containing different symbiont types, and found that the host transcriptomic states grouped according to Symbiodinium genotype rather than thermal stress. As the first study that links coral host transcriptomic patterns to the clade content of their Symbiodinium community, our results provide a critical step to elucidating the molecular basis of the apparent variability seen among different coral-Symbiodinium partnerships. © 2010 Blackwell Publishing Ltd.

  13. A two-step real-time PCR assay for quantitation and genotyping of human parvovirus 4.

    Science.gov (United States)

    Väisänen, E; Lahtinen, A; Eis-Hübinger, A M; Lappalainen, M; Hedman, K; Söderlund-Venermo, M

    2014-01-01

    Human parvovirus 4 (PARV4) of the family Parvoviridae was discovered in a plasma sample of a patient with an undiagnosed acute infection in 2005. Currently, three PARV4 genotypes have been identified, however, with an unknown clinical significance. Interestingly, these genotypes seem to differ in epidemiology. In Northern Europe, USA and Asia, genotypes 1 and 2 have been found to occur mainly in persons with a history of injecting drug use or other parenteral exposure. In contrast, genotype 3 appears to be endemic in sub-Saharan Africa, where it infects children and adults without such risk behaviour. In this study, a novel straightforward and cost-efficient molecular assay for both quantitation and genotyping of PARV4 DNA was developed. The two-step method first applies a single-probe pan-PARV4 qPCR for screening and quantitation of this relatively rare virus, and subsequently, only the positive samples undergo a real-time PCR-based multi-probe genotyping. The new qPCR-GT method is highly sensitive and specific regardless of the genotype, and thus being suitable for studying the clinical impact and occurrence of the different PARV4 genotypes. Copyright © 2013 Elsevier B.V. All rights reserved.

  14. Detection of HCV genotypes using molecular and radio-isotopic methods

    International Nuclear Information System (INIS)

    Ahmad, N.; Baig, S.M.; Shah, W.A.; Khattak, K.F.; Khan, B.; Qureshi, J.A.

    2004-01-01

    Hepatitis C virus (HCV) accounts for most cases of acute and chronic non-A and non-B liver diseases. Persistent HCV infection may lead to liver cirrhosis and hepatocellular carcinoma. Six major HCV genotypes have been recognized. Infection with different genotypes results in different clinical pictures and responses to antiviral therapy. In the area of Faisalabad (Punjab province of Pakistan), the prevalence and molecular epidemiology of Hepatitis C virus infection had never been investigated before. In this study, we have made an attempt to determine the prevalence, distribution and clinical significance of HCV infection in 1100 suspected patients of liver disease by nested reverse transcriptase polymerase chain reaction (RTPCR) over a period of four years. HCV genotypes of isolates were determined by dot-blot hybridization with genotype specific radiolabeled probes in 337 subjects. The proportion of patients with HCV genotypes 1,2,3 and 4 were 37.38%, 1.86%, 16.16% and 0.29% respectively. Mixed infection of HCV genotype was detected in 120 (35.6%) patients, whereas 31 (9.1%) samples remained unclassified. This study revealed changing epidemiology of hepatitis C virus genotype 1 and 3 in the patients. Multiple infection of HCV genotype in the same patient may be of great clinical and pathological importance and interest. (author)

  15. Prevalence of hepatitis-C virus genotypes and potential transmission risks in Malakand Khyber Pakhtunkhwa, Pakistan.

    Science.gov (United States)

    Nazir, Nausheen; Jan, Muhammad Rasul; Ali, Amjad; Asif, Muhammad; Idrees, Muhammad; Nisar, Mohammad; Zahoor, Muhammad; Abd El-Salam, Naser M

    2017-08-22

    Hepatitis C virus (HCV) is a leading cause of chronic liver disease and frequently progresses towards liver cirrhosis and Hepatocellular Carcinoma (HCC). This study aimed to determine the prevalence of HCV genotypes and their association with possible transmission risks in the general population of Malakand Division. Sum of 570 serum samples were collected during March 2011 to January 2012 from suspected patients visited to different hospitals of Malakand. The suspected sera were tested using qualitative PCR and were then subjected to molecular genotype specific assay. Quantitative PCR was also performed for determination of pre-treatment viral load in confirmed positive patients. Out of 570 serum samples 316 sera were seen positive while 254 sera were found negative using qualitative PCR. The positive samples were then subjected to genotyping assay out of 316, type-specific PCR fragments were seen in 271 sera while 45 samples were found untypable genotypes. Genotype 3a was seen as a predominant genotype (63.3%) with a standard error of ±2.7%. Cramer's V statistic and Liklihood-Ratio statistical procedures are used to measure the strength and to test the association, respectively, between the dependent variable, genotype, and explanatory variables (e.g. gender, risk, age and area/districts). The dependent variable, genotype, is observed statistically significant association with variable risk factors. This implies that the genotype is highly dependent on how the patient was infected. In contrast, the other covariates, for example, gender, age, and district (area) no statistical significant association are observed. The association between gender-age indicates that the mean age of female was older by 10.5 ± 2.3 years with 95% confidence level using t-statistic. It was concluded from the present study that the predominant genotype was 3a in the infected population of Malakand. This study also highlights the high prevalence rate of untypable genotypes which an

  16. Genotyping of clinical isolates of Acanthamoeba genus in Venezuela.

    Science.gov (United States)

