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Sample records for human faecal samples

  1. Citrobacter europaeus sp. nov., isolated from water and human faecal samples.

    Science.gov (United States)

    Ribeiro, Teresa G; Clermont, Dominique; Branquinho, Raquel; Machado, Elisabete; Peixe, Luísa; Brisse, Sylvain

    2017-01-01

    Strains 97/79T and A121, recovered respectively from human faeces and well water, were compared to currently known species of the genus Citrobacter using genotypic and phenotypic approaches. Multilocus sequence analysis based on housekeeping genes fusA, leuS, pyrG, rpoB and recN, showed that the two strains formed a distinct phylogenetic lineage within the genus Citrobacter. Average nucleotide identity (ANI) between strains 97/79T and A121 was 99.2 %, whereas ANI values of strain 97/79T with the type strains of closely related species of the genus Citrobacter, C. werkmanii, C. braakii, C. freundii, C. youngae and C. pasteurii, were all below 93.0 %. The ability to metabolize different compounds also discriminated strains 97/79T and A121 from other species of the genus Citrobacter. Based on these results, strains 97/79T and A121 represent a novel species of the genus Citrobacter, for which the name Citrobacter europaeus sp. nov. is proposed, with strain 97/79T (=CIP 106467T=DSM 103031T) as the type strain. The DNA G+C content of strain 97/79T is 52.0 %.

  2. Molecular Detection of Strongyloides ratti in Faecal Samples from ...

    African Journals Online (AJOL)

    the detection of DNA from Strongyloides ratti (an animal model of S. stercoralis) in faecal samples of wild Brown rats ... Human parasite S. stercoralis, which was discovered for ... species on the agar plate surface [4]. The ... based technique have been developed. PCR has .... Reproductive system without seminal receptacle.

  3. Streptococcus caviae sp. nov., isolated from Guinea pig faecal samples

    NARCIS (Netherlands)

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

    2017-01-01

    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 2

  4. Multiparametric monitoring of microbial faecal pollution reveals the dominance of human contamination along the whole Danube River.

    Science.gov (United States)

    Kirschner, A K T; Reischer, G H; Jakwerth, S; Savio, D; Ixenmaier, S; Toth, E; Sommer, R; Mach, R L; Linke, R; Eiler, A; Kolarevic, S; Farnleitner, A H

    2017-11-01

    The microbial faecal pollution of rivers has wide-ranging impacts on a variety of human activities that rely on appropriate river water quality. Thus, detailed knowledge of the extent and origin of microbial faecal pollution is crucial for watershed management activities to maintain safe water use. In this study, the microbial faecal pollution levels were monitored by standard faecal indicator bacteria (SFIB) along a 2580 km stretch of the Danube, the world's most international river, as well as the Danube's most important tributaries. To track the origin of faecal pollution, host-associated Bacteroidetes genetic faecal marker qPCR assays for different host groups were applied in concert with SFIB. The spatial resolution analysis was followed by a time resolution analysis of faecal pollution patterns over 1 year at three selected sites. In this way, a comprehensive faecal pollution map of the total length of the Danube was created, combining substantiated information on both the extent and origin of microbial faecal pollution. Within the environmental data matrix for the river, microbial faecal pollution constituted an independent component and did not cluster with any other measured environmental parameters. Generally, midstream samples representatively depicted the microbial pollution levels at the respective river sites. However, at a few, somewhat unexpected sites, high pollution levels occurred in the lateral zones of the river while the midstream zone had good water quality. Human faecal pollution was demonstrated as the primary pollution source along the whole river, while animal faecal pollution was of minor importance. This study demonstrates that the application of host-associated genetic microbial source tracking markers in concert with the traditional concept of microbial faecal pollution monitoring based on SFIB significantly enhances the knowledge of the extent and origin of microbial faecal pollution patterns in large rivers. It constitutes a

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

    Science.gov (United States)

    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 (<0.10mg/L) with the pH ranging between 5.5 and 7.3 and turbidity between 0.14-1.76 NTU. Since 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 (<0.10mg/ L) in all samples as well as in both tap water and commercially bottled drinking water, with the pH ranged between 5.5-7.3, ineffective disinfection of water source as a contributing factor to such high counts of faecal coliforms in ice cubes also could not be ruled out. Therefore, a periodical, yet comprehensive check on the food outlets, including that of ice cube is crucial in ensuring better food and water for human consumption.

  6. Bacteriophages as indicators of human and animal faecal contamination in raw and treated wastewaters from Tunisia.

    Science.gov (United States)

    Yahya, M; Hmaied, F; Jebri, S; Jofre, J; Hamdi, M

    2015-05-01

    We aimed at quantifying bacteriophages in raw and treated wastewaters of human and animal origin in Tunisia to assess their usefulness for tracking the origin of faecal pollution and in the follow-up of effectiveness of water treatments process. The concentrations of bacteriophages in wastewater samples were determined by double layer agar technique. Somatic coliphages and F-specific RNA bacteriophages were present in all types of samples in high concentrations. The values of Escherichia coli were variable depending on geographical location. On the other hand, bacteriophages infecting strain GA17 were detected preferably when human faecal contamination was occurred. Bacteriophages appear as a feasible and widely applicable manner to detect faecal contamination in Tunisia. On the other hand, phages infecting GA17 could be good markers for tracking the origin of faecal pollution in the area studied. The reuse of treated wastewaters can be a solution to meet the needs of water in the geographical area of study. Bacteriophages seem to predict differently the presence of faecal contamination in water than bacterial indicators. Consequently, they can be a valuable additional tool to improve water resources management for minimizing health risks. © 2015 The Society for Applied Microbiology.

  7. 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

  8. Comparative analysis of cultural isolation and PCR based assay for detection of Campylobacter jejuni in food and faecal samples

    Directory of Open Access Journals (Sweden)

    Harkanwaldeep Singh

    2011-03-01

    Full Text Available In the present study, the efficacy of polymerase chain reaction (PCR based on mapA gene of C. jejuni was tested for detection of Campylobacter jejuni in naturally infected as well as spiked faecal and food samples of human and animal origin. Simultaneously, all the samples were subjected to the cultural isolation of organism and biochemical characterization. The positive samples resulted in the amplification of a DNA fragment of size ~589 bp in PCR assay whereas the absence of such amplicon in DNA extracted from E. coli, Listeria, Salmonella and Staphylococcus confirmed the specificity of the primers. Of randomly collected 143 faecal samples comprising human diarrheic stools (43, cattle diarrheic faeces (48 and poultry faecal swabs (52 only 4, 3 and 8, respectively, could be detected by isolation whereas 6, 3 and 10, respectively, were found positive by PCR. However, among food samples viz. beef (30, milk (35, cheese (30, only one beef sample was detected both by culture as well as PCR. Additionally, PCR was found to be more sensitive for C. jejuni detection in spiked faecal and food samples (96.1% each as relative to culture isolation which could detect the organism in 86.7% and 80% samples, respectively. The results depicted the superior efficacy of PCR for rapid screening of samples owing to its high sensitivity, specificity and automation potential.

  9. Detection and dissemination of the colistin resistance gene, mcr-1, from isolates and faecal samples in China.

    Science.gov (United States)

    Chen, Xia; Zhao, Xiaofei; Che, Jie; Xiong, Yanwen; Xu, Yanmei; Zhang, Lifeng; Lan, Ruiting; Xia, Lining; Walsh, Timothy R; Xu, Jianguo; Lu, Jinxing; Li, Juan

    2017-03-01

    A recently identified colistin resistance gene, mcr-1, has been reported in many countries. In this study, we established a new real-time PCR method to detect it. We used a real-time PCR method to detect the mcr-1 gene in a variety of isolates and faecal samples from 20 provinces and municipal cities in China. Of the 2330 isolates (from 10 species) screened, 54 (2.3 %) isolates were positive for mcr-1. All of the mcr-1-positive isolates that were identified belonged to Escherichia coli strains, among which 9, 1, and 44 were identified as enteropathogenic E. coli, enteroadherent E. coli, and non-pathogenic E. coli, respectively. The majority of the mcr-1-positive isolates were obtained from farm animals from eight provinces and municipal cities across China. A total of 337 faecal samples, including 229 human and 108 pet animal faecal samples, were also screened for the mcr-1 gene. Of the 337 samples analyzed, six and eight human and pet animal faecal samples were positive for the mcr-1 gene, respectively. The data demonstrate that the mcr-1 gene is highly prevalent in human and animal populations in China. This occurrence suggests that active surveillance of the mcr-1 gene is imperative in curtailing its spread.

  10. Evaluation of an immunochromatographic dip strip test for simultaneous detection of Cryptosporidium spp, Giardia duodenalis, and Entamoeba histolytica antigens in human faecal samples.

    Science.gov (United States)

    Goñi, P; Martín, B; Villacampa, M; García, A; Seral, C; Castillo, F J; Clavel, A

    2012-08-01

    Immunochromatographic (IC) tests may play an important role in the future diagnosis of parasitic diseases because of their speed and simplicity of use. A recently developed test to detect Cryptosporidium spp, Giardia duodenalis and Entamoeba histolytica was evaluated. Microscopy and PCR were the "gold standard" reference techniques and the results of this IC test were compared with those obtained with ELISA and IC single test for the three parasites. One hundred sixty stool samples were assayed. Using microscopy, 22 samples were diagnosed as positive for Cryptosporidium spp., 31 for Giardia duodenalis, 41 for Entamoeba histolytica/dispar, and 68 had a negative diagnosis for the three parasites. Results of IC tests show sensitivities of 70-72% for Cryptosporidium, 90-97% for Giardia and 62.5% for Entamoeba histolytica. Specificities were of 93.6-94.9%, >99% and 96.1%, respectively. In all diagnoses, agreement with microscopy and PCR was over 90%, except in the triple test and microscopy in E. histolytica detection that was 76.3%, due to the inability of microscopy to differentiate E. histolytica from nonpathogenic species such as E. dispar or E. moshkovskii. The triple stool immunoassays provide adequate sensitivities and specificities for use in outbreak situations, for screening proposals and for massive assays in endemic areas where a large number of samples must be analysed or as complementary test for individual diagnosis.

  11. Presence of Clostridium difficile in pig faecal samples and wild animal species associated with pig farms.

    Science.gov (United States)

    Andrés-Lasheras, S; Bolea, R; Mainar-Jaime, R C; Kuijper, E; Sevilla, E; Martín-Burriel, I; Chirino-Trejo, M

    2017-02-01

    To determine the presence of Clostridium difficile on fattening pig farms in north-eastern Spain. Twenty-seven farms were sampled. Pools of pig faecal samples (n = 210), samples of intestinal content from common farm pest species (n = 95) and environment-related samples (n = 93) were collected. Isolates were tested for toxin genes of C. difficile, and typed by PCR-ribotyping and toxinotyping. The minimal inhibitory concentrations of six antimicrobial agents were determined using Etest. Thirty-four isolates were obtained from 12 farms, and 30 (88·2%) had toxin genes. Seven ribotypes were identified. Ribotype 078 and its variant 126 were predominant (52·9%). The same ribotypes were isolated from different animal species on the same farm. None of the isolates were resistant to metronidazole or vancomycin. Clostridium difficile was common within the pig farm environment. Most of the positive samples came from pest species or were pest-related environmental samples. Pest species were colonized with toxigenic and antimicrobial-resistant C. difficile strains of the same ribotypes that are found in humans and pigs. Rodents and pigeons may transmit toxigenic and antimicrobial-resistant C. difficile strains that are of the same ribotypes as those occuring in humans. © 2016 The Society for Applied Microbiology.

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

    Directory of Open Access Journals (Sweden)

    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.

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

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    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.

  14. Reducing sampling error in faecal egg counts from black rhinoceros (Diceros bicornis).

    Science.gov (United States)

    Stringer, Andrew P; Smith, Diane; Kerley, Graham I H; Linklater, Wayne L

    2014-04-01

    Faecal egg counts (FECs) are commonly used for the non-invasive assessment of parasite load within hosts. Sources of error, however, have been identified in laboratory techniques and sample storage. Here we focus on sampling error. We test whether a delay in sample collection can affect FECs, and estimate the number of samples needed to reliably assess mean parasite abundance within a host population. Two commonly found parasite eggs in black rhinoceros (Diceros bicornis) dung, strongyle-type nematodes and Anoplocephala gigantea, were used. We find that collection of dung from the centre of faecal boluses up to six hours after defecation does not affect FECs. More than nine samples were needed to greatly improve confidence intervals of the estimated mean parasite abundance within a host population. These results should improve the cost-effectiveness and efficiency of sampling regimes, and support the usefulness of FECs when used for the non-invasive assessment of parasite abundance in black rhinoceros populations.

  15. Administration of Bacillus coagulans in calves: recovery from faecal samples and evaluation of functional aspects of spores.

    Science.gov (United States)

    Ripamonti, Barbara; Agazzi, Alessandro; Baldi, Antonella; Balzaretti, Claudia; Bersani, Carla; Pirani, Silvia; Rebucci, Raffaella; Savoini, Giovanni; Stella, Simone; Stenico, Alberta; Domeneghini, Cinzia

    2009-12-01

    An investigation was carried out into the recovery from calf faeces of Bacillus coagulans spores added to the feed as probiotic. For this purpose, Bacillus coagulans spores (9 log₁₀ CFU g⁻¹) were given daily to 10 calves during the whole farming periods; another 10 calves acted as controls. Throughout the trial the faecal spore counts were significantly (P < 0.01) higher in the treated group than in the controls (averaging 2.1 x 10⁵ vs 3.7 x 10⁴ CFU g⁻¹). Bacterial cells were recovered from faecal samples and ribotyping matched the strain isolated from faecal sample to the clone administered to the animals. In addition, the recovered cells were found to maintain their functionality aspects of acid production, survival in artificial gastric juice and in the presence of bile, and attachment to human intestinal epithelial cells. The results further elucidate the fate of spore formers administered to calves, and this will help in the development of new species-specific nutritional strategies.

  16. 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.

  17. Antigenotoxicity of probiotics and prebiotics on faecal water-induced DNA damage in human colon adenocarcinoma cells.

    Science.gov (United States)

    Burns, Anthony J; Rowland, Ian R

    2004-07-13

    Six strains of lactic acid producing bacteria (LAB) were incubated (1 x 10(8)cfu/ml) with genotoxic faecal water from a human subject. HT29 human adenocarcinoma cells were then challenged with the resultant samples and DNA damage measured using the single cell gel electrophoresis (comet) assay. The LAB strains investigated were Bifidobacterium sp. 420, Bifidobacterium Bb12, Lactobacillus plantarum, Streptococcus thermophilus, Lactobacillus bulgaricus and Enterococcus faecium. DNA damage was significantly decreased by all bacteria used with the exception of Strep. thermophilus. Bif. Bb12 and Lact. plantarum showed the greatest protective effect against DNA damage. Incubation of faecal water with different concentrations of Bif. Bb12 and Lact. plantarum revealed that the decrease in genotoxicity was related to cell density. Non-viable (heat treated) probiotic cells had no effect on faecal water genotoxicity. In a second study, HT29 cells were cultured in the presence of supernatants of incubations of probiotics with various carbohydrates including known prebiotics; the HT29 cells were then exposed to faecal water. Overall, incubations involving Lact. plantarum with the fructooligosaccharide (FOS)-based prebiotics Inulin, Raftiline, Raftilose and Actilight were the most effective in increasing the cellular resistance to faecal water genotoxicity, whereas fermentations with Elixor (a galactooligosaccharide) and Fibersol (a maltodextrin) were less effective. Substantial reductions in faecal water-induced DNA damage were also seen with supernatants from incubation of prebiotics with Bif. Bb12. The supernatant of fermentations involving Ent. faecium and Bif. sp. 420 generally had less potent effects on genotoxicity although some reductions with Raftiline and Elixor fermentations were apparent.

  18. Faecal carriage of Pseudomonas aeruginosa in healthy humans: antimicrobial susceptibility and global genetic lineages.

    Science.gov (United States)

    Estepa, Vanesa; Rojo-Bezares, Beatriz; Torres, Carmen; Sáenz, Yolanda

    2014-07-01

    The aim of this study was to analyse the Pseudomonas aeruginosa faecal carriage rate in 98 healthy humans and to perform the phenotypic and genotypic characterization of recovered isolates. The genetic relatedness among the isolates was analysed by pulsed-field gel electrophoresis and multilocus sequence typing that was compared with worldwide epidemic clones. Pseudomonas aeruginosa was isolated from eight healthy individuals (8.2%), and two of them remained colonized after 5 months (in one case by the same clone). All 10 isolates (one/sample) were susceptible to 14 tested antipseudomonal agents and lacked integron structures. Six pulsed-field gel electrophoresis patterns and six sequence types (ST245, ST253, ST254, ST274, ST663 and the new one, ST1059) were identified among them. Four groups of OprD alterations were detected based on mutations and deletions related to PAO1 reference strain in our carbapenem-susceptible strains. This is the first study focused on P. aeruginosa from faecal samples of healthy humans that provides additional insights into the antimicrobial resistance and genetic diversity of P. aeruginosa. Although the isolates were antimicrobial susceptible, most of the sequence types detected were genetically related to Spanish epidemic clones or globally spread sequence types, such as ST274 and ST253.

  19. Prevalence of the mcr-1 colistin resistance gene in extended-spectrum β-lactamase-producing Escherichia coli from human faecal samples collected in 2012 in rural villages in Shandong Province, China.

    Science.gov (United States)

    Bi, Zhenwang; Berglund, Björn; Sun, Qiang; Nilsson, Maud; Chen, Baoli; Tärnberg, Maria; Ding, Lilu; Stålsby Lundborg, Cecilia; Bi, Zhenqiang; Tomson, Göran; Yao, Jingjing; Gu, Zhanying; Yin, Xiao; Kou, Zengqiang; Nilsson, Lennart E

    2017-04-01

    Since its initial discovery in China in 2015, the plasmid-mediated colistin resistance gene mcr-1 has been reported in Escherichia coli isolated from clinical samples, animals and meat worldwide. In this study, 706 extended-spectrum β-lactamase (ESBL)-producing E. coli from 411 persons were detected in a collection of faecal samples from 1000 rural residents in three counties in Shandong Province, China. These isolates were screened for mcr-1 and phenotypic colistin resistance. The gene was found in 3.5% of the isolates (from 4.9% of persons) from all three counties. All isolates with phenotypic colistin resistance carried mcr-1. These data indicate that commensal carriage of ESBL-producing E. coli with mcr-1 among persons in rural China was already present in 2012 and that mcr-1 was the most important colistin resistance mechanism. Interventions are necessary to minimise further dissemination of mcr-1, which would limit the future usefulness of colistin as a last-resort antibiotic. Copyright © 2017 Elsevier B.V. and International Society of Chemotherapy. All rights reserved.

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

    Science.gov (United States)

    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.

  1. Molecular analysis of the human faecal archaea in a southern Indian population

    Indian Academy of Sciences (India)

    SANDYA B RANI; RAMADASS BALAMURUGAN; BALAKRISHNAN S RAMAKRISHNA

    2017-03-01

    Archaea are an important constituent of the human gut microbiota, but there is no information on human gut archaea inan Indian population. In this study, faecal samples were obtained from different age groups (neonatal babies, preschoolchildren, school-going children, adolescents, adults and elderly) of a southern Indian population, and from atribal population also resident in southern India). 16S rRNA gene sequences specific to Archaea were amplified frompooled faecal DNA in each group, sequenced, and aligned against the NCBI database. Of the 806 adequate sequencesin the study, most aligned with 22 known sequences. There were 9 novel sequences in the present study. All sequenceswere deposited in the GenBank nucleotide sequence database with the following accession numbers: KF607113 -KF607918. Methanobrevibacter was the most prevalent genus among all the age groups accounting for 98% inneonates, 96% in post-weaning, and 100% each in preschool, school and adult population. In the elderly, Methanobrevibacteraccounted for 96% and in tribal adults, 99% of the clones belonged to Methanobrevibacter genus. Othergenera detected included Caldisphaera, Halobaculum, Methanosphaeraand Thermogymnomonas. Methanobrevibactersmithii predominated in all age groups, accounting for 749 (92.9%) of the 806 sequences. Archaea can befound in the faeces of southern Indian residents immediately after birth. Methanobrevibacter smithii was the dominantfaecal archeon in all age groups, with other genera being found at the extremes of age.

  2. 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.

  3. Evaluation of five commercial methods for the extraction and purification of DNA from human faecal samples for downstream molecular detection of the enteric protozoan parasites Cryptosporidium spp., Giardia duodenalis, and Entamoeba spp.

    Science.gov (United States)

    Paulos, Silvia; Mateo, Marta; de Lucio, Aida; Hernández-de Mingo, Marta; Bailo, Begoña; Saugar, José M; Cardona, Guillermo A; Fuentes, Isabel; Mateo, María; Carmena, David

    2016-08-01

    High quality, pure DNA is required for ensuring reliable and reproducible results in molecular diagnosis applications. A number of in-house and commercial methods are available for the extraction and purification of genomic DNA from faecal material, each one offering a specific combination of performance, cost-effectiveness, and easiness of use that should be conveniently evaluated in function of the pathogen of interest. In this comparative study the marketed kits QIAamp DNA stool mini (Qiagen), SpeedTools DNA extraction (Biotools), DNAExtract-VK (Vacunek), PowerFecal DNA isolation (MoBio), and Wizard magnetic DNA purification system (Promega Corporation) were assessed for their efficacy in obtaining DNA of the most relevant enteric protozoan parasites associated to gastrointestinal disease globally. A panel of 113 stool specimens of clinically confirmed patients with cryptosporidiosis (n=29), giardiasis (n=47) and amoebiasis by Entamoeba histolytica (n=3) or E. dispar (n=10) and apparently healthy subjects (n=24) were used for this purpose. Stool samples were aliquoted in five sub-samples and individually processed by each extraction method evaluated. Purified DNA samples were subsequently tested in PCR-based assays routinely used in our laboratory. The five compared methods yielded amplifiable amounts of DNA of the pathogens tested, although performance differences were observed among them depending on the parasite and the infection burden. Methods combining chemical, enzymatic and/or mechanical lysis procedures at temperatures of at least 56°C were proven more efficient for the release of DNA from Cryptosporidium oocysts. Copyright © 2016 Elsevier B.V. All rights reserved.

  4. Reverse transcriptase real-time PCR for detection and quantification of viable Campylobacter jejuni directly from poultry faecal samples

    DEFF Research Database (Denmark)

    Bui, Thanh Xuan; Wolff, Anders; Madsen, Mogens

    2012-01-01

    and quantification of viable Campylobacter jejuni directly from chicken faecal samples. The results of this method anda DNA-based quantitative real-time PCR (qPCR) method were compared with those of a bacterial culture method. Using bacterial culture andRT-qPCR methods, viable C. jejuni cells could be detected......Campylobacter spp. is the most common cause of bacterial diarrhoea in humans worldwide. Therefore, rapid and reliable methods fordetection and quantification of this pathogen are required. In this study, we have developed a reverse transcription quantitative real-time PCR(RT-qPCR) for detection...... for up to 5 days in both the C. jejuni spiked and the naturally contaminated faecalsamples. We found that no RT-qPCR signals were obtained when viable C. jejuni cells could not be counted by the culture method. In contrast,using a DNA-based qPCR method, dead or non-viable Campylobacter cells were...

  5. Molecular differentiation of cryptic stage ofEchinococcus granulosusand Taenia species from faecal and environmental samples

    Institute of Scientific and Technical Information of China (English)

    Diganta Pan; Sumanta De; Asit Kumar Bera; Subhashis Bandyopadhyay; Subrata Kumar Das; Debasis Bhattacharya

    2010-01-01

    Objective:To differentiate cryptic stage ofEchinococcus granulosus(E. granulosus) andTaenia by PCR-RFLP and sequence information of amplicon.Methods: DNA were isolated from metacestodes stage ofTaenia andE. granulosus using DNA isolation kit (Q-BIOgene kit, USA), the amplified and purified DNA product was then cloned and sent for sequencing. The generating sequence information was used for amplicons identification.Results:Out of 112 faecal and environmental samples, 16 exhibited positive result. The product size of amplicon positive for E. granulosus was 310 bp; whereas, forTaenia spp. sizes varied from 379 to 388 bp. Restriction profile of actin II with Csp61 also differedTaenia spp. andE. granulosus.Conclusions: The result of the study indicated that, the primers were useful to differentiate cryptic stage of the two genera which is yet to be reported earlier.

  6. A comparison of the efficiency of five different commercial DNA extraction kits for extraction of DNA from faecal samples.

    Science.gov (United States)

    Claassen, Shantelle; du Toit, Elloise; Kaba, Mamadou; Moodley, Clinton; Zar, Heather J; Nicol, Mark P

    2013-08-01

    Differences in the composition of the gut microbiota have been associated with a range of diseases using culture-independent methods. Reliable extraction of nucleic acid is a key step in identifying the composition of the faecal microbiota. Five widely used commercial deoxyribonucleic acid (DNA) extraction kits (QIAsymphony® Virus/Bacteria Midi Kit (kit QS), ZR Fecal DNA MiniPrep™ (kit Z), QIAamp® DNA Stool Mini Kit (kit QA), Ultraclean® Fecal DNA Isolation Kit (kit U) and PowerSoil® DNA Isolation Kit (kit P)) were evaluated, using human faecal samples. Yield, purity and integrity of total genomic DNA were compared spectrophotometrically and using gel electrophoresis. Three bacteria, commonly found in human faeces were quantified using real time polymerase chain reaction (qPCR) and total bacterial diversity was studied using denaturing gradient gel electrophoresis (DGGE) as well as terminal restriction fragment length polymorphism (T-RFLP). The measurements of DNA yield and purity exhibited variations between the five kits tested in this study. Automated kit QS exhibited the best quality and highest quantity of DNA. All kits were shown to be reproducible with CV values≤0.46 for DNA extraction. qPCR results showed that all kits were uniformly efficient for extracting DNA from the selected target bacteria. DGGE and T-RFLP produced the highest diversity scores for DNA extracted using kit Z (H'=2.30 and 1.27) and kit QS (H'=2.16 and 0.94), which also extracted the highest DNA yields compared to the other kits assessed. Copyright © 2013 Elsevier B.V. All rights reserved.

  7. [Protozoans in superficial waters and faecal samples of individuals of rural populations of the Montes municipality, Sucre state, Venezuela].

    Science.gov (United States)

    Mora, Leonor; Martínez, Indira; Figuera, Lourdes; Segura, Merlyn; Del Valle, Guilarte

    2010-12-01

    In Sucre state, the Manzanares river is threatened by domestic, agricultural and industrial activities, becoming an environmental risk factor for its inhabitants. In this sense, the presence of protozoans in superficial waters of tributaries of the Manzanares river (Orinoco river, Quebrada Seca, San Juan river), Montes municipality, Sucre state, as well as the analysis of faecal samples from inhabitants of towns bordering these tributaries were evaluated. We collected faecal and water samples from may 2006 through april 2007. The superficial water samples were processed after centrifugation by the direct examination and floculation, using lugol, modified Kinyoun and trichromic colorations. Fecal samples where analyzed by direct examination with physiological saline solution and the modified Ritchie concentration method and using the other colorations techniques above mentioned. The most frequently observed protozoans in superficial waters in the three tributaries were: Amoebas, Blastocystis sp, Endolimax sp., Chilomastix sp. and Giardia sp. Whereas in faecal samples, Blastocystis hominis, Endolimax nana and Entaomeba coli had the greatest frequencies in the three communities. The inhabitants of Orinoco La Peña turned out to be most susceptible to these parasitic infections (77.60%), followed by San Juan River (46.63%) and Quebrada Seca (39.49%). The presence of pathogenic and nonpathogenic protozoans in superficial waters demonstrates the faecal contamination of the tributaries, representing a constant focus of infection for their inhabitants, inferred by the observation of the same species in both types of samples.

  8. Temporal Variation of Faecal Shedding of Escherichia coli 0157:H7 in A Dairy Herd Producing Raw Milk for Direct Human Consumption

    Science.gov (United States)

    Merialdi, Giuseppe; Bardasi, Lia; Stancampiano, Laura; Taddei, Roberta; Delogu, Mauro; Di Francesco, Antonietta; Guarniero, Ilaria; Grilli, Ester; Fustini, Mattia; Bonfante, Elena; Giacometti, Federica

    2014-01-01

    The objective of this study was to analyse over time the evolution of E. coli O157:H7 faecal shedding in a dairy herd producing raw milk for direct human consumption. The study was performed between October 2012 and September 2013 in an average size Italian dairy farm where animals are housed inside the barn all over the year. The farm housed about 140 animals during the study – 70 cows and 70 calves and heifers. Twenty-six animals were randomly selected from both the cows and young animals group, and faecal sampling was performed rectally six times two months apart in each animal. Eleven animals were culled during the study and a total of 285 faecal samples were collected. At each faecal sampling, three trough water samples and two trough feed samples were also collected for a total of 36 water samples and 24 feed samples. Samples were analysed by real time polymerase chain reaction (RT-PCR) and culture. Overall, 16 (5.6%) faecal samples were positive for E. coli O157 by RT-PCR. Cultural examination found 9 (3.1%) samples positive for E. coli O157; all the isolates were positive for stx1, stx 2 and eae genes. One (4.1%) feed sample was positive for E. coli O157 by RT-PCR; none of the water samples was positive for E. coli O157. The model highlighted a general significant reduction of the number of positive samples observed during the study from the first to the sixth sampling (P=0.000) and a positive relation between the presence of positive samples and average environmental temperature (P=0.003). The results of the study showed that in an Italian dairy farm housing animals all year, faecal shedding of E. coli O157 followed the same temporal trend reported for other types of farming. The enhanced faecal shedding during warmer months may have a significant impact on environmental contamination and the safety of raw milk and its byproducts.

  9. Temporal variation of faecal shedding of Escherichia coli O157:H7 in a dairy herd producing raw milk for direct human consumption

    Directory of Open Access Journals (Sweden)

    Giuseppe Merialdi

    2014-09-01

    Full Text Available The objective of this study was to analyse over time the evolution of E. coli O157:H7 faecal shedding in a dairy herd producing raw milk for direct human consumption. The study was performed between October 2012 and September 2013 in an average size Italian dairy farm where animals are housed inside the barn all over the year. The farm housed about 140 animals during the study – 70 cows and 70 calves and heifers. Twenty-six animals were randomly selected from both the cows and young animals group, and faecal sampling was performed rectally six times two months apart in each animal. Eleven animals were culled during the study and a total of 285 faecal samples were collected. At each faecal sampling, three trough water samples and two trough feed samples were also collected for a total of 36 water samples and 24 feed samples. Samples were analysed by real time polymerase chain reaction (RT-PCR and culture. Overall, 16 (5.6% faecal samples were positive for E. coli O157 by RT-PCR. Cultural examination found 9 (3.1% samples positive for E. coli O157; all the isolates were positive for stx1, stx 2 and eae genes. One (4.1% feed sample was positive for E. coli O157 by RT-PCR; none of the water samples was positive for E. coli O157. The model highlighted a general significant reduction of the number of positive samples observed during the study from the first to the sixth sampling (P=0.000 and a positive relation between the presence of positive samples and average environmental temperature (P=0.003. The results of the study showed that in an Italian dairy farm housing animals all year, faecal shedding of E. coli O157 followed the same temporal trend reported for other types of farming. The enhanced faecal shedding during warmer months may have a significant impact on environmental contamination and the safety of raw milk and its byproducts.

  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. 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...

  12. 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...

  13. 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 was ...

  14. 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

    . 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...... faeces (EPG) was estimated every fourth day until day 28 post set up (p.s.) by a concentration McMaster-method. Larval cultures were prepared on day 0, 12 and 28 p.s. and the larval yield determined. For C. oncophora, the EPG was significantly higher in vacuum packed samples after 28 days as compared...

  15. 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.

  16. Double sampling of a faecal immunochemical test is not superior to single sampling for detection of colorectal neoplasia: a colonoscopy controlled prospective cohort study

    NARCIS (Netherlands)

    F.A. Oort (Frank); S.T. Van Turenhout (Sietze T.); V.M.H. Coupé (Veerle); R.W.M. van der Hulst (René); E.I.C. Wesdorp (Eric); J.S. Terhaar sive Droste (Jochim); I.B. Larbi (Ilhame); S.L. Kanis (Shannon); E. Van Hengel (Edwin); A.A. Bouman (Anneke); C.J.L.M. Meijer (Chris); C.J.J. Mulder (Chris)

    2011-01-01

    markdownabstract__Background:__ A single sampled faecal immunochemical test (FIT) has moderate sensitivity for colorectal cancer and advanced adenomas. Repeated FIT sampling could improve test sensitivity. The aim of the present study is to determine whether any of three different strategies of doub

  17. Description of Helicobacter valdiviensis sp. nov., an Epsilonproteobacteria isolated from wild bird faecal samples.

    Science.gov (United States)

    Collado, Luis; Jara, Ronald; González, Susana

    2014-06-01

    Two Gram-stain-negative, gently curved rod-shaped isolates (WBE14(T) and WBE19), recovered from wild bird faecal samples in the city of Valdivia (Southern Chile) were subjected to a polyphasic taxonomic study. Results of a genus-specific PCR indicated that these isolates belonged to the genus Helicobacter. This was further confirmed by a phylogenetic analyses based on the 16S rRNA, 60 kDa heat-shock protein (cpn60) and gyrase subunit B (gyrB) genes, where both strains formed a novel phylogenetic line within this genus. The 16S rRNA gene sequence similarity of strain WBE14(T) to the type strains of all other species of the genus Helicobacter examined ranged from 89.4 to 97.0%; Helicobacter brantae and Helicobacter pametensis were the most closely related species. However, on the basis of the protein-coding genes Helicobacter pullorum and Helicobacter canadensis are the most closely related species. These data, together with their different morphological and biochemical characteristics, revealed that these strains represent a novel species, for which the name Helicobacter valdiviensis sp. nov. is proposed, with the type strain WBE14(T) ( = CECT 8410(T) = LMG 27920(T)).

  18. 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.

  19. 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 (Pcoffees) induced a significant increase in the growth of Bifidobacterium spp. relative to the control vessel at 10 h after exposure (Pcoffee) induced a significant increase in the growth of Bifidobacterium spp. (P<0·05). CGA alone also induced a significant increase in the growth of the Clostridium coccoides-Eubacterium rectale group (P<0·05). This selective metabolism and subsequent amplification of specific bacterial populations could be beneficial to host health.