    Wagner, Carolina; Reyes-Batlle, María; Ysea, María Alejandra Vethencourt; Pérez, Mónica V Galindo; de Rondón, Carmen Guzmán; Paduani, Anaibeth J Nessi; Pérez, Angelyseb Dorta; López-Arencibia, Atteneri; Sifaoui, Ines; de Galindo, María Virginia Pérez; de Suárez, Eva Pérez; Martínez-Carretero, Enrique; Valladares, Basilio; Piñero, José E; Lorenzo-Morales, Jacob

    2016-12-01

    Free-living amoebae of Acanthamoeba genus are opportunistic pathogens distributed worldwide. Strains included in this genus are causative agents of a fatal encephalitis and a sight-threating keratitis in humans and other animals. In this study, 550 clinical samples which were collected between 1984 and 2014 from different patients with suspected infections due to Acanthamoeba were initially screened for the presence of this amoebic genus at the Laboratorio de Amibiasis-Escuela de Bioanálisis at the Universidad Central de Venezuela. Samples were cultured in 2% Non-Nutrient agar plates seeded with a layer of heat killed Escherichia coli. From the 550 clinical samples included in this study, 18 of them were positive for Acanthamoeba genus after culture identification. Moreover, positive samples were confirmed after amplification of the Diagnostic Fragment 3 (DF3) of the Acanthamoeba18S rDNA genus and sequencing was carried out in order to genotype the isolated strains of Acanthamoeba. Furthermore, the pathogenic potential of the strains was checked by performing thermotolerance and osmotolerance assays. Sequencing of the DF3 region resulted in the identification of genotype T4 in all the isolated strains. Moreover, most isolates were thermotolerant or both thermotolerant and osmotolerant and thus were classified as potentially pathogenic strains. To the best of our knowledge, this is the first report on the molecular characterization at the genotype level of Acanthamoeba strains in Venezuela.

  17. Monitoring ovarian cycle and pregnancy in the giant anteater (Myrmecophaga tridactyla) by faecal progestagen and oestrogen analysis.

    Science.gov (United States)

    Patzl, M; Schwarzenberger, F; Osmann, C; Bamberg, E; Bartmann, W

    1998-10-01

    Oestrogen and progestagen metabolites were measured in the faeces of five female giant anteaters (Myrmecophaga tridactyla), to characterise the oestrous cycle and pregnancy. Faecal samples were collected twice weekly for a minimum of 6 months, and immunoreactive progestagens and oestrogens were analysed using enzyme immunoassays (EIA). For progestagens, two antibodies that cross-reacted with 20alpha-hydroxy- or 20-oxo-progestagens were used. Both assays effectively monitored ovarian cyclicity; however, the concentrations obtained using the antibody for 20alpha-hydroxy-progestagens were higher, and the hormonal changes were more pronounced. Regular ovarian cycles were identified in three of the five females. Average (+/-SEM) length of the oestrous cycle (n=10) was 51.4+/-5.6 days. Peak concentrations of 20alpha-hydroxy-progestagens ranged from 80-660 ng/g of faeces and those of oestrogens from 20-100 ng/g. Hormone concentrations were measured during parts of two pregnancies and during four post-partum periods. The length of one gestation (from oestrous oestrogen peak until parturition) was 184 days. In the second half of gestation, progestagen concentration started to increase above luteal phase values; in the week before parturition it was approximately 20 times higher than those during the luteal phase. Concentrations of excreted oestrogens began to increase after two thirds of gestation and exceeded that of the follicular phase by approximately 2.5-fold in the week before parturition. Onset of ovarian cyclicity after parturition varied from 4-11 weeks. In conclusion, the measurement of faecal immunoreactive progestagens and oestrogens in the giant anteater indicated an ovarian cycle of approximately 7 weeks in length and provided potentially useful data for successful breeding management.

  18. Act Fast as Time Is Less: High Faecal Carriage of Carbapenem-Resistant Enterobacteriaceae in Critical Care Patients.

    Science.gov (United States)

    Saseedharan, Sanjith; Sahu, Manisa; Pathrose, Edwin Joseph; Shivdas, Sarita

    2016-09-01

    Carbapenem-resistant Enterobacteriaceae (CRE) are drug-resistant Gram-negative bacteria that are present in the community as well as in hospitals. Their infection and colonisation puts critically ill patients at high risk due to the drug-resistant nature of the strains and possible spreading of these organisms, even in a hospital environment. To examine the presence and types of Enterobacteriaceae species in patients admitted directly from the community. The present study was a one-month pilot conducted in the ICU of a tertiary care hospital in Mumbai, India in 2015. Faecal samples of patients admitted from the community directly to the ICU were analysed using tests like MHT (Modified Hodge) and EDTA for the presence of IMP (action on Imipenem) and KPC ( Klebsiella Test Pneumoniae Carbapenemase) producing strains of Enterobacteriaceae . Polymerase Chain Reaction (PCR) was performed to look for VIM , IMP , NDM 1, OXA , and KPC genes. Antibiotic Sensitivity Test was carried out as per CLSI guidelines. The results showed an alarming level of faecal carriage rates in adult ICU patients. Klebsiella pneumonia was the most common carbapenem-resistant isolate, closely followed by Escherichia coli . PCR results revealed nine strains were positive for bla (KPC) gene, from which 7 were Klebsiella pneumoniae and one each of Escherichia coli and Klebsiella oxytoca was observed. Antibiotic Sensitivity Test results showed that the isolates had maximum sensitivity to Colistin (100%) and Tigecycline (95%). These levels indicate that in the absence of CRE screenings, proper isolation of carrier patients is not possible, leading to possible spreading of these resistant bacteria strains in ICUs. A longer period of study is required to obtain more substantial data to validate the results of this pilot.