  20. Increased DNA amplification success of non-invasive genetic samples by successful removal of inhibitors from faecal samples collected in the field

    DEFF Research Database (Denmark)

    Hebert, Louise; Darden, Safi K.; Pedersen, Bo Vest;

    2011-01-01

    The use of non-invasive genetic sampling (NGS) is becoming increasingly important in the study of wild animal populations. Obtaining DNA from faecal samples is of particular interest because faeces can be collected without deploying sample capture devices. However, PCR amplification of DNA...... extracted from faeces is problematic because of high concentrations of inhibitors. Here we present a method for increasing the successful application of donor DNA extracted from faecal samples through inhibitor reduction. After standard extraction with a DNA stool kit we used a ‘Concentrated Chelex...... Treatment’ (CCT) that increased the amplification success from 31.7 to 61.4% of loci. Our results suggest that darker supernatant and samples with more precipitate contain more inhibitors than lighter samples and samples with little or no precipitate. We expect the use of this technique to have wide...

  1. An assessment of Bacteroides fragilis group organisms as indicators of human faecal pollution.

    Science.gov (United States)

    Allsop, K; Stickler, D J

    1985-01-01

    Membrane filtration techniques were used to enumerate Bacteroides fragilis group (BFG) organisms and Escherichia coli in a variety of natural waters, the influents and effluents from three types of sewage treatment plants and faeces of various animals. The results suggest that BFG organisms die off more rapidly than E. coli in water and that animal faeces are not a significant source of BFG. It is suggested that the ratio of BFG to E. coli in water may be used to indicate the proximity of a source of human faecal contamination.

  2. A Comparison of Microscopy and Enzyme Linked Immunosorbent Assay for Diagnosis of Giardia lamblia in Human Faecal Specimens.

    Science.gov (United States)

    Jahan, Noor; Khatoon, Razia; Ahmad, Siraj

    2014-11-01

    Giardia lamblia, a flagellate protozoa, is a common causative agent of parasitic diarrhoeal diseases of humans. Laboratory diagnosis mainly consists of direct microscopic examination of stool specimen for trophozoite and cysts of Giardia. However, due to intermittent faecal excretion of parasite, the case may be miss diagnosed and the patient may continue excreting the parasite and infecting others. Therefore, other mode of diagnosis should be looked for, which overcome the above drawbacks of microscopy used alone for diagnosis. The present study was done to evaluate the efficacy of RIDASCREEN Giardia (ELISA) test in comparison to direct microscopy in the diagnosis of Giardia lamblia in stool specimens from patients with diarrhea and other gastrointestinal symptoms. A total of 1680 patients were included in the study and three faecal specimens were taken from each patient which was divided into two parts. One part was used for direct wet mount examination and second part was used to put ELISA by using RIDASCREEN Giardia test. Out of 1680 stool samples, 380 specimens (22.6%) were found to be positive for Giardia lamblia. Maximum cases were detected by RIDASCREEN Giardia (ELISA) test with sensitivity of 100% and specificity of 91.5%. Maximum cases of giardiasis were detected in children less than 10 y of age (12.8%). RIDASCREEN Giardia test is a rapid and effective method with high sensitivity and specificity and detects Giardia antigens in stool specimens even when the count of parasite is low, thus reducing the chances of missing even the asymptomatic cases.

  3. The Composition of Human Milk and Infant Faecal Microbiota Over the First Three Months of Life: A Pilot Study

    Science.gov (United States)

    Murphy, Kiera; Curley, David; O’Callaghan, Tom F.; O’Shea, Carol-Anne; Dempsey, Eugene M.; O’Toole, Paul W.; Ross, R. Paul; Ryan, C. Anthony; Stanton, Catherine

    2017-01-01

    Human milk contains a diverse array of bioactives and is also a source of bacteria for the developing infant gut. The aim of this study was to characterize the bacterial communities in human milk and infant faeces over the first 3 months of life, in 10 mother-infant pairs. The presence of viable Bifidobacterium and Lactobacillus in human milk was also evaluated. MiSeq sequencing revealed a large diversity of the human milk microbiota, identifying over 207 bacterial genera in milk samples. The phyla Proteobacteria and Firmicutes and the genera Pseudomonas, Staphylococcus and Streptococcus were the predominant bacterial groups. A core of 12 genera represented 81% of the microbiota relative abundance in milk samples at week 1, 3 and 6, decreasing to 73% at week 12. Genera shared between infant faeces and human milk samples accounted for 70–88% of the total relative abundance in infant faecal samples, supporting the hypothesis of vertical transfer of bacteria from milk to the infant gut. In addition, identical strains of Bifidobacterium breve and Lactobacillus plantarum were isolated from the milk and faeces of one mother-infant pair. Vertical transfer of bacteria via breastfeeding may contribute to the initial establishment of the microbiota in the developing infant intestine. PMID:28094284

  4. Results of parasitological examinations of faecal samples from cats and dogs in Germany between 2003 and 2010.

    Science.gov (United States)

    Barutzki, Dieter; Schaper, Roland

    2011-08-01

    In a retrospective study, the results of parasitological examinations of faecal samples from 8,560 cats and 24,677 dogs between January 2003 and December 2010 in Germany were analysed. 30.4 % of the examined dogs and 22.8 % of the cats were infected with endoparasites. The examination of the faecal samples from dogs revealed stages of Giardia spp. (18.6 %), Toxocara canis (6.1 %), Toxascaris leonina (0.6 %), Ancylostomatidae (2.2 %), Trichuris vulpis (1.2 %), Capillaria spp. (1.3 %), Crenosoma vulpis (0.4 %), Angiostrongylus vasorum (0.5 %), Taeniidae (0.4 %), Dipylidiidae (canis (2.4 %), Sarcocystis spp. (2.2 %) and Hammondia heydorni/Neospora caninum (0.3 %). Dogs in the age groups up to 3 months and > 3 up to 6 months of age showed significantly higher infection rates with Giardia spp. (37.5 % and 38.2 %, respectively), Toxocara canis (12.0 % and 12.4 %, respectively), Toxascaris leonina (1.1 % and 1.6 %, respectively), Isospora spp. (23.4 % and 11.8 %, respectively), I. ohioensis-complex (15.6 % and 7.2 %, respectively) and I. canis (11.8 % and 5.2 %, respectively) compared to older dogs. In faecal samples from cats, stages of Giardia spp. (12.6 %), Toxocara cati (4.7 %), Toxascaris leonina (0.1 %), Ancylostoma tubaeforme (0.2 %), Aelurostrongylus abstrusus (0.5 %), Capillaria spp. (1.0 %), Taeniidae (0.6 %), Dipylidium caninum ( 3 up to 6 months of age showed significantly higher infection rates with Giardia spp. (19.5 % and 24.0 %, respectively), T. cati (8.1 % and 6.9 %, respectively), Isospora spp. (12.8 % and 8.6 %, respectively), I. felis (10.0 % and 5.9%, respectively) and I. rivolta (4.6 % and 2.9%, respectively) compared to older cats.

  5. 454 pyrosequencing analysis on faecal samples from a randomized DBPC trial of colicky infants treated with Lactobacillus reuteri DSM 17938.

    Directory of Open Access Journals (Sweden)

    Stefan Roos

    Full Text Available OBJECTIVE: To analyze the global microbial composition, using large-scale DNA sequencing of 16 S rRNA genes, in faecal samples from colicky infants given L. reuteri DSM 17938 or placebo. METHODS: Twenty-nine colicky infants (age 10-60 days were enrolled and randomly assigned to receive either Lactobacillus reuteri (10(8 cfu or a placebo once daily for 21 days. Responders were defined as subjects with a decrease of 50% in daily crying time at day 21 compared with the starting point. The microbiota of faecal samples from day 1 and 21 were analyzed using 454 pyrosequencing. The primers: Bakt_341F and Bakt_805R, complemented with 454 adapters and sample specific barcodes were used for PCR amplification of the 16 S rRNA genes. The structure of the data was explored by using permutational multivariate analysis of variance and effects of different variables were visualized with ordination analysis. RESULTS: The infants' faecal microbiota were composed of Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes as the four main phyla. The composition of the microbiota in infants with colic had very high inter-individual variability with Firmicutes/Bacteroidetes ratios varying from 4000 to 0.025. On an individual basis, the microbiota was, however, relatively stable over time. Treatment with L. reuteri DSM 17938 did not change the global composition of the microbiota, but when comparing responders with non-responders the group responders had an increased relative abundance of the phyla Bacteroidetes and genus Bacteroides at day 21 compared with day 0. Furthermore, the phyla composition of the infants at day 21 could be divided into three enterotype groups, dominated by Firmicutes, Bacteroidetes, and Actinobacteria, respectively. CONCLUSION: L. reuteri DSM 17938 did not affect the global composition of the microbiota. However, the increase of Bacteroidetes in the responder infants indicated that a decrease in colicky symptoms was linked to changes of

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

    DEFF Research Database (Denmark)

    Katakweba, A. A. S.; Møller, K. S.; Muumba, J.

    2015-01-01

    AIM: 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. METHODS AND RESULTS: 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......, 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. CONCLUSIONS: Antibiotic resistant bacteria were not more frequently found...

  7. Comparison of Toxocara eggs in hair and faecal samples from owned dogs and cats collected in Ankara, Turkey.

    Science.gov (United States)

    Öge, Hatice; Öge, Semih; Özbakış, Gökben; Gürcan, Safa

    2014-12-15

    This study was undertaken to determine the prevalence of Toxocara eggs on hair and in faeces of healthy owned cats and dogs and to make comparisons between data (sex, age, host factor, etc.) collected from dogs and cats. Toxocara eggs were found on the hair of 14% of 100 dogs and 22% of 100 cats. In total, 58 and 136 eggs were recovered from the hair samples of examined cats and dogs, respectively. Of the total number of eggs, 2 were classified as embryonated in cats. One of the eggs recovered was embryonating in dogs. The maximum number of eggs was found in the tail bottom of cats (28 eggs) and dogs (58 eggs). As well as finding Toxocara eggs in dogs and cats hair, we also found eggs of some helminthic parasites; such as Dicrocoelium sp., Fasciola sp., Taenia sp., Dipylidium caninum and Toxascaris leonina. In addition, faecal samples of same dogs and cats were also examined by two techniques (centrifugal flotation and sedimentation): Toxocara eggs were found in 5% and 13% of dogs and cats faeces, respectively. But, 14% of the dogs and 22% of the cats were positive for Toxocara eggs on hair. The prevalence of eggs in faecal samples was lower than those detected from hair samples (P dogs and cats without internal infections were shown to have eggs on their hair and so uninfected animals also pose a threat in terms of the eggs present on their hair, albeit a small risk. Copyright © 2014 Elsevier B.V. All rights reserved.

  8. Detection and characterisation of bisegmented double-stranded RNA viruses (picobirnaviruses) in human faecal specimens.

    Science.gov (United States)

    Gallimore, C I; Appleton, H; Lewis, D; Green, J; Brown, D W

    1995-02-01

    The prevalence of picobirnaviruses (PBVs) in human stools was investigated by polyacrylamide gel electrophoresis (PAGE) analysis of 832 faecal specimens collected between 1982 and 1993 from patients in various clinical groups. Similar prevalences (9-13%) were detected in patients with or without gastroenteritis and throughout the age range of 3 to > 65 years. Two methods for the extraction of nucleic acid, a phenol/chloroform method and a guanidinium thiocynate (GTC)/silica method, were compared. Detection of PBVs by PAGE was three times more sensitive following RNA extraction by the GTC/silica method. Characterisation of three strains was carried out. Segment sizes ranged from 1.625 to 1.95 kilo base pairs (Kbp) and 2.2 to 2.5 Kbp for the fast and slow migrating bands, respectively. The nuclic acid was shown to be double-stranded RNA (dsRNA) by nuclease digestion. PBV-like particles were detected by electron microscopy in two PAGE-positive stools. Virion diameters ranged from 35 to 41 nm and a buoyant density of 1.38-1.4 g/ml in caesium chloride (CsCl) was demonstrated. These findings suggest that PBVs are widespread in humans in the United Kingdom. However, no disease association could be demonstrated.

  9. Comparison of real-time PCR and Kato smear microscopy for the detection of hookworm infections in three consecutive faecal samples from schoolchildren in Ghana

    NARCIS (Netherlands)

    van Mens, Suzan P.; Aryeetey, Yvonne; Yazdanbakhsh, Maria; van Lieshout, Lisette; Boakye, Daniel; Verweij, Jaco J.

    2013-01-01

    The classic technique used to detect hookworm infections in population-based surveys is microscopic examination of Kato thick smears of multiple faecal samples per person as variation in soil-transmitted helminth egg output is common. As an alternative to this time-consuming and logistically difficu

  10. You can pool faecal samples from individual pigs to test for Porcine Circovirus Type 2 and Lawsonia intracellularis using real-time PCRs

    DEFF Research Database (Denmark)

    Holyoake, Patricia K.; Hjulsager, Charlotte Kristiane; Larsen, Lars Erik;

    Introduction Real-time PCR tests have been developed to detect and quantify Porcine Circovirus type 2 (PCV2) and Lawsonia intracellularis in pigs’ faeces. Pooling of individual faecal samples is often used to reduce the costs of diagnostic testing. The objective of this study was to evaluate any ...

  11. Evaluating the interaction of faecal pellet deposition rates and DNA degradation rates to optimize sampling design for DNA-based mark-recapture analysis of Sonoran pronghorn.

    Science.gov (United States)

    Woodruff, S P; Johnson, T R; Waits, L P

    2015-07-01

    Knowledge of population demographics is important for species management but can be challenging in low-density, wide-ranging species. Population monitoring of the endangered Sonoran pronghorn (Antilocapra americana sonoriensis) is critical for assessing the success of recovery efforts, and noninvasive DNA sampling (NDS) could be more cost-effective and less intrusive than traditional methods. We evaluated faecal pellet deposition rates and faecal DNA degradation rates to maximize sampling efficiency for DNA-based mark-recapture analyses. Deposition data were collected at five watering holes using sampling intervals of 1-7 days and averaged one pellet pile per pronghorn per day. To evaluate nuclear DNA (nDNA) degradation, 20 faecal samples were exposed to local environmental conditions and sampled at eight time points from one to 124 days. Average amplification success rates for six nDNA microsatellite loci were 81% for samples on day one, 63% by day seven, 2% by day 14 and 0% by day 60. We evaluated the efficiency of different sampling intervals (1-10 days) by estimating the number of successful samples, success rate of individual identification and laboratory costs per successful sample. Cost per successful sample increased and success and efficiency declined as the sampling interval increased. Results indicate NDS of faecal pellets is a feasible method for individual identification, population estimation and demographic monitoring of Sonoran pronghorn. We recommend collecting samples sampling interval of four to seven days in summer conditions (i.e., extreme heat and exposure to UV light) will achieve desired sample sizes for mark-recapture analysis while also maximizing efficiency [Corrected]. © 2014 John Wiley & Sons Ltd.

  12. Effect of yoghurt containing Bifidobacterium lactis Bb12® on faecal excretion of secretory immunoglobulin A and human beta-defensin 2 in healthy adult volunteers.

    Science.gov (United States)

    Kabeerdoss, Jayakanthan; Devi, R Shobana; Mary, R Regina; Prabhavathi, D; Vidya, R; Mechenro, John; Mahendri, N V; Pugazhendhi, Srinivasan; Ramakrishna, Balakrishnan S

    2011-12-23

    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. 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. 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.

  13. 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.

  14. Detection of vancomycin-resistant enterococci from faecal samples of Iberian wolf and Iberian lynx, including Enterococcus faecium strains of CC17 and the new singleton ST573.

    Science.gov (United States)

    Gonçalves, Alexandre; Igrejas, Gilberto; Radhouani, Hajer; López, María; Guerra, Ana; Petrucci-Fonseca, Francisco; Alcaide, Eva; Zorrilla, Irene; Serra, Rodrigo; Torres, Carmen; Poeta, Patrícia

    2011-12-01

    The aim of this study was to perform the molecular characterization of vancomycin resistant enterococci (VRE) within the faecal flora of Iberian wolf and Iberian lynx. The association with other resistance genes and the detection of virulence genes were also analysed. From 2008 to 2010, 365 faecal samples from Iberian wolf and Iberian lynx were collected and tested for VRE recovery. Mechanisms of resistance to vancomycin and other antibiotics, as well as genes encoding virulence factors were detected through PCR. Multilocus Sequence Typing (MLST) was performed for Enterococcus faecium strains. VRE were recovered in 8 of the 365 analysed samples. The vanA gene was identified in two E. faecium isolates recovered from Iberian wolf faecal samples and the remaining six showed intrinsic resistance (3 vanC1-E. gallinarum and 3 vanC2-E. casseliflavus, from Iberian wolf and Iberian lynx faecal samples, respectively). One vanA-containing isolate showed tetracycline and erythromycin resistance [with erm(B) and tet(L) genes] and the other one also exhibited ampicillin and kanamycin resistance [with erm(B), tet(M) and aph(3')-III genes]. One of the vanA-isolates revealed a new sequence type named ST573 and the other one belonged to the CC17 clonal complex (ST18). The hyl gene was detected in one E. casseliflavus and three E. gallinarum but not among vanA-positive isolates, and the occurrence of cylA and cylL genes was confirmed in two E. casseliflavus isolates. A low prevalence of VRE has been detected in faecal samples of Iberian wolf and Iberian lynx and strains with an acquired mechanism of resistance to vancomycin have not been detected among Iberian lynx.

  15. In vitro fermentation by human faecal bacteria of total and purified dietary fibres from brown seaweeds.

    Science.gov (United States)

    Michel, C; Lahaye, M; Bonnet, C; Mabeau, S; Barry, J L

    1996-02-01

    The in vitro degradation of dietary fibre from three brown seaweeds (Himanthalia elongata, Laminaria digitata and Undaria pinnatifida) was studied, using human faecal flora. Two sets of fibre were tested: (1) total algal fibres extracted from the whole algae, mainly composed of alginates, and (2) purified fibres (sulphated fucans, Na-alginates and laminarans) representative of those contained in the whole brown algae. Mannuronate, one algal component, was also investigated. Substrate disappearance and short-chain fatty acid (SCFA) production were monitored after 6, 12 and 24 h fermentation. Gas production was followed hourly during the first 9 h and then at 12 and 24 h. Sugarbeet fibre was used as a fermentation reference substrate. According to the fermentative indices used, most of each of the total algal fibres disappeared after 24 h (range 60-76%) but, unlike the reference substrate, they were not completely metabolized to SCFA (range 47-62%). Among the purified algal fibres, disappearance of laminarans was approximately 90% and metabolism to SCFA was approximately 85% in close agreement with the fermentation pattern of reference fibres. Sulphated fucans were not degraded. Na-alginates exhibited a fermentation pattern quite similar to those of the whole algal fibres with a more pronounced discrepancy between disappearance and production of SCFA: disappearance was approximately 83% but metabolism was only approximately 57%. Mannuronate was slowly fermented but its metabolism corresponded to its disappearance from the fermentative medium. Thus, the characteristic fermentation pattern of the total fibres from the three brown algae investigated was attributed to the peculiar fermentation of alginates, and mannuronate was shown not to be directly involved.

  16. GC-MS method for determining faecal sterols as biomarkers of human and pastoral animal presence in freshwater sediments.

    Science.gov (United States)

    Battistel, Dario; Piazza, Rossano; Argiriadis, Elena; Marchiori, Enrico; Radaelli, Marta; Barbante, Carlo

    2015-11-01

    In order to determine sterols and stanols in freshwater sediments to reconstruct the past presence of humans and pastoral animals, we developed an analytical method based on pressurised liquid extraction (PLE), clean-up performed using solid phase extraction (SPE) and sterol determination using gas chromatography-mass spectrometry (GC-MS) analysis. PLE extraction conditions were optimised using dichloromethane (DCM) and DCM/methanol mixtures. Clean-up was performed with 2 g silica SPE cartridges, and the concentrated extracts were eluted with 70 mL DCM. Extraction yield was evaluated using an in-house reference material spiked with (13)C-labelled cholesterol and aged for 10 days. In comparison with pre-extraction, where the sediment is extracted and then spiked with a known analyte concentration, this approach preserves the original composition of the sediment. DCM and DCM/methanol mixtures resulted in high extraction yields ranging from 86 to 92 % with good reproducibility (relative standard deviation (RSD) 5-8 %). PLE extraction yields obtained with DCM as the extracting solvent were about 1.5 times higher than extractions using an ultrasonic bath. The solvent extraction mixture and matrix composition strongly affected the solvent extraction composition where higher overall recoveries (70-80 %) for each compound were obtained with DCM. The extraction mixture and matrix composition also affected the analyte concentrations, resulting in a method precision ranging from 1 to 18 %. Diatomaceous earth spiked with 10 to 100 ng of sterols, and environmental samples fortified with suitable amounts of sterols provided apparent recovery values ranging from 90 to 110 %. We applied the method to environmental samples both close to and upstream from sewage discharge zones, resulting in substantially higher faecal sterol (FeSt) concentrations near the sewage. In addition, we also applied the method to a 37-cm freshwater sediment core in order to evaluate its applicability for

  17. Effect of oral spiramycin on the faecal and oral bacteria in human volunteers.

    Science.gov (United States)

    Andremont, A; Trancrède, C; Desnottes, J F

    1991-03-01

    Six healthy adult volunteers were treated with 1 g of oral spiramycin twice daily for five days, and their oral and faecal microbial flora were studied. Mean saliva and serum concentrations of the antibiotic never exceeded 2.1 +/- 1.1 mg/l. The number of volunteers whose oral cavity was colonized by Enterobacteriaceae, group D streptococci, staphylococci, and fungi remained unchanged following treatment. The mean count of anaerobic faecal bacteria was 10.3 +/- 0.6 log10 cfu/g initially. This did not change significantly during the treatment, nor did the composition of the predominant anaerobic flora. Mean counts of group D streptococci were 1000 times lower than those of anaerobes before treatment, and also remained unchanged during therapy. No overgrowth of fungi, staphylococci, or Pseudomonas aeruginosa was observed. No significant modifications occurred in the mean total count of faecal Enterobacteriaceae (7.9 +/- 0.4 versus 7.4 +/- 1.0 log10 cfu/g of faeces before and during treatment respectively). However, faecal concentrations of highly spiramycin-resistant Enterobacteriaceae (MIC greater than or equal to 512 mg/l) increased from 4.8 +/- 1.2 to 7.0 +/- 1.8 log10 cfu/g during treatment. The MIC50 value of spiramycin for anaerobes, Enterobacteriaceae, and group D streptococci were 0.125, 64, and 0.5 mg/l respectively before treatment, and these increased to 1024, 512 and 1024 mg/l respectively during treatment. This was attributed to the rise in the faecal concentrations of spiramycin, which reached 689 +/- 48 micrograms/g of faeces on the fifth day of treatment. These concentrations decreased rapidly on cessation of treatment.

  18. Campylobacter ornithocola sp. nov., a novel member of the Campylobacter lari group isolated from wild bird faecal samples.

    Science.gov (United States)

    Cáceres, Alberto; Muñoz, Ivo; Iraola, Gregorio; Díaz-Viraqué, Florencia; Collado, Luis

    2017-06-01

    During a study on the prevalence and diversity of campylobacteria in wild birds faecal samples from the city of Valdivia (southern Chile) 17 Gram-stain-negative, curved-rod-shaped isolates, were initially identified as Campylobacter lari by PCR-RFLP. Further identification by 16S rRNA sequence analysis revealed that they formed a distinct group in the genus Campylobacter. This unique position was confirmed by the results of analysis of rpoB, atpA and cpn60 gene sequences. The average nucleotide identity between the representative strain WBE38T and the type strain of the most closely related taxon C. larisubsp.concheus (LMG 11760) was 90.8 %. The oxidase and urease activity of the novel isolates enabled them to be phenotypically differentiated from species of the genus Campylobacter with validly published names. Therefore, on the basis of phenotypic, genetic and genomic characterizations, the results of this study clearly indicate that these strains represent a novel species within the genus Campylobacter, for which the name Campylobacter ornithocola sp. nov. is proposed, with the type strain WBE38T (=CECT 9147T=LMG 29815T).

  19. Detection of Bifidobacteriurn longum in faecal samples after orogastric intubation using immunological test systems

    OpenAIRE

    Dreher, R M; Gerhard, J.; Schönborn, W.; Lauer, E.

    2011-01-01

    A simple method based on a sandwich-ELISA was developed to study the passage and the viability of a bifidobacterial species after oral application of lyophilized preparation. Rabbits were immunized with a formaldehyde-inactivated strain of the species Bifidobacterium longum resulting in a highly specific antiserum. The cross-reaction of most of 46 selected, representative strains of 14 bifidobacterial species from animal and human sources was negligibly low. Only two strains of B. angulatum a...

  20. Application of real-time PCR for the differentiation of Entamoeba histolytica and E. dispar in cyst-positive faecal samples from 130 immigrants living in Spain.

    Science.gov (United States)

    Gutiérrez-Cisneros, M J; Cogollos, R; López-Vélez, R; Martín-Rabadán, P; Martínez-Ruiz, R; Subirats, M; Merino, F J; Fuentes, I

    2010-03-01

    In an effort to improve the diagnosis of intestinal amoebiasis, a real-time PCR has been used for the detection and differentiation of Entamoeba histolytica and E. dispar infections in African or South American immigrants who live in Spain. Faecal samples from all of the 130 subjects had apparently been found to contain E. histolytica/E. dispar cysts by microscopical examination. Using the real-time PCR, E. histolytica DNA was detected in faecal samples from only 10 (7.7%) of the immigrants, with E. dispar DNA detected in the samples from another 117 (90.0%) of the subjects. The use of such PCR in the routine investigation of patients found positive for E. histolytica/E. dispar cysts (by microscopy) is recommended, especially in non-endemic areas.

  1. Pooling sheep faecal samples for the assessment of anthelmintic drug efficacy using McMaster and Mini-FLOTAC in gastrointestinal strongyle and Nematodirus infection.

    Science.gov (United States)

    Kenyon, Fiona; Rinaldi, Laura; McBean, Dave; Pepe, Paola; Bosco, Antonio; Melville, Lynsey; Devin, Leigh; Mitchell, Gillian; Ianniello, Davide; Charlier, Johannes; Vercruysse, Jozef; Cringoli, Giuseppe; Levecke, Bruno

    2016-07-30

    In small ruminants, faecal egg counts (FECs) and reduction in FECs (FECR) are the most common methods for the assessment of intensity of gastrointestinal (GI) nematodes infections and anthelmintic drug efficacy, respectively. The main limitation of these methods is the time and cost to conduct FECs on a representative number of individual animals. A cost-saving alternative would be to examine pooled faecal samples, however little is known regarding whether pooling can give representative results. In the present study, we compared the FECR results obtained by both an individual and a pooled examination strategy across different pool sizes and analytical sensitivity of the FEC techniques. A survey was conducted on 5 sheep farms in Scotland, where anthelmintic resistance is known to be widespread. Lambs were treated with fenbendazole (4 groups), levamisole (3 groups), ivermectin (3 groups) or moxidectin (1 group). For each group, individual faecal samples were collected from 20 animals, at baseline (D0) and 14 days after (D14) anthelmintic administration. Faecal samples were analyzed as pools of 3-5, 6-10, and 14-20 individual samples. Both individual and pooled samples were screened for GI strongyle and Nematodirus eggs using two FEC techniques with three different levels of analytical sensitivity, including Mini-FLOTAC (analytical sensitivity of 10 eggs per gram of faeces (EPG)) and McMaster (analytical sensitivity of 15 or 50 EPG).For both Mini-FLOTAC and McMaster (analytical sensitivity of 15 EPG), there was a perfect agreement in classifying the efficacy of the anthelmintic as 'normal', 'doubtful' or 'reduced' regardless of pool size. When using the McMaster method (analytical sensitivity of 50 EPG) anthelmintic efficacy was often falsely classified as 'normal' or assessment was not possible due to zero FECs at D0, and this became more pronounced when the pool size increased. In conclusion, pooling ovine faecal samples holds promise as a cost-saving and efficient

  2. Rapid sample preparation for detection and identification of avian influenza virus from chicken faecal samples using magnetic bead microsystem

    DEFF Research Database (Denmark)

    Dhumpa, Raghuram; Bu, Minqiang; Handberg, Kurt

    2010-01-01

    Avian influenza virus (AIV) is an infectious agent of birds and mammals. AIV is causing huge economic loss and can be a threat to human health. Reverse transcriptase polymerase chain reaction (RT-PCR) has been used as a method for the detection and identification of AIV virus. Although RT...

  3. Fate of Extended-Spectrum β-Lactamase-Producing Escherichia coli from Faecal Sources in Surface Water and Probability of Human Exposure through Swimming

    NARCIS (Netherlands)

    Schijven, Jack F; Blaak, Hetty; Schets, Franciska M; de Roda Husman, Ana Maria

    2015-01-01

    The goal of this study was to determine the fate of ESBL-producing Escherichia coli (ESBL-EC) emitted from faecal sources in surface water, and the probability of human exposure through swimming. Concentrations of ESBL-EC were measured in recreational waters and in source waters, being water in ditc

  4. Locating hybrid individuals in the red wolf (Canis rufus) experimental population area using a spatially targeted sampling strategy and faecal DNA genotyping.

    Science.gov (United States)

    Adams, Jennifer R; Lucash, Chris; Schutte, Leslie; Waits, Lisette P

    2007-05-01

    Hybridization with coyotes (Canis latrans) continues to threaten the recovery of endangered red wolves (Canis rufus) in North Carolina and requires the development of new strategies to detect and remove coyotes and hybrids. Here, we combine a spatially targeted faecal collection strategy with a previously published reference genotype data filtering method and a genetic test for coyote ancestry to screen portions of the red wolf experimental population area for the presence of nonred wolf canids. We also test the accuracy of our maximum-likelihood assignment test for identifying hybrid individuals using eight microsatellite loci instead of the original 18 loci and compare its performance to the Bayesian approach implemented in newhybrids. We obtained faecal DNA genotypes for 89 samples, 73 of which were matched to 23 known individuals. The performance of two sampling strategies - comprehensive sweep and opportunistic spot-check was evaluated. The opportunistic spot-check sampling strategy required less effort than the comprehensive sweep sampling strategy but identified fewer individuals. Six hybrids or coyotes were detected and five of these individuals were subsequently captured and removed from the population. The accuracy and power of the genetic test for coyote ancestry is decreased when using eight loci; however, nonred wolf canids are identified with high frequency. This combination of molecular and traditional field-based approaches has great potential for addressing the challenge of hybridization in other species and ecosystems.

  5. Heterogeneous distributions of Escherichia coli O157 within naturally infected bovine faecal pats.

    Science.gov (United States)

    Robinson, Susan E; Brown, Patrick E; John Wright, E; Bennett, Malcolm; Hart, C Anthony; French, Nigel P

    2005-03-15

    Escherichia coli O157 is an important human pathogen for which cattle are considered a reservoir. This paper describes and models the variation in counts of E. coli O157 that exists within individual bovine faecal pats. The presence and concentration of E. coli O157 in faecal samples was determined using a combination of direct spiral plating followed by a more sensitive isolation procedure. The data were modelled using multilevel random effect models, in which the random effects were allowed to be correlated to allow for the fact that pooled and individual samples come from the same pat. Up to a two log difference in the concentration of E. coli O157 was demonstrated in samples from different areas within a faecal pat. Pooling of individual samples from throughout the faecal pat and processing it as one composite sample allows this heterogeneity to be overcome.

  6. Influence of sample return time and ambient temperature on the performance of an immunochemical faecal occult blood test with a new buffer for colorectal cancer screening.

    Science.gov (United States)

    Dancourt, Vincent; Hamza, Samia; Manfredi, Sylvain; Drouillard, Antoine; Bidan, Jeanne-Marie; Faivre, Jean; Lepage, Come

    2016-03-01

    The haemoglobin concentration measured by faecal immunochemical tests (FIT) may be decreased in cases of delayed sample return or high temperature. It is an issue of great importance. The aim of this study was to investigate the effects of sample return time and of season on the performance of an FIT (FOB-Gold) with a new buffer. The study included 20 371 participants involved in the French organized colorectal cancer (CRC) screening programme. The probability of a positive screening test, detection rates and positive predictive values for CRC and advanced adenoma were analysed according to sample return time and season of screening. A sample of positive FIT was stored for 7 days in an incubator at 20°C or 30°C. The positivity rate was 4.1% for a sample return time of up to 3 days, 4.1% for 4-5 days and 4.6% for 6-7 days (P=0.25). In multivariate analysis, there was no association between positivity rates, detection rates and positive predictive values for CRC and advanced adenoma and the sample return time or the season of screening. At a constant temperature of 20°C, there was a decrease in the haemoglobin concentration of 5.1% after 7 days. The decrease reached 20.5% at a temperature of 30°C. It was only 4.5% during the first 4 days of storage in the incubator. With the new buffer, delay in sample return or season did not affect the clinical outcome. When temperatures reach 30°C, the faecal sample must be returned promptly.

  7. 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.

  8. Serotipos de Campylobacter jejuni ssp. jejuni aislado en carne de ave para consumo humano y en muestras de heces de niños con diarrea Campylobacter jejuni ssp. jejuni serotypes in avian meat for human consumption and in faecal samples of children with diarrhoea

    Directory of Open Access Journals (Sweden)

    H. Fernández

    2005-01-01

    Full Text Available Considerando a las aves de consumo como un importante reservorio de C. jejuni ssp jejuni y sus subproductos alimenticios como principal vehículo, fueron serotipificadas 50 cepas aisladas de carne de ave para consumo humano, correlacionándolas epidemiológicamente con los serotipos encontrados en 50 cepas aisladas de niños con diarrea. Las cepas de C.jejuni ssp jejuni fueron serotipificadas mediante la técnica de hemaglutinación pasiva descrita por Penner, utilizando un kit comercial (DENKA SEIKEN, conteniendo los 25 sueros tipificadores para los serotipos descritos como los más frecuentes. Los serotipos A, B, F, L, N e Y fueron aislados concomitantemente en ambos tipos de muestras. Los serotipos de mayor aislamiento en las muestras de origen humano fueron Z2 (16% y Z5 (12%, mientras que en las de origen aviar fueron los serotipos A (28%, C (10%, L (10% e Y (10%. Al no coexistir los serotipos Z y C, en ambos grupos muestrales, es posible inferir la existencia de otros reservorios y vehículos que estén actuando como agentes transmisores de esta bacteria al ser humano.Having in mind that fowl and avian byproducts for human consumption are important reservoirs and vehicles for C. jejuni ssp. jejuni, a serotyping study was conducted in 50 strains isolated from avian meat and 50 isolated from human diarrhoeic stools. C. jejuni ssp. jejuni serotyping was carried out using a commercial kit with 25 antisera (DENKA SEIKEN, based on the Penner’s passive haemagglutination technique. Serotypes A, B, F, L, N e Y were concomitantly found in both kinds of samples. Serotypes Z2 (16% and Z5 (12% were the most frequently found in human strains, whereas serotypes A (28%, C (10%, L (10% and Y (10% were the most frequently isolated from avian samples. However, serotypes Z and C did not coexist in both types of samples. The latter results suggest that additionally to fowl and avian meat, there might be other animal reservoirs and vehicles that could act as

  9. Faecal microbiota of cats with insulin-treated diabetes mellitus.

    Science.gov (United States)

    Bell, Erin T; Suchodolski, Jan S; Isaiah, Anitha; Fleeman, Linda M; Cook, Audrey K; Steiner, Jörg M; Mansfield, Caroline S

    2014-01-01

    Microorganisms within the gastrointestinal tract significantly influence metabolic processes within their mammalian host, and recently several groups have sought to characterise the gastrointestinal microbiota of individuals affected by metabolic disease. Differences in the composition of the gastrointestinal microbiota have been reported in mouse models of type 2 diabetes mellitus, as well as in human patients. Diabetes mellitus in cats has many similarities to type 2 diabetes in humans. No studies of the gastrointestinal microbiota of diabetic cats have been previously published. The objectives of this study were to compare the composition of the faecal microbiota of diabetic and non-diabetic cats, and secondarily to determine if host signalment and dietary factors influence the composition of the faecal microbiota in cats. Faecal samples were collected from insulin-treated diabetic and non-diabetic cats, and Illumina sequencing of the 16S rRNA gene and quantitative PCR were performed on each sample. ANOSIM based on the unweighted UniFrac distance metric identified no difference in the composition of the faecal microbiota between diabetic and non-diabetic cats, and no significant differences in the proportions of dominant bacteria by phylum, class, order, family or genus as determined by 16S rRNA gene sequencing were identified between diabetic and non-diabetic cats. qPCR identified a decrease in Faecalibacterium spp. in cats aged over ten years. Cat breed or gender, dietary carbohydrate, protein or fat content, and dietary formulation (wet versus dry food) did not affect the composition of the faecal microbiota. In conclusion, the composition of the faecal microbiota was not altered by the presence of diabetes mellitus in cats. Additional studies that compare the functional products of the microbiota in diabetic and non-diabetic cats are warranted to further investigate the potential impact of the gastrointestinal microbiota on metabolic diseases such as

  10. In vitro fermentation of 12 dietary fibres by faecal inoculum from pigs and humans

    NARCIS (Netherlands)

    Jonathan, M.C.; Borne, van den J.J.G.C.; Wiechen, van P.; Souza Da Silva, C.; Schols, H.A.; Gruppen, H.

    2012-01-01

    In vitro fermentation of twelve dietary fibers by fecal inocula from pigs and humans were performed. The fibers included homoglucans, mannans, fructans, polyuronides, and complex heteroglycans. Gas production, short chain fatty acid production and fiber degradation products were monitored during

  11. Detection dog efficacy for collecting faecal samples from the critically endangered Cross River gorilla (Gorilla gorilla diehli) for genetic censusing.

    Science.gov (United States)

    Arandjelovic, Mimi; Bergl, Richard A; Ikfuingei, Romanus; Jameson, Christopher; Parker, Megan; Vigilant, Linda

    2015-02-01

    Population estimates using genetic capture-recapture methods from non-invasively collected wildlife samples are more accurate and precise than those obtained from traditional methods when detection and resampling rates are high. Recently, detection dogs have been increasingly used to find elusive species and their by-products. Here we compared the effectiveness of dog- and human-directed searches for Cross River gorilla (Gorilla gorilla diehli) faeces at two sites. The critically endangered Cross River gorilla inhabits a region of high biodiversity and endemism on the border between Nigeria and Cameroon. The rugged highland terrain and their cryptic behaviour make them difficult to study and a precise population size for the subspecies is still lacking. Dog-directed surveys located more fresh faeces with less bias than human-directed survey teams. This produced a more reliable population estimate, although of modest precision given the small scale of this pilot study. Unfortunately, the considerable costs associated with use of the United States-based detection dog teams make the use of these teams financially unfeasible for a larger, more comprehensive survey. To realize the full potential of dog-directed surveys and increase cost-effectiveness, we recommend basing dog-detection teams in the countries where they will operate and expanding the targets the dogs are trained to detect.

  12. 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.

    Science.gov (United States)

    Jensen, A N; Nielsen, L R; Baggesen, D L

    2013-05-03

    There is a need for more sensitive detection methods to improve effectiveness of control programmes of Salmonella enterica subsp. enterica serotypes (Salmonella) in cattle. We assessed the performance of a rapid, molecular-based, real-time PCR (rt-PCR) method against the conventional 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 50 CFU 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 (<1 CFU/g). Hence, the evaluated rt-PCR method did not provide a sensitive alternative to the BCRM for detection of bacteria in faecal samples of sub-clinically, Salmonella-infectious cattle.

  13. Prebiotics, faecal transplants and microbial network units to stimulate biodiversity of the human gut microbiome

    NARCIS (Netherlands)

    Van den Abbeele, Pieter; Verstraete, Willy; El Aidy, Sahar; Geirnaert, Annelies; Van de Wiele, Tom

    2013-01-01

    Accumulating evidence demonstrates the intimate association between human hosts and the gut microbiome. Starting at birth, the sterile gut of the newborn acquires a diverse spectrum of microbes, needed for immunological priming. However, current practices (caesarean sections, use of formula milk) de

  14. Prebiotics, faecal transplants and microbial network units to stimulate biodiversity of the human gut microbiome

    NARCIS (Netherlands)

    Van den Abbeele, Pieter; Verstraete, Willy; El Aidy, Sahar; Geirnaert, Annelies; Van de Wiele, Tom

    2013-01-01

    Accumulating evidence demonstrates the intimate association between human hosts and the gut microbiome. Starting at birth, the sterile gut of the newborn acquires a diverse spectrum of microbes, needed for immunological priming. However, current practices (caesarean sections, use of formula milk) de

  15. Changes in behaviour and faecal glucocorticoid levels in response to increased human activities during weekends in the pin-tailed sandgrouse

    Science.gov (United States)

    Casas, Fabián; Benítez-López, Ana; Tarjuelo, Rocío; Barja, Isabel; Viñuela, Javier; García, Jesús T.; Morales, Manuel B.; Mougeot, Francois

    2016-12-01

    Human recreational activities are becoming increasingly widespread and frequent, a fact that may potentially exacerbate their effects on wildlife. These human-related disturbances on animals may induce behavioural and physiological changes that can ultimately affect their fitness, showing a similar anti-predator response that against natural predator or other threats. Here, we combine the use of behavioural and physiological approaches to assess the potential effect of winter human activities on a threatened farmland bird in Europe, the pin-tailed sandgrouse ( Pterocles alchata). We compared before, during and after weekend variations in human activity rates, pin-tailed sandgrouse behaviour (flocking and flying behaviour, interspecific association in mixed flocks and habitat use) and faecal glucocorticoid metabolite concentrations. Human disturbances, in particular those associated with hunting activities, peaked during weekends. Sandgrouse showed significant behavioural changes (increased sandgrouse-only flock sizes, increased proportion of birds flying and changes in habitat use) during weekends and higher faecal glucocorticoid metabolite concentrations after the weekends compared with during or before weekends. Therefore, physiological stress levels could be modulated by behavioural adjustments such as increased flock sizes and changes in habitat use that may allow sandgrouse to cope with increased human disturbance rates during weekends. Nevertheless, temporal and spatial organization of hunting days among groups of estates might be good strategies to buffer these potential adverse effects on wintering pin-tailed sandgrouse and other steppe species of conservation concern, while preserving a socio-economically important activity such as hunting.

  16. 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

    2016-03-01

    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

  17. Description of a novel viral tool to identify and quantify ovine faecal pollution in the environment.

    Science.gov (United States)

    Rusiñol, Marta; Carratalà, Anna; Hundesa, Ayalkibet; Bach, Alex; Kern, Anita; Vantarakis, Apostolos; Girones, Rosina; Bofill-Mas, Sílvia

    2013-08-01

    Farmed animals such as sheep, cattle, swine and poultry play an important role in microbial contamination of water, crops and food, and introduce large quantities of pathogens into the environment. The ability to determine the origin of faecal pollution in water resources is essential when establishing a robust and efficient water management system. Animal-specific viruses have previously been suggested as microbial source tracking tools, but specific ovine viral markers have not been reported before now. Previous studies have shown that polyomaviruses are host-specific, highly prevalent and are commonly excreted in urine. Furthermore, they have been reported to infect several vertebrate species but not sheep. That situation encouraged the study of a new putative ovine polyomavirus (OPyV) and its use to determine whether faecal pollution originates from ovine faecal/urine contamination. Putative OPyV DNA was amplified from ovine urine and faecal samples using a broad-spectrum nested PCR (nPCR). Specific nested PCR and quantitative PCR assays were developed and applied to faecal and environmental samples, including sheep slurries, slaughterhouse wastewater effluents, urban sewage and river water samples. Successful amplification by PCR was achieved in sheep urine samples, sheep slaughterhouse wastewater and downstream sewage effluents. The assay was specific and was negative in samples of human, bovine, goat, swine and chicken origin. Ovine faecal pollution was detected in river water samples by applying the designed methods. These results provide a quantitative tool for the analysis of OPyV as a suitable viral indicator of sheep faecal contamination that may be present in the environment.

  18. Evaluation of Bacteroides fragilis GB-124 bacteriophages as novel human-associated faecal indicators in the United States

    Science.gov (United States)

    Phages infecting human-associated Bacteroides fragilis (GB-124 phages) have been employed in the European Union (EU) to identify human fecal pollution, but their utility for U.S. was unclear. Primary sewage effluent samples were collected seasonally from seven wastewater treatme...

  19. Evaluation of Bacteroides fragilis GB-124 bacteriophages as novel human-associated faecal indicators in the United States

    Science.gov (United States)

    Phages infecting human-associated Bacteroides fragilis (GB-124 phages) have been employed in the European Union (EU) to identify human fecal pollution, but their utility for U.S. was unclear. Primary sewage effluent samples were collected seasonally from seven wastewater treatme...

  20. Validation of a 20-h real-time PCR method for screening of Salmonella in poultry faecal samples

    DEFF Research Database (Denmark)

    Löfström, Charlotta; Hansen, Flemming; Hoorfar, Jeffrey

    2010-01-01

    for 18 ± 2 h, centrifugation of a 1-ml subsample, DNA extraction on the pellet and PCR. The total analysis time is 20 h. The validation study included comparative and collaborative trials, based on the recommendations from the Nordic organization for validation of alternative microbiological methods...... (NordVal). The comparative trial was performed against a reference method from the Nordic Committee on Food Analysis (NMKL187, 2007) using 132 artificially and naturally contaminated samples. The limit of detection (LOD50) was found to be 24 and 33 CFU/sample for the PCR and NMKL187 methods......Efficient and rapid monitoring of Salmonella in the poultry production chain is necessary to assure safe food. The objective was to validate an open-formula real-time PCR method for screening of Salmonella in poultry faeces (sock samples). The method consists of incubation in buffered peptone water...

  1. [Results of parasitological examinations of faecal samples from horses, ruminants, pigs, dogs, cats, hedgehogs and rabbits between 1998 and 2002].

    Science.gov (United States)

    Epe, C; Coati, N; Schnieder, T

    2004-06-01

    The results of coproscopical examinations in horses, ruminants, pigs, dogs, cats, hedgehogs and rabbits between 1998 and 2002 are presented. In 4399 samples from horses 37.4% stages of strongylids, 1.4% anoplocephalids, 1.3% Strongyloides westeri, 0.9% Parascaris equorum, 0.04% Oxyuris equi, 0.04% Eimeria sp. and 0.04% Fasciola hepatica were found. In 998 samples of cattle 22.1% stages of strongylids, 11.2% of Eimeria spp., 3.5% of cryptosporidium, 2.9% of Moniezia spp., 1.3% of Trichuris spp., 0.7% of Dictyocaulus sp., 0.6% of Fasciola hepatica, 0.6% of Strongyloides sp., 0.5% of Nematodirus spp. and 0.4% of Capillaria sp. could be detected. In 524 samples of sheep 60.7% eggs of strongylids, 43.1% oozysts of Eimeria spp., 11.1% stages of Nematodirus spp., 9.5% of Moniezia spp., 7.8% of Trichuris spp., 6.7% of Strongyloides sp., 1.7% of Fasciola hepatica, 1% of Capillaria spp., 0.4% of protostrongylidae, 0.2% of Skrjabinema sp. and 0.2% of Dictyocaulus sp. were found. 33.9% of the 118 samples of goats that were examined were positive for oocysts of Eimeria spp., 30.5% for eggs of strongylids, 6.8% for Nematodirus spp., 4.2% for Trichuris spp., 3.4% for Moniezia spp., 0.8 for protostrongylids and 0.8% for Strongyloides sp. 5.7% of 1427 samples of pigs contained stages of strongylids, 1.5% of Ascaris suum, 0.4% of Isospora, 0.3% of Eimeria spp., 0.3% of Trichuris sp., 0.1% of Giardia sp., 0.1% of cryptosproidium as well as 0.1% of metastrongylids. In 1281 of the samples of dogs 2.3% Giardia sp., 2.3% Isospora sp., 2.2% Toxocara canis, 1.4% ancylostomids, 0.8% taeniids, 0.6% larvae of Crenosoma sp., 0.2% Capillaria sp, 0.2% Trichuris vulpis and 0.2% Hammondia-like oocysts were found. In 441 samples of cats 10.7% stages of Isospora sp., 3.9% eggs of Toxocara cati, 1.6% of ancylostomids, 1.4% of taeniids, 1.1% of Giardia sp., 0.7% of Toxoplasma-like oocysts, 0.7% of Aelurostrongylus abstrusus, 0.5% of Toxascaris leonina and 0.2% of Capillaria spp. were found

  2. Isolation of bacteriophage host strains of Bacteroides species suitable for tracking sources of animal faecal pollution in water.

    Science.gov (United States)

    Gómez-Doñate, Marta; Payán, Andrey; Cortés, Ivania; Blanch, Anicet R; Lucena, Francisco; Jofre, Juan; Muniesa, Maite

    2011-06-01

    Microbial source tracking (MST) methods allow the identification of specific faecal sources. The aim is to detect the sources of faecal pollution in a water body to allow targeted, efficient and cost-effective remediation efforts in the catchment. Bacteriophages infecting selected host strains of Bacteroides species are used as markers to track faecal contaminants in water. By using a suitable Bacteroides host from a given faecal origin, it is possible to specifically detect bacteriophages of this faecal origin. It can thus be used to detect specific phages of Bacteroides for MST. With this objective, we isolated several Bacteroides strains from pig, cow and poultry faeces by applying a previously optimized methodology used to isolate the host strains from humans. The isolated strains belonged to Bacteroides fragilis and Bacteroides thetaiotaomicron. These strains, like most Bacteroides species, detected phages of the Siphoviridae morphology. Using the newly isolated host strains for phage enumeration in a range of samples, we showed that these detect phages in faecal sources that coincide with their own origin (70-100% of the samples), and show no detection or very low percentages of detection of phages from other animal origins (from 0 to 20% of the samples). Only strains isolated from pig wastewater detected phages in 50% of human sewage samples. Nevertheless, those strains detecting phages from faecal origins other than their own detected fewer phages (2-3 log₁₀ pfu·100 ml⁻¹) than the phages detected by the specific strain of the same origin. On the basis of our results, we propose that faecal source tracking with phages infecting specific Bacteroides host strains is a useful method for MST. In addition, the method presented here is feasible in laboratories equipped with only basic microbiological equipment, it is more rapid and cost-effective than other procedures and it does not require highly qualified staff. © 2011 Society for Applied Microbiology

  3. Faecal carriage of extended-spectrum β-lactamase-producing Enterobacteriaceae among humans in Java, Indonesia, in 2001-2002.

    Science.gov (United States)

    Severin, Juliëtte A; Lestari, Endang Sri; Kloezen, Wendy; Lemmens-den Toom, Nicole; Mertaniasih, Ni Made; Kuntaman, Kuntaman; Purwanta, Marijam; Duerink, D Offra; Hadi, Usman; van Belkum, Alex; Verbrugh, Henri A; Goessens, Wil H

    2012-04-01

    To characterise commensal Escherichia coli and other Enterobacteriaceae with reduced susceptibility to cefotaxime that were collected in a large survey carried out among 3995 patients and healthy persons in two urban regions on Java, Indonesia, in 2001-2002. The putative extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae were analysed using double-disk synergy tests, isoelectric focusing, PCR assays, DNA sequencing, and pulsed-field gel electrophoresis (PFGE). On the day of discharge after five or more days of hospitalisation, at least 95 of 999 (9.5%) patients carried ESBL-positive Enterobacteriaceae as dominant faecal flora. Six patients were simultaneously colonised with E. coli and Klebsiella pneumoniae isolates with ESBL activity. On admission, only 6 of 998 (0.6%) patients were colonised. Faecal carriage of ESBL-producing Enterobacteriaceae among healthy persons or persons visiting a public health centre was not detected. The 107 ESBL-positive strains included 68 E. coli, 35 K. pneumoniae, and four other Enterobacteriaceae. bla(CTX-M-15) was the most prevalent ESBL in both E. coli (47.1%) and K. pneumoniae (45.7%), but the E. coli O25b-ST131 clone was virtually absent. Other ESBL types found were: SHV-2, -2a, -5, -12, CTX-M-3, -9, -14, and TEM-19. PFGE revealed extensive genetic diversity among the isolates. In 2001-2002, faecal carriage of ESBL-producing Enterobacteriaceae as dominant flora in Indonesia was almost exclusively hospital-associated. The presence of various bla(ESBL) genes and the extensive genetic diversity among isolates argue against a single/dominant strain outbreak. © 2012 Blackwell Publishing Ltd.

  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. Ammonia production by human faecal bacteria, and the enumeration, isolation and characterization of bacteria capable of growth on peptides and amino acids

    Directory of Open Access Journals (Sweden)

    Richardson Anthony J

    2013-01-01

    Full Text Available Abstract Background The products of protein breakdown in the human colon are considered to be detrimental to gut health. Amino acid catabolism leads to the formation of sulfides, phenolic compounds and amines, which are inflammatory and/or precursors to the formation of carcinogens, including N-nitroso compounds. The aim of this study was to investigate the kinetics of protein breakdown and the bacterial species involved. Results Casein, pancreatic casein hydrolysate (mainly short-chain peptides or amino acids were incubated in vitro with suspensions of faecal bacteria from 3 omnivorous and 3 vegetarian human donors. Results from the two donor groups were similar. Ammonia production was highest from peptides, followed by casein and amino acids, which were similar. The amino acids metabolized most extensively were Asp, Ser, Lys and Glu. Monensin inhibited the rate of ammonia production from amino acids by 60% (P = 0.001, indicating the involvement of Gram-positive bacteria. Enrichment cultures were carried out to investigate if, by analogy with the rumen, there was a significant population of asaccharolytic, obligately amino acid-fermenting bacteria (‘hyper-ammonia-producing’ bacteria; HAP in the colon. Numbers of bacteria capable of growth on peptides or amino acids alone averaged 3.5% of the total viable count, somewhat higher than the rumen. None of these were HAP, however. The species enriched included Clostridium spp., one of which was C. perfringens, Enterococcus, Shigella and Escherichia coli. Conclusions Protein fermentation by human faecal bacteria in the absence of sugars not only leads to the formation of hazardous metabolic products, but also to the possible proliferation of harmful bacteria. The kinetics of protein metabolism were similar to the rumen, but HAP bacteria were not found.

  6. The effect of Yucca schidigera extract on canine and feline faecal volatiles occurring concurrently with faecal aroma amelioration.

    Science.gov (United States)

    Lowe, J A; Kershaw, S J; Taylor, A J; Linforth, R S

    1997-01-01

    Addition of Yucca schidigera extract (YSE) products to canine or feline diets improved faecal aroma as monitored by a human panel. Odour port-gas chromatography (GC) indicated different odour component types in dog faecal volatiles and, in particular, 'faecal'-type odours due to methyl sulfides. GC-mass spectrometry demonstrated several chemical compound classes present in faecal volatiles and quantitation in the cat indicated apparently significant changes in the concentrations of several compounds on YSE treatment, although these were not necessarily aroma components. The potential for direct YSE alteration of aroma perception in a mixture of volatiles, possibly by binding, was demonstrated.

  7. 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

    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......There is a need for more sensitive detection methods to improve effectiveness of control programmes of Salmonella enterica subsp. enterica serotypes (Salmonella) in cattle. We assessed the performance of a rapid, molecular-based, real-time PCR (rt-PCR) method against the conventional...

  8. 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

  9. Comparison of sensitivity and faecal egg counts of Mini-FLOTAC using fixed stool samples and Kato-Katz technique for the diagnosis of Schistosoma mansoni and soil-transmitted helminths.

    Science.gov (United States)

    Coulibaly, Jean T; Ouattara, Mamadou; Becker, Sören L; Lo, Nathan C; Keiser, Jennifer; N'Goran, Eliézer K; Ianniello, Davide; Rinaldi, Laura; Cringoli, Giuseppe; Utzinger, Jürg

    2016-12-01

    Accurate diagnostic tools for human helminthiasis are crucial for epidemiological surveys, improved patient management, and evaluation of community-based intervention studies. However, the diagnosis of intestinal schistosomiasis and soil-transmitted helminthiasis heavily relies on stool microscopy using the Kato-Katz technique, which has a low sensitivity. The Mini-FLOTAC method is an alternative microscopy-based technique, but its diagnostic performance using sodium acetate-acetic acid-formalin-(SAF)-fixed stool specimens has not been validated. The fixation of stool samples for later examination in a laboratory may reduce logistical and financial barriers of prevalence surveys by not requiring field laboratories. We compared the diagnostic accuracy of the Kato-Katz technique using fresh stool samples with the Mini-FLOTAC technique, employing matched stool samples that were fixed in SAF. Three consecutive stool samples from 149 school-aged children in Côte d'Ivoire were subjected to quintuplicate Kato-Katz thick smears examined on the same day. From the remaining stool, approximately 2g was fixed in 10ml of SAF for about 3 months, and then subjected to the Mini-FLOTAC method, using two flotation solutions (FS2 and FS7). The combined results of multiple Kato-Katz and Mini-FLOTAC readings revealed prevalences of Schistosoma mansoni, Trichuris trichiura and hookworm of 99.3%, 72.5% and 7.4%, respectively. Employing a Bayesian latent class analysis to estimate the true sensitivity of the diagnostic approaches, the sensitivity of Mini-FLOTAC using FS2 was 50.1% (95% Bayesian credible interval (BCI): 30.9-70.2%) for hookworm and 68.0% (95% BCI: 34.9-93.5%) for T. trichiura. When applying Mini-FLOTAC using FS7, the sensitivity was 89.9% (95% BCI: 86.9-97.4%) for S. mansoni, 37.2% (95% BCI: 17.2-60.6%) for hookworm and 67.7% (95% BCI: 33.0-93.0%) for T. trichiura. The specificity ranged from 80.1-95.0% in all Mini-FLOTAC tests. Mini-FLOTAC revealed higher arithmetic mean

  10. Development and testing of an optimized method for DNA-based identification of jaguar (Panthera onca) and puma (Puma concolor) faecal samples for use in ecological and genetic studies.

    Science.gov (United States)

    Haag, Taiana; Santos, Anelisie S; De Angelo, Carlos; Srbek-Araujo, Ana Carolina; Sana, Dênis A; Morato, Ronaldo G; Salzano, Francisco M; Eizirik, Eduardo

    2009-07-01

    The elusive nature and endangered status of most carnivore species imply that efficient approaches for their non-invasive sampling are required to allow for genetic and ecological studies. Faecal samples are a major potential source of information, and reliable approaches are needed to foster their application in this field, particularly in areas where few studies have been conducted. A major obstacle to the reliable use of faecal samples is their uncertain species-level identification in the field, an issue that can be addressed with DNA-based assays. In this study we describe a sequence-based approach that efficiently distinguishes jaguar versus puma scats, and that presents several desirable properties: (1) considerably high amplification and sequencing rates; (2) multiple diagnostic sites reliably differentiating the two focal species; (3) high information content that allows for future application in other carnivores; (4) no evidence of amplification of prey DNA; and (5) no evidence of amplification of a nuclear mitochondrial DNA insertion known to occur in the jaguar. We demonstrate the reliability and usefulness of this approach by evaluating 55 field-collected samples from four locations in the highly fragmented Atlantic Forest biome of Brazil and Argentina, and document the presence of one or both of these endangered felids in each of these areas.

  11. EVALUATION OF CISPLATIN-INDUCED PICA BEHAVIOUR IN RATS BY MEASURING FAECAL CARMINE-DYE EXCRETION: AN IMPROVED EXPERIMENTAL MODEL TO SCREEN SAMPLES WITH ANTI-EMETIC PROPERTIES

    Directory of Open Access Journals (Sweden)

    Rajesh S.

    2012-02-01

    Full Text Available The objective of the present study is to evaluate the Cisplatin-induced pica behaviour in rats by measuring faecal carmine dye excretion and to evaluate the anti-emetic effect of drugs on Cisplatin-induced pica behaviour in rats. Thirty-two rats were divided into 4 groups of 8 animals each. Rats from group I and II received DM water (10ml/kg p.o. Rats from group III and IV received Himalaya Anti-emetic Tablets (HAT 250 mg/kg p.o. and ondansetron 4mg/kg p.o, respectively. After one hour of the assigned treatment, all the animals except in group I were injected with Cisplatin 3mg/kg i.p. Rats in group I were injected with saline (1ml/kg i.p.. All the animals were fed with normal as well as kaolin pellets (impregnated with carmine dye. The faeces of each rat was collected after 72 hrs of drug administration and analysed for the carmine content.Cisplatin injection (3mg/kg caused a significant increase in kaolin consumption, which was indicated by increased carmine dye excretion in faeces compared to control. Pre-treatment with HAT and ondansetron significantly suppressed kaolin consumption induced by Cisplatin. The present findings showed that the exact kaolin consumption can be quantified by measuring the faecal excretion of carmine, which was added in kaolin pellets and this can be a sensitive model to study the anti-emetic potential of drugs, overcoming the inherent disadvantages of measuring direct kaolin intake. Pre-treatment with ondansetron and HAT significantly decreased kaolin consumption in rats-induced by Cisplatin injection, which was further shown by decrease in faecal excretion of carmine, indicating anti-emetic potential of tested drugs.

  12. The potential impact of density dependent fecundity on the use of the faecal egg count reduction test for detecting drug resistance in human hookworms.

    Directory of Open Access Journals (Sweden)

    Andrew C Kotze

    Full Text Available Current efforts to control human soil-transmitted helminth (STH infections involve the periodic mass treatment of people, particularly children, in all endemic areas, using benzimidazole and imidothiazole drugs. Given the fact that high levels of resistance have developed to these same drugs in roundworms of livestock, there is a need to monitor drug efficacy in human STHs. The faecal egg count reduction test (FECRT, in which faecal egg output is measured pre- and post-drug treatment, is presently under examination by WHO as a means of detecting the emergence of resistance. We have examined the potential impact of density dependent fecundity on FECRT data. Recent evidence with the canine hookworm indicates that the density dependent egg production phenomenon shows dynamic properties in response to drug treatment. This will impact on measurements of drug efficacy, and hence drug resistance. It is likely that the female worms that survive a FECRT drug treatment in some human cases will respond to the relaxation of density dependent constraints on egg production by increasing their egg output significantly compared to their pre-treatment levels. These cases will therefore underestimate drug efficacy in the FECRT. The degree of underestimation will depend on the ability of the worms within particular hosts to increase their egg output, which will in turn depend on the extent to which their egg output is constrained prior to the drug treatment. As worms within different human cases will likely be present at quite different densities prior to a proposed FECRT, there is potential for the effects of this phenomenon on drug efficacy measurements to vary considerably within any group of potential FECRT candidates. Measurement of relative drug efficacy may be improved by attempting to ensure a consistent degree of underestimation in groups of people involved in separate FECRTs. This may be partly achieved by omission of cases with the heaviest infections

  13. Effect of yoghurt containing Bifidobacterium lactis Bb12® on faecal excretion of secretory immunoglobulin A and human beta-defensin 2 in healthy adult volunteers

    National Research Council Canada - National Science Library

    Kabeerdoss, Jayakanthan; Devi, R Shobana; Mary, R Regina; Prabhavathi, D; Vidya, R; Mechenro, John; Mahendri, N V; Pugazhendhi, Srinivasan; Ramakrishna, Balakrishnan S

    2011-01-01

    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...

  14. Detection and source identification of faecal pollution in non-sewered catchment by means of host-specific molecular markers.

    Science.gov (United States)

    Ahmed, W; Powell, D; Goonetilleke, A; Gardner, T

    2008-01-01

    Multiple host-specific molecular markers were used to detect the sources of faecal pollution in a mixed land use non-sewered catchment in Southeast Queensland, Australia. These markers included human-specific Bacteroides (HF183 and HF134), cattle-specific Bacteroides (CF128), dog-specific Bacteroides (BacCan) and human-specific enterococci surface protein (esp) markers. The sensitivity and specificity of these markers were determined by testing 197 faecal samples from 13 host groups. The overall sensitivity and specificity of these markers was high (sensitivity>/=85% and specificity>/=93%) indicating their suitability for detecting the sources of faecal pollution. Of the 16 samples collected from the study area, 14 (87%) were positive for at least one of the molecular marker tested. Amongst all the markers, cattle-specific CF128 was more prevalent than others, followed by human-specific HF183 which was consistently detected in samples collected from sites within close proximity to urban development. Significant correlations were found between E. coli and enterococci concentrations with the positive/negative results of human-specific Bacteroides HF183 (psources of human faecal pollution in surface waters in Southeast Queensland, Australia.

  15. Detection of vancomycin-resistant Enterococcus faecalis ST6-vanB2 and E. faecium ST915-vanA in faecal samples of wild Rattus rattus in Spain.

    Science.gov (United States)

    Lozano, Carmen; González-Barrio, David; García, Jesús T; Ceballos, Sara; Olea, Pedro P; Ruiz-Fons, Francisco; Torres, Carmen

    2015-05-15

    The detection of vancomycin-resistant-enterococci (VRE) among wild animals represents a worrisome public health concern. The objectives of the study were to determine the possible presence of VRE in faecal samples of wild small mammals in Spain, to characterize the vancomycin resistance mechanisms and genetic lineages of recovered isolates and to know the diversity of enterococcal species in these animals. A total of 155 faecal samples from small mammals were inoculated in Slanetz-Bartley agar supplemented or not with vancomycin (Van-SB/SB plates). The antimicrobial susceptibility profile to 12 antimicrobials and the presence of 20 antimicrobial resistance genes was analyzed. The structure of Tn1546 and the presence of gelE, cylA, asa, esp and hyl genes was studied. Multilocus-sequence-typing (MLST) technique was also performed. VRE isolates were recovered in Van-SB plates in 11 samples. Two samples contained vanB2-positive E. faecalis isolates of lineage ST6, which showed a multiresistance phenotype and harboured the virulence genes gelE and asa. One sample contained a vancomycin-resistant E. faecium isolate of the new lineage ST915, with the vanA gene included into Tn1546 (truncated with IS1542 and IS1216 elements). The vanB2 and vanA isolates were obtained from Rattus rattus. The remaining eight VRE-positive samples contained species with intrinsic vancomycin-resistance mechanisms: E. casseliflavus (n=5) and E. gallinarum (n=3). One hundred and forty-seven vancomycin-susceptible-enterococcal isolates were obtained in SB plates, and E. faecalis and E. faecium were the most frequent detected species. This is the first report of vanB2-containing enterococci in wild animals.

  16. FRNA Bacteriophages as Viral Indicators of Faecal Contamination in Mexican Tropical Aquatic Systems

    Science.gov (United States)

    Diaz-Avalos, Carlos; Lopez-Vidal, Yolanda; Castillo-Rojas, Gonzalo; Mazari-Hiriart, Marisa

    2017-01-01

    A particular challenge to water safety in populous intertropical regions is the lack of reliable faecal indicators to detect microbiological contamination of water, while the numerical relationships of specific viral indicators remain largely unexplored. The aim of this study was to investigate the numerical relationships of FRNA-bacteriophage genotypes, adenovirus 41, and human adenoviruses (HADV) in Mexican surface water systems to assess sewage contamination. We studied the presence of HADV, HADV41 and FRNA bacteriophage genotypes in water samples and quantified by qPCR and RT-qPCR. Virus and water quality indicator variances, as analyzed by principal component analysis and partial least squared regression, followed along the major percentiles of water faecal enterococci. FRNA bacteriophages adequately deciphered viral and point source water contamination. The strongest correlation for HADV was with FRNA bacteriophage type II, in water samples higher than the 50th percentiles of faecal enterococci, thus indicating urban pollution. FRNA bacteriophage genotypes I and III virus indicator performances were assisted by their associations with electrical conductivity and faecal enterococci. In combination, our methods are useful for inferring water quality degradation caused by sewage contamination. The methods used have potential for determining source contamination in water and, specifically, the presence of enteric viruses where clean and contaminated water have mixed. PMID:28114378

  17. FRNA Bacteriophages as Viral Indicators of Faecal Contamination in Mexican Tropical Aquatic Systems.

    Science.gov (United States)

    Arredondo-Hernandez, Luis Jose Rene; Diaz-Avalos, Carlos; Lopez-Vidal, Yolanda; Castillo-Rojas, Gonzalo; Mazari-Hiriart, Marisa

    2017-01-01

    A particular challenge to water safety in populous intertropical regions is the lack of reliable faecal indicators to detect microbiological contamination of water, while the numerical relationships of specific viral indicators remain largely unexplored. The aim of this study was to investigate the numerical relationships of FRNA-bacteriophage genotypes, adenovirus 41, and human adenoviruses (HADV) in Mexican surface water systems to assess sewage contamination. We studied the presence of HADV, HADV41 and FRNA bacteriophage genotypes in water samples and quantified by qPCR and RT-qPCR. Virus and water quality indicator variances, as analyzed by principal component analysis and partial least squared regression, followed along the major percentiles of water faecal enterococci. FRNA bacteriophages adequately deciphered viral and point source water contamination. The strongest correlation for HADV was with FRNA bacteriophage type II, in water samples higher than the 50th percentiles of faecal enterococci, thus indicating urban pollution. FRNA bacteriophage genotypes I and III virus indicator performances were assisted by their associations with electrical conductivity and faecal enterococci. In combination, our methods are useful for inferring water quality degradation caused by sewage contamination. The methods used have potential for determining source contamination in water and, specifically, the presence of enteric viruses where clean and contaminated water have mixed.