  19. Effects of feeding polydextrose on faecal characteristics, microbiota and fermentative end products in healthy adult dogs.

    Science.gov (United States)

    Beloshapka, Alison N; Wolff, Amanda K; Swanson, Kelly S

    2012-08-01

    Polydextrose is a potential prebiotic, but has not been well tested in dogs. Thus, the objective of the present study was to determine the effects of polydextrose on faecal characteristics, microbial populations and fermentative end products in healthy adult dogs. A total of eight adult hound dogs (3.5 (sem 0.5) years; 20 (sem 0.5) kg) were randomly allotted to one of four test diets containing the following concentrations of polydextrose: (1) 0 % (control); (2) 0.5 %; (3) 1.0 %; or (4) 1.5 %. A Latin square design was used, with each treatment period lasting 14 d (days 0-10 adaptation; days 11-14 fresh and total faecal collection). All dogs were fed to maintain body weight. Data were evaluated for linear and quadratic effects using SAS software. Although apparent total tract DM digestibility was unaffected, total tract crude protein digestibility tended to decrease (P dogs.

  20. Detection and genotyping of Chlamydia species responsible for reproductive disorders in Algerian small ruminants.

    Science.gov (United States)

    Merdja, Salah-Eddine; Khaled, Hamza; Aaziz, Rachid; Vorimore, Fabien; Bertin, Claire; Dahmani, Ali; Bouyoucef, Abdallah; Laroucau, Karine

    2015-02-01

    Chlamydiosis in small ruminants is a zoonotic disease mainly related to Chlamydia abortus. This bacterium is responsible for abortions and reproductive disorders in sheep and goats. Stillbirth and infertility, leading to important economic losses, are also associated with this pathology. In Algeria, abortion cases are frequently reported by veterinarians but, except for brucellosis which is a notifiable disease in this country, abortive diseases are in general poorly studied. In order to detect and genotype Chlamydia species in small ruminants in different areas of Algeria, a study was conducted on samples collected from females (164 blood samples and 199 vaginal swabs) between October 2011 and March 2013. Serum samples were tested with a C. abortus-specific indirect ELISA test. Fourteen samples (8.5 %), from six farms (6/20, 30 %) were tested positive. Vaginal swabs were analysed with a real-time PCR targeting all Chlamydiaceae spp. Thirty samples (15 %) were diagnosed positive in 16 farms (16/25, 64 %). Positive samples were all re-tested with a C. abortus- and a C. pecorum-specific real-time PCR. Finally, 13/30 (43.3 %) and 6/30 (20 %) were identified as C. abortus and C. pecorum, respectively. Enough concentrated C. abortus samples were genotyped by multi-loci variable number of tandem repeat (VNTR) analysis (MLVA), and all were related to the genotype [2] group which mainly includes French C. abortus isolates. C. pecorum-positive samples were genotyped by multi-locus sequence typing (MLST). Interestingly, two of them were successfully genotyped and showed identical MLST sequences to VB2, AB10, E58 and SBE, a group which includes C. pecorum isolates considered as highly pathogenic. These findings suggest a possible role of C. abortus and C. pecorum strains in the aetiology of abortion in Algerian small ruminants.

  1. A comparative study of faecal occult blood kits in a colorectal cancer screening program in a cohort of healthy construction workers.

    LENUS (Irish Health Repository)

    Shuhaibar, M

    2012-02-01

    BACKGROUND: The incidence of colorectal cancer (CRC) has been increasing. We evaluated uptake rates and outcomes of faecal immunochemical test (FIT) and Guaiac test (gFOBT) kits as part of a two-step CRC screening. METHODS: A 3-year CRC screening program for a defined population of construction workers was conducted. Those satisfying the inclusion criteria were provided with gFOBT or FIT kits. Individuals testing positive were invited for a colonoscopy. RESULTS: A total of 909 faecal testing kits were distributed. Age range was 53-60 years. Compliance rate was higher for FIT (58.3%) as compared to gFOBT (46.7%) (p = 0.0006). FIT detected adenomatous polyps and CRC in 37.5 and 25%, respectively, whereas; gFOBT detected 23.5 and 18%. Colonoscopies were normal in 53 and 25% tested positive by gFOBT and FIT, respectively (p = 0.016). CONCLUSION: The FIT was more cost-effective when compared with gFOBT with higher return rate, sensitivity and specificity. A comparative study of faecal occult blood kits in a CRC screening program in a healthy cohort of construction workers.