  18. Fasciola hepatica: Specificity of a coproantigen ELISA test for diagnosis of fasciolosis in faecal samples from cattle and sheep concurrently infected with gastrointestinal nematodes, coccidians and/or rumen flukes (paramphistomes), under field conditions.

    Science.gov (United States)

    Kajugu, P-E; Hanna, R E B; Edgar, H W; McMahon, C; Cooper, M; Gordon, A; Barley, J P; Malone, F E; Brennan, G P; Fairweather, I

    2015-09-15

    Chronic fasciolosis is often diagnosed by faecal egg counting (FEC), following concentration of the eggs in the sample by a zinc sulphate floatation method. However, concentration by a sedimentation technique gives improved sensitivity. Interpretation of FEC results for fasciolosis is complicated by factors such as the long pre-patent period and irregular egg shedding. Thus, FEC reduction tests (FECRT), when used alone, are not completely reliable for diagnosis of anthelmintic susceptibility or resistance in local fluke populations, especially when parasite burdens are small. A Fasciola hepatica coproantigen ELISA test has been introduced which more accurately reflects the presence of flukes in the host bile ducts in late pre-patent infections, and absence of flukes following successful chemotherapeutic intervention. The aim of the present study was to elucidate the specificity of the F. hepatica coproantigen ELISA technique, particularly regarding potential cross-reactivity with rumen fluke (paramphistome), gastrointestinal nematode and coccidian infections. The method involved parallel testing of a large battery of faecal samples from field-infected cattle and sheep using floatation and sedimentation FECs and coproantigen analysis. No evidence was found for significant false positivity in the F. hepatica coproantigen ELISA due to paramphistome, coccidian and/or gastrointestinal nematode co-infections. With sedimentation FECs less than 10 F. hepatica eggs per gram (epg), the likelihood of a positive coproantigen result for the sample progressively decreased. Diagnosis of fasciolosis should be based on consideration of both FEC and coproantigen ELISA findings, to ensure optimum sensitivity for pre-patent and low-level infections.

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

    Science.gov (United States)

    Sistiaga, Ainara; Mallol, Carolina; Galván, Bertila; Summons, Roger Everett

    2014-01-01

    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.

  20. 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.

  1. Ileal and faecal protein digestibility measurement in humans and other non-ruminants - a comparative species view

    NARCIS (Netherlands)

    Hendriks, W.H.; Baal, van J.; Bosch, G.

    2012-01-01

    A comparative non-ruminant species view of the contribution of the large intestinal metabolism to inaccuracies in nitrogen and amino acid absorption measurements is provided to assess potential implications for the determination of crude protein/amino acid digestibility in adult humans consuming low

  2. Characterisation of faecal protease activity in irritable bowel syndrome with diarrhoea: origin and effect of gut transit.

    Science.gov (United States)

    Tooth, David; Garsed, Klara; Singh, Gulzar; Marciani, Luca; Lam, Ching; Fordham, Imogen; Fields, Annie; Banwait, Rawinder; Lingaya, Melanie; Layfield, Robert; Hastings, Maggie; Whorwell, Peter; Spiller, Robin

    2014-05-01

    Faecal serine proteases (FSPs) may play a role in irritable bowel syndrome with diarrhoea (IBS-D), but their origin is unclear. We aimed to structurally characterise them and define the impact of colonic cleansing and transit time. Faecal samples were obtained from 30 healthy volunteers (HV) and 79 patients with IBS-D participating in a trial of ondansetron versus placebo. Colonic transit was measured using radio-opaque markers. Samples were also obtained from 24 HV before and after colonic cleansing with the osmotic laxative MoviPrep. FSPs were purified from faecal extracts using benzamidine-Sepharose affinity chromatography. SDS-PAGE profiled components were identified using trypsinolysis and tandem mass spectrometry. Functional protease activity in faecal extracts was measured using a colorimetric assay based on the proteolysis of azo-casein. Protein analysis identified the most abundant FSPs as being of human origin and probably derived from pancreatic juice. Functional assays showed increased faecal protease (FP) and amylase in patients with IBS-D compared with HV. Those with higher amylase had significantly higher FP and greater anxiety. FP activity correlated negatively with whole gut transit in patients with IBS-D (Spearman r=-0.32, p=0.005) and HV (r=-0.55, p=0.014). Colon cleansing caused a significant rise in FP activity in HV from a baseline of median (IQR) 253 (140-426) to 1031 (435-2296), levels similar to those seen in patients with IBS-D. FSP activity correlated positively with days/week with urgency. The most abundant FSPs are of human origin. Rapid transit through the colon and/or decreased (possibly bacterial) proteolytic degradation increases their faecal concentration and could contribute to visceral hypersensitivity in patients with IBS-D. NCT00745004.

  3. Faecal mucus degrading glycosidases in ulcerative colitis and Crohn's disease.

    Science.gov (United States)

    Rhodes, J M; Gallimore, R; Elias, E; Allan, R N; Kennedy, J F

    1985-08-01

    Because the normal faecal flora includes bacteria which can produce mucus-digesting glycosidases, it follows that increased digestion of colonic mucus by these bacterial enzymes could be important in the pathogenesis of ulcerative colitis. Faecal activities of potential mucus-degrading glycosidases have therefore been assayed in samples from patients with inflammatory bowel disease and normal controls. The enzymes alpha-D-galactosidase, beta-D-galactosidase, beta-NAc-D-glucosaminidase alpha-L-fucosidase and neuraminidase were assayed. Considerable glycosidase activity was present in most faecal samples. Similar activities of all the enzymes assayed were found in faeces from patients with ulcerative colitis, Crohn's disease and normal controls and there was no significant correlation with disease activity. These results imply that relapse of ulcerative colitis is not initiated by increased degradation of colonic mucus by faecal glycosidases but do not exclude a role for bacterial mucus degradation in the pathogenesis of ulcerative colitis.

  4. REDUCTION OF FAECAL MICROBIOLOGICAL INDICATORS IN DIFFERENT COMPOST TOILETS

    OpenAIRE

    Møller, J.; Forslund, A.; Dalsgaard, A.

    2003-01-01

    Large variations in numbers of faecal indicator bacteria were found irrespective of the storage time of collected human faeces. Little heat seemed generated from composting processes when bin units were stored locally in households. The low reduction in microbiological parameters and very limited temperature increase were generally corroborated by the results obtained in experiment 2 when pathogen indicators were added to thoroughly mixed faecal matter. Even though Salmonella died of rapidly ...

  5. Determination of total selenium and Se-77 in isotopically enriched human samples by ICP-dynamic reaction cell-MS

    DEFF Research Database (Denmark)

    Sloth, Jens Jørgen; Larsen, Erik Huusfeldt; Bügel, Susanne H.;

    2003-01-01

    This paper describes an analytical method for the simultaneous quantitative determination of total selenium (Se) and Se-77 in isotopically enriched human plasma, urine and faeces by inductively coupled plasma- dynamic reaction cell- mass spectrometry ( ICP- DRC- MS). The samples originated from...... and the digested faecal samples were diluted using an aqueous diluent containing 0.5% Triton X-100, 2% nitric acid and 3% methanol. Selenium was detected as Se-76, Se-77 and Se-80 by ICP- DRC- MS. Selenium originating from the natural isotope abundance yeast and other selenium sources from the diet was determined...

  6. Antimicrobial resistance in the Bacteroides fragilis group in faecal microbiota from healthy Danish children.

    Science.gov (United States)

    Sydenham, Thomas Vognbjerg; Jensen, Betina Hebbelstrup; Petersen, Andreas Munk; Krogfelt, Karen Angeliki; Justesen, Ulrik Stenz

    2017-05-01

    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 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 in faecal microbiota exists. Copyright © 2017 Elsevier B.V. and International Society of Chemotherapy. All rights reserved.

  7. Utility of faecal calprotectin analysis in adult inflammatory bowel disease

    Institute of Scientific and Technical Information of China (English)

    Lyn A Smith; Daniel R Gaya

    2012-01-01

    The inflammatory bowel diseases (IBD),Crohn's disease and ulcerative colitis,are chronic relapsing,remitting disorders.Diagnosis,along with assessment of disease activity and prognosis present challenges to managing clinicians.Faecal biomarkers,such as faecal calprotectin,are a non-invasive method which can be used to aid these decisions.Calprotectin is a calcium and zinc binding protein found in the cytosol of human neutrophils and macrophages.It is released extracellularly in times of cell stress or damage and can be detected within faeces and thus can be used as a sensitive marker of intestinal inflammation.Faecal calprotectin has been shown to be useful in the diagnosis of IBD,correlates with mucosal disease activity and can help to predict response to treatment or relapse.With growing evidence supporting its use,over the last decade this faecal biomarker has significantly changed the way IBD is managed.

  8. Detection of Campylobacter in human and animal field samples in Cambodia.

    Science.gov (United States)

    Osbjer, Kristina; Tano, Eva; Chhayheng, Leang; Mac-Kwashie, Akofa Olivia; Fernström, Lise-Lotte; Ellström, Patrik; Sokerya, Seng; Sokheng, Choup; Mom, Veng; Chheng, Kannarath; San, Sorn; Davun, Holl; Boqvist, Sofia; Rautelin, Hilpi; Magnusson, Ulf

    2016-06-01

    Campylobacter are zoonotic bacteria and a leading cause of human gastroenteritis worldwide with Campylobacter jejuni and C. coli being the most commonly detected species. The aim of this study was to detect Campylobacter in humans and livestock (chickens, ducks, pigs, cattle, water buffalo, quail, pigeons and geese) in rural households by routine culturing and multiplex PCR in faecal samples frozen before analysis. Of 681 human samples, 82 (12%) tested positive by PCR (C. jejuni in 66 samples and C. coli in 16), but none by routine culture. Children were more commonly Campylobacter positive (19%) than adult males (8%) and females (7%). Of 853 livestock samples, 106 (12%) tested positive by routine culture and 352 (41%) by PCR. Campylobacter jejuni was more frequent in chickens and ducks and C. coli in pigs. In conclusion, Campylobacter proved to be highly prevalent by PCR in children (19%), ducks (24%), chickens (56%) and pigs (72%). Routine culturing was insufficiently sensitive in detecting Campylobacter in field samples frozen before analysis. These findings suggest that PCR should be the preferred diagnostic method for detection of Campylobacter in humans and livestock where timely culture is not feasible. © 2016 The Authors. APMIS published by John Wiley & Sons Ltd on behalf of Scandinavian Societies for Medical Microbiology and Pathology.

  9. 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.

  10. 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 (Pcombination 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.

  11. Use of probiotics to reduce faecal shedding of Shiga toxin-producing Escherichia coli in sheep.

    Science.gov (United States)

    Rigobelo, E E C; Karapetkov, N; Maestá, S A; Avila, F A; McIntosh, D

    2015-03-01

    Shiga toxin-producing Escherichia coli (STEC) are zoonotic, foodborne pathogens of humans. Ruminants, including sheep, are the primary reservoirs of STEC and there is a need to develop intervention strategies to reduce the entry of STEC into the food chain. The initiation of the majority of bacterial, enteric infections involves colonisation of the gut mucosal surface by the pathogen. However, probiotic bacteria can serve to decrease the severity of infection via a number of mechanisms including competition for receptors and nutrients, and/or the synthesis of organic acids and bacteriocins that create an environment unfavourable for pathogen development. The aim of the current study was to determine whether the administration of a probiotic mixture to sheep experimentally infected with a non-O157 STEC strain, carrying stx1, stx2 and eae genes, was able to decrease faecal shedding of the pathogen. The probiotic mixture contained Lactobacillus acidophilus, Lactobacillus helveticus, Lactobacillus bulgaricus, Lactobacillus lactis, Streptococcus thermophilus and Enterococcus faecium. The numbers of non-O157 STEC in faecal samples collected from sheep receiving daily doses of the probiotic mixture were significantly lower at the 3rd, 5th and 6th week post-inoculation when compared to the levels recorded in untreated animals. It was concluded that administration of the probiotic mixture reduced faecal shedding of non-O157 STEC in sheep, and holds potential as a pre-harvest intervention method to reduce transmission to humans.

  12. Usefulness of Chromogenic CromoCen® AGN agar medium for the identification of the genus Aeromonas: Assessment of faecal samples.

    Science.gov (United States)

    Aguilera-Arreola, M G; Portillo-Muñoz, M I; Rodríguez-Martínez, C; Castro-Escarpulli, G

    2012-08-01

    Selective screening media for the detection and identification of Aeromonas strains are needed to guide primary isolation procedures in the clinical laboratory. This study compared the selective CromoCen® AGN chromogenic agar medium for the detection and identification of Aeromonas strains that were isolated from various samples against the conventional selective agar media that are commonly used for the isolation of this organism in food, environmental and clinical samples. The Miles and Misra and ecometric methods were used to evaluate the microbiological performance of CromoCen® AGN chromogenic agar medium, which was shown to be satisfactory. A total of 14 reference Aeromonas strains, 44 wild strains and 106 clinical stool specimens were examined using both non-chromogenic selective agars that are commonly used for Aeromonas isolation and CromoCen® AGN agar. The latter exhibited 94.73% sensitivity and 100% specificity for the various samples. On CromoCen® AGN agar medium, Aeromonas formed colonies with light green, greenish and salmon pigments with or without a surrounding wide transparent zone (halo) of 2-3mm in diameter around the entire border. This medium is recommended for the isolation and potential identification of the Aeromonas genus.

  13. A Real-Time PCR Assay for Bat SARS-Like Coronavirus Detection and Its Application to Italian Greater Horseshoe Bat Faecal Sample Surveys

    Directory of Open Access Journals (Sweden)

    Andrea Balboni

    2012-01-01

    Full Text Available Bats are source of coronaviruses closely related to the severe acute respiratory syndrome (SARS virus. Numerous studies have been carried out to identify new bat viruses related to SARS-coronavirus (bat-SARS-like CoVs using a reverse-transcribed-polymerase chain reaction assay. However, a qualitative PCR could underestimate the prevalence of infection, affecting the epidemiological evaluation of bats in viral ecology. In this work an SYBR Green-real time PCR assay was developed for diagnosing infection with SARS-related coronaviruses from bat guano and was applied as screening tool in a survey carried out on 45 greater horseshoe bats (Rhinolophus ferrumequinum sampled in Italy in 2009. The assay showed high sensitivity and reproducibility. Its application on bats screening resulted in a prevalence of 42%. This method could be suitable as screening tool in epidemiological surveys about the presence of bat-SARS-like CoVs, consequently to obtain a more realistic scenario of the viral prevalence in the population.

  14. 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.

  15. Immunoglobulin coating of faecal bacteria in inflammatory bowel disease

    NARCIS (Netherlands)

    van der Waaij, LA; Kroese, FGM; Visser, A; Nelis, FG; Westerveld, BD; Jansen, PLM; Hunter, JO

    2004-01-01

    Objective An inappropriate mucosal immune response to the commensal bacterial flora may play a role in the pathogenesis of inflammatory bowel disease (IBD). In this study we determined the percentage of immunoglobulin-coated bacteria in the stools of patients and controls. Methods Faecal samples wer

  16. 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.

  17. Evaluation of an Immunoassay-Based Algorithm for Screening and Identification of Giardia and Cryptosporidium Antigens in Human Faecal Specimens from Saudi Arabia

    Directory of Open Access Journals (Sweden)

    Yousry Hawash

    2014-01-01

    Full Text Available An immunoassay-based algorithm, involving three commercial kits, was introduced and evaluated for screening and identification of Giardia/Cryptosporidium antigens in human stool specimens. Initially, Giardia/Cryptosporidium Chek kit (TechLab, an enzyme-linked immunosorbent assay (ELISA, was adopted for screening. The ELISA-positive reactions were subsequently characterised by RIDA Quick Giardia and RIDA Quick Cryptosporidium immunochromatographic kits (R-Biopharm. A gold standard test comprising PCR and microscopy was used for preparing control samples. Performance of individual kits was tested against these samples which included 50 Giardia-positive, 40 Cryptosporidium-positive, and 70 Cryptosporidium/Giardia-negative. For Cryptosporidium, specificities of the ELISA and RIDA Quick Cryptosporidium kits were 95.71% and 100%, respectively. Both kits demonstrated sensitivity of 95%. For Giardia, the ELISA and RIDA Quick Giardia kits showed sensitivities of 100% and 97.5%, respectively. Specificities obtained by the ELISA and RIDA Quick Giardia were 95.7% and 100%, respectively. Based on the results of two reference PCRs, on 250 random samples, the algorithm exhibited sensitivity, specificity, positive predictive value, and negative predictive value of 97.06%, 100.00%, 100.00%, and 98.91%, respectively. In conclusion, this immunoassay-based algorithm can be used as routine test in diagnostic laboratories for screening and identification of a large number of samples.

  18. SIFAT KIMIA SELAI BUAH NAGA, KOMPOSISI MIKROFLORA DAN PROFIL SCFA FESES RELAWAN [Chemical Properties of Drugon Fruit Jam, Microflora Composition and SCFA Profile of Human Volunteer Faecal

    Directory of Open Access Journals (Sweden)

    Nurhayati

    2015-12-01

    Full Text Available Dragon fruit contains oligosaccharides, Including prebiotic ingredients, that are namely raffinose, stachyose, and fructo-oligosaccharides. The heat treatment process like jam producing can affect the functional properties of a food material. The aim of the research wereto know the effect of jam processing on chemical properties, and their prebiotic properties. Evaluation of the prebiotic properties was conducted by in vivo method i.e. probiotic and enterobacteria population of volunteers faecal (microflora composition, prebiotic index (PI value and Short Chain Fatty Acid (SCFA profile. The result showed that the processing of dragon fruit into jams decreased water content, β-sianin and dissolved particles but increased the Insoluble Indigestible Fraction (IIF. The PI value of dragon fruit jam were 1.70 for white dragon jam and 1.18 for red dragon fruit. The jam processing decreased PI value up to 0.49 (red dragon fruit jam and 0.54 (white dragon fruit jam. The fresh dragon fruit and the jam produced short chain fatty acid (SCFA i.e. acetic and propionic acid. It can be concluded that prebiotic properties of white dragon fruit better than red dragon fruit.

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

    Directory of Open Access Journals (Sweden)

    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

  20. 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

  1. Effects of natural environmental conditions on faecal glucocorticoid metabolite concentrations in jaguars (Panthera onca) in Belize.

    Science.gov (United States)

    Mesa-Cruz, J Bernardo; Brown, Janine L; Kelly, Marcella J

    2014-01-01

    In situ studies that rely on non-invasive faecal hormone monitoring are subject to problems due to potential changes in hormone concentrations in samples exposed to field conditions. In this study, we conducted an environmental validation for measurement of faecal glucocorticoid metabolites (FGMs) in jaguars (Panthera onca). We collected fresh faeces (e.g. no older than 8 h) from jaguars (six males and four females), housed at the Belize Zoo, and exposed them randomly to two environmental conditions: shade and sun. A control (first sub-sample) was immediately frozen, after which sub-samples were frozen daily over a 5 day period in both the dry and wet seasons. We quantified FGMs using a cortisol enzyme immunoassay (EIA) and a corticosterone radioimmunoassay (RIA), both capable of identifying relevant metabolites. Results indicated that FGMs assessed with the cortisol EIA were stable for 5 days during the dry season but for jaguar faeces to sun or shade had no effect on FGM concentrations, despite significant differences in weather parameters. Analysis of faecal morphology proved unreliable in identifying faecal age. We conclude that the corticosterone RIA is suitable for assessing FGMs in free-ranging Belizean jaguars by surveying the same transects every 3-4 days in both seasons. The cortisol EIA can be used during the dry season, but there are possible shifts in metabolite immunoactivity in wet conditions. Assessment of adrenal activity in jaguars ranging areas of varying human disturbance is a timely application of this methodology in Belize.

  2. The Effect of Lactulose on the Composition of the Intestinal Microbiota and Short-chain Fatty Acid Production in Human Volunteers and a Computer-controlled Model of the Proximal Large Intestine

    NARCIS (Netherlands)

    Venema, K.; Nuenen, M.H.M.C. van; Heuvel, E.G. van den; Pool, W.; Vossen, J.M.B.M. van der

    2003-01-01

    The objective of this study was to compare the in vivo effect of lactulose on faecal parameters with the effect in a dynamic, computer-controlled in vitro model of the proximal large intestine (TIM-2). Faecal samples from 10 human volunteers collected before (non-adapted) and after 1 week of

  3. The effects of freezing on faecal microbiota as determined using MiSeq sequencing and culture-based investigations.

    Directory of Open Access Journals (Sweden)

    Fiona Fouhy

    Full Text Available High-throughput sequencing has enabled detailed insights into complex microbial environments, including the human gut microbiota. The accuracy of the sequencing data however, is reliant upon appropriate storage of the samples prior to DNA extraction. The aim of this study was to conduct the first MiSeq sequencing investigation into the effects of faecal storage on the microbiota, compared to fresh samples. Culture-based analysis was also completed.Seven faecal samples were collected from healthy adults. Samples were separated into fresh (DNA extracted immediately, snap frozen on dry ice and frozen for 7 days at -80°C prior to DNA extraction or samples frozen at -80°C for 7 days before DNA extraction. Sequencing was completed on the Illumina MiSeq platform. Culturing of total aerobes, anaerobes and bifidobacteria was also completed.No significant differences at phylum or family levels between the treatment groups occurred. At genus level only Faecalibacterium and Leuconostoc were significantly different in the fresh samples compared to the snap frozen group (p = 0.0298; p = 0.0330 respectively. Diversity analysis indicated that samples clustered based on the individual donor, rather than by storage group. No significant differences occurred in the culture-based analysis between the fresh, snap or -80°C frozen samples.Using the MiSeq platform coupled with culture-based analysis, this study highlighted that limited significant changes in microbiota occur following rapid freezing of faecal samples prior to DNA extraction. Thus, rapid freezing of samples prior to DNA extraction and culturing, preserves the integrity of the microbiota.

  4. The capacity of short-chain fructo-oligosaccharides to stimulate faecal bifidobacteria: a dose-response relationship study in healthy humans

    Directory of Open Access Journals (Sweden)

    Simoneau Guy

    2006-03-01

    Full Text Available Abstract Background Short-chain fructo-oligosaccharides (scFOS are well-known for their bifidogenicity. In a large study comprising 200 healthy volunteers, we determined the bifidogenic properties of 7 non-digestible carbohydrates administered at a dose of 10 g/d in the diet; we analysed dose-response relationships of the bifidogenic substrates at doses ranging from 2.5 to 10 g/d in comparison with a placebo. The aim of this presentation is to give more details about the dose-response effects of short-chain fructo-oligosaccharides (scFOS. Methods Forty healthy volunteers (18 males, 22 females eating their usual diets were randomly divided into 5 groups of 8 subjects and received scFOS at a dose of 2.5, 5.0, 7.5 and 10 g/d or a placebo for 7 d. Stools were collected before (day (d 8 and at the end (day (d 15 of sugar consumption, and tolerance was evaluated using a daily chart. Results (m ± SEM Bifidobacteria counts increase was higher in scFOS than in placebo group for all doses tested [2.5 g/d (from 9.15 ± 0.59 to 9.39 ± 0.70; P = 0.02; 5 g/d (from 10.21 ± 0.21 to 10.67 ± 0.22; P = 0.03; 7.5 g/d (from 9.28 ± 0.49 to 9.85 ± 0.35;P = 0.01; 10 g/d (from 9.00 ± 0.81 to 10.18 ± 0.60; P = 0.003]. A significant correlation between the ingested dose of scFOS and faecal bifidobacteria counts was observed at d15 (r2 = 0.307, P Conclusion This study showed that scFOS is bifidogenic and well tolerated at doses ranging from 2.5 to 10 g/d, and that there is a dose-response relationship in healthy volunteers.

  5. Faecal sterols as indicators of sewage contamination in estuarine sediments of the Tay Estuary, Scotland: an extended baseline survey

    Science.gov (United States)

    Reeves, A. D.; Patton, D.

    2005-06-01

    Sterol ratios are used to identify sources, occurrence and partitioning of faecal matter in sediments of the Tay Estuary, Scotland. The 5β/(5α+5β) ratio is used to discriminate between sewage and biogenic sterol sources by comparing the concentrations of coprostanols to cholesterol plus coprostanols. This index shows unambiguous sewage pollution in the Invergowrie Bay area (values >0.7). The coprostanol/epicoprostanol index is used to differentiate between human and non-human faecal inputs. Ratios confirmed the primary source as human-derived faecal material. The coprostanol/cholesterol ratio was calculated in order to elucidate the contribution of different biogenic sources to the sedimentary sterol budget. Ratios of >1 clearly indicate faecal sterol sources. Invergowrie Bay displayed no sterol signature other than sewage. A biogenic source of cholesterol influenced total sterol concentrations upstream of the City of Dundee. Attention is directed to the potential role of density fronts in compartmentalization of faecal material in bottom sediments.

  6. 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

  7. Faecal phytic acid and its relation to other putative markers of risk for colorectal cancer.

    OpenAIRE

    Owen, R W; Weisgerber, U M; Spiegelhalder, B; Bartsch, H

    1996-01-01

    AIMS--Phytic acid, a major constituent of cereals, pulses, and seeds has been advocated as an important antioxidant component of dietary fibre that affords possible protection against colorectal cancer. This is supported by experimental studies showing it has antineoplastic activity in animal models of both colon and breast cancer. To date the concentration of faecal phytic acid in human clinical groups has not been evaluated. Therefore the faecal phytic acid content of adenoma patients drawn...

  8. Faecal short chain fatty acid pattern and allergy in early childhood.

    Science.gov (United States)

    Sandin, Anna; Bråbäck, Lennart; Norin, Elisabeth; Björkstén, Bengt

    2009-05-01

    To investigate whether functional changes of the gut flora over time were related to sensitization and allergic symptoms at four years of age. The levels of short chain fatty acids (SCFAs) in faecal samples at one (n = 139) and four (n = 53) years of age were related to the development of positive skin prick tests (SPT) and allergic symptoms during the first four years of life. Faecal acetic (p diversity.

  9. Dielectric characterisation of human tissue samples

    NARCIS (Netherlands)

    Rossum, W.L. van; Nennie, F.; Deiana, D.; Veen, A.J. van der; Monni, S.

    2014-01-01

    The electrical properties of tissues samples are required for investigation and simulation purposes in biomedical applications of EM sensors. While available open literature mostly deals with ex-vivo characterization of isolated tissues, knowledge on dielectric properties of these tissues in their o

  10. Pattern designation of PCBs in human samples

    Energy Technology Data Exchange (ETDEWEB)

    Wolff, M.S.; Fischbein, A.; Rosenman, K.D.; Levin, S.M.

    1986-03-01

    In order to asses the nature of PCB exposures in humans, statistical measures of PCB patterns in blood serum (as Aroclor 1254 or 1260) were made in 348 cases, representing several exposed and non-exposed groups. Although the cases were not representative of any population, most (252/348) had an Arcolor 1260 pattern, with evidence that PCB congeners in blood serum were usually derived from both Aroclor 1254 and 1260. The method is readily applied to routine packed column gc analysis.

  11. Forensic Identification of Human Blood: comparison of two one-step presumptive tests for blood screening of crime scene samples.

    Directory of Open Access Journals (Sweden)

    Ana Flávia Belchior Andrade

    2014-08-01

    Full Text Available Blood is the most common body fluid found at crime scenes. One-step presumptive tests have been designed as a rapid immunological test for the qualitative detection of human hemoglobin in stool samples (faecal occult blood their usefulness for forensic purposes has been demonstrated before. In this study we compare Hexagon OBTI kit and FOB One-step Bioeasy kit sensitivity in the analysis of diluted blood samples. With Hexagon OBTI, positive test results are achieved in whole blood dilutions up to 1:1.000. Sensitivity decreased with aged samples, if samples were not stored under low temperatures regardless of which presumptive test is used. Whole blood tests must take into consideration that “hook” effect may interfere. Comparing both tests, OBTI Hexagon Kit is more sensible to detect diluted blood, showing a wider detection window in all conditions. This is interesting when analyzing forensic samples as forensic analysts usually do not know about the history of the analyzed sample before its collection.

  12. Antimicrobial resistance in commensal faecal Escherichia coli of hospitalised horses

    Directory of Open Access Journals (Sweden)

    Bryan Jill

    2010-06-01

    Full Text Available Abstract The objective of this study was to examine the impact of hospitalisation and antimicrobial drug administration on the prevalence of resistance in commensal faecal E. coli of horses. Faecal samples were collected from ten hospitalised horses treated with antimicrobials, ten hospitalised horses not treated with antimicrobials and nine non-hospitalised horses over a consecutive five day period and susceptibility testing was performed on isolated E. coli. Results revealed that hospitalisation alone was associated with increased prevalence of antimicrobial resistance and multidrug resistance in commensal E. coli of horses. Due to the risk of transfer of resistance between commensal and pathogenic bacteria, veterinarians need to be aware of possible resistance in commensal bacteria when treating hospitalised horses.

  13. Detection of vanA-containing Enterococcus species in faecal microbiota of gilthead seabream (Sparus aurata).

    Science.gov (United States)

    Barros, Joana; Andrade, Margarida; Radhouani, Hajer; López, Maria; Igrejas, Gilberto; Poeta, Patricia; Torres, Carmen

    2012-01-01

    Vancomycin-resistant Enterococcus faecalis, E. faecium and E. durans isolates with the genotype vanA were detected in 7 of 118 faecal samples (5.9%) of natural gilthead seabream recovered off the coast of Portugal, and one vancomycin-resistant isolate/sample was further characterized. The genes erm(B), tet(L), tet(M), aac(6')-aph(2"), aph(3')-IIIa and/or ant(6)-Ia were identified in most of the 7 vancomycin-resistant enterococci. Sequence types ST273, ST313 and ST76 were detected in three E. faecium isolates and ST6 in two E. faecalis isolates. VanA-containing enterococci are suggested to be disseminated in fish in marine ecosystems close to areas of human activity.

  14. Screening for colorectal cancer and advanced colorectal neoplasia in kidney transplant recipients: cross sectional prevalence and diagnostic accuracy study of faecal immunochemical testing for haemoglobin and colonoscopy.

    Science.gov (United States)

    Collins, Michael G; Teo, Edward; Cole, Stephen R; Chan, Choy-Yoke; McDonald, Stephen P; Russ, Graeme R; Young, Graeme P; Bampton, Peter A; Coates, P Toby

    2012-07-25

    To investigate whether screening kidney transplant recipients aged over 50 years for colorectal cancer with a faecal immunochemical test for haemoglobin might be justified, by determining the prevalence of advanced colorectal neoplasia and evaluating the diagnostic accuracy of faecal haemoglobin testing compared with colonoscopy in a population of kidney transplant recipients at otherwise average risk. Cross sectional prevalence and diagnostic accuracy study with index test of faecal haemoglobin and reference standard of colonoscopy. Outpatient clinics in metropolitan and regional hospitals in South Australia. 229 kidney transplant recipients aged 50 years and over, who were at least 6 months (mean 9.0 (SD 8.4) years) post-transplant and otherwise at average risk of colorectal cancer, completed the study between June 2008 and October 2011. Faecal immunochemical testing (Enterix Insure) for human haemoglobin, followed by colonoscopy with histological evaluation of retrieved samples. Prevalence of advanced colorectal neoplasia, defined as an adenoma at least 10 mm in diameter, villous features, high grade dysplasia, or colorectal cancer; sensitivity, specificity, and predictive values of faecal haemoglobin testing for advanced neoplasia compared with colonoscopy. Advanced colorectal neoplasia was found in 29 (13%, 95% confidence interval 9% to 18%) participants, including 2% (n=4) with high grade dysplasia and 2% (n=5) with colorectal cancer. Faecal testing for haemoglobin was positive in 12% (n=28); sensitivity, specificity, and positive and negative predictive values for advanced neoplasia were 31.0% (15.3% to 50.8%), 90.5% (85.6% to 94.2%), 32.1% (15.9% to 52.4%), and 90.1% (85.1% to 93.8%). Colonoscopy was well tolerated, with no significant adverse outcomes. To identify one case of advanced neoplasia, 8 (6 to 12) colonoscopies were needed. Kidney transplant recipients aged over 50 years have a high prevalence of advanced colorectal neoplasia. Faecal haemoglobin

  15. Isolation of Campylobacter from human stool samples

    Directory of Open Access Journals (Sweden)

    S M Salim

    2014-01-01

    Full Text Available Context: Campylobacter is an undetected cause of diarrhoea especially under 5 years of age in most of the countries. Isolation of this organism is difficult, expensive and cumbersome. Aims: Our objective of this study was to isolate this pathogen from the stool specimens on routinely available blood containing laboratory media using the candle jar for creating the microaerophilic atmosphere in our setup. Settings and Designs: A descriptive study. Materials and Methods: A total of 50 stool samples were inoculated onto selective and non-selective media with and without filtration using a 0.45 μm membrane. The inoculated media were simultaneously incubated in microaerophilic conditions using the Anoxomat as well as in candle jars at temperatures 37°C and 42°C. The culture isolates were confirmed by standard phenotypic tests. A simplex polymerase chain reaction (PCR targeting the 16S ribosomal deoxyribonucleic acid of Campylobacter was performed on the deoxyribonucleic acid (DNA of the culture isolates as well as on the DNA extracted from the stool filtrates. Statistical Analysis: Data was expressed as a proportion. Results: Campylobacter could be isolated in 5 out of 50 stool samples using both the Anoxomat as well as the candle jar. Furthermore, we did not find any difference between the isolation using the selective and blood containing media as well as the different incubation temperatures. All the five were confirmed phenotypically and genotypically to be Campylobacter jejuni. The PCR results corroborated with that of the culture. Conclusions: Isolation by culture was as sensitive as that of the PCR.

  16. Effect of soy on faecal dry matter content and excretion of Brachyspira hyodysenteriae in pigs

    Science.gov (United States)

    Grahofer, Alexander; Overesch, Gudrun; Nathues, Heiko; Zeeh, Friederike

    2016-01-01

    The aim of this study was to investigate the effect of a soy diet on the excretion of Brachyspira hyodysenteriae in five farms with subclinically infected pigs. The effects on general health, faecal consistency and dry matter were analysed. In total, 200 pigs of different ages (group 1 feed ration was replaced by pure soy on two consecutive days. Faecal scores were used to determine faecal consistency and a microwave method to assess faecal dry matter content (FDMC). In age group 1, soy feeding resulted in a statistically significant decrease of the FDMC of 2.5 per cent compared with group C and in age group 2 in a significant increase of 2.2 per cent compared with group C at day 2. Overall seven (T: 5, C: 2) out of 597 faecal samples tested positive for B hyodysenteriae by PCR. In conclusion, a high soy diet applied over two days influenced the faecal consistency and the FDMC in growers, finishers and sows under field conditions. Further investigations with more sensitive diagnostic methods are needed to prove a potential influence of a high soy diet on the detection rate of B hyodysenteriae in subclinically infected herds. PMID:27239320

  17. 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.

  18. Faecal Excretion of Glycosphingolipids of Breast-fed and Formula-fed Infants

    OpenAIRE

    Larson, G.; Falk, P; Hynsjö, L.; Midtvedt, A. -C.; Midtvedt, T

    2011-01-01

    Faecal samples of six healthy breast-fed, or formula-fed, infants were collected at intervals up to 9 mth of age and analysed for their contents of sphingolipids. Comparisons were made with faecal samples of one older child and one adult. The mean faccal content of sphingolipids during the first 9 mth of life (8.2 μmol sphingosine/g dry stool) was significantly less than that of meconium samples (23.3 μmol/gj but higher than that of adult stools (1.2 μmol/g). Sphingomyelin excretion ...

  19. 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...... in faecal microbiota exists....

  20. Relationship Between Gastrointestinal Parasite Infection and Faecal Protein Excretion in Moghani ewes

    Directory of Open Access Journals (Sweden)

    S. Hassanpour

    2011-06-01

    Full Text Available The aim of this study was to investigate relationship between Faecal Egg Counts (FECs and protein excretion in naturally acquired nematode infected Moghani ewes. Thirty-five Moghani ewes (aged from 6 to 12 months and average of body weight 32±3 kg were selected among the naturally acquired nematode infected animals which their infection had confirmed by McMaster flotation method. The animals were divided into 5 groups according to the FECs (470. Faecal samples were taken directly from the rectum of each animal in early morning and kept in individual sampling containers under 4ºC. Faecal parameters such as Crude Protein (CP, Dry Matter (DM, Organic Matter (OM and ash were determined using the Kjeldahl method following the standard procedures. Data were processed in excel and statistical analysis was performed using SPSS/ver. 17 software. Our data indicates that there was a significant difference among groups for the faecal ash and OM values (p0.1, r = - 0.290 in the naturally acquired nematode infected Moghani ewes. In conclusion, the FECs was not a good indication for interpretation of faecal protein excretion in nematode infected sheep.

  1. Detection of porcine rotavirus from tissue and faecal specimens

    Directory of Open Access Journals (Sweden)

    Prabha Suji

    2009-01-01

    Full Text Available Porcine small intestinal sub-mucosa is a cell-free collagen matrix that has demonstrated its ability as a scaffold material. Transplantation poses special hazards because grafted tissues and organs transmit pathogens efficiently, especially viruses. Rotavirus is thought to be confined to the intestine, causing acute diarrhoea. The purpose of this study was to evaluate the porcine intestinal tissue scaffold for Rotavirus and to study the incidence of this virus among pig herds. Only one isolate was successfully adapted to grow in cell line MA 104 from faecal samples. This isolate was further confirmed by reverse transcriptase polymerase chain reaction and sequence analysis.

  2. Baseline concentrations of faecal sterols and assessment of sewage input into different inlets of Admiralty Bay, King George Island, Antarctica.

    Science.gov (United States)

    Martins, César C; Aguiar, Sabrina N; Wisnieski, Edna; Ceschim, Liziane M M; Figueira, Rubens C L; Montone, Rosalinda C

    2014-01-15

    The Antarctic region is one of the best preserved environments in the world. However, human activities such as the input of sewage result in the alteration of this pristine site. We report baseline values of faecal sterols in Admiralty Bay, Antarctica. Four sediment cores were collected during the 2006/2007 austral summer at the Ezcurra (THP and BAR), Mackelar (REF) and Martel (BTP) inlets. Concentrations of faecal sterols (coprostanol+epicoprostanol) were sterols in core layers for THP, BAR, REF and BTP, were 0.04 ± 0.02, 0.03 ± 0.01, 0.07 ± 0.01 and 0.04 ± 0.02 μg g(-1), respectively. These results established as natural contributions of faecal sterols, suggesting that these markers can be useful indicators of human-derived faecal input and contributing to monitoring programs to prevent anthropogenic impacts. Copyright © 2013 Elsevier Ltd. All rights reserved.

  3. 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.

  4. Nocturnal faecal soiling and anal masturbation.

    OpenAIRE

    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.

  5. Approach-Induced Biases in Human Information Sampling

    Science.gov (United States)

    Hunt, Laurence T.; Rutledge, Robb B.; Malalasekera, W. M. Nishantha; Kennerley, Steven W.; Dolan, Raymond J.

    2016-01-01

    Information sampling is often biased towards seeking evidence that confirms one’s prior beliefs. Despite such biases being a pervasive feature of human behavior, their underlying causes remain unclear. Many accounts of these biases appeal to limitations of human hypothesis testing and cognition, de facto evoking notions of bounded rationality, but neglect more basic aspects of behavioral control. Here, we investigated a potential role for Pavlovian approach in biasing which information humans will choose to sample. We collected a large novel dataset from 32,445 human subjects, making over 3 million decisions, who played a gambling task designed to measure the latent causes and extent of information-sampling biases. We identified three novel approach-related biases, formalized by comparing subject behavior to a dynamic programming model of optimal information gathering. These biases reflected the amount of information sampled (“positive evidence approach”), the selection of which information to sample (“sampling the favorite”), and the interaction between information sampling and subsequent choices (“rejecting unsampled options”). The prevalence of all three biases was related to a Pavlovian approach-avoid parameter quantified within an entirely independent economic decision task. Our large dataset also revealed that individual differences in the amount of information gathered are a stable trait across multiple gameplays and can be related to demographic measures, including age and educational attainment. As well as revealing limitations in cognitive processing, our findings suggest information sampling biases reflect the expression of primitive, yet potentially ecologically adaptive, behavioral repertoires. One such behavior is sampling from options that will eventually be chosen, even when other sources of information are more pertinent for guiding future action. PMID:27832071

  6. The ameliorating effect of Yucca schidigera extract on canine and feline faecal aroma.

    Science.gov (United States)

    Lowe, J A; Kershaw, S J

    1997-01-01

    Addition of Yucca schidigera extract (YSE) products to canine or feline diets improved the character and reduced the intensity of faecal aroma as monitored by a human panel. The general condition of the animals was not adversely affected as monitored by faecal pH, food retention time, and blood cell counts. Blood urea increased significantly in YSE-treated cats, possibly due to the saponins of YSE affecting gut wall permeability. This finding contrasts with previously published reports of a reduction in blood urea on the addition of sarsaponin (from YSE) to rat diets and of YSE products to poultry and cattle diets.

  7. External Quality Assessment in the Evaluation of Laboratory Performance of Faecal Culture.

    Science.gov (United States)

    Kiiskinen, Salla J; Ojanen, Tarja; Björkman, Yvonne; Laitinen, Harri; Siitonen, Anja

    2017-01-01

    In Finland, all laboratories carrying out diagnostics of infectious diseases in humans are approved by the Regional State Administrative Agencies and are obligated to participate in External Quality Assurance rounds. Performance in these rounds is thought to reflect the quality of laboratory work. In the 6-year study period, 17 Finnish laboratories received 48 simulated faecal specimens for the culturing of diarrhoeal pathogens, yielding altogether 586 faecal culture External Quality Control specimens and 581 reports. The results were correct in 92% of all reports and in 67% of all specimens. False-negative Salmonella results were given for 2 of the 18 specimens, one with biochemically atypical Salmonella strain and the other with a low count of Salmonella cells. False-negative Shigella report was given for 6 of the 7 specimens in some participating laboratory. Detection of all common faecal pathogens is especially relevant to patient safety, public health, and epidemiological surveillance.

  8. Human-Robot Site Survey and Sampling for Space Exploration

    Science.gov (United States)

    Fong, Terrence; Bualat, Maria; Edwards, Laurence; Flueckiger, Lorenzo; Kunz, Clayton; Lee, Susan Y.; Park, Eric; To, Vinh; Utz, Hans; Ackner, Nir

    2006-01-01

    NASA is planning to send humans and robots back to the Moon before 2020. In order for extended missions to be productive, high quality maps of lunar terrain and resources are required. Although orbital images can provide much information, many features (local topography, resources, etc) will have to be characterized directly on the surface. To address this need, we are developing a system to perform site survey and sampling. The system includes multiple robots and humans operating in a variety of team configurations, coordinated via peer-to-peer human-robot interaction. In this paper, we present our system design and describe planned field tests.

  9. Generic Modelling of Faecal Indicator Organism Concentrations in the UK

    Directory of Open Access Journals (Sweden)

    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.

  10. Analysis of the microbial diversity in faecal material of the endangered blue whale, Balaenoptera musculus.

    Science.gov (United States)

    Guass, Olivia; Haapanen, Lisa Meier; Dowd, Scot E; Širović, Ana; McLaughlin, Richard William

    2016-07-01

    Using bacterial and fungal tag-encoded FLX-Titanium amplicon pyrosequencing, the microbiota of the faecal material of two blue whales living in the wild off the coast of California was investigated. In both samples the most predominant bacterial phylum was the Firmicutes with Clostridium spp. being the most dominant bacteria. The most predominant fungi were members of the phylum Ascomycota with Metschnikowia spp. being the most dominant. In this study, we also preliminarily characterised the culturable anaerobic bacteria from the faecal material, using traditional culture and 16S rRNA gene sequencing approaches. In total, three bacterial species belonging to the phylum Firmicutes were identified.

  11. In silico analyses of metagenomes from human atherosclerotic plaque samples

    DEFF Research Database (Denmark)

    Mitra, Suparna; Drautz-Moses, Daniela I; Alhede, Morten

    2015-01-01

    a challenge. RESULTS: To investigate microbiome diversity within human atherosclerotic tissue samples, we employed high-throughput metagenomic analysis on: (1) atherosclerotic plaques obtained from a group of patients who underwent endarterectomy due to recent transient cerebral ischemia or stroke. (2...

  12. A DNA methylation fingerprint of 1628 human samples

    Science.gov (United States)

    Fernandez, Agustin F.; Assenov, Yassen; Martin-Subero, Jose Ignacio; Balint, Balazs; Siebert, Reiner; Taniguchi, Hiroaki; Yamamoto, Hiroyuki; Hidalgo, Manuel; Tan, Aik-Choon; Galm, Oliver; Ferrer, Isidre; Sanchez-Cespedes, Montse; Villanueva, Alberto; Carmona, Javier; Sanchez-Mut, Jose V.; Berdasco, Maria; Moreno, Victor; Capella, Gabriel; Monk, David; Ballestar, Esteban; Ropero, Santiago; Martinez, Ramon; Sanchez-Carbayo, Marta; Prosper, Felipe; Agirre, Xabier; Fraga, Mario F.; Graña, Osvaldo; Perez-Jurado, Luis; Mora, Jaume; Puig, Susana; Prat, Jaime; Badimon, Lina; Puca, Annibale A.; Meltzer, Stephen J.; Lengauer, Thomas; Bridgewater, John; Bock, Christoph; Esteller, Manel

    2012-01-01

    Most of the studies characterizing DNA methylation patterns have been restricted to particular genomic loci in a limited number of human samples and pathological conditions. Herein, we present a compromise between an extremely comprehensive study of a human sample population with an intermediate level of resolution of CpGs at the genomic level. We obtained a DNA methylation fingerprint of 1628 human samples in which we interrogated 1505 CpG sites. The DNA methylation patterns revealed show this epigenetic mark to be critical in tissue-type definition and stemness, particularly around transcription start sites that are not within a CpG island. For disease, the generated DNA methylation fingerprints show that, during tumorigenesis, human cancer cells underwent a progressive gain of promoter CpG-island hypermethylation and a loss of CpG methylation in non-CpG-island promoters. Although transformed cells are those in which DNA methylation disruption is more obvious, we observed that other common human diseases, such as neurological and autoimmune disorders, had their own distinct DNA methylation profiles. Most importantly, we provide proof of principle that the DNA methylation fingerprints obtained might be useful for translational purposes by showing that we are able to identify the tumor type origin of cancers of unknown primary origin (CUPs). Thus, the DNA methylation patterns identified across the largest spectrum of samples, tissues, and diseases reported to date constitute a baseline for developing higher-resolution DNA methylation maps and provide important clues concerning the contribution of CpG methylation to tissue identity and its changes in the most prevalent human diseases. PMID:21613409

  13. Effect of special Hungarian probiotic kefir on faecal microflora

    Institute of Scientific and Technical Information of China (English)

    Mária Figler; Gyula Mózsik; Béla Schaffer; Beáta Gasztonyi; Pongrác (A)cs; Béla Szili; Regina Rab; Sándor Szakály

    2006-01-01

    AIM: To investigate the effect of a four-week consumption of a special Hungarian probiotic agent (Biofir(R)) on the faecal microflora in human healthy subjects.METHODS: The effect of Biofir(R) with 106/cm3 initial germs on the faecal microflora was studied in 120healthy volunteers (71 females, 49 males). The traditional Russian type kefir was used as control. The various germ groups and pH values were determined in wk 2, 4and 6.RESULTS: The number of all microbes increased during the 4-week probiotic treatment. The number of microbes increased 4.3-fold in the control group and 6.8-fold in Biofir-treated group. The probiotic kefir caused multiplication of the probiotic flora, meanwhile the undesired bacteria multiplied in the control group. No significant change of pH values of the faeces was found in both groups.CONCLUSION: The Hungarian probiotic kefir (Biofir(R)) is capable of promoting multiplication of probiotic bacterial flora in the large bowel.

  14. Virulence factors and bacteriocins in faecal enterococci of wild boars.

    Science.gov (United States)

    Poeta, Patricia; Igrejas, Gilberto; Costa, Daniela; Sargo, Roberto; Rodrigues, Jorge; Torres, Carmen

    2008-10-01

    The production of antimicrobial, haemolytic and gelatinase activities was tested in 67 enterococci (39 E. faecium, 24 E. hirae, 2 E. faecalis, and 2 Enterococcus spp.), recovered from faecal samples of wild boars. In addition, the presence of genes encoding bacteriocin and virulence factors was also analysed by PCR and sequencing. Production of antimicrobial activity was checked in all enterococci against 9 indicator bacteria and it was detected in 11 E. faecium isolates (16.5%); eight and two of them harboured the genes encoding enterocin A + enterocin B and enterocin L50A/B, respectively. Sixty-seven per cent of our enterococci harboured different combinations of genes of the cyl operon, but none of them contained the complete cyl L(L)L(S)ABM operon, necessary for cytolysin expression. The presence of gel E gene, associated with the fsr ABC locus, was identified in 4 E. faecium and two E. faecalis isolates, exhibiting all of them gelatinase activity. beta -hemolytic activity was not found in our isolates. Both cpd and ace genes, encoding respectively the accessory colonisation factor and pheromone, were detected in two E. faecalis isolates, and the hyl gene, encoding hyalorunidase, in two E. faecium isolates, one of them gelatinase-positive. Genes encoding bacteriocins and virulence factors are widely disseminated among faecal enterococci of wild boars and more studies should be carried out to know the global distribution of these determinants in enterococci of different ecosystems.

  15. Flatography: Detection of gastrointestinal diseases by faecal gas analysis

    Institute of Scientific and Technical Information of China (English)

    Evelien; F; de; Groot; Tim; G; de; Meij; Daniel; J; Berkhout; Marc; P; van; der; Schee; Nanne; K; de; Boer

    2015-01-01

    Patients presenting with gastro-intestinal symptoms might suffer from a range of possible underlying diseases. An unmet need exists for novel cost-effective,reproducible, easy-to-perform and non-invasive tests. Hippocrates used body odours to diagnose diseases circa 460 before Christ. The art of diagnostic smelling is making a promising high-tech come-back with portable "electronic diagnostic noses". Analysis of faecal volatile organic compounds is a novel field in metabolomics with considerable potential to improve the diagnosis, phenotyping and monitoring of gastro-intestinal disease. Challenges will be to mature over the coming years by development of a standardized methodology for stool sample collection, storage, handling and analysis. Furthermore, key volatiles need to be identified to improve test accuracy and sensitivity by development of sensors tailored toward the accurate identification of disease specific volatiles. If these challenges are adequately faced, analysis of faecal volatiles has realistic potential to considerably improve screening, diagnosis and disease monitoring for gastro-intestinal diseases.

  16. 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.

  17. Groundbreaking Mars Sample Return for Science and Human Exploration

    Science.gov (United States)

    Cohen, Barbara; Draper, David; Eppler, Dean; Treiman, Allan

    2012-01-01

    Partnerships between science and human exploration have recent heritage for the Moon (Lunar Precursor Robotics Program, LPRP) and nearearth objects (Exploration Precursor Robotics Program, xPRP). Both programs spent appreciable time and effort determining measurements needed or desired before human missions to these destinations. These measurements may be crucial to human health or spacecraft design, or may be desired to better optimize systems designs such as spacesuits or operations. Both LPRP and xPRP recommended measurements from orbit, by landed missions and by sample return. LPRP conducted the Lunar Reconnaissance Orbiter (LRO) and Lunar Crater Observation and Sensing Satellite (LCROSS) missions, providing high-resolution visible imagery, surface and subsurface temperatures, global topography, mapping of possible water ice deposits, and the biological effects of radiation [1]. LPRP also initiated a landed mission to provide dust and regolith properties, local lighting conditions, assessment of resources, and demonstration of precision landing [2]. This mission was canceled in 2006 due to funding shortfalls. For the Moon, adequate samples of rocks and regolith were returned by the Apollo and Luna programs to conduct needed investigations. Many near-earth asteroids (NEAs) have been observed from the Earth and several have been more extensively characterized by close-flying missions and landings (NEAR, Hayabusa, Rosetta). The current Joint Robotic Precursor Activity program is considering activities such as partnering with the New Frontiers mission OSIRIS-Rex to visit a NEA and return a sample to the Earth. However, a strong consensus of the NEO User Team within xPRP was that a dedicated mission to the asteroid targeted by humans is required [3], ideally including regolith sample return for more extensive characterization and testing on the Earth.

  18. Sampling strategy for estimating human exposure pathways to consumer chemicals

    Directory of Open Access Journals (Sweden)

    Eleni Papadopoulou

    2016-03-01

    Full Text Available Human exposure to consumer chemicals has become a worldwide concern. In this work, a comprehensive sampling strategy is presented, to our knowledge being the first to study all relevant exposure pathways in a single cohort using multiple methods for assessment of exposure from each exposure pathway. The selected groups of chemicals to be studied are consumer chemicals whose production and use are currently in a state of transition and are; per- and polyfluorinated alkyl substances (PFASs, traditional and “emerging” brominated flame retardants (BFRs and EBFRs, organophosphate esters (OPEs and phthalate esters (PEs. Information about human exposure to these contaminants is needed due to existing data gaps on human exposure intakes from multiple exposure pathways and relationships between internal and external exposure. Indoor environment, food and biological samples were collected from 61 participants and their households in the Oslo area (Norway on two consecutive days, during winter 2013-14. Air, dust, hand wipes, and duplicate diet (food and drink samples were collected as indicators of external exposure, and blood, urine, blood spots, hair, nails and saliva as indicators of internal exposure. A food diary, food frequency questionnaire (FFQ and indoor environment questionnaire were also implemented. Approximately 2000 samples were collected in total and participant views on their experiences of this campaign were collected via questionnaire. While 91% of our participants were positive about future participation in a similar project, some tasks were viewed as problematic. Completing the food diary and collection of duplicate food/drink portions were the tasks most frequent reported as “hard”/”very hard”. Nevertheless, a strong positive correlation between the reported total mass of food/drinks in the food record and the total weight of the food/drinks in the collection bottles was observed, being an indication of accurate performance

  19. 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.

  20. [Fusarium graminearum presence in wheat samples for human consumption].

    Science.gov (United States)

    Martinez, Mauro; Castañares, Eliana; Dinolfo, María I; Pacheco, Walter G; Moreno, María V; Stenglein, Sebastián A

    2014-01-01

    One of the most important diseases in cereal crops is Fusarium head blight, being Fusarium graminearum the main etiological agent. This fungus has the ability to produce a wide spectrum and quantity of toxins, especially deoxynivalenol (DON). During the last crop season (2012-2013) the climatic conditions favored Fusarium colonization. The objective of this work was to determine the presence of this fungus as well as the DON content in 50 wheat grain samples. Our results showed that 80% of the samples were contaminated with Fusarium graminearum. Twenty four percent (24%) of the samples contained ≥ 1μg/g DON, 26% ranged from 0,5 and 0,99μg/g, and the remaining 50% had values lower than 0,5μg/g. Correlation was found between the presence of Fusarium graminearum and DON. It is necessary to establish DON limit values in wheat grains for human consumption.

  1. Evaluation of Faecal Salmonella Shedding Among Dogs at Seven Animal Shelters across Texas.

    Science.gov (United States)

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

    2016-11-01

    Estimates of prevalence of faecal Salmonella shedding among dogs in the United States have varied widely. Surveillance among shelter dogs has been limited, although dogs in animal shelters may be at elevated risk of Salmonella infection because of their previous exposure history as well as factors inherent to shelter environments. Our objectives were to estimate the prevalence of Salmonella shedding among shelter dogs across Texas, to identify risk factors for shedding and to characterize the isolates. Using a repeated cross-sectional study design, we collected faecal samples from dogs on two or three visits to each of seven Texas animal shelters between May 2013 and December 2014. Standard bacteriologic culture methods were used to isolate Salmonella from samples, and isolates were characterized via serotyping and anti-microbial susceptibility testing. The prevalence of faecal Salmonella shedding among sampled dogs was 4.9% (27/554), and within-shelter prevalence ranged from 1.9% to 8.3%. There was a marginal association (P = 0.09) between watery faecal samples and positive Salmonella status, as estimated by a logistic regression model that controlled for shelter as a random effect. However, over 60% of Salmonella-positive dogs had grossly normal faeces. Salmonella prevalence did not vary significantly by age group or sex. The most common serovars were Newport (22%) and Javiana (15%), both of which were widespread among shelters. Resistance to anti-microbial agents was uncommon. The prevalence of faecal Salmonella shedding among shelter dogs in Texas appears to be comparable to that seen among pet dogs in general. © 2016 Blackwell Verlag GmbH.

  2. Steroid Biomarkers Revisited – Improved Source Identification of Faecal Remains in Archaeological Soil Material

    Science.gov (United States)

    Prost, Katharina; Birk, Jago Jonathan; Lehndorff, Eva; Gerlach, Renate; Amelung, Wulf

    2017-01-01

    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. PMID:28060808

  3. Distribution of phylogroups and co-resistance to antimicrobial agents in ampicillin resistant Escherichia coli isolated from healthy humans and from patients with bacteraemia

    DEFF Research Database (Denmark)

    Haugaard, A.; Hammerum, A. M.; Porsbo, Lone Jannok;

    In 2002-03, 31 ampicillin resistant faecal isolates were collected from healthy humans. Moreover, 31 ampicillin resistant blood isolates from patients with bacte-raemia were collected in 2000-02. All isolates were tested positive for the pres-ence of blaTEM. Isolates were characterized by minimum...... inhibitory concentration to antimicrobial agents and examined by PCR to determine their phylogroups. The phylotyping grouped the faecal samples into A (13%), B1 (10%), B2 (42%), D (19%), NT (16%) while the blood isolates grouped into A (16%), B1 (0%), B2 (48%), D (32%) and NT (3%). The frequency...... of resistance in faecal and blood isolates (F/B) was: tetracycline (48%/48%), gentamicin (0%/10%), ciprofloxacin (3%,13%), sulfonamide (68%/77%) and trimethoprim (39%/39%). Conclusion: B2 was the most prevalent phylogroup found both in faecal isolates collected from healthy humans and in blood isolates from...

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

    DEFF Research Database (Denmark)

    Maeda, Yasuko; Høyer, Morten; Lundby, Lilli;

    2011-01-01

    for this review. The incidence of faecal incontinence following radiotherapy for prostate cancer varied from 1.6% to 58%. The mechanism of faecal incontinence was not entirely clear but it is most likely due to injury to the nerve plexus of the rectal muscular layer. Correlation between rectal dose...... the spatial distribution of radiation to the rectum may identify a more direct linkage between radiation damage and faecal incontinence....

  5. Estimating Sampling Selection Bias in Human Genetics: A Phenomenological Approach

    Science.gov (United States)

    Risso, Davide; Taglioli, Luca; De Iasio, Sergio; Gueresi, Paola; Alfani, Guido; Nelli, Sergio; Rossi, Paolo; Paoli, Giorgio; Tofanelli, Sergio

    2015-01-01

    This research is the first empirical attempt to calculate the various components of the hidden bias associated with the sampling strategies routinely-used in human genetics, with special reference to surname-based strategies. We reconstructed surname distributions of 26 Italian communities with different demographic features across the last six centuries (years 1447–2001). The degree of overlapping between "reference founding core" distributions and the distributions obtained from sampling the present day communities by probabilistic and selective methods was quantified under different conditions and models. When taking into account only one individual per surname (low kinship model), the average discrepancy was 59.5%, with a peak of 84% by random sampling. When multiple individuals per surname were considered (high kinship model), the discrepancy decreased by 8–30% at the cost of a larger variance. Criteria aimed at maximizing locally-spread patrilineages and long-term residency appeared to be affected by recent gene flows much more than expected. Selection of the more frequent family names following low kinship criteria proved to be a suitable approach only for historically stable communities. In any other case true random sampling, despite its high variance, did not return more biased estimates than other selective methods. Our results indicate that the sampling of individuals bearing historically documented surnames (founders' method) should be applied, especially when studying the male-specific genome, to prevent an over-stratification of ancient and recent genetic components that heavily biases inferences and statistics. PMID:26452043

  6. Effects of iron supplementation on dominant bacterial groups in the gut, faecal SCFA and gut inflammation: a randomised, placebo-controlled intervention trial in South African children.

    Science.gov (United States)

    Dostal, Alexandra; Baumgartner, Jeannine; Riesen, Nathalie; Chassard, Christophe; Smuts, Cornelius M; Zimmermann, Michael B; Lacroix, Christophe

    2014-08-28

    Fe supplementation is a common strategy to correct Fe-deficiency anaemia in children; however, it may modify the gut microbiota and increase the risk for enteropathogenic infection. In the present study, we studied the impact of Fe supplementation on the abundance of dominant bacterial groups in the gut, faecal SCFA concentration and gut inflammation in children living in rural South Africa. In a randomised, placebo-controlled intervention trial of 38 weeks, 6- to 11-year-old children with Fe deficiency received orally either tablets containing 50 mg Fe as FeSO₄ (n 22) for 4 d/week or identical placebo (n 27). In addition, Fe-sufficient children (n 24) were included as a non-treated reference group. Faecal samples were analysed at baseline and at 2, 12 and 38 weeks to determine the effects of Fe supplementation on ten bacterial groups in the gut (quantitative PCR), faecal SCFA concentration (HPLC) and gut inflammation (faecal calprotectin concentration). At baseline, concentrations of bacterial groups in the gut, faecal SCFA and faecal calprotectin did not differ between Fe-deficient and Fe-sufficient children. Fe supplementation significantly improved Fe status in Fe-deficient children and did not significantly increase faecal calprotectin concentration. Moreover, no significant effect of Fe treatment or time × treatment interaction on the concentrations of bacterial groups in the gut or faecal SCFA was observed compared with the placebo treatment. Also, there were no significant differences observed in the concentrations of any of the bacterial target groups or faecal SCFA at 2, 12 or 38 weeks between the three groups of children when correcting for baseline values. The present study suggests that in African children with a low enteropathogen burden, Fe status and dietary Fe supplementation did not significantly affect the dominant bacterial groups in the gut, faecal SCFA concentration or gut inflammation.

  7. 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.

  8. Recognition of human face based on improved multi-sample

    Institute of Scientific and Technical Information of China (English)

    LIU Xia; LI Lei-lei; LI Ting-jun; LIU Lu; ZHANG Ying

    2009-01-01

    In order to solve the problem caused by variation illumination in human face recognition, we bring forward a face recognition algorithm based on the improved muhi-sample. In this algorithm, the face image is processed with Retinex theory, meanwhile, the Gabor filter is adopted to perform the feature extraction. The experimental results show that the application of Retinex theory improves the recognition accuracy, and makes the algorithm more robust to the variation illumination. The Gabor filter is more effective and accurate for extracting more useable facial local features. It is proved that the proposed algorithm has good recognition accuracy and it is stable under variation illumination.

  9. 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

  10. Duodenal and faecal microbiota of celiac children: molecular, phenotype and metabolome characterization.

    Science.gov (United States)

    Di Cagno, Raffaella; De Angelis, Maria; De Pasquale, Ilaria; Ndagijimana, Maurice; Vernocchi, Pamela; Ricciuti, Patrizia; Gagliardi, Francesca; Laghi, Luca; Crecchio, Carmine; Guerzoni, Maria Elisabetta; Gobbetti, Marco; Francavilla, Ruggiero

    2011-10-04

    Epidemiology of celiac disease (CD) is increasing. CD mainly presents in early childhood with small intestinal villous atrophy and signs of malabsorption. Compared to healthy individuals, CD patients seemed to be characterized by higher numbers of Gram-negative bacteria and lower numbers Gram-positive bacteria. This study aimed at investigating the microbiota and metabolome of 19 celiac disease children under gluten-free diet (treated celiac disease, T-CD) and 15 non-celiac children (HC). PCR-denaturing gradient gel electrophoresis (DGGE) analyses by universal and group-specific primers were carried out in duodenal biopsies and faecal samples. Based on the number of PCR-DGGE bands, the diversity of Eubacteria was the higher in duodenal biopsies of T-CD than HC children. Bifidobacteria were only found in faecal samples. With a few exceptions, PCR-DGGE profiles of faecal samples for Lactobacillus and Bifidobacteria differed between T-CD and HC. As shown by culture-dependent methods, the levels of Lactobacillus, Enterococcus and Bifidobacteria were confirmed to be significantly higher (P = 0.028; P = 0.019; and P = 0.023, respectively) in fecal samples of HC than in T-CD children. On the contrary, cell counts (CFU/ml) of presumptive Bacteroides, Staphylococcus, Salmonella, Shighella and Klebsiella were significantly higher (P = 0.014) in T-CD compared to HC children. Enterococcus faecium and Lactobacillus plantarum were the species most diffusely identified. This latter species was also found in all duodenal biopsies of T-CD and HC children. Other bacterial species were identified only in T-CD or HC faecal samples. As shown by Randomly Amplified Polymorphic DNA-PCR analysis, the percentage of strains identified as lactobacilli significantly (P = 0.011) differed between T-CD (ca. 26.5%) and HC (ca. 34.6%) groups. The metabolome of T-CD and HC children was studied using faecal and urine samples which were analyzed by gas-chromatography mass spectrometry

  11. Duodenal and faecal microbiota of celiac children: molecular, phenotype and metabolome characterization

    Directory of Open Access Journals (Sweden)

    Guerzoni Maria

    2011-10-01

    Full Text Available Abstract Background Epidemiology of celiac disease (CD is increasing. CD mainly presents in early childhood with small intestinal villous atrophy and signs of malabsorption. Compared to healthy individuals, CD patients seemed to be characterized by higher numbers of Gram-negative bacteria and lower numbers Gram-positive bacteria. Results This study aimed at investigating the microbiota and metabolome of 19 celiac disease children under gluten-free diet (treated celiac disease, T-CD and 15 non-celiac children (HC. PCR-denaturing gradient gel electrophoresis (DGGE analyses by universal and group-specific primers were carried out in duodenal biopsies and faecal samples. Based on the number of PCR-DGGE bands, the diversity of Eubacteria was the higher in duodenal biopsies of T-CD than HC children. Bifidobacteria were only found in faecal samples. With a few exceptions, PCR-DGGE profiles of faecal samples for Lactobacillus and Bifidobacteria differed between T-CD and HC. As shown by culture-dependent methods, the levels of Lactobacillus, Enterococcus and Bifidobacteria were confirmed to be significantly higher (P = 0.028; P = 0.019; and P = 0.023, respectively in fecal samples of HC than in T-CD children. On the contrary, cell counts (CFU/ml of presumptive Bacteroides, Staphylococcus, Salmonella, Shighella and Klebsiella were significantly higher (P = 0.014 in T-CD compared to HC children. Enterococcus faecium and Lactobacillus plantarum were the species most diffusely identified. This latter species was also found in all duodenal biopsies of T-CD and HC children. Other bacterial species were identified only in T-CD or HC faecal samples. As shown by Randomly Amplified Polymorphic DNA-PCR analysis, the percentage of strains identified as lactobacilli significantly (P = 0.011 differed between T-CD (ca. 26.5% and HC (ca. 34.6% groups. The metabolome of T-CD and HC children was studied using faecal and urine samples which were analyzed by gas

  12. Comparison of faecal microbiota in Blastocystis-positive and Blastocystis-negative irritable bowel syndrome patients.

    Science.gov (United States)

    Nagel, Robyn; Traub, Rebecca J; Allcock, Richard J N; Kwan, Marcella M S; Bielefeldt-Ohmann, Helle

    2016-08-31

    We investigated whether the carriage of Blastocystis in IBS patients was associated with differences in the faecal microbiota. Forty patients with diarrhoea-predominant IBS (26 Blastocystis-positive and 14 Blastocystis-negative) and 57 healthy controls (HC) (42 Blastocystis-positive and 15 Blastocystis-negative) submitted faecal samples for metataxonomic analysis of the 16S ribosomal RNA gene. Differences in the relative abundance of bacteria in these IBS and HC groups were evaluated from phylum to genus level. Significant changes were observed in two dominant phyla in IBS patients, regardless of Blastocystis infection status, namely a rise in Firmicutes and a statistically significant reduction in relative abundance of Bacteroidetes (with a threefold increase in the Firmicutes to Bacteoridetes ratio). Significant differences at genus level in IBS subjects compared to HC were also observed for many bacterial species. However, further clinical subgroup analysis of Blastocystis-positive and Blastocystis-negative subjects, regardless of symptoms, showed no significant differences at the phylum or genus level in IBS-P compared to IBS-N. Significant differences in the faecal microbiota between diarrhoea-predominant IBS patients and healthy controls were confirmed, but the carriage of Blastocystis did not significantly alter the faecal microbiota. If Blastocystis-positive patients represent a separate clinical subtype of IBS, this group is not identified by changes in the microbiota.