  2. COMT val108/158 met genotype affects neural but not cognitive processing in healthy individuals.

    Science.gov (United States)

    Dennis, Nancy A; Need, Anna C; LaBar, Kevin S; Waters-Metenier, Sheena; Cirulli, Elizabeth T; Kragel, James; Goldstein, David B; Cabeza, Roberto

    2010-03-01

    The relationship between cognition and a functional polymorphism in the catechol-O-methlytransferase (COMT) gene, val108/158met, is one of debate in the literature. Furthermore, based on the dopaminergic differences associated with the COMT val108/158met genotype, neural differences during cognition may be present, regardless of genotypic differences in cognitive performance. To investigate these issues the current study aimed to 1) examine the effects of COMT genotype using a large sample of healthy individuals (n = 496-1218) and multiple cognitive measures, and using a subset of the sample (n = 22), 2) examine whether COMT genotype effects medial temporal lobe (MTL) and frontal activity during successful relational memory processing, and 3) investigate group differences in functional connectivity associated with successful relational memory processing. Results revealed no significant group difference in cognitive performance between COMT genotypes in any of the 19 cognitive measures. However, in the subset sample, COMT val homozygotes exhibited significantly decreased MTL and increased prefrontal activity during both successful relational encoding and retrieval, and reduced connectivity between these regions compared with met homozygotes. Taken together, the results suggest that although the COMT val108/158met genotype has no effect on cognitive behavioral measures in healthy individuals, it is associated with differences in neural process underlying cognitive output.

  3. Human Papilloma Virus Genotype Distribution in Cervical lesions in Zanjan, Iran

    Science.gov (United States)

    Ahmadi, Shahrzad; Goudarzi, Hossein; Jalilvand, Ahmad; Esmaeilzadeh, Abdolreza

    2017-12-29

    Objective: Cervical cancer is one of the most common cancers among women all over the world, and main cause is persistent infection with high risk human papillomavirus (HPV) strains. It has been reported that the distribution and prevalence of HPV types varies by geographical region, so that this is important for prevention by type-specific vaccines. The aim of current study was to determine the genotype distribution of HPV using the INNO-LiPA genotyping assay in Zanjan province, North West Iran. Methods: A total of 112 formalin-fixed paraffin embedded (FFPE) tissue samples from cases of low-grade intraepithelial lesion (LSIL), high-grade intraepithelial lesion (HSIL) and squamous cell carcinoma (SCC) were collected. The polymerase chain reaction (PCR) was used to amplify DNA for genotyping. Results: Among the 112 samples from females (ranging from 20 to 69 years, mean age 43.8 ± 10.1) tested for HPV DNA, 50 samples were positive. Based on results of genotyping, most common HPV genotypes were HPV18 (48%) followed by HPV-6 (24%), HPV73 (16%), HPV-51(8%), HPV-31(8%), HPV-16 (8%), HPV-56 (4%), HPV-44 (4%). Conclusion: While HPV infection is the major etiological factor for cervical cancer, presence was relatively low in our survey. In the positive cases, however, HPV18 was the most common in line with many other populations. The fact that types vary among different populations must clearly be taken into account in design of vaccines for our country. Creative Commons Attribution License

  4. Methods of developing core collections based on the predicted genotypic value of rice ( Oryza sativa L.).

    Science.gov (United States)

    Li, C T; Shi, C H; Wu, J G; Xu, H M; Zhang, H Z; Ren, Y L

    2004-04-01

    The selection of an appropriate sampling strategy and a clustering method is important in the construction of core collections based on predicted genotypic values in order to retain the greatest degree of genetic diversity of the initial collection. In this study, methods of developing rice core collections were evaluated based on the predicted genotypic values for 992 rice varieties with 13 quantitative traits. The genotypic values of the traits were predicted by the adjusted unbiased prediction (AUP) method. Based on the predicted genotypic values, Mahalanobis distances were calculated and employed to measure the genetic similarities among the rice varieties. Six hierarchical clustering methods, including the single linkage, median linkage, centroid, unweighted pair-group average, weighted pair-group average and flexible-beta methods, were combined with random, preferred and deviation sampling to develop 18 core collections of rice germplasm. The results show that the deviation sampling strategy in combination with the unweighted pair-group average method of hierarchical clustering retains the greatest degree of genetic diversities of the initial collection. The core collections sampled using predicted genotypic values had more genetic diversity than those based on phenotypic values.

  5. Genotypic frequency of Caveolin-1 (CAV1 T29107A polymorphism in the Iranian patients with breast cancer

    Directory of Open Access Journals (Sweden)

    Ahmad Hamta

    2016-09-01

    Full Text Available Introduction: Caveolin-1 (Cav-1 is a scaffolding protein found in special structures of plasma membrane, known as Caveolae. Cav-1 can regulate many intracellular processes, including signal transmission and cholesterol metabolism. This protein plays an important role in the growth and differentiation of breast tissue and acts as a tumor suppressor gene as well. The aim of this study was to determine the genotypic frequency of Cav-1 T29107A (rs7804372 polymorphism and its association with susceptibility to breast cancer among the female population in Kermanshah, Iran. Methods: A total of 120 patients with breast cancer and an equal number of non-cancer individuals (control group, matched for age and gender with the patients, were selected in this study. The paraffin tissues of the patients from 2006 to 2013 were collected from Imam Reza hospital, Kermanshah, and 2.5 cc blood sample was taken from non-cancer individuals. The genomic DNA was extracted from paraffin tissues and blood by salting out method. The genotype of samples was determined by RFLP-PCR method, and Sau3A1 enzyme was used for RFLP analysis. Results: The distribution of Cav-1 T29107A genotype was found to be significantly different between breast cancer patients and control group (p=0.004. Among the patients, 84 (70% samples had genotype TT, 29 (24.78% genotype AT and 7 (5.83% genotype AA. As for the control group, however, 59 (49.17% samples had genotype TT, 49 (40.83% genotype AT and 12 (10% genotype AA. Conclusion: The results of this study showed that genotype TT is associated with an increased risk of susceptibility to breast cancer.