  13. Human papillomavirus detection from human immunodeficiency virus-infected Colombian women's paired urine and cervical samples.

    Science.gov (United States)

    Munoz, Marina; Camargo, Milena; Soto-De Leon, Sara C; Sanchez, Ricardo; Parra, Diana; Pineda, Andrea C; Sussmann, Otto; Perez-Prados, Antonio; Patarroyo, Manuel E; Patarroyo, Manuel A

    2013-01-01

    Infection, coinfection and type-specific human papillomavirus (HPV) distribution was evaluated in human immunodeficiency virus (HIV)-positive women from paired cervical and urine samples. Paired cervical and urine samples (n = 204) were taken from HIV-positive women for identifying HPV-DNA presence by using polymerase chain reaction (PCR) with three generic primer sets (GP5+/6+, MY09/11 and pU1M/2R). HPV-positive samples were typed for six high-risk HPV (HR-HPV) (HPV-16, -18, -31, -33, -45 and -58) and two low-risk (LR-HPV) (HPV-6/11) types. Agreement between paired sample results and diagnostic performance was evaluated. HPV infection prevalence was 70.6% in cervical and 63.2% in urine samples. HPV-16 was the most prevalent HPV type in both types of sample (66.7% in cervical samples and 62.0% in urine) followed by HPV-31(47.2%) in cervical samples and HPV-58 (35.7%) in urine samples. There was 55.4% coinfection (infection by more than one type of HPV) in cervical samples and 40.2% in urine samples. Abnormal Papanicolau smears were observed in 25.3% of the women, presenting significant association with HPV-DNA being identified in urine samples. There was poor agreement of cervical and urine sample results in generic and type-specific detection of HPV. Urine samples provided the best diagnosis when taking cytological findings as reference. In conclusion including urine samples could be a good strategy for ensuring adherence to screening programs aimed at reducing the impact of cervical cancer, since this sample is easy to obtain and showed good diagnostic performance.

  14. Human papillomavirus detection from human immunodeficiency virus-infected Colombian women's paired urine and cervical samples.

    Directory of Open Access Journals (Sweden)

    Marina Munoz

    Full Text Available Infection, coinfection and type-specific human papillomavirus (HPV distribution was evaluated in human immunodeficiency virus (HIV-positive women from paired cervical and urine samples. Paired cervical and urine samples (n = 204 were taken from HIV-positive women for identifying HPV-DNA presence by using polymerase chain reaction (PCR with three generic primer sets (GP5+/6+, MY09/11 and pU1M/2R. HPV-positive samples were typed for six high-risk HPV (HR-HPV (HPV-16, -18, -31, -33, -45 and -58 and two low-risk (LR-HPV (HPV-6/11 types. Agreement between paired sample results and diagnostic performance was evaluated. HPV infection prevalence was 70.6% in cervical and 63.2% in urine samples. HPV-16 was the most prevalent HPV type in both types of sample (66.7% in cervical samples and 62.0% in urine followed by HPV-31(47.2% in cervical samples and HPV-58 (35.7% in urine samples. There was 55.4% coinfection (infection by more than one type of HPV in cervical samples and 40.2% in urine samples. Abnormal Papanicolau smears were observed in 25.3% of the women, presenting significant association with HPV-DNA being identified in urine samples. There was poor agreement of cervical and urine sample results in generic and type-specific detection of HPV. Urine samples provided the best diagnosis when taking cytological findings as reference. In conclusion including urine samples could be a good strategy for ensuring adherence to screening programs aimed at reducing the impact of cervical cancer, since this sample is easy to obtain and showed good diagnostic performance.

  15. Antibiotic resistance in faecal bacteria isolated from horses receiving virginiamycin for the prevention of pasture-associated laminitis.

    Science.gov (United States)

    Menzies-Gow, N J; Young, N J

    2011-09-28

    Enterococcus faecium, a major cause of potentially life-threatening hospital-acquired human infections, can be resistant to several antimicrobials, such that streptogramin quinupristin-dalfopristin (Q/D) is one of the few antibiotics still effective. Consequently use of the streptogramin virginiamycin as an animal growth promoter was banned in the EU in 1999 as some believed this contributed to the emergence of Q/D resistant E. faecium. Virginiamycin is advocated for preventing equine pasture-associated laminitis, but its effect on equine faecal bacterial Q/D resistance has not been determined. Faecal samples were obtained from horses receiving virginiamycin, horses co-grazing and horses not exposed to virginiamycin. Streptogramin resistant E. faecium were cultured from 70% (21/30) of animals treated with virginiamycin, 75% (18/24) of co-grazing animals and 69% (11/16) of animals not exposed. ermB and vatD genes were detected using real time PCR in 63% and 66% of animals treated with virginiamycin, 75% and 71% of co-grazing animals and 63% and 69% of animals not exposed. Antimicrobial resistance genes were present only in samples which had cultured Q/D resistant E. faecium. There was no significant difference between groups with respect to antimicrobial resistance. The gene load of vatD was significantly (p=0.04) greater in unexposed animals compared to those treated with virginiamycin. The use of virginiamycin to prevent pasture-associated laminitis does not appear to be related to an increased Q/D resistance frequency. However, in view of the high frequency of resistance within all groups, the horse is a reservoir of Q/D resistant genes and clones that potentially could be transferred transiently to humans.

  16. Spectrophotometric assay of creatinine in human serum sample

    Directory of Open Access Journals (Sweden)

    Avinash Krishnegowda

    2017-05-01

    Full Text Available A new spectrophotometric method for the analysis of creatinine concentration in human serum samples is developed. The method explores the oxidation of p-methylamino phenol sulfate (Metol in the presence of copper sulfate and creatinine which yields an intense violet colored species with maximum absorbance at 530 nm. The calibration graph of creatinine by fixed time assay ranged from 4.4 to 620 μM. Recovery of creatinine in human serum samples varied from 101% to 106%. Limit of detection and limit of quantification were 0.145 μM and 0.487 μM respectively. Sandell’s sensitivity was 0.112 μg cm−2 and molar absorptivity was 0.101 × 104 L mol−1 cm−1. Within day precision was 2.5–4.8% and day-to-day precision range was 3.2–7.8%. The robustness and ruggedness of the method expressed in RSD values ranged from 0.78% to 2.12% and 1.32% to 3.46% respectively, suggesting that the developed method was rugged. This method provides good sensitivity and is comparable to standard Jaffe’s method with comparatively less interference from foreign substances.

  17. Rapid extraction and preservation of genomic DNA from human samples.

    Science.gov (United States)

    Kalyanasundaram, D; Kim, J-H; Yeo, W-H; Oh, K; Lee, K-H; Kim, M-H; Ryew, S-M; Ahn, S-G; Gao, D; Cangelosi, G A; Chung, J-H

    2013-02-01

    Simple and rapid extraction of human genomic DNA remains a bottleneck for genome analysis and disease diagnosis. Current methods using microfilters require cumbersome, multiple handling steps in part because salt conditions must be controlled for attraction and elution of DNA in porous silica. We report a novel extraction method of human genomic DNA from buccal swab and saliva samples. DNA is attracted onto a gold-coated microchip by an electric field and capillary action while the captured DNA is eluted by thermal heating at 70 °C. A prototype device was designed to handle four microchips, and a compatible protocol was developed. The extracted DNA using microchips was characterized by qPCR for different sample volumes, using different lengths of PCR amplicon, and nuclear and mitochondrial genes. In comparison with a commercial kit, an equivalent yield of DNA extraction was achieved with fewer steps. Room-temperature preservation for 1 month was demonstrated for captured DNA, facilitating straightforward collection, delivery, and handling of genomic DNA in an environment-friendly protocol.

  18. FANTOM5 CAGE profiles of human and mouse samples

    KAUST Repository

    Noguchi, Shuhei

    2017-08-29

    In the FANTOM5 project, transcription initiation events across the human and mouse genomes were mapped at a single base-pair resolution and their frequencies were monitored by CAGE (Cap Analysis of Gene Expression) coupled with single-molecule sequencing. Approximately three thousands of samples, consisting of a variety of primary cells, tissues, cell lines, and time series samples during cell activation and development, were subjected to a uniform pipeline of CAGE data production. The analysis pipeline started by measuring RNA extracts to assess their quality, and continued to CAGE library production by using a robotic or a manual workflow, single molecule sequencing, and computational processing to generate frequencies of transcription initiation. Resulting data represents the consequence of transcriptional regulation in each analyzed state of mammalian cells. Non-overlapping peaks over the CAGE profiles, approximately 200,000 and 150,000 peaks for the human and mouse genomes, were identified and annotated to provide precise location of known promoters as well as novel ones, and to quantify their activities.

  19. Imbalances in faecal and duodenal Bifidobacterium species composition in active and non-active coeliac disease

    Directory of Open Access Journals (Sweden)

    Sanz Yolanda

    2008-12-01

    Full Text Available Abstract Background Gut bifidobacteria are believed to influence immune-related diseases. The objective of this study was to assess the possible relationships between the gut bifidobacteria composition and coeliac disease (CD in children. A total of 48 faecal samples (30 and 18 samples from active and no active CD patients, respectively and 33 duodenal biopsy specimens of CD patients (25 and 8 samples from active and non-active CD patients, respectively were analysed. Samples (30 faecal samples and 8 biopsies from a control age-matched group of children were also included for comparative purposes. Gut Bifidobacterium genus and species were analyzed by real-time PCR. Results Active and non-active CD patients showed lower numbers of total Bifidobacterium and B. longum species in faeces and duodenal biopsies than controls, and these differences were particularly remarkable between active CD patients and controls. B. catenulatum prevalence was higher in biopsies of controls than in those of active and non-active CD patients, whereas B. dentium prevalence was higher in faeces of non-active CD patients than in controls. Correlations between levels of Bifidobacterium and B. longum species in faecal and biopsy samples were detected in both CD patients and controls. Conclusion Reductions in total Bifidobacterium and B. longum populations were associated with both active and non-active CD when compared to controls. These bacterial groups could constitute novel targets for adjuvant dietary therapies although the confirmation of this hypothesis would require further investigations.

  20. Faecal pollution along the southeastern coast of Florida and insight into the use of pepper mild mottle virus as an indicator.

    Science.gov (United States)

    Symonds, E M; Sinigalliano, C; Gidley, M; Ahmed, W; McQuaig-Ulrich, S M; Breitbart, M

    2016-11-01

    To identify faecal pollution along the southeastern Florida coast and determine the performance of a reverse transcription-quantitative polymerase chain reaction (RT-qPCR) method for pepper mild mottle virus (PMMoV). In 2014, bimonthly surface water samples were collected from inlets, exposed to runoff and septic seepage, and coastal sites, exposed to ocean outfalls. Analysis of culturable enterococci and a suite of microbial source tracking (MST) markers (BacHum, CowM2, DogBact, HF183, HPyV, PMMoV) revealed faecal pollution, primarily of human origin, at all sites. Since PMMoV was detected more frequently than other MST markers, the process limits of quantification (undiluted to 10(-2) dilution) and detection (10(-2) dilution) for the RT-qPCR method were determined by seeding untreated wastewater into the coastal waters. Simulated quantitative microbial risk assessment, employing human norovirus as a reference pathogen, calculated a 0·286 median risk of gastrointestinal illness associated with the PMMoV limit of detection. All sites met the U.S. EPA recreational water criteria, despite detection of domestic wastewater-associated MST markers. PMMoV correlated only with human-associated MST markers. This study demonstrated that PMMoV is an important domestic wastewater-associated marker that should be included in the MST toolbox; therefore, future studies should thoroughly investigate the health risks associated with its detection and quantification in environmental waters. © 2016 The Society for Applied Microbiology.

  1. The influence of Lactobacillus casei DN 114 001 on the activity of faecal enzymes and genotoxicity of faecal water in the presence of heterocyclic aromatic amines.

    Science.gov (United States)

    Nowak, Adriana; Śliżewska, Katarzyna; Błasiak, Janusz; Libudzisz, Zdzisława

    2014-12-01

    High activity of bacterial enzymes in human colon and genotoxicity of faecal water (FW) are biomarkers of the harmful action of microbiota. The aim of the present study was to assess the activity of β-glucuronidase and β-glucosidase and the genotoxicity of FW in vitro after incubation with 2-amino-3-methyl-3H-imidazo[4,5-f]quinoline (IQ) or 2-amino-1-methyl-6-phenyl-1H-imidazo[4,5-b]pyridine (PhIP) and probiotic Lactobacillus casei DN 114 001 (Actimel). Our results indicate, that IQ and PhIP greatly increased the activity of faecal enzymes (it was up to four times higher, as measured by spectrophotometric methods) and the genotoxicity of FW (% DNA in the tail was up to 3.2 times higher, as evaluated by the comet assay on Caco-2 cells) in 15 individuals from three age-dependent groups (breast-fed children, adults aged 30-40 years, elderly aged 75-85 years). Lb. casei DN 114 001 decreased the activity of faecal enzymes and the genotoxicity of FW exposed to PhIP and IQ mostly to control values. The activity of faecal enzymes after incubation with IQ was reduced by 71.8% in the FW of children, 37.5% in adults and 64.2% in elderly (β-glucuronidase); as well as by 59.9% in children and 87.9% in elderly (β-glucosidase). For PhIP the reduction was by 59.0% in the FW of children, 50.0% in adults and 81.2% in elderly (β-glucuronidase) and by 20.2% in children, 20.7% in adults and 84.1% in elderly (β-glucosidase). Lb. casei DN 114 001 also decreased the genotoxicity of FW to the greatest extent in adults after incubation with IQ (by 65.4%) and PhIP (by 69.6%) and it was found to correlate positively with the decrease in faecal enzymes activity. In conclusion, Lb. casei DN 114 001 may exert the protective effects against genotoxic and possibly pro-carcinogenic effects of food processing-derived chemicals present in faecal water. Copyright © 2014. Published by Elsevier Ltd.

  2. Isolation of Cancer Stem Cells From Human Prostate Cancer Samples

    Science.gov (United States)

    Vidal, Samuel J.; Quinn, S. Aidan; de la Iglesia-Vicente, Janis; Bonal, Dennis M.; Rodriguez-Bravo, Veronica; Firpo-Betancourt, Adolfo; Cordon-Cardo, Carlos; Domingo-Domenech, Josep

    2014-01-01

    The cancer stem cell (CSC) model has been considerably revisited over the last two decades. During this time CSCs have been identified and directly isolated from human tissues and serially propagated in immunodeficient mice, typically through antibody labeling of subpopulations of cells and fractionation by flow cytometry. However, the unique clinical features of prostate cancer have considerably limited the study of prostate CSCs from fresh human tumor samples. We recently reported the isolation of prostate CSCs directly from human tissues by virtue of their HLA class I (HLAI)-negative phenotype. Prostate cancer cells are harvested from surgical specimens and mechanically dissociated. A cell suspension is generated and labeled with fluorescently conjugated HLAI and stromal antibodies. Subpopulations of HLAI-negative cells are finally isolated using a flow cytometer. The principal limitation of this protocol is the frequently microscopic and multifocal nature of primary cancer in prostatectomy specimens. Nonetheless, isolated live prostate CSCs are suitable for molecular characterization and functional validation by transplantation in immunodeficient mice. PMID:24686446

  3. Phylogenetic analysis of Escherichia coli strains isolated from human samples

    Directory of Open Access Journals (Sweden)

    Abdollah Derakhshandeh

    2013-12-01

    Full Text Available Escherichia coli (E. coli is a normal inhabitant of the gastrointestinal tract of vertebrates, including humans. Phylogenetic analysis has shown that E. coli is composed of four main phylogenetic groups (A, B1, B2 and D. Group A and B1 are generally associated with commensals, whereas group B2 is associated with extra-intestinal pathotypes. Most enteropathogenic isolates, however, are assigned to group D. In the present study, a total of 102 E. coli strains, isolated from human samples, were used. Phylogenetic grouping was done based on the Clermont triplex PCR method using primers targeted at three genetic markers, chuA, yjaA and TspE4.C2. Group A contained the majority of the collected isolates (69 isolates, 67.64%, followed by group B2 (18 isolates, 17.64% and D (15 isolates, 14.7% and no strains were found to belong to group B1. The distribution of phylogenetic groups in our study suggests that although the majority of strains were commensals, the prevalence of enteropathogenic and extra-intestinal pathotypes was noteworthy. Therefore, the role of E. coli in human infections including diarrhea, urinary tract infections and meningitis should be considered.

  4. Understanding the mechanisms of faecal microbiota transplantation.

    Science.gov (United States)

    Khoruts, Alexander; Sadowsky, Michael J

    2016-09-01

    This Review summarizes mechanistic investigations in faecal microbiota transplantation (FMT), which has increasingly been adapted into clinical practice as treatment for Clostridium difficile infection (CDI) that cannot be eliminated with antibiotics alone. Administration of healthy donor faecal microbiota in this clinical situation results in its engraftment and restoration of normal gut microbial community structure and functionality. In this Review, we consider several main mechanisms for FMT effectiveness in treatment of CDI, including direct competition of C. difficile with commensal microbiota delivered by FMT, restoration of secondary bile acid metabolism in the colon and repair of the gut barrier by stimulation of the mucosal immune system. Some of these mechanistic insights suggest possibilities for developing novel, next-generation CDI therapeutics. FMT might also have potential applications for non-CDI indications. The gut can become a reservoir of other potential antibiotic-resistant pathogens under pressure of antibiotic treatments, and restoration of normal microbial community structure by FMT might be a promising approach to protect against infections with these pathogens as well. Finally, FMT could be considered for multiple chronic diseases that are associated with some form of dysbiosis. However, considerable research is needed to optimize the FMT protocols for such applications before their therapeutic promise can be evaluated.

  5. Metabolic and inflammatory faecal markers in collagenous colitis

    DEFF Research Database (Denmark)

    Wildt, Signe; Lassen, Inge Nordgaard; Bendtsen, Flemming

    2007-01-01

    To evaluate the excretion of the inflammatory and metabolic faecal markers calprotectin, lactoferrin, and short-chain fatty acids in symptomatic and quiescent collagenous colitis.......To evaluate the excretion of the inflammatory and metabolic faecal markers calprotectin, lactoferrin, and short-chain fatty acids in symptomatic and quiescent collagenous colitis....

  6. Validation of a new scoring system: Rapid assessment faecal incontinence score

    Institute of Scientific and Technical Information of China (English)

    Fernando; de; la; Portilla; Arantxa; Calero-Lillo; Rosa; M; Jiménez-Rodríguez; Maria; L; Reyes; Manuela; Segovia-González; María; Victoria; Maestre; Ana; M; García-Cabrera

    2015-01-01

    AIM: To implement a quick and simple test- rapid assessment faecal incontinence score(RAFIS) and show its reliability and validity.METHODS: From March 2008 through March 2010, we evaluated a total of 261 consecutive patients, including 53 patients with faecal incontinence. Demographic and comorbidity information was collected. In a single visit, patients were administered the RAFIS. The results obtained with the new score were compared with those of both Wexner score and faecal incontinence quality of life scale(FIQL) questionnaire. The patient withoutinfluence of the surgeon completed the test. The role of surgeon was explaining the meaning of each section and how he had to fill. Reliability of the RAFIS score was measured using intra-observer agreement and Cronbach’s alpha(internal consistency) coefficient. Multivariate analysis of the main components within the different scores was performed in order to determine whether all the scores measured the same factor and to conclude whether the information could be encompassed in a single factor. A sample size of 50 patients with faecal incontinence was estimated to be enough to detect a correlation of 0.55 or better at 5% level of significance with 80% power.RESULTS: We analysed the results obtained by 53 consecutive patients with faecal incontinence(median age 61.55 ± 12.49 years) in the three scoring systems. A total of 208 healthy volunteers(median age 58.41 ± 18.41 years) without faecal incontinence were included in the study as negative controls. Pearson’s correlation coefficient between "state" and "leaks" was excellent(r = 0.92, P < 0.005). Internal consistency in the comparison of "state" and "leaks" yielded also excellent correlation(Cronbach’s α = 0.93). Results in each score were compared using regression analysis and a correlation value of r = 0.98 was obtained with Wexner score. As regards FIQL questionnaire, the values of "r " for the different subscales of the questionnaire were: "lifestyle" r

  7. Selection of bacteria originating from a human intestinal microbiota in the gut of previously germ-free rats

    DEFF Research Database (Denmark)

    Licht, Tine Rask; Madsen, Bodil; Wilcks, Andrea

    2007-01-01

    Denaturing gradient gel electrophoresis (DGGE) was applied to separate PCR-amplified 16S rRNA genes originating from human microbiota associated (HMA) rat faeces as well as from the human faecal sample used for inoculation of the animals. Subsequently, a total of 15 dominant bands were excised fr...

  8. Managing faecal retention and incontinence in neurodisability.

    Science.gov (United States)

    Pierce, E; Cowan, P; Stokes, M

    The large number of patients with faecal retention and/or incontinence in continuing care wards and rehabilitation units presents a considerable challenge. In order to maintain dignity and minimize the unpleasant odour so commonly associated with these wards and units, effective bowel management should be planned for individual patients. For an effective bowel management regime a team approach should be adopted, involving, where possible, the patient and carer as well as all the health professionals administering the care. Two case studies illustrate the use of assessment and management of bowel problems in patients with severe complex neurodisability. Bowel dysfunction in this patient population, in general, is poorly covered in the literature. The present article, by relating theory to practice, offers information and guidance for nurses working with patients who have bowel-related problems.

  9. Faecal microbiota transplantation: Key points to consider.

    Science.gov (United States)

    Bourlioux, P

    2015-05-01

    Faecal microbiota transplantation (FMT) from a healthy donor has become the gold standard treatment for patients suffering from recurrent Clostridium difficile infection where antibiotic treatment (with vancomycin, metronidazole or fidaxomicin) has failed. FMT eradicates C. difficile and helps restore the recipient's intestinal flora, but its mechanism of action remains unclear. Since FMT's complex and highly variable composition cannot be easily characterized - nor its quality routinely assessed - FMT as a sui generis biologic drug cannot conform to existing standards for preparation. Clearly, donors must be carefully selected and the raw material prepared under close microbiological control, but FMT should also conform to manufacturing and laboratory practice standards for which international consensus can only be achieved with further experience. The objective should be to engage biomedical research to develop protocols that help elucidate the mechanism of action of FMT and support the production of safe and efficacious products. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

  10. Further evaluation of an updated PCR assay for the detection of Schistosoma mansoni DNA in human stool samples

    Directory of Open Access Journals (Sweden)

    Luciana I Gomes

    2009-12-01

    Full Text Available A previously reported sensitive PCR assay for the detection of Schistosoma mansoni DNA was updated and evaluated. Changes in the DNA extraction method, including the use of a worldwide available commercial kit and the inclusion of additional quality control measures, increased the robustness of the test, as confirmed by the analysis of 67 faecal samples from an endemic area in Brazil. The PCR assay is at hand as a proven, reliable diagnostic test for the control of schistosomiasis in specific settings.

  11. Diversity and functions of the sheep faecal microbiota: a multi?omic characterization

    OpenAIRE

    Tanca, A.; Fraumene, C.; Manghina, V.; Palomba, A; Abbondio, M.; Deligios, M.; Pagnozzi, D.; Addis, M.F.; Uzzau, S.

    2017-01-01

    Summary Little is currently known on the microbial populations colonizing the sheep large intestine, despite their expected key role in host metabolism, physiology and immunity. This study reports the first characterization of the sheep faecal microbiota composition and functions, obtained through the application of a multi?omic strategy. An optimized protocol was first devised for DNA extraction and amplification from sheep stool samples. Then, 16S rDNA sequencing, shotgun metagenomics and s...

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

    Science.gov (United States)

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

    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 >100TTC/100mL 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 (>10TTC/100mL) 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.

  13. Molecular Diagnosis of Strongyloides Stercoralis Infection by PCR Detection of Specific DNA in Human Stool Samples

    Directory of Open Access Journals (Sweden)

    Eb Kia

    2011-06-01

    Full Text Available Background: Strongyloidiasis is mostly an asymptomatic infection and diagnosis of latent infec­tions is difficult due to limitations of current parasitological and serological methods. This study was conducted to set up a PCR-based method for molecular diagnosis of Strongyloides stercor­alis infection by detection of copro-DNA in stool samples.Methods: A total of 782 fresh stool samples were collected and examined by agar plate culture. Among those sixteen stool samples, which confirmed to be infected with S. stercoralis were exam­ined as positive control to set up each single and nested PCR, using two primer sets design­ing to amplify partial ribosomal DNA of S. stercoralis genome. Since, single PCR method yielded higher efficacy in detecting positive samples, in the second step, 30 stool samples, which found negative for S. stercoralis by agar plate culture of single stool sample, were examined by sin­gle PCR. Data analysis was performed using McNemar's χ2 test, with consideration of a P-value of <0.05 as indication of significant difference.Results: In amplification of DNA extracted from stool samples, single PCR detected S. stercor­alis DNA target in all 16 positive samples, while nested PCR amplified DNA in only 75% of sam­ples. In the second step, single PCR amplified S. stercoralis extracted DNA in 5 out of 30 sam­ples which were negative by coproculture.Conclusion: Single PCR method amplifying a short (100bp target represented more efficacies for detection of S. stercoralis in faecal examination compared to agar plate culture and nested PCR, which amplified longer target.

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

    Directory of Open Access Journals (Sweden)

    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.

  15. Faecal Salmonella shedding in fattening pigs in relation to the presence of Salmonella antibodies in three pig production systems

    DEFF Research Database (Denmark)

    Bonde, Marianne Kjær; Sørensen, Jan Tind

    2012-01-01

    Human salmonellosis originating from pork is an important zoonotic disease, and the production of outdoor pigs may increase the risk of contaminating the food chain with Salmonella from environmental sources. The prevalence of faecal Salmonella shedding has therefore been compared in organic...

  16. Irritable bowel syndrome and active inflammatory bowel disease diagnosed by faecal gas analysis.

    Science.gov (United States)

    Aggio, R B M; White, P; Jayasena, H; de Lacy Costello, B; Ratcliffe, N M; Probert, C S J

    2017-01-01

    Inflammatory bowel disease and irritable bowel syndrome may present in a similar manner. Measuring faecal calprotectin concentration is often recommended to rule out inflammatory bowel disease, however, there are no tests to positively diagnose irritable bowel syndrome and invasive tests are still used to rule out other pathologies. To investigate a platform technology for diagnosing inflammatory bowel disease and irritable bowel syndrome based on faecal gas. The platform technology is composed of a gas chromatography column coupled to a metal oxide gas sensor (OdoReader) and a computer algorithm. The OdoReader separates the volatile compounds from faecal gas and the computer algorithm identifies resistance patterns associated with specific medical conditions and builds classification models. This platform was applied to faecal samples from 152 patients: 33 patients with active inflammatory bowel disease; 50 patients with inactive inflammatory bowel disease; 28 patients with irritable bowel syndrome and 41 healthy donors (Control). The platform classified samples with accuracies from 75% to 100% using rigorous validation schemes: namely leave-one-out cross-validation, 10-fold cross-validation, double cross-validation and their Monte Carlo variations. The most clinically important findings, after double cross-validation, were the accuracy of active Crohn's disease vs. irritable bowel syndrome (87%; CI 84-89%) and irritable bowel syndrome vs. controls (78%; CI 76-80%). These schemes provide an estimate of out-of-sample predictive accuracy for similar populations. This is the first description of an investigation for the positive diagnosis of irritable bowel syndrome, and for diagnosing inflammatory bowel disease. © 2016 John Wiley & Sons Ltd.

  17. Faecal microbiota transplantation: a sui generis biological drug, not a tissue.

    Science.gov (United States)

    Megerlin, F; Fouassier, E; Lopert, R; Bourlioux, P

    2014-07-01

    Responding to Smith et al. (Nature, 2014), this paper argues that for medical use, faecal microbiota transplantation (FMT) should be considered a sui generis biological drug, rather than a tissue. Smith and colleagues' thesis is based on possible undesirable economic consequences of this designation--not on its scientific and conceptual basis. The faecal transplant (including gut microbiota, metabolites, mucus, human cells, viruses, fungi, etc.) is not a tissue; it is of topographic--not cellular--human origin. We consider the donor a bioreactor, producing the faecal substrate of therapeutic interest. The debate is of singular importance as the FDA considers FMT a drug and released a new guidance for public consultation in February 2014, whereas to date the European Medicines Agency has not promulgated its position. The UK's National Institute for Heath and Care Excellence does not consider FMT to involve the transplantation of body tissue, and in March 2014 the French regulatory agency ANSM expressly declared it to be a drug. As FM is a complex and highly variable admixture, its components cannot be completely characterized, and to date, compositional quality cannot be assessed. We consider FMT to be a sui generis biologic drug, albeit one prepared with unconventional raw material under microbiologic control. The possibility of associating identified bacterial species with particular diseases and cultivating selected bacteria of therapeutic interest would certainly define a second generation of microbiome therapeutics, but is still speculative. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

  18. 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.

  19. 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

  20. Enumeration of faecal indicator bacteria in large water volumes using on site membrane filtration to assess water treatment efficiency

    NARCIS (Netherlands)

    Hijnen, W.A.M.; Veendaal, D.; Speld, W.M.H. van der; Visser, Ate; Hoogenboezem, W.; Kooij, D. van der

    2000-01-01

    Sample volumes as tested in routine microbiological methods for determining the presence and absence of faecal indicator bacteria in water are too small to assess the actual concentration in the last stages of a water treatment. Consequently no accurate information can be obtained about the removal

  1. Enumeration of faecal indicator bacteria in large water volumes using on site membrane filtration to assess water treatment efficiency

    NARCIS (Netherlands)

    Hijnen, W.A.M.; Veendaal, D.; Speld, W.M.H. van der; Visser, Ate; Hoogenboezem, W.; Kooij, D. van der

    2000-01-01

    Sample volumes as tested in routine microbiological methods for determining the presence and absence of faecal indicator bacteria in water are too small to assess the actual concentration in the last stages of a water treatment. Consequently no accurate information can be obtained about the removal

  2. The sensitivity of direct faecal examination, direct faecal flotation, modified centrifugal faecal flotation and centrifugal sedimentation/flotation in the diagnosis of canine spirocercosis

    Directory of Open Access Journals (Sweden)

    J. Christie

    2011-04-01

    Full Text Available Several faecal examination techniques have shown variable sensitivity in demonstrating Spirocerca lupi (S. lupi eggs. The objective of this study was to determine which faecal examination technique, including a novel modified centrifugal flotation technique, was most sensitive to diagnose spirocercosis. Ten coproscopic examinations were performed on faeces collected from 33 dogs confirmed endoscopically to have spirocercosis. The tests included a direct faecal examination, a faecal sedimentation/flotation test, 4 direct faecal flotations and 4 modified faecal centrifugal flotations. These latter 2 flotation tests utilised 4 different faecal flotation solutions:NaNO3 (SG 1.22,MgSO4 (SG 1.29,ZnSO4 (SG 1.30 and sugar (SG 1.27. The sensitivity of the tests ranged between 42 %and 67 %, with theNaNO3 solution showing the highest sensitivity in both the direct and modified-centrifugal flotations. The modified NaNO3 centrifugal method ranked 1st with the highest mean egg count (45.24±83, and was superior (i.e. higher egg count and significantly different (P< 0.05 compared with the routine saturated sugar,ZnSO4 andMgSO4 flotation methods. The routine NaNO3 flotation method was also superior and significantly different (P < 0.05 compared with the routine ZnSO4 andMgSO4 flotation methods. Fifteen per cent (n=5 of dogs had neoplastic oesophageal nodules and a further 18 % (n = 6 had both neoplastic and non-neoplastic nodules. S. lupi eggs were demonstrated in 40%of dogs with neoplastic nodules only and 72.9 % of the dogs with non-neoplastic nodules. The mean egg count in the non-neoplastic group (61 was statistically greater (P = 0.02 than that of the neoplastic group (1. The results show that faecal examination using a NaNO3 solution is the most sensitive in the diagnosis of spirocercosis. The modified centrifugal flotation faecal method using this solution has the highest egg count. The study also found that dogs with neoplastic nodules shed

  3. The sensitivity of direct faecal examination, direct faecal flotation, modified centrifugal faecal flotation and centrifugal sedimentation/flotation in the diagnosis of canine spirocercosis.