  6. Microbiome changes associated with sustained eradication of Clostridium difficile after single faecal microbiota transplantation in children with and without inflammatory bowel disease.

    Science.gov (United States)

    Hourigan, S K; Chen, L A; Grigoryan, Z; Laroche, G; Weidner, M; Sears, C L; Oliva-Hemker, M

    2015-09-01

    Little data are available regarding the effectiveness and associated microbiome changes of faecal microbiota transplantation (FMT) for Clostridium difficile infection (CDI) in children, especially in those with inflammatory bowel disease (IBD) with presumed underlying dysbiosis. To investigate C. difficile eradication and microbiome changes with FMT in children with and without IBD. Children with a history of recurrent CDI (≥3 recurrences) underwent FMT via colonoscopy. Stool samples were collected pre-FMT and post-FMT at 2-10 weeks, 10-20 weeks and 6 months. The v4 hypervariable region of the 16S rRNA gene was sequenced. C. difficile toxin B gene polymerase chain reaction was performed. Eight children underwent FMT for CDI; five had IBD. All had resolution of CDI symptoms. All tested had eradication of C. difficile at 10-20 weeks and 6 months post-FMT. Pre-FMT patient samples had significantly decreased bacterial richness compared with donors (P = 0.01), in those with IBD (P = 0.02) and without IBD (P = 0.01). Post-FMT, bacterial diversity in patients increased. Six months post-FMT, there was no significant difference between bacterial diversity of donors and patients without IBD; however, bacterial diversity in those with IBD returned to pre-FMT baseline. Microbiome composition at 6 months in IBD-negative patients more closely approximated donor composition compared to IBD-positive patients. FMT gives sustained C. difficile eradication in children with and without IBD. FMT-restored diversity is sustained in children without IBD. In those with IBD, bacterial diversity returns to pre-FMT baseline by 6 months, suggesting IBD host-related mechanisms modify faecal microbiome diversity. © 2015 John Wiley & Sons Ltd.

  7. A multiplex PCR for the simultaneous detection and genotyping of the Echinococcus granulosus complex.

    Directory of Open Access Journals (Sweden)

    Ghalia Boubaker

    Full Text Available Echinococcus granulosus is characterized by high intra-specific variability (genotypes G1-G10 and according to the new molecular phylogeny of the genus Echinococcus, the E. granulosus complex has been divided into E. granulosus sensu stricto (G1-G3, E. equinus (G4, E. ortleppi (G5, and E. canadensis (G6-G10. The molecular characterization of E. granulosus isolates is fundamental to understand the spatio-temporal epidemiology of this complex in many endemic areas with the simultaneous occurrence of different Echinococcus species and genotypes. To simplify the genotyping of the E. granulosus complex we developed a single-tube multiplex PCR (mPCR allowing three levels of discrimination: (i Echinococcus genus, (ii E. granulosus complex in common, and (iii the specific genotype within the E. granulosus complex. The methodology was established with known DNA samples of the different strains/genotypes, confirmed on 42 already genotyped samples (Spain: 22 and Bulgaria: 20 and then successfully applied on 153 unknown samples (Tunisia: 114, Algeria: 26 and Argentina: 13. The sensitivity threshold of the mPCR was found to be 5 ng Echinoccoccus DNA in a mixture of up to 1 µg of foreign DNA and the specificity was 100% when template DNA from closely related members of the genus Taenia was used. Additionally to DNA samples, the mPCR can be carried out directly on boiled hydatid fluid or on alkaline-lysed frozen or fixed protoscoleces, thus avoiding classical DNA extractions. However, when using Echinococcus eggs obtained from fecal samples of infected dogs, the sensitivity of the mPCR was low (<40%. Thus, except for copro analysis, the mPCR described here has a high potential for a worldwide application in large-scale molecular epidemiological studies on the Echinococcus genus.

  8. Genotyping of circulating measles strains in Italy in 2010

    Directory of Open Access Journals (Sweden)

    Melissa Baggieri

    2014-12-01

    Full Text Available INTRODUCTION: The European Regional Office of the World Health Organization developed a strategic approach to stop the indigenous transmission of measles in its 53 Member States by 2015. In Italy, laboratory surveillance activity is implemented by the National Reference Laboratory for Measles and Rubella at the Italian National Institute of Health (Istituto Superiore di Sanità, Rome. The role of the National Reference Laboratory is to strengthen surveillance systems through rigorous case investigation and laboratory confirmation of suspected sporadic cases and outbreaks. Genetic characterization of wild-type measles virus is an essential component of the laboratory-based surveillance. This study describes the molecular characterization of measles virus strains isolated during 2010. METHODS: Dried blood spots, urine and oral fluid samples were collected from patients with a suspected measles infection. Serological tests were performed on capillary blood, and viral detection was performed on urine and oral fluid samples through molecular assay. Positive samples were sequenced and phylogenetically analysed. RESULTS AND DISCUSSION: The phylogenetic analysis showed a co-circulation of genotypes D4 and D8, and sporadic cases associated to genotypes D9 and B3. Then, molecular epidemiology of measles cases permitted to establish that D4 and D8 were the endemic genotypes in Italy during 2010.