    Science.gov (United States)

    Christie, J; Schwan, E V; Bodenstein, L L; Sommerville, J E M; van der Merwe, L L

    2011-06-01

    Several faecal examination techniques have shown variable sensitivity in demonstrating Spirocerca lupi (S. lupi) eggs. The objective of this study was to determine which faecal examination technique, including a novel modified centrifugal flotation technique, was most sensitive to diagnose spirocercosis. Ten coproscopic examinations were performed on faeces collected from 33 dogs confirmed endoscopically to have spirocercosis. The tests included a direct faecal examination, a faecal sedimentation/flotation test, 4 direct faecal flotations and 4 modified faecal centrifugal flotations. These latter 2 flotation tests utilised 4 different faecal flotation solutions: NaNO3 (SG 1.22), MgSO4 (SG 1.29), ZnSO4 (SG 1.30) and sugar (SG 1.27). The sensitivity of the tests ranged between 42% and 67%, with the NaNO3 solution showing the highest sensitivity in both the direct and modified-centrifugal flotations. The modified NaNO3 centrifugal method ranked 1st with the highest mean egg count (45.24 +/- 83), and was superior (i.e. higher egg count) and significantly different (P < 0.05) compared with the routine saturated sugar, ZnSO4 and MgSO4 flotation methods. The routine NaNO3 flotation method was also superior and significantly different (P < 0.05) compared with the routine ZnSO4 and MgSO4 flotation methods. Fifteen per cent (n = 5) of dogs had neoplastic oesophageal nodules and a further 18% (n = 6) had both neoplastic and non-neoplastic nodules. S. lupi eggs were demonstrated in 40% of dogs with neoplastic nodules only and 72.9% of the dogs with non-neoplastic nodules. The mean egg count in the non-neoplastic group (61) was statistically greater (P = 0.02) than that of the neoplastic group (1). The results show that faecal examination using a NaNO3 solution is the most sensitive in the diagnosis of spirocercosis. The modified centrifugal flotation faecal method using this solution has the highest egg count. The study also found that dogs with neoplastic nodules shed

  4. High faecal glucocorticoid levels predict mortality in ring-tailed lemurs (Lemur catta)

    Science.gov (United States)

    Ethan Pride, R

    2005-01-01

    Glucocorticoid levels are commonly used as measures of stress in wild animal populations, but their relevance to individual fitness in a wild population has not been demonstrated. In this study I followed 93 ring-tailed lemurs (Lemur catta) at Berenty Reserve in Madagascar, collecting 1089 faecal samples from individually recognized animals, and recording their survival over a 2 year period. I evaluated faecal glucocorticoid levels as predictors of individual survival to the end of the study. Animals with high glucocorticoid levels had a significantly higher mortality rate. This result suggests that glucocorticoid measures can be useful predictors of individual survival probabilities in wild populations. The ‘stress landscape’ indicated by glucocorticoid patterns may approximate the fitness landscape to which animals adapt. PMID:17148128

  5. Level and transport pattern of faecal coliform bacteria from tropical urban catchments.

    Science.gov (United States)

    Chow, M F; Yusop, Z; Toriman, M E

    2013-01-01

    Urbanization and frequent storms play important roles in increasing faecal bacteria pollution, especially for tropical urban catchments. However, only little information on the faecal bacteria levels from different land use types and the factors that influence bacteria concentrations is available. Thus, the objectives of this study were to quantify the levels and transport mechanism of faecal coliforms (FCs) from residential and commercial catchments. Stormwaters were sampled and the runoff flow rates were measured from both catchments during four storm events in Skudai, Malaysia. The samples were then analysed for FC, biochemical oxygen demand (BOD5), chemical oxygen demand (COD), total suspended solids (TSS) and ammoniacal-nitrogen (NH3-N) concentrations. Intra-storm and inter-storm characteristics of FC bacteria were investigated in order to identify the level and transport pattern of FC. The commercial catchment showed significantly higher event mean concentration (EMC) of FC than the residential catchment. For the residential catchment, the highest bacterial concentrations occurred during the early part of stormwater runoff with peak concentrations usually preceding the peak flow. First flush effect was more prevalent at the residential catchment.

  6. Coprophilic amoebae and flagellates, including Guttulinopsis, Rosculus and Helkesimastix, characterise a divergent and diverse rhizarian radiation and contribute to a large diversity of faecal-associated protists.

    Science.gov (United States)

    Bass, David; Silberman, Jeffrey D; Brown, Matthew W; Pearce, Rebecca A; Tice, Alexander K; Jousset, Alexandre; Geisen, Stefan; Hartikainen, Hanna

    2016-05-01

    A wide diversity of organisms utilize faecal habitats as a rich nutrient source or a mechanism to traverse through animal hosts. We sequenced the 18S rRNA genes of the coprophilic, fruiting body-forming amoeba Guttulinopsis vulgaris and its non-fruiting relatives Rosculus 'ithacus' CCAP 1571/3, R. terrestris n. sp. and R. elongata n. sp. and demonstrate that they are related to the coprophilic flagellate Helkesimastix in a strongly supported, but highly divergent 18S sister clade. PCR primers specific to both clades were used to generate 18S amplicons from a range of environmental and faecal DNA samples. Phylogenetic analysis of the cloned sequences demonstrated a high diversity of uncharacterised sequence types within this clade, likely representing previously described members of the genera Guttulinopsis, Rosculus and Helkesimastix, as well as so-far unobserved organisms. Further, an Illumina MiSeq sequenced set of 18S V4-region amplicons generated from faecal DNAs using universal eukaryote primers showed that core-cercozoan assemblages in faecal samples are as diverse as those found in more conventionally examined habitats. These results reveal many novel lineages, some of which appear to occur preferentially in faecal material, in particular cercomonads and glissomonads. More broadly, we show that faecal habitats are likely untapped reservoirs of microbial eukaryotic diversity.

  7. 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.

  8. [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

  9. Comparação de duas técnicas de isolamento do Mycobacterium avium subsp. paratuberculosis em amostras de fezes de ovinos com suspeita clínica de paratuberculose Comparison of two techniques of isolation of Mycobacterium avium subsp. paratuberculosis in faecal samples of ovine with clinical suspicion of paratuberculosis

    Directory of Open Access Journals (Sweden)

    Ana Cláudia Coelho

    2009-05-01

    . Culture was positive in 2.0% of faecal samples. Isolation was obtained using Löwenstein Jensen® with mycobactin® J, and the Middlebrook® 7H11 with OADC®. The Löwenstein Jensen® with mycobactin® J was that provided highest amount of isolations. The percentages of isolation in each culture media were 2.0% (6/300 to Löwenstein Jensen® with micobactina J, and 1.0% (3/300 to Middlebrook® 7H11/OADC. The three positive samples in Middlebrook® 7H11/OADC were also positive in Löwenstein Jensen® with micobactina J. In the Middlebrook® 7H11/OADC alone there was no sample growth. The results of this study suggest that culture media of Löwenstein-Jensen® with micobactina® J is more effective for the isolation of sheep strains in Portugal.

  10. Faecal incontinence: Current knowledges and perspectives

    Institute of Scientific and Technical Information of China (English)

    2016-01-01

    Faecal incontinence (FI) is a disabling and frequentsymptom since its prevalence can vary between 5%and 15% of the general population. It has a particularnegative impact on quality of life. Many tools arecurrently available for the treatment of FI, from conservativemeasures to invasive surgical treatments. Theconservative treatment may be dietetic measures,various pharmacological agents, anorectal rehabilitation,posterior tibial nerve stimulation, and transanal irrigation.If needed, patients may have miniinvasive approachessuch as sacral nerve modulation or antegrade irrigation.In some cases, a surgical treatment is proposed, mainlyexternal anal sphincter repair. Although these differenttherapeutic options are available, new techniques arearriving allowing new hopes for the patients. Moreover,most of them are non-invasive such as local applicationof an α1-adrenoceptor agonist, stem cell injections,rectal injection of botulinum toxin, acupuncture. Newmore invasive techniques with promising results arealso coming such as anal magnetic sphincter andantropylorus transposition. This review reports the maincurrent available treatments of FI and the developingtherapeutics tools.

  11. Faecal calprotectin: Management in inflammatory bowel disease

    Institute of Scientific and Technical Information of China (English)

    José; Manuel; Benítez; Valle; García-Sánchez

    2015-01-01

    Inflammatory bowel disease(IBD) is a chronic and relapsing disorder which leads to an inflammation of the gastrointestinal tract. A tailored therapy to achieve mucosal healing with the less adverse events has become a key issue in the management of IBD. In the past, the clinical remission was the most important factor to consider for adapting diagnostic procedures and therapeutic strategies. However, there is no a good correlation between symptoms and intestinal lesions, so currently the goals of treatment are to achieve not only the control of symptoms, but deep remission, which is related with a favourable prognosis. Thus, the determination of biological markers or biomarkers of intestinal inflammation play a crucial role. Many biomarkers have been extensively evaluated in IBD showing significant correlation with endoscopic lesions, risk of recurrence and response to treatment. One of the most important markers is faecal calprotectin(FC). Despite calprotectin limitations, this biomarker represents a reliable and noninvasive alternative to reduce the need for endoscopic procedures. FC has demonstrated its performance for regular monitoring of IBD patients, not only to the diagnosis for discriminating IBD from non-IBD diagnosis, but for assessing disease activity, relapse prediction and response to therapy. Although, FC provides better results than other biomarkers such as C-reactive protein and erythrocyte sedimentation rate, these surrogate markers of intestinal inflammation should not be used isolation but in combination with other clinical, endoscopic, radiological or/and histological parameters enabling a comprehensive assessment of IBD patients.

  12. Detection of parasitizing coccidia and determination of host crane species, sex and genotype by faecal DNA analysis.

    Science.gov (United States)

    Honma, H; Suyama, Y; Nakai, Y

    2011-11-01

    In Japan, the three main crane species are the endangered red-crowned crane (Grus japonensis) inhabiting Hokkaido, the northernmost island of Japan; the vulnerable hooded crane (Grus monacha); and the vulnerable white-naped crane (Grus vipio). Both the hooded and white-naped cranes migrate in winter to Izumi in Kyushu, the southern island of Japan. In this study, we investigated the cranes and their coccidian parasites, through a targeted molecular approach using faecal DNA to develop a noninvasive method for infectious disease research. To determine the origin of noninvasively collected faecal samples, host species were identified by sequencing a region of approximately 470 bp of the mitochondrial 16S ribosomal RNA gene in the faecal DNA. Furthermore, to avoid sample redundancy, individual determination was performed by fragment analysis using microsatellite and sex-linked markers. For microsatellite genotyping, previously reported markers and markers isolated in this study were examined, and seven loci for red-crowned cranes, eight for hooded cranes and six for white-naped cranes displayed polymorphisms. A low error rate was demonstrated by comparing microsatellite data generated from faecal DNA samples with that generated from feather DNA samples, indicating a high reliability. Polymerase chain reaction-based capillary electrophoresis (PCR-CE), employing genetic markers in the second internal transcribed spacer (ITS2) of nuclear ribosomal DNA, was employed to detect crane coccidia. The sensitivity of detection of PCR-CE using faecal DNA was inferior to that with traditional microscopy; however, our results suggest that PCR-CE can depict crane coccidia diversity with higher resolution and it is a useful tool to characterize community composition of coccidia in detail.

  13. Faecal carriage of ESBL-producing Enterobacteriaceae and carbapenem-resistant Gram-negative bacilli in community settings.

    Science.gov (United States)

    Villar, Hugo Edgardo; Baserni, Marisa Noemí; Jugo, Monica Beatriz

    2013-08-15

    The aim of this study was to determine the prevalence of intestinal carriage of extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae and carbapenem-resistant Gram-negative bacilli in the community in Buenos Aires, Argentina. Faecal samples from 164 non-hospitalized patients were cultured on CHROMagar KPC and CHROMagar ESBL plates. Isolates resistant to third-generation cephalosporins or carbapenems were selected for further study. The minimal inhibitory concentration (MIC) of the isolates was determined using the E-test method. The phenotypic detection of ESBLs and carbapenemases was performed using the double-disc synergy test. The rate of faecal carriage of Enterobacteriaceae resistant to third-generation cephalosporins was 26.8%. Escherichia coli represented a large majority (75%) of the isolates recovered. Thirty-three ESBL-producing isolates were detected from 31 faecal samples (18.9% of the collected specimens). Eight carbapenem-resistant Gram-negative bacilli were recovered from eight specimens (4.9%). This study revealed a high prevalence of faecal carriage of multidrug-resistant Gram-negative bacteria, including ESBLs, in Buenos Aires. Therefore, the use of surveillance cultures will be helpful for tracking and monitoring the spread of ESBL-producing Enterobacteriaceae within community settings.

  14. Temporal and farm-management-associated variation in faecal pat prevalence of Arcobacter spp. in ruminants.

    Science.gov (United States)

    Grove-White, D H; Leatherbarrow, A J H; Cripps, P J; Diggle, P J; French, N P

    2014-04-01

    In a 2-year longitudinal study of adult animals on 15 dairy farms and four sheep farms in Lancashire, UK, Arcobacter spp. were isolated from all farms although not at every sampling occasion. Faecal samples were collected and cultured using standard techniques for isolation of campylobacters. Assignment to species was via PCR assays. Apparent prevalence of Arcobacter spp. was higher in dairy cattle compared to sheep (40.1% vs. 8%, P Arcobacter spp. and Campylobacter jejuni although this may in part be an artefact of laboratory test method sensitivity, whereby a relative increase in the frequency of one bacterial species would reduce the sensitivity of detecting the other.

  15. Cost-effective screening of pooled faecal specimens from patients with nosocomial diarrhoea for Clostridium perfringens enterotoxin

    Directory of Open Access Journals (Sweden)

    C Vaishnavi

    2011-01-01

    Full Text Available Purpose: Clostridium perfringens is a significant cause of nosocomial AAD. The prevalence of C. perfringens enterotoxin (CPE-positive stool specimens in hospitalised patients is very low in the Indian setting making the diagnostics very expensive. Therefore, a cost-effective diagnostic approach to screen faecal specimens for CPE was devised. Materials and Methods: Faecal specimens from 540 hospitalised patients with various ailments and from 340 healthy subjects were investigated for CPE. An aliquot of pooled faecal supernatants was made by mixing 100 μl each of 10 specimens to be tested. Each aliquot was investigated for the presence of CPE by an enzyme immunoassay. A repetition of the assay was done with individual specimens of the pooled aliquots from each positive well as seen visually by colour development. Results: Of the 540 patient specimens tested, 405 (75% patients were on antibiotics, the predominant ones being cephalosporins, penicillin, quinolones, aminoglycosides, etc. During the time of sampling, diarrhoea was present in 481 (89%, abdomen pain in 203 (37.6% and fever in 242 (44.8% patients. C. perfringens enterotoxin was positive in nine wells of the 540 pooled test specimens whereas all of the pooled 340 control samples were negative. Repeat of individual specimens comprising the nine wells with positive samples helped to identify the individual patients positive for CPE. Conclusion: Only two CPE kits were needed for a total of 880 faecal specimens tested. The cost-effective diagnostic approach to screen faecal specimens for CPE, as described herein will help to save institutional resources.

  16. Hanging drop cultures of human testis and testis cancer samples

    DEFF Research Database (Denmark)

    Jørgensen, Anne; Young, J; Nielsen, J E

    2014-01-01

    limited by the lack of experimental models. The aim of this study was to establish an experimental tissue culture model to maintain normal and malignant germ cells within their niche and allow investigation of treatment effects. METHODS: Human testis and testis cancer specimens from orchidectomies were...

  17. Successful carnivore identification with faecal DNA across a fragmented Amazonian landscape.

    Science.gov (United States)

    Michalski, Fernanda; Valdez, Fernanda Pedone; Norris, Darren; Zieminski, Chris; Kashivakura, Cyntia Kayo; Trinca, Cristine S; Smith, Heath B; Vynne, Carly; Wasser, Samuel K; Metzger, Jean Paul; Eizirik, Eduardo

    2011-09-01

    The use of scat surveys to obtain DNA has been well documented in temperate areas, where DNA preservation may be more effective than in tropical forests. Samples obtained in the tropics are often exposed to high humidity, warm temperatures, frequent rain and intense sunlight, all of which can rapidly degrade DNA. Despite these potential problems, we demonstrate successful mtDNA amplification and sequencing for faeces of carnivores collected in tropical conditions and quantify how sample condition and environmental variables influence the success of PCR amplification and species identification. Additionally, the feasibility of genotyping nuclear microsatellites from jaguar (Panthera onca) faeces was investigated. From October 2007 to December 2008, 93 faecal samples were collected in the southern Brazilian Amazon. A total of eight carnivore species was successfully identified from 71% of all samples obtained. Information theoretic analysis revealed that the number of PCR attempts before a successful sequence was an important negative predictor across all three responses (success of species identification, success of species identification from the first sequence and PCR amplification success), whereas the relative importance of the other three predictors (sample condition, season and distance from forest edge) varied between the three responses. Nuclear microsatellite amplification from jaguar faeces had lower success rates (15-44%) compared with those of the mtDNA marker. Our results show that DNA obtained from faecal samples works efficiently for carnivore species identification in the Amazon forest and also shows potential for nuclear DNA analysis, thus providing a valuable tool for genetic, ecological and conservation studies.

  18. High-protein/high red meat and high-carbohydrate weight-loss diets do not differ in their effect on faecal water genotoxicity tested by use of the WIL2-NS cell line and with other biomarkers of bowel health.

    Science.gov (United States)

    Benassi-Evans, Bianca; Clifton, Peter; Noakes, Manny; Fenech, Michael

    2010-12-21

    The impact of popular weight-loss diets with different macronutrient profiles on bowel health in humans has not been previously assessed. The aim of this study was to investigate whether a high-protein/high red meat (HP) diet influences faecal water genotoxicity and other standard biomarkers of bowel health differently compared with a high-carbohydrate (HC) diet. Thirty-three male subjects were randomly assigned to a HP (35% protein, 40% carbohydrate) or HC (17% protein, 58% carbohydrate) isocaloric energy-restricted dietary intervention consisting of 12 weeks intensive weight loss followed by weight maintenance for up to 52 weeks. Faecal samples were collected at 0, 12 and 52 weeks. Faecal water genotoxicity was assessed in the WIL2-NS human B lymphoblastoid cell line by means of the cytokinesis-block micronucleus cytome assay. Average weight loss after 12 weeks was 9.3 ± 0.7kg for both diets, with no further change in weight at 52 weeks. Two-way ANOVA showed a significant effect with time (Pacid excretion, phenol or p-cresol. Results suggest that HP and HC weight-loss diets may modify the carcinogenic profile of the bowel contents such that weight loss may exert a beneficial effect by reducing genotoxic load in the short term; however, these results require verification against a non-weight-loss control. 2010 Elsevier B.V. All rights reserved.

  19. Longitudinal prevalence, faecal shedding and molecular characterisation of Campylobacter spp. and Salmonella enterica in sheep.

    Science.gov (United States)

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

    2014-11-01

    Faecal excretion of Campylobacter spp. and Salmonella enterica in sheep in Australia was determined using a quantitative multiplex PCR (qPCR) targeting the Campylobacter spp. purine biosynthesis gene (PurA) and the S. enterica outer membrane protein (ompF). The mutiplex qPCR was specific and Campylobacter spp. and S. enterica were each detected with a sensitivity of 5 organisms/µL faecal DNA extract. This multiplex qPCR was used to determine the prevalence and concentration of Campylobacter spp. and S. enterica in 3412 faecal samples collected from 1189 lambs on eight farms across South Australia (n = 2 farms), New South Wales (n = 1), Victoria (n = 2) and Western Australia (n = 3) at three sampling periods (weaning, post-weaning and pre-slaughter). The overall prevalences of Campylobacter spp. and S. enterica were 13.3% and 5.0%, respectively, with the highest prevalence for Campylobacter spp. in South Australia and the highest prevalence for S. enterica in New South Wales. Campylobacter jejuni was the only Campylobacter sp. identified from a subset of 120 positive samples sequenced at the 16S locus. S. enterica serovar Typhimurium was the only serovar of S. enterica identified from a subset of 120 positive samples sequenced at the ompF locus. Across all states, Campylobacter spp. had the highest median bacterial concentration in faeces at weaning and post-weaning (medians of 3.4 × 10(6) and 1.1 × 10(5), respectively), whereas S. enterica had the highest median bacterial concentration at pre-slaughter (1.8 × 10(5)/g faeces).

  20. Characterizing healthy samples for studies of human cognitive aging

    OpenAIRE

    Geldmacher, David S.; Levin, Bonnie E.; Wright, Clinton B.

    2012-01-01

    Characterizing the cognitive declines associated with aging, and differentiating them from the effects of disease in older adults, are important goals for human neuroscience researchers. This is also an issue of public health urgency in countries with rapidly aging populations. Progress toward understanding cognitive aging is complicated by numerous factors. Researchers interested in cognitive changes in healthy older adults need to consider these complexities when they design and interpre...

  1. Effects of dietary bran and the colon carcinogen 1,2-dimethylhydrazine on faecal. beta. -glucuronidase activity in mice

    Energy Technology Data Exchange (ETDEWEB)

    London, J.F.; Clapp, N.K.; Henke, M.A.

    1981-01-01

    To evaluate the physiological changes that might provide either mechanistic or prognostic information in colon carcinogenesis, we treated 8-wk-old male BALB/c mice with semisynthetic bran diets containing 20% by weight of either soya bean, winter wheat, or corn bran and gave ten weekly injections (from age 11 to 21 wk) of 20 mg 1,2-dimethylhydrazine (DMH)/kg body weight. Appropriate controls were included. Faecal samples were collected 11 to 13 wk after completion of DMH treatment and after 24 to 26 wk of continuous bran diet feeding. Daily faecal ..beta..-glucuronidase activity fluctuations were observed, but these were not statistically significant. Faecal enzyme activity varied depending upon the type of bran diet (control > wheat > soya bean > corn). DMH generally depressed faecal enzyme activity to a statistically significant degree (P < 0.03). These results demonstrate the persistent enzyme alterations produced by DMH and the assay's sensitivity for detecting such change. Further, the effects of diet suggest that dietary brans cause physiological changes that have the potential to modify colon carcinogenesis.

  2. 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.

  3. The design and initial patient evaluation of an integrated care pathway for faecal incontinence: a qualitative study.

    Science.gov (United States)

    Rimmer, Craig John; Gill, Kathryn Ann; Greenfield, Sheila; Dowswell, George

    2015-10-01

    condition may have led to potential bias when discussing their beliefs or experiences. As with most qualitative studies, our aim was to identify a range of experiences rather than define our participant sample as being representative. Our participant sample was diverse in the key characteristics but a longitudinal study may reveal further important aspects of an ICP for FI. An integrated care pathway for faecal incontinence appears to have potential to address the long-standing service delivery issues that have blighted continence services historically.

  4. 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.

  5. influence of sampling depth and post-sampling analysis time on the ...

    African Journals Online (AJOL)

    coliform bacteria were significantly higher in the 3 m water depth samples than in the surface water samples ... of total or faecal coliforms with potential pathogenic Vibrio groups. ... Paradise is released directly to the ocean at this point.

  6. 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

  7. A SYBR(®) Green-based real-time PCR method for improved detection of mcr-1-mediated colistin resistance in human stool samples.

    Science.gov (United States)

    Donà, Valentina; Bernasconi, Odette J; Kasraian, Sara; Tinguely, Regula; Endimiani, Andrea

    2017-06-01

    The aim of this study was to design a rapid and sensitive real-time PCR (rt-PCR) method for colistin resistance mcr-1 gene detection in human faecal samples. Stools (n=88) from 36 volunteers were analysed. To isolate mcr-1-producing Enterobacteriaceae, samples were enriched overnight in Luria-Bertani (LB) broth containing 2mg/L colistin and were then plated on selective agar plates with 4mg/L colistin. A SYBR(®) Green-based rt-PCR targeting mcr-1 was then designed. For method validation and to establish the limit of detection (LOD), total DNA was extracted from mcr-1-negative and mcr-1-positive Escherichia coli. rt-PCR was also performed with DNA extracted from 88 native stools and after enriching them in LB broth containing colistin. Based on the culture approach, three unique volunteers resulted colonised with mcr-1-harboring E. coli strains. For culture isolates, rt-PCR exhibited a LOD of 10 genomic copies/reaction, with both sensitivity and specificity of 100%. Nevertheless, when testing native stools, only two of the three mcr-1-positive specimens were detected. However, after enrichment in LB broth containing colistin, the rt-PCR was strongly positive for all culture-positive samples. The average cycle threshold was 22, granting rapid and confident detection of positive specimens within 30 cycles. No false positives were observed for the remaining 85 culture-negative specimens. A rapid rt-PCR for detection of mcr-1 from stool specimens was developed. The detection rate was increased by testing selective broth enrichments. This approach also has the advantage of concomitant isolation of mcr-1-harboring strains for further antimicrobial susceptibility and genetic testing. Copyright © 2017 International Society for Chemotherapy of Infection and Cancer. Published by Elsevier Ltd. All rights reserved.

  8. Sampling Based Trajectory Planning for Robots in Dynamic Human Environments

    DEFF Research Database (Denmark)

    Svenstrup, Mikael

    2010-01-01

    Open-ended human environments, such as pedestrian streets, hospital corridors, train stations etc., are places where robots start to emerge. Hence, being able to plan safe and natural trajectories in these dynamic environments is an important skill for future generations of robots. In this work...... method for selecting the best trajectory in the RRT, according to the cost of traversing a potential field. Furthermore the RRT expansion is enhanced to direct the search and account for the kinodynamic robot constraints. A model predictive control (MPC) approach is taken to accommodate...

  9. Sampling

    CERN Document Server

    Thompson, Steven K

    2012-01-01

    Praise for the Second Edition "This book has never had a competitor. It is the only book that takes a broad approach to sampling . . . any good personal statistics library should include a copy of this book." —Technometrics "Well-written . . . an excellent book on an important subject. Highly recommended." —Choice "An ideal reference for scientific researchers and other professionals who use sampling." —Zentralblatt Math Features new developments in the field combined with all aspects of obtaining, interpreting, and using sample data Sampling provides an up-to-date treat

  10. [Analysis of human tissue samples for volatile fire accelerants].

    Science.gov (United States)

    Treibs, Rudolf

    2014-01-01

    In police investigations of fires, the cause of a fire and the fire debris analysis regarding traces of fire accelerants are important aspects for forensic scientists. Established analytical procedures were recently applied to the remains of fire victims. When examining lung tissue samples, vapors inhaled from volatile ignitable liquids could be identified and differentiated from products of pyrolysis caused by the fire. In addition to the medico-legal results this evidence allowed to draw conclusions as to whether the fire victim was still alive when the fire started.

  11. 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...

  12. 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...

  13. Analysis of repeated tests for interferon-gamma (IFN-gamma) response and faecal excretion for diagnosis of subclinical paratuberculosis in Danish cattle

    DEFF Research Database (Denmark)

    Huda, A.; Lind, Peter; Christoffersen, Anna-Bodil;

    2003-01-01

    A total of 315 cattle were tested for infection with Mycobacterium avium subsp. paratuberculosis (M. paratuberculosis) at three consecutive samplings, using the interferon-gamma (IFN-gamma) test on whole blood and bacteriological culture of faecal samples. Of 205 cattle from 10 infected herds 99...

  14. Vegetable dietary fibres made with minimal processing improve health-related faecal parameters in a valid rat model.

    Science.gov (United States)

    Monro, John; Mishra, Suman; Redman, Claire; Somerfield, Sheryl; Ng, Jovyn

    2016-06-15

    Dietary fibre-induced faecal bulking and hydration are important contributors to large bowel function and health, and are affected by the dietary fibre structure. To determine faecal bulk-related parameters for vegetable dietary fibres with retained structure, cold water fragmentation of vegetables was used to make minimally processed vegetable fibres (MPVF) from swede, broccoli and asparagus. A valid adult rat model was used to subject the fibres to processes of hind gut fermentation and faecal accumulation similar to those in humans. All the MPVFs had high faecal bulking indexes (FBIs, mean ± sem: wheat bran (reference), 100 ± 6.0; asparagus 168 ± 5.7; swede 135 ± 6.1; broccoli 135 ± 5.9; broccoli rind 205 ± 10.4), and caused large increases in the theoretical colonic water load at 10 g per 100 g diet (increase over baseline (%): wheat bran, 137 ± 8.3; asparagus, 236 ± 25, swede 193 ± 8.8; broccoli 228 ± 12; broccoli rind 223 ± 8.5). Faecal bulking by MPVFs was much greater than by fermentable extracted polysaccharides such as pectin and raftilose, or by commercial fibres made from highly processed cell walls. The results show natural, non-degraded vegetable fibres with retained botanical structure have beneficial effects not provided by structure-less fermentable dietary fibres. Dietary fibre-deficient diets supplemented with prebiotics cannot, therefore, adequately substitute for varied diets containing adequate vegetables, fruits and wholegrain cereals in which fermentation is associated with enough retained structure to conserve physicochemical properties of benefit to colonic function.

  15. Bacteriophages and genetic mobilization in sewage and faecally polluted environments

    Science.gov (United States)

    Muniesa, Maite; Imamovic, Lejla; Jofre, Juan

    2011-01-01

    Summary Bacteriophages are one of the most abundant entities on the planet and are present in high concentrations within humans and animals, mostly in the gut. Phages that infect intestinal bacteria are released by defecation and remain free in extra‐intestinal environments, where they usually persist for longer than their bacterial hosts. Recent studies indicate that a large amount of the genetic information in bacterial genomes and in natural environments is of phage origin. In addition, metagenomic analysis reveals that a substantial number of bacterial genes are present in viral DNA in different environments. These facts support the belief that phages can play a significant role in horizontal gene transfer between bacteria. Bacteriophages are known to transfer genes by generalized and specialized transduction and indeed there are some examples of phages found in the environment carrying and transducing genes of bacterial origin. A successful transduction in the environment requires certain conditions, e.g. phage and bacterial numbers need to exceed certain threshold concentrations, the bacteria need to exist in an infection‐competent physiological state, and lastly, the physical conditions in the environment (pH, temperature, etc. of the supporting matrix) have to be suitable for phage infection. All three factors are reviewed here, and the available information suggests: (i) that the number of intestinal bacteria and phages in faecally contaminated environments guarantees bacteria–phage encounters, (ii) that transduction to intestinal bacteria in the environment is probable, and (iii) that transduction is more frequent than previously thought. Therefore, we suggest that phage‐mediated horizontal transfer between intestinal bacteria, or between intestinal and autochthonous bacteria in extra‐intestinal environments, might take place and that its relevance for the emergence of new bacterial strains and potential pathogens should not be ignored. PMID

  16. Bacteriophages and genetic mobilization in sewage and faecally polluted environments.

    Science.gov (United States)

    Muniesa, Maite; Imamovic, Lejla; Jofre, Juan

    2011-11-01

    Bacteriophages are one of the most abundant entities on the planet and are present in high concentrations within humans and animals, mostly in the gut. Phages that infect intestinal bacteria are released by defecation and remain free in extra-intestinal environments, where they usually persist for longer than their bacterial hosts. Recent studies indicate that a large amount of the genetic information in bacterial genomes and in natural environments is of phage origin. In addition, metagenomic analysis reveals that a substantial number of bacterial genes are present in viral DNA in different environments. These facts support the belief that phages can play a significant role in horizontal gene transfer between bacteria. Bacteriophages are known to transfer genes by generalized and specialized transduction and indeed there are some examples of phages found in the environment carrying and transducing genes of bacterial origin. A successful transduction in the environment requires certain conditions, e.g. phage and bacterial numbers need to exceed certain threshold concentrations, the bacteria need to exist in an infection-competent physiological state, and lastly, the physical conditions in the environment (pH, temperature, etc. of the supporting matrix) have to be suitable for phage infection. All three factors are reviewed here, and the available information suggests: (i) that the number of intestinal bacteria and phages in faecally contaminated environments guarantees bacteria-phage encounters, (ii) that transduction to intestinal bacteria in the environment is probable, and (iii) that transduction is more frequent than previously thought. Therefore, we suggest that phage-mediated horizontal transfer between intestinal bacteria, or between intestinal and autochthonous bacteria in extra-intestinal environments, might take place and that its relevance for the emergence of new bacterial strains and potential pathogens should not be ignored.

  17. Human papillomavirus self-sampling for screening nonattenders

    DEFF Research Database (Denmark)

    Lam, Janni Uyen Hoa; Rebolj, Matejka; Ejegod, Ditte Møller

    2017-01-01

    In organized cervical screening programs, typically 25% of the invited women do not attend. The Copenhagen Self-sampling Initiative (CSi) aimed to gain experiences on participation among screening nonattenders in the Capital Region of Denmark. Here, we report on the effectiveness of different...... region of Denmark were identified via the organized national invitation module. Screening history was obtained via the nationwide pathology registry. Twenty-four thousand women were invited, and as an alternative to the regular communication platforms (letter and phone), women could request a home test...... via a mobile-friendly webpage. Instruction material and video-animation in several languages were made available online. Chi-square test was used to test differences. Out of all invited, 31.7% requested a home test, and 20% returned it to the laboratory. In addition, 10% were screened at the physician...

  18. 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 food. Faecal DM excretion has a considerable impact on faecal Ca losses in a practical feeding situation. In conclusion, Ca requirements for maintenance may vary with food DM intake and digestibility.

  19. Reducing sample complexity of polyclonal human autoantibodies by chromatofocusing.

    Science.gov (United States)

    Hagemann, Sascha; Faude, Alexander; Rabenstein, Monika; Balzer-Geldsetzer, Monika; Nölker, Carmen; Bacher, Michael; Dodel, Richard

    2010-08-15

    Chromatofocusing was performed in order to separate a polyclonal antigen-specific mixture of human immunoglobulins (IgGs) that would then allow for further analyses of as few different IgGs as possible. Because polyclonal IgGs only differ by amino acid sequence and possible post-translational modifications but not by molecular weight, we chose chromatofocusing for protein separation by different isoelectric points. We isolated antigen-specific IgGs from commercially available intravenous immunoglobulins (IVIG) using a combination of affinity- and size exclusion-chromatography and in order to reduce the complexity of the starting material IVIG was then replaced by single-donor plasmapheresis material. Using two-dimensional gel electrophoresis (2-DE), we observed a clear decrease in the number of different light and heavy chains in the chromatofocusing peak as compared to the starting material. In parallel, we monitored slight problems with the selected peak in isoelectric focusing as the first dimension of 2-DE, displayed in by the less proper focusing of the spots. When we tested whether IgGs were binding to their specific antigen after chromatofocusing, we were able to show that they were still in native conformation. In conclusion, we showed that chromatofocusing can be used as a first step in the analysis of mixtures of very similar proteins, e.g. polyclonal IgG preparations, in order to minimize the amount of different proteins in separated fractions in a reproducible way. Copyright 2010 Elsevier B.V. All rights reserved.

  20. 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.

  1. Characterization of the Blastocystis-specific faecal IgA immune response in pigs.

    Science.gov (United States)

    Wang, W; Cuttell, L; Traub, R J; Owen, H; Bielefeldt-Ohmann, H

    2014-10-01

    Blastocystis is an intestinal protist found in many species including humans and pigs. It has a controversial pathogenesis and has been implicated as a potential cause of irritable bowel syndrome. Our previous studies identified pigs as potential animal models for blastocystosis by demonstrating that they were likely natural hosts of Blastocystis and can harbour subtypes (ST) in common with humans. Furthermore, our finding of a lack of intestinal histopathology associated with Blastocystis infection in pigs is also a consistent finding in examined infected humans. In this study, we aimed to identify and characterize the Blastocystis-specific mucosal IgA response in pigs by immunoblotting, using pig faecal antibodies and Blastocystis antigen. Faeces from 233 pigs representing three age groups (sows/boars, growers/weaners and piglets) and including five dexamethasone-immunosuppressed research pigs were tested. The majority (81·5%) of the pigs had faecal IgA reactivity against Blastocystis proteins of molecular weights of 17·5-120 kDa. Reactivity to a >250 kDa protein was found in 18·5% of pigs. Notably, immunosuppressed pigs and piglets were statistically more likely to have reactivity to this protein compared to growers/weaners and sows/boars, respectively. These results corroborate other findings suggesting that compromised immunity may predispose to blastocystosis and support our contention that pigs are potentially good models for pathogenesis studies. © 2014 John Wiley & Sons Ltd.