  9. Hepatitis B virus genotypes circulating in Brazil: molecular characterization of genotype F isolates

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    Virgolino Helaine A

    2007-11-01

    Full Text Available Abstract Background Hepatitis B virus (HBV isolates have been classified in eight genotypes, A to H, which exhibit distinct geographical distributions. Genotypes A, D and F are predominant in Brazil, a country formed by a miscegenated population, where the proportion of individuals from Caucasian, Amerindian and African origins varies by region. Genotype F, which is the most divergent, is considered indigenous to the Americas. A systematic molecular characterization of HBV isolates from different parts of the world would be invaluable in establishing HBV evolutionary origins and dispersion patterns. A large-scale study is needed to map the region-by-region distribution of the HBV genotypes in Brazil. Results Genotyping by PCR-RFLP of 303 HBV isolates from HBsAg-positive blood donors showed that at least two of the three genotypes, A, D, and F, co-circulate in each of the five geographic regions of Brazil. No other genotypes were identified. Overall, genotype A was most prevalent (48.5%, and most of these isolates were classified as subgenotype A1 (138/153; 90.2%. Genotype D was the most common genotype in the South (84.2% and Central (47.6% regions. The prevalence of genotype F was low (13% countrywide. Nucleotide sequencing of the S gene and a phylogenetic analysis of 32 HBV genotype F isolates showed that a great majority (28/32; 87.5% belonged to subgenotype F2, cluster II. The deduced serotype of 31 of 32 F isolates was adw4. The remaining isolate showed a leucine-to-isoleucine substitution at position 127. Conclusion The presence of genotypes A, D and F, and the absence of other genotypes in a large cohort of HBV infected individuals may reflect the ethnic origins of the Brazilian population. The high prevalence of isolates from subgenotype A1 (of African origin indicates that the African influx during the colonial slavery period had a major impact on the circulation of HBV genotype A currently found in Brazil. Although most genotype F

  10. Echinococcus granulosus sensu lato genotypes infecting humans--review of current knowledge.

    Science.gov (United States)

    Alvarez Rojas, Cristian A; Romig, Thomas; Lightowlers, Marshall W

    2014-01-01

    Genetic variability in the species group Echinococcus granulosus sensu lato is well recognised as affecting intermediate host susceptibility and other biological features of the parasites. Molecular methods have allowed discrimination of different genotypes (G1-10 and the 'lion strain'), some of which are now considered separate species. An accumulation of genotypic analyses undertaken on parasite isolates from human cases of cystic echinococcosis provides the basis upon which an assessment is made here of the relative contribution of the different genotypes to human disease. The allocation of samples to G-numbers becomes increasingly difficult, because much more variability than previously recognised exists in the genotypic clusters G1-3 (=E. granulosus sensu stricto) and G6-10 (Echinococcus canadensis). To accommodate the heterogeneous criteria used for genotyping in the literature, we restrict ourselves to differentiate between E. granulosus sensu stricto (G1-3), Echinococcus equinus (G4), Echinococcus ortleppi (G5) and E. canadensis (G6-7, G8, G10). The genotype G1 is responsible for the great majority of human cystic echinococcosis worldwide (88.44%), has the most cosmopolitan distribution and is often associated with transmission via sheep as intermediate hosts. The closely related genotypes G6 and G7 cause a significant number of human infections (11.07%). The genotype G6 was found to be responsible for 7.34% of infections worldwide. This strain is known from Africa and Asia, where it is transmitted mainly by camels (and goats), and South America, where it appears to be mainly transmitted by goats. The G7 genotype has been responsible for 3.73% of human cases of cystic echinococcosis in eastern European countries, where the parasite is transmitted by pigs. Some of the samples (11) could not be identified with a single specific genotype belonging to E. canadensis (G6/10). Rare cases of human cystic echinococcosis have been identified as having been caused by

  11. Short Communication: A Simple Method for Performing Worm-Egg Counts on Sodium Acetate Formaldehyde-Preserved Samples

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    Wayne Melrose

    2012-01-01

    Full Text Available The Kato Katz method is the most common way of performing worm-egg counts on human faecal samples, but it must be done in the field using freshly collected samples. This makes it difficult to use in remote, poorly accessible situations. This paper describes a simple method for egg counts on preserved samples collected in the field and sent to a central location for further processing.

  12. Genomic Variants Revealed by Invariably Missing Genotypes in Nelore Cattle.

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    Joaquim Manoel da Silva

    Full Text Available High density genotyping panels have been used in a wide range of applications. From population genetics to genome-wide association studies, this technology still offers the lowest cost and the most consistent solution for generating SNP data. However, in spite of the application, part of the generated data is always discarded from final datasets based on quality control criteria used to remove unreliable markers. Some discarded data consists of markers that failed to generate genotypes, labeled as missing genotypes. A subset of missing genotypes that occur in the whole population under study may be caused by technical issues but can also be explained by the presence of genomic variations that are in the vicinity of the assayed SNP and that prevent genotyping probes from annealing. The latter case may contain relevant information because these missing genotypes might be used to identify population-specific genomic variants. In order to assess which case is more prevalent, we used Illumina HD Bovine chip genotypes from 1,709 Nelore (Bos indicus samples. We found 3,200 missing genotypes among the whole population. NGS re-sequencing data from 8 sires were used to verify the presence of genomic variations within their flanking regions in 81.56% of these missing genotypes. Furthermore, we discovered 3,300 novel SNPs/Indels, 31% of which are located in genes that may affect traits of importance for the genetic improvement of cattle production.

  13. Bulk Genotyping of Biopsies Can Create Spurious Evidence for Hetereogeneity in Mutation Content.

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    Rumen Kostadinov

    2016-04-01

    Full Text Available When multiple samples are taken from the neoplastic tissues of a single patient, it is natural to compare their mutation content. This is often done by bulk genotyping of whole biopsies, but the chance that a mutation will be detected in bulk genotyping depends on its local frequency in the sample. When the underlying mutation count per cell is equal, homogenous biopsies will have more high-frequency mutations, and thus more detectable mutations, than heterogeneous ones. Using simulations, we show that bulk genotyping of data simulated under a neutral model of somatic evolution generates strong spurious evidence for non-neutrality, because the pattern of tissue growth systematically generates differences in biopsy heterogeneity. Any experiment which compares mutation content across bulk-genotyped biopsies may therefore suggest mutation rate or selection intensity variation even when these forces are absent. We discuss computational and experimental approaches for resolving this problem.

  14. Bulk Genotyping of Biopsies Can Create Spurious Evidence for Hetereogeneity in Mutation Content.

    Science.gov (United States)

    Kostadinov, Rumen; Maley, Carlo C; Kuhner, Mary K

    2016-04-01

    When multiple samples are taken from the neoplastic tissues of a single patient, it is natural to compare their mutation content. This is often done by bulk genotyping of whole biopsies, but the chance that a mutation will be detected in bulk genotyping depends on its local frequency in the sample. When the underlying mutation count per cell is equal, homogenous biopsies will have more high-frequency mutations, and thus more detectable mutations, than heterogeneous ones. Using simulations, we show that bulk genotyping of data simulated under a neutral model of somatic evolution generates strong spurious evidence for non-neutrality, because the pattern of tissue growth systematically generates differences in biopsy heterogeneity. Any experiment which compares mutation content across bulk-genotyped biopsies may therefore suggest mutation rate or selection intensity variation even when these forces are absent. We discuss computational and experimental approaches for resolving this problem.

  15. The relationship between faecal-associated and mucosal-associated microbiota in irritable bowel syndrome patients and healthy subjects

    NARCIS (Netherlands)

    Rangel, I.; Sundin, J.; Fuentes Enriquez de Salamanca, S.; Repsilber, D.; Vos, de W.M.; Brummer, R.J.

    2015-01-01

    BACKGROUND: The faecal-associated microbiota is commonly seen as a surrogate of the mucosal-associated microbiota. However, previous studies indicate that they are different. Furthermore, analyses of the mucosal microbiota are commonly done after standard bowel cleansing, affecting the microbial

  16. Comparison of the endogenous ileal and faecal amino acid excretion in the dog (Canis familiaris) and the rat (Rattus rattus) determined under protein-free feeding and peptide alimentation.

    Science.gov (United States)

    Hendriks, W H; Sritharan, K; Hodgkinson, S M

    2002-10-01

    The aim of the study was to determine and compare the endogenous ileal excretions of nitrogen and amino acids under protein-free and peptide alimentation by the dog and rat. Two diets were prepared, one that was devoid of protein and the other containing 23% enzyme hydrolysed casein. Chromic oxide was included in the diets as an indigestible marker. A total of 10 mixed breed dogs were fed hourly either a protein-free or enzymatically hydrolysed casein diet for a total of 10 days. A faecal sample was obtained from each dog on day 9 while digesta was obtained from the terminal 20 cm of the ileum directly after euthanasia on day 10. A total of 12 8-week-old Sprague-Dawley rats received the same diets as the dogs. A faecal sample from each rat was obtained on day 7 while ileal digesta samples were obtained on day 8. The endogenous ileal excretions of most amino acids were greater in the dogs and rats that received the enzymatically hydrolysed casein diet compared with those receiving the protein free diet. Whereas the pattern of endogenous amino acid excretion was similar in the rats and dogs, the dogs excreted a significantly greater amount of nitrogen (1.91 vs. 2.27 and 1.63 vs. 4.12 g/kg dry matter intake for the protein-free and peptide alimentation method, respectively) and all amino acids except for glycine, isoleucine and leucine. Endogenous ileal amino acid excretions are higher in dogs compared to omnivorous animals such as rats and pigs but similar to the carnivorous cat.

  17. Antimicrobial resistance in the Bacteroides fragilis group in faecal microbiota from healthy Danish children

    DEFF Research Database (Denmark)

    Sydenham, Thomas Vognbjerg; Jensen, Betina Hebbelstrup; Petersen, Andreas Munk

    2017-01-01

    The Bacteroides fragilis group constitute a significant portion of the human gut microbiota and comprise a major proportion of anaerobic bacteria isolated in human infections. We established a baseline of antimicrobial susceptibility rates in the B. fragilis group in the intestinal tract of relat......The Bacteroides fragilis group constitute a significant portion of the human gut microbiota and comprise a major proportion of anaerobic bacteria isolated in human infections. We established a baseline of antimicrobial susceptibility rates in the B. fragilis group in the intestinal tract...... of relatively antibiotic-naive healthy Danish children. From 174 faecal samples collected from children attending day care, 359 non-duplicate isolates were screened for antimicrobial susceptibility. Of these, 0.0%, 1.9%, 5.0% and 21.2% of isolates were intermediate-susceptible or resistant to metronidazole......, meropenem, piperacillin/tazobactam and clindamycin, respectively. Eighteen additional studies reporting susceptibility rates in the B. fragilis group bacteria were identified by conducting a literature search. Heterogeneity among results from studies of B. fragilis group antimicrobial susceptibility rates...

  18. Pelvic floor muscle training for prevention and treatment of urinary and faecal incontinence in antenatal and postnatal women.

    Science.gov (United States)

    Woodley, Stephanie J; Boyle, Rhianon; Cody, June D; Mørkved, Siv; Hay-Smith, E Jean C

    2017-12-22

    About one-third of women have urinary incontinence and up to one-tenth have faecal incontinence after childbirth. Pelvic floor muscle training (PFMT) is commonly recommended during pregnancy and after birth for both prevention and treatment of incontinence.This is an update of a review previously published in 2012. To determine the effectiveness of pelvic floor muscle training (PFMT) in the prevention or treatment of urinary and faecal incontinence in pregnant or postnatal women. We searched the Cochrane Incontinence Specialised Register (16 February 2017) and reference lists of retrieved studies. Randomised or quasi-randomised trials in pregnant or postnatal women. One arm of the trial included PFMT. Another arm was no PFMT, usual antenatal or postnatal care, another control condition, or an alternative PFMT intervention. Review authors independently assessed trials for inclusion and risk of bias. We extracted data and checked them for accuracy. Populations included: women who were continent (PFMT for prevention), women who were incontinent (PFMT for treatment) at randomisation and a mixed population of women who were one or the other (PFMT for prevention or treatment). We assessed quality of evidence using the GRADE approach. The review included 38 trials (17 of which were new for this update) involving 9892 women from 20 countries. Overall, trials were small to moderate sized, and the PFMT programmes and control conditions varied considerably and were often poorly described. Many trials were at moderate to high risk of bias. Other than two reports of pelvic floor pain, trials reported no harmful effects of PFMT.Prevention of urinary incontinence: compared with usual care, continent pregnant women performing antenatal PFMT may have had a lower risk of reporting urinary incontinence in late pregnancy (62% less; risk ratio (RR) for incontinence 0.38, 95% confidence interval (CI) 0.20 to 0.72; 6 trials, 624 women; low-quality evidence). Similarly, antenatal PFMT

  19. Heterogeneity and compartmentalization of Pneumocystis carinii f. sp. hominis genotypes in autopsy lungs

    DEFF Research Database (Denmark)

    Helweg-Larsen, J; Lundgren, Bettina; Lundgren, Jens Dilling

    2001-01-01

    . Not all genotypes present in the lungs at autopsy were detected in the diagnostic respiratory samples. Compartmentalization of specific ITS and mtLSU rRNA sequence types was observed in different lung segments. In conclusion, the interpretation of genotype data and in particular ITS sequence types...

  20. Occurrence of human-associated Bacteroidetes genetic source tracking markers in raw and treated wastewater of municipal and domestic origin and comparison to standard and alternative indicators of faecal pollution

    Science.gov (United States)

    Mayer, R.E.; Bofill-Mas, S.; Egle, L.; Reischer, G.H.; Schade, M.; Fernandez-Cassi, X.; Fuchs, W.; Mach, R.L.; Lindner, G.; Kirschner, A.; Gaisbauer, M.; Piringer, H.; Blaschke, A.P.; Girones, R.; Zessner, M.; Sommer, R.; Farnleitner, A.H.

    2016-01-01

    This was a detailed investigation of the seasonal occurrence, dynamics, removal and resistance of human-associated genetic Bacteroidetes faecal markers (GeBaM) compared with ISO-based standard faecal indicator bacteria (SFIB), human-specific viral faecal markers and one human-associated Bacteroidetes phage in raw and treated wastewater of municipal and domestic origin. Characteristics of the selected activated sludge wastewater treatment plants (WWTPs) from Austria and Germany were studied in detail (WWTPs, n = 13, connected populations from 3 to 49000 individuals), supported by volume-proportional automated 24-h sampling and chemical water quality analysis. GeBaM were consistently detected in high concentrations in raw (median log10 8.6 marker equivalents (ME) 100 ml−1) and biologically treated wastewater samples (median log10 6.2–6.5 ME 100 ml−1), irrespective of plant size, type and time of the season (n = 53–65). GeBaM, Escherichia coli, and enterococci concentrations revealed the same range of statistical variability for raw (multiplicative standard deviations s* = 2.3–3.0) and treated wastewater (s* = 3.7–4.5), with increased variability after treatment. Clostridium perfringens spores revealed the lowest variability for raw wastewater (s* = 1.5). In raw wastewater correlations among microbiological parameters were only detectable between GeBaM, C. perfringens and JC polyomaviruses. Statistical associations amongst microbial parameters increased during wastewater treatment. Two plants with advanced treatment were also investigated, revealing a minimum log10 5.0 (10th percentile) reduction of GeBaM in the activated sludge membrane bioreactor, but no reduction of the genetic markers during UV irradiation (254 nm). This study highlights the potential of human-associated GeBaM to complement wastewater impact monitoring based on the determination of SFIB. In addition, human-specific JC polyomaviruses and adenoviruses seem to be a valuable support if