  2. Assessment of human exposure to airborne fungi in agricultural confinements: personal inhalable sampling versus stationary sampling.

    Science.gov (United States)

    Adhikari, Atin; Reponen, Tiina; Lee, Shu-An; Grinshpun, Sergey A

    2004-01-01

    Accurate exposure assessment to airborne fungi in agricultural environments is essential for estimating the associated occupational health hazards of workers. The objective of this pilot study was to compare personal and stationary sampling for assessing farmers' exposure to airborne fungi in 3 different agricultural confinements located in Ohio, USA (hog farm, dairy farm, and grain farm), using Button Personal Inhalable Samplers. Personal exposures were measured with samplers worn by 3 subjects (each carrying 2 samplers) during 3 types of activities, including animal feeding in the hog farm, cleaning and animal handling in the dairy farm, and soybean unloading and handling in the grain farm. Simultaneously, the stationary measurements were performed using 5 static Button Samplers and 1 revolving Button Sampler. The study showed that the total concentration of airborne fungi ranged from 1.4 x 10(4)-1.2 x 10(5) spores m(-3) in 3 confinements. Grain unloading and handling activity generated highest concentrations of airborne fungi compared to the other 2 activities. Prevalent airborne fungi belonged to Cladosporium, Aspergillus/Penicillium, Ascospores, smut spores, Epicoccum, Alternaria, and Basidiospores. Lower coefficients of variations were observed for the fungal concentrations measured by personal samplers (7-12%) compared to the concentrations measured by stationary samplers (27-37%). No statistically significant difference was observed between the stationary and personal measurement data for the total concentrations of airborne fungi (p > 0.05). Revolving stationary and static stationary Button Samplers demonstrated similar performance characteristics for the collection of airborne fungi. This reflects the low sensitivity of the sampler's efficiency to the wind speed and direction. The results indicate that personal exposure of agricultural workers in confinements may be adequately assessed by placing several Button Samplers simultaneously operating in a

  3. Antimicrobial resistance risk factors and characterisation of faecal E. coli isolated from healthy Labrador retrievers in the United Kingdom.

    Science.gov (United States)

    Schmidt, Vanessa M; Pinchbeck, Gina L; Nuttall, Tim; McEwan, Neil; Dawson, Susan; Williams, Nicola J

    2015-04-01

    Antimicrobial resistant bacteria are increasingly detected from canine samples but few studies have examined commensal isolates in healthy community dogs. We aimed to characterise faecal Escherichia coli from 73 healthy non-veterinarian-visiting and non-antimicrobial treated Labrador retrievers, recruited from dog shows in the North West United Kingdom between November 2010 and June 2011. Each enrolled dog provided one faecal sample for our study. E. coli were isolated from 72/73 (99%) faecal samples. Disc diffusion susceptibility tests were determined for a range of antimicrobials, including phenotypic extended-spectrum beta-lactamase (ESBL) and AmpC-production. PCR assay detected phylogenetic groups and resistance genes (blaCTX-M, blaSHV, blaTEM, blaOXA, blaCIT, qnr), and conjugation experiments were performed to investigate potential transfer of mobile genetic elements. Multivariable logistic regression examined potential risk factors from owner-questionnaires for the presence of antimicrobial resistant faecal E. coli. Antimicrobial resistant, multi-drug resistant (≥3 antimicrobial classes; MDR) and AmpC-producing E. coli were detected in 63%, 30% and 16% of samples, respectively. ESBL-producing E. coli was detected from only one sample and conjugation experiments found that blaCTX-M and blaCIT were transferred from commensal E. coli to a recipient strain. Most isolates were phylogenetic groups B1 and A. Group B2 isolates were associated with lower prevalence of resistance to at least one antimicrobial (PE. coli were surprisingly prevalent in this group of non-antimicrobial treated and non-veterinarian-visiting dogs and consumption of raw meat was a significant risk factor for antimicrobial resistance. These findings are of concern due to the increasing popularity of raw-meat canine diets, and the potential for opportunistic infection, zoonotic transmission and transmission of antimicrobial resistant determinants from commensal isolates to potential pathogenic

  4. 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.

  5. Preliminary monitoring of faecal indicator organisms of surface water ...

    African Journals Online (AJOL)

    Preliminary monitoring of faecal indicator organisms of surface water: A case study ... in Mvudi River used as a source of domestic water for people who live around it. ... of Water Affairs and Forestry of South Africa (DWAF) and the World Health ...

  6. Faecal Parasitology: Concentration Methodology Needs to be Better Standardised

    Science.gov (United States)

    Manser, Monika M.; Saez, Agatha Christie Santos; Chiodini, Peter L.

    2016-01-01

    Aim To determine whether variation in the preservative, pore size of the sieve, solvent, centrifugal force and centrifugation time used in the Ridley-Allen Concentration method for examining faecal specimens for parasite stages had any effect on their recovery in faecal specimens. Methods A questionnaire was sent to all participants in the UK NEQAS Faecal Parasitology Scheme. The recovery of parasite stages was compared using formalin diluted in water or formalin diluted in saline as the fixative, 3 different pore sizes of sieve, ether or ethyl acetate as a solvent, 7 different centrifugal forces and 6 different centrifugation times according to the methods described by participants completing the questionnaire. Results The number of parasite stages recovered was higher when formalin diluted in water was used as fixative, a smaller pore size of sieve was used, ethyl acetate along with Triton X 100 was used as a solvent and a centrifugal force of 3,000 rpm for 3 minutes were employed. Conclusions This study showed that differences in methodology at various stages of the concentration process affect the recovery of parasites from a faecal specimen and parasites present in small numbers could be missed if the recommended methodology is not followed. PMID:27073836

  7. Faecal Parasitology: Concentration Methodology Needs to be Better Standardised.

    Directory of Open Access Journals (Sweden)

    Monika M Manser

    2016-04-01

    Full Text Available To determine whether variation in the preservative, pore size of the sieve, solvent, centrifugal force and centrifugation time used in the Ridley-Allen Concentration method for examining faecal specimens for parasite stages had any effect on their recovery in faecal specimens.A questionnaire was sent to all participants in the UK NEQAS Faecal Parasitology Scheme. The recovery of parasite stages was compared using formalin diluted in water or formalin diluted in saline as the fixative, 3 different pore sizes of sieve, ether or ethyl acetate as a solvent, 7 different centrifugal forces and 6 different centrifugation times according to the methods described by participants completing the questionnaire.The number of parasite stages recovered was higher when formalin diluted in water was used as fixative, a smaller pore size of sieve was used, ethyl acetate along with Triton X 100 was used as a solvent and a centrifugal force of 3,000 rpm for 3 minutes were employed.This study showed that differences in methodology at various stages of the concentration process affect the recovery of parasites from a faecal specimen and parasites present in small numbers could be missed if the recommended methodology is not followed.

  8. Optimization of techniques for multiple platform testing in small, precious samples such as human chorionic villus sampling.

    Science.gov (United States)

    Pisarska, Margareta D; Akhlaghpour, Marzieh; Lee, Bora; Barlow, Gillian M; Xu, Ning; Wang, Erica T; Mackey, Aaron J; Farber, Charles R; Rich, Stephen S; Rotter, Jerome I; Chen, Yii-der I; Goodarzi, Mark O; Guller, Seth; Williams, John

    2016-11-01

    Multiple testing to understand global changes in gene expression based on genetic and epigenetic modifications is evolving. Chorionic villi, obtained for prenatal testing, is limited, but can be used to understand ongoing human pregnancies. However, optimal storage, processing and utilization of CVS for multiple platform testing have not been established. Leftover CVS samples were flash-frozen or preserved in RNAlater. Modifications to standard isolation kits were performed to isolate quality DNA and RNA from samples as small as 2-5 mg. RNAlater samples had significantly higher RNA yields and quality and were successfully used in microarray and RNA-sequencing (RNA-seq). RNA-seq libraries generated using 200 versus 800-ng RNA showed similar biological coefficients of variation. RNAlater samples had lower DNA yields and quality, which improved by heating the elution buffer to 70 °C. Purification of DNA was not necessary for bisulfite-conversion and genome-wide methylation profiling. CVS cells were propagated and continue to express genes found in freshly isolated chorionic villi. CVS samples preserved in RNAlater are superior. Our optimized techniques provide specimens for genetic, epigenetic and gene expression studies from a single small sample which can be used to develop diagnostics and treatments using a systems biology approach in the prenatal period. © 2016 John Wiley & Sons, Ltd. © 2016 John Wiley & Sons, Ltd.

  9. QMRAcatch - faecal microbial quality of water resources in a river-floodplain area affected by urban sources and recreational visitors

    Science.gov (United States)

    Derx, Julia; Schijven, Jack; Sommer, Regina; Kirschner, Alexander; Farnleitner, Andreas H.; Blaschke, Alfred Paul

    2016-04-01

    QMRAcatch, a tool to simulate microbial water quality including infection risk assessment, was previously developed and successfully tested at a Danube river site (Schijven et al. 2015). In the tool concentrations of target faecal microorganisms and viruses (TMVs) are computed at a point of interest (PI) along the main river and the floodplain river at daily intervals for a one year period. Even though faecal microbial pathogen concentrations in water resources are usually below the sample limit of detection, this does not ensure, that the water quality complies with a certain required health based target. The aim of this study was therefore to improve the predictability of relevant human pathogenic viruses, i.e. enterovirus and norovirus, in the studied river/floodplain area. This was done by following an innovative calibration strategy based on human-associated microbial source tracking (MST) marker data which were determined following the HF183 TaqMan assay (Green et al. 2011). The MST marker is strongly associated with human faeces and communal sewage, occurring there in numbers by several magnitudes higher than for human enteric pathogens (Mayer et al 2015). The calibrated tool was then evaluated with measured enterovirus concentrations at the PI and in the floodplain river. In the simulation tool the discharges of 5 wastewater treatment plants (WWTPs) were considered with point discharges along a 200 km reach of the Danube river. The MST marker and target virus concentrations at the PI at a certain day were computed based on the concentrations of the previous day, plus the wastewater concentrations times the WWTP discharge divided by the river discharge. A ratio of the river width was also considered, over which the MST marker and virus particles have fully mixed with river water. In the tool, the excrements from recreational visitors frequenting the floodplain area every day were assumed to be homogeneously distributed in the area. A binomial distributed

  10. Adaptation of faecal microbiota in sows after diet changes and consequences for in vitro fermentation capacity.

    Science.gov (United States)

    Sappok, M A; Peréz Gutiérrez, O; Smidt, H; Pellikaan, W F; Verstegen, M W A; Bosch, G; Hendriks, W H

    2015-09-01

    In vitro gas production studies are routinely used to assess the metabolic capacity of intestinal microbiota to ferment dietary fibre sources. The faecal inocula used during the in vitro gas production procedure are most often obtained from animals adapted to a certain diet. The present study was designed to assess whether 19 days of adaptation to a diet are sufficient for faecal inocula of pigs to reach a stable microbial composition and activity as determined by in vitro gas production. Eighteen multiparous sows were allotted to one of two treatments for three weeks: a diet high in fibre (H) or a diet low in fibre (L). After this 3-week period, the H group was transferred to the low fibre diet (HL-treatment) while the L group was transferred to the diet high in fibre (LH-treatment). Faecal samples were collected from each sow at 1, 4, 7, 10, 13, 16 and 19 days after the diet change and prepared as inoculum used for incubation with three contrasting fermentable substrates: oligofructose, soya pectin and cellulose. In addition, inocula were characterised using a phylogenetic microarray targeting the pig gastrointestinal tract microbiota. Time after diet change had an effect (Pmicrobiota and in composition of the microbiota over time. Adaptation of the microbiota as assessed by gas production occurred faster for LH-animals for fast fermentable substrates compared with HL-animals. Overall, adaptation of the large intestinal microbiota of sows as a result of ingestion of low and high fibre diets seems to take longer than 19 days, especially for the ability to ferment slowly fermentable substrates.

  11. 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.

  12. Effect of physical training on nutrient digestibility and faecal fermentative parameters in Standardbred horses.

    Science.gov (United States)

    Goachet, A G; Harris, P; Philippeau, C; Julliand, V

    2014-12-01

    This study aimed at evaluating, in previously inactive Standardbreds horses, the effect of 5 weeks of an exercise training programme on nutrient digestibility and faecal fermentative parameters (FFPs). As an increase in digestibility had previously been reported in trained endurance horses, we hypothesized that similar results would be found in horses being trained for other types of exercise on a different type of diet. After 3 weeks of dietary adaptation, a digestibility trial (DT1) was undertaken, over 3 days, in eight untrained Standardbreds with a fresh faecal sample being collected on the second day for FFP determinations. Six of the eight horses undertook a training programme, and after 5 weeks of exercise, the DT and the FFP measurements were then repeated (DT2). DT2 began after 3 days of inactivity. The same natural meadow hay (H) and pelleted complementary feed (CF) were fed throughout. For 5 days before the DTs, horses were fed 2.1% BW on a dry matter basis (55:45 ratio H:CF). Body weight and body condition score remained constant. Apparent digestibility of dry matter, organic matter, neutral detergent fibre, hemicellulose, crude protein and gross energy, as well as faecal total volatile fatty acids (VFA), acetate and propionate concentrations were significantly (p digestibility and FFP. Training may improve dietary energy supply, in particular via increased hindgut VFA production. The potential improvement of digestive efficiency with training should be taken into account when formulating nutritional recommendations for the exercising horse, particularly when performing light work, which is low-intensity exercise for 1-3 h per week.

  13. The effect of fermented liquid feeding on the faecal microbiology and colostrum quality of farrowing sows.

    Science.gov (United States)

    Demecková, V; Kelly, D; Coutts, A G P; Brooks, P H; Campbell, A

    2002-11-15

    This study investigated the effects of fermented liquid feed (FLF) on the lactic acid bacteria (LAB):Coliform (L:C) ratio in the faeces of farrowing sows and the quality of sow colostrum. Eighteen multiparous sows were randomly allocated to one of three dietary treatments for approximately 2 weeks prior to farrowing and for 3 weeks after parturition. The three dietary treatments were dry pelleted feed (DPF), nonfermented liquid feed (NFLF), and fermented liquid feed (FLF). A rifampicin-resistant mutant of Lactobacillus plantarum was used to ferment liquid feed. Coliforms and lactic acid bacteria (LAB) in the faeces of farrowing sows and piglets were estimated by standard microbiological techniques. Intestinal epithelial cells (IEC-6) and blood lymphocytes were used to evaluate the mitogenic activity of colostral samples taken at parturition. Results demonstrated that while the LAB population was not significantly affected by dietary treatment, significant differences in coliform population were observed in the sow faecal samples taken 7 days after parturition. Faeces excreted from sows fed FLF had significantly (P feed fed sows (53433 +/- 1568 and 1231 +/- 61.4 CPM, respectively). The combined effects of enhanced maternal/passive immunity and the reduction in the level of environmental contamination with faecal pathogens, achieved by FLF, may be important in achieving improved health status for both sows and piglets.

  14. Human DNA quantification and sample quality assessment: Developmental validation of the PowerQuant(®) system.

    Science.gov (United States)

    Ewing, Margaret M; Thompson, Jonelle M; McLaren, Robert S; Purpero, Vincent M; Thomas, Kelli J; Dobrowski, Patricia A; DeGroot, Gretchen A; Romsos, Erica L; Storts, Douglas R

    2016-07-01

    Quantification of the total amount of human DNA isolated from a forensic evidence item is crucial for DNA normalization prior to short tandem repeat (STR) DNA analysis and a federal quality assurance standard requirement. Previous commercial quantification methods determine the total human DNA and total human male DNA concentrations, but provide limited information about the condition of the DNA sample. The PowerQuant(®) System includes targets for quantification of total human and total human male DNA as well as targets for evaluating whether the human DNA is degraded and/or PCR inhibitors are present in the sample. A developmental validation of the PowerQuant(®) System was completed, following SWGDAM Validation Guidelines, to evaluate the assay's specificity, sensitivity, precision and accuracy, as well as the ability to detect degraded DNA or PCR inhibitors. In addition to the total human DNA and total human male DNA concentrations in a sample, data from the degradation target and internal PCR control (IPC) provide a forensic DNA analyst meaningful information about the quality of the isolated human DNA and the presence of PCR inhibitors in the sample that can be used to determine the most effective workflow and assist downstream interpretation.

  15. 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

  16. Bacteria-human somatic cell lateral gene transfer is enriched in cancer samples.

    Directory of Open Access Journals (Sweden)

    David R Riley

    Full Text Available There are 10× more bacterial cells in our bodies from the microbiome than human cells. Viral DNA is known to integrate in the human genome, but the integration of bacterial DNA has not been described. Using publicly available sequence data from the human genome project, the 1000 Genomes Project, and The Cancer Genome Atlas (TCGA, we examined bacterial DNA integration into the human somatic genome. Here we present evidence that bacterial DNA integrates into the human somatic genome through an RNA intermediate, and that such integrations are detected more frequently in (a tumors than normal samples, (b RNA than DNA samples, and (c the mitochondrial genome than the nuclear genome. Hundreds of thousands of paired reads support random integration of Acinetobacter-like DNA in the human mitochondrial genome in acute myeloid leukemia samples. Numerous read pairs across multiple stomach adenocarcinoma samples support specific integration of Pseudomonas-like DNA in the 5'-UTR and 3'-UTR of four proto-oncogenes that are up-regulated in their transcription, consistent with conversion to an oncogene. These data support our hypothesis that bacterial integrations occur in the human somatic genome and may play a role in carcinogenesis. We anticipate that the application of our approach to additional cancer genome projects will lead to the more frequent detection of bacterial DNA integrations in tumors that are in close proximity to the human microbiome.

  17. 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.

  18. 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.

  19. 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 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.

  20. Mitochondrial Respiration Chain Enzymatic Activities in the Human Brain: Methodological Implications for Tissue Sampling and Storage.

    Science.gov (United States)

    Ronsoni, Marcelo Fernando; Remor, Aline Pertile; Lopes, Mark William; Hohl, Alexandre; Troncoso, Iris H Z; Leal, Rodrigo Bainy; Boos, Gustavo Luchi; Kondageski, Charles; Nunes, Jean Costa; Linhares, Marcelo Neves; Lin, Kátia; Latini, Alexandra Susana; Walz, Roger

    2016-04-01

    Mitochondrial respiratory chain complexes enzymatic (MRCCE) activities were successfully evaluated in frozen brain samples. Epilepsy surgery offers an ethical opportunity to study human brain tissue surgically removed to treat drug resistant epilepsies. Epilepsy surgeries are done with hemodynamic and laboratory parameters to maintain physiology, but there are no studies analyzing the association among these parameters and MRCCE activities in the human brain tissue. We determined the intra-operative parameters independently associated with MRCCE activities in middle temporal neocortex (Cx), amygdala (AMY) and head of hippocampus (HIP) samples of patients (n = 23) who underwent temporal lobectomy using multiple linear regressions. MRCCE activities in Cx, AMY and HIP are differentially associated to trans-operative mean arterial blood pressure, O2 saturation, hemoglobin, and anesthesia duration to time of tissue sampling. The time-course between the last seizure occurrence and tissue sampling as well as the sample storage to biochemical assessments were also associated with enzyme activities. Linear regression models including these variables explain 13-17 % of MRCCE activities and show a moderate to strong effect (r = 0.37-0.82). Intraoperative hemodynamic and laboratory parameters as well as the time from last seizure to tissue sampling and storage time are associated with MRCCE activities in human samples from the Cx, AMYG and HIP. Careful control of these parameters is required to minimize confounding biases in studies using human brain samples collected from elective neurosurgery.

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

    Science.gov (United States)

    Hill, Cian J; Brown, Jillian R M; Lynch, Denise B; Jeffery, Ian B; Ryan, C Anthony; Ross, R Paul; Stanton, Catherine; O'Toole, Paul W

    2016-05-10

    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. Use of the storage vials increased the quality of extracted bacterial DNA by reduction of DNA shearing. When infant and elderly datasets were examined separately, no differences in microbiota composition were observed due to storage. When the two datasets were combined, there was a difference according to a Wilcoxon test in the relative proportions of Faecalibacterium, Sporobacter, Clostridium XVIII, and Clostridium XlVa after 1 week's storage compared to immediately extracted samples. After 2 weeks' storage, Bacteroides abundance was also significantly different, showing an apparent increase from week 1 to week 2. The microbiota composition of infant samples was more affected than that of elderly samples by storage, with significantly higher Spearman distances between paired freshly extracted and stored samples (p microbiota profiles were analysed at the operational taxonomic unit (OTU) level, three infant datasets in the study did not cluster together, while only one elderly dataset did not. The lower microbiota diversity of the infant gut microbiota compared to the elderly gut microbiota (p microbiota samples, but may be less appropriate for lower diversity samples. Differences between fresh and stored samples mean that where storage is

  2. A duplex PCR for rapid and simultaneous detection of Brucella spp. in human blood samples.

    Science.gov (United States)

    Mirnejad, Reza; Mohamadi, Mozafar; Piranfar, Vahbeh; Mortazavi, Seied Mojtaba; Kachuei, Reza

    2013-06-01

    To design a duplex PCR for rapid and simultaneous detection of Brucella species. in human blood samples. Fifty-two peripheral bloods samples were collected from suspicious patients with brucellosis. Following DNA extraction, PCR assay were performed, using three primers that could simultaneously identify and differentiate three major species of pathogenic Brucella in humans and animals. Of the 52 peripheral bloods samples tested, 25 sample (48%) showed positive reactions in PCR. Twelve samples were positive for Brucella abortus 39 (B. abortus 39) (23%), 13 for Brucella melitensis 39 (B. melitensis 39) (25%) and 0 for Brucella ovis 39 (B. ovis 39) (0%). This work demonstrates that in case where specific primers were utilized, duplex PCR has proved to be a simple, fast, and relatively inexpensive method for simultaneous detection of important species of Brucella in clinical samples. Copyright © 2013 Hainan Medical College. Published by Elsevier B.V. All rights reserved.

  3. A duplex PCR for the rapid and simultaneous detection of Brucella spp. in human blood samples

    Institute of Scientific and Technical Information of China (English)

    Reza Mirnejad; Mozafar mohamadi; Vahbeh Piranfar; Seied Mojtaba Mortazavi; Reza Kachuei

    2013-01-01

    Objective: To design a duplex PCR for rapid and simultaneous detection of Brucella species. in human blood samples. Methods: Fifty-two peripheral bloods samples were collected from suspicious patients with brucellosis. Following DNA extraction, PCR assay were performed, using three primers that could simultaneously identify and differentiate three major species of pathogenic Brucella in humans and animals. Results: Of the 52 peripheral bloods samples tested, 25 sample (48%) showed positive reactions in PCR. Twelve samples were positive for Brucella abortus (B. abortus) (23%), 13 for Brucella melitensis (B. melitensis) (25%) and 0 for Brucella ovis (B. ovis) (0%). Conclusions: This work de=monstrates that in case where specific primers were utilized, duplex PCR has proved to be a simple, fast, and relatively inexpensive method for simultaneous detection of important species of Brucella in clinical samples.

  4. Urinary, biliary and faecal excretion of rocuronium in humans

    NARCIS (Netherlands)

    Proost, JH; Eriksson, LI; Mirakhur, RK; Wierda, JMKH

    2000-01-01

    The excretion of rocuronium and its potential metabolites was studied in 38 anaesthetized patients, ASA I-III and 21-69 yr old. Rocuronium bromide was administered as an i.v. bolus dose of 0.3 or 0.9 mg kg(-1). in Part A of the study, the excretion into urine and bile, and the liver content were stu

  5. Differential Decay of Human Faecal Bacteroides in Marine and Freshwater

    Science.gov (United States)

    Gene sequences from Bacteroides and relatives are being considered for the enumeration of aquatic fecal contamination and estimation of public health risk. To interpret these data, it is necessary to understand the decay of molecular and cultivated indicators and pathogens in en...

  6. Factors Involved in the In Vitro Fermentability of Short Carbohydrates in Static Faecal Batch Cultures

    Directory of Open Access Journals (Sweden)

    Eva Gietl

    2012-01-01

    Full Text Available In recent years, research has focused on the positive effects of prebiotics on intestinal health and gut microbiota. The relationship between their chemical structure and their fermentation pattern by human intestinal microbiota is still not well understood. The aim of this study was to improve understanding of this relationship and identify factors that may be used to design galactooligosaccharides that reach more distal regions than commercial prebiotics which mainly target the proximal colon. The following factors were investigated: monomer type, linkage, substitution, and degree of polymerisation. Total organic acid production from sugars by faecal bacteria was fitted to a model which allowed an estimate of the time when half of the maximal organic acid concentration was reached (T50 in static faecal batch cultures. The different factors can be grouped by their effectiveness at prolonging fermentation time as follows: substitution is most effective, with methylgalactose, β-galactose-pentaacetate, D-fucose, and galactitol fermented more slowly than D-galactose. Monomers and linkage also influence fermentation time, with L rhamnose, arabinose, melezitose, and xylose being fermented significantly slower than D-glucose (P<0.05, maltose, isomaltose, cellobiose, and gentiobiose showing that Glcα1-6Glc and Glcβ1-4Glc were utilised slowest. Chain length had the smallest effect on fermentation time.

  7. 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...

  8. Ecological impact of MCB3837 on the normal human microbiota.

    Science.gov (United States)

    Rashid, Mamun-Ur; Dalhoff, Axel; Bäckström, Tobias; Björkhem-Bergman, Linda; Panagiotidis, Georgios; Weintraub, Andrej; Nord, Carl Erik

    2014-08-01

    MCB3837 is a novel, water-soluble, injectable prodrug that is rapidly converted to the active substance MCB3681 in vivo following intravenous (i.v.) administration. Both MCB3837 and MCB3681 are oxazolidinone-quinolone hybrid molecules. The purpose of the present study was to investigate the effect of MCB3681 on the human skin, nose, oropharyngeal and intestinal microbiota following administration of MCB3837. Twelve healthy male subjects received i.v. MCB3837 (6 mg/kg body weight) once daily for 5 days. Skin, nose, saliva and faecal samples were collected on Day -1 (pre dose), during administration on Days 2 and 5, and post dose on Days 8, 12 and 19. Micro-organisms were identified to genus level. No measurable concentrations of MCB3681 were found in any saliva samples or in the faecal samples on Day -1. On Day 2, 10 volunteers had faecal MCB3681 concentrations between 16.5 mg/kg faeces and 275.1mg/kg faeces; no MCB3681 in faeces could be detected in two of the volunteers. On Day 5, all volunteers had faecal concentrations of MCB3681 ranging from 98.9 to 226.3 mg/kg. MCB3681 caused no ecological changes in the skin, nasal and oropharyngeal microbiota. The numbers of enterococci, bifidobacteria, lactobacilli and clostridia decreased in the intestinal microbiota during administration of the drug. Numbers of Escherichia coli, other enterobacteria and Candida were not affected during the study. There was no impact on the number of Bacteroides. The faecal microbiota was normalised on Day 19. No new colonising aerobic or anaerobic Gram-positive bacteria with MCB3681 minimum inhibitory concentrations of ≥4 mg/L were found. Copyright © 2014 Elsevier B.V. and the International Society of Chemotherapy. All rights reserved.

  9. Effect of isomalt consumption on faecal microflora and colonic metabolism in healthy volunteers.

    Science.gov (United States)

    Gostner, A; Blaut, M; Schäffer, V; Kozianowski, G; Theis, S; Klingeberg, M; Dombrowski, Y; Martin, D; Ehrhardt, S; Taras, D; Schwiertz, A; Kleessen, B; Lührs, H; Schauber, J; Dorbath, D; Menzel, T; Scheppach, W

    2006-01-01

    Due to its low digestibility in the small intestine, a major fraction of the polyol isomalt reaches the colon. However, little is known about effects on the intestinal microflora. During two 4-week periods in a double-blind, placebo-controlled, cross-over design, nineteen healthy volunteers consumed a controlled basal diet enriched with either 30 g isomalt or 30 g sucrose daily. Stools were collected at the end of each test phase and various microbiological and luminal markers were analysed. Fermentation characteristics of isomalt were also investigated in vitro. Microbiological analyses of faecal samples indicated a shift of the gut flora towards an increase of bifidobacteria following consumption of the isomalt diet compared with the sucrose diet (Pisomalt phase, the activity of bacterial beta-glucosidase decreased (Pisomalt (P=0.055). Faecal SCFA, lactate, bile acids, neutral sterols, N, NH3, phenol and p-cresol were not affected by isomalt consumption. In vitro, isomalt was metabolized in several bifidobacteria strains and yielded high butyrate concentrations. Isomalt, which is used widely as a low-glycaemic and low-energy sweetener, has to be considered a prebiotic carbohydrate that might contribute to a healthy luminal environment of the colonic mucosa.

  10. Characterization of faecal microbial communities of dairy cows fed diets containing ensiled Moringa oleifera fodder.

    Science.gov (United States)

    Sun, Jiajie; Zeng, Bin; Chen, Zujing; Yan, Shijuan; Huang, Wenjie; Sun, Baoli; He, Qian; Chen, Xiaoyang; Chen, Ting; Jiang, Qingyan; Xi, Qianyun; Zhang, Yongliang

    2017-01-30

    Moringa oleifera (M. oleifera) is a remarkable species with high nutritional value and good biomass production, which can be used as livestock fodder. In this study, we examined changes in the faecal microbiota of thirty dairy cows in response to alternative M. oleifera diets and their effects on nutrient digestion, milk traits and the faecal concentrations of short-chain fatty acids. No differences in milk yield and constituents were found between the control and the M. oleifera alternative groups. Cows fed M. oleifera silage had lower dry matter digestibility, as well as the propionate and isovalerate concentrations in M. oleifera treated group. Using 16S rDNA gene sequencing, 1,299,556 paired-end reads were obtained. Clustering analysis revealed 13 phyla and 93 genera across all samples. Firmicutes and Bacteroidetes were the co-dominant phyla. Ten taxa displayed a significant difference in response to the high M. oleifera diet. In addition, strong correlations between Akkermansia and Prevotella with milk yield and protein indicated that some bacterial groups could be used to improve milk traits. Our results provided an insight into the microbiome-associated responses to M. oleifera in livestock diets, and could aid the development of novel applications of M. oleifera.

  11. Characterization of faecal microbial communities of dairy cows fed diets containing ensiled Moringa oleifera fodder

    Science.gov (United States)

    Sun, Jiajie; Zeng, Bin; Chen, Zujing; Yan, Shijuan; Huang, Wenjie; Sun, Baoli; He, Qian; Chen, Xiaoyang; Chen, Ting; Jiang, Qingyan; Xi, Qianyun; Zhang, Yongliang

    2017-01-01

    Moringa oleifera (M. oleifera) is a remarkable species with high nutritional value and good biomass production, which can be used as livestock fodder. In this study, we examined changes in the faecal microbiota of thirty dairy cows in response to alternative M. oleifera diets and their effects on nutrient digestion, milk traits and the faecal concentrations of short-chain fatty acids. No differences in milk yield and constituents were found between the control and the M. oleifera alternative groups. Cows fed M. oleifera silage had lower dry matter digestibility, as well as the propionate and isovalerate concentrations in M. oleifera treated group. Using 16S rDNA gene sequencing, 1,299,556 paired-end reads were obtained. Clustering analysis revealed 13 phyla and 93 genera across all samples. Firmicutes and Bacteroidetes were the co-dominant phyla. Ten taxa displayed a significant difference in response to the high M. oleifera diet. In addition, strong correlations between Akkermansia and Prevotella with milk yield and protein indicated that some bacterial groups could be used to improve milk traits. Our results provided an insight into the microbiome-associated responses to M. oleifera in livestock diets, and could aid the development of novel applications of M. oleifera. PMID:28134261

  12. Faecal contamination of a municipal drinking water distribution system in association with Campylobacter jejuni infections.

    Science.gov (United States)

    Pitkänen, Tarja; Miettinen, Ilkka T; Nakari, Ulla-Maija; Takkinen, Johanna; Nieminen, Kalle; Siitonen, Anja; Kuusi, Markku; Holopainen, Arja; Hänninen, Marja-Liisa

    2008-09-01

    After heavy rains Campylobacter jejuni together with high counts of Escherichia coli, other coliforms and intestinal enterococci were detected from drinking water of a municipal distribution system in eastern Finland in August 2004. Three patients with a positive C. jejuni finding, who had drunk the contaminated water, were identified and interviewed. The pulsed-field gel electrophoresis (PFGE) genotypes from the patient samples were identical to some of the genotypes isolated from the water of the suspected contamination source. In addition, repetitive DNA element analysis (rep-PCR) revealed identical patterns of E. coli and other coliform isolates along the distribution line. Further on-site technical investigations revealed that one of the two rainwater gutters on the roof of the water storage tower had been in an incorrect position and rainwater had flushed a large amount of faecal material from wild birds into the drinking water. The findings required close co-operation between civil authorities, and application of cultivation and genotyping techniques strongly suggested that the municipal drinking water was the source of the infections. The faecal contamination associated with failures in cleaning and technical management stress the importance of instructions for waterworks personnel to perform maintenance work properly.

  13. Antibiotic-resistant commensal Escherichia coli in faecal droplets from bats and poultry in Nigeria

    Directory of Open Access Journals (Sweden)

    Anthonia Olufunke Oluduro

    2012-09-01

    Full Text Available The prevalence of antibiotic resistance and plasmid carriage among commensal faecal Escherichia coli isolates of bats, broilers and free-range chickens in Ile-Ife, Osun State, Nigeria was studied. A total of 125 E. coli isolates were recovered from the fresh faecal samples of bats, broilers and free-range chickens on eosin methylene blue agar plates and characterised using standard biochemical tests. The susceptibility of the isolates to antibiotics was performed using the disk diffusion method. All isolates developed resistance to antibiotics to varying degrees; resistance to augumentin, amoxicillin and tetracycline was significantly higher (p0.05 with the exception of ciprofloxacin, pefloxacin gentamicin and ofloxacin. A total of 90% of the bat isolates developed multiple antibiotic resistance with 28 multiple antibiotic resistance patterns. The free-range chicken and broiler isolates displayed 10 and 38 multiple antibiotic resistance patterns, respectively. Resistance was mostly plasmid-mediated with molecular weights ranging between 0.91 kb and 40.42 kb. Antibiotic resistance and plasmid carriage among the commensal E. coli isolates studied was relatively high and may be implicated in zoonotic infections.

  14. Faecal biomarkers of intestinal health and disease in children

    Directory of Open Access Journals (Sweden)

    Tamara ePang

    2014-01-01

    Full Text Available The identification of various faecal biomarkers has provided insight into the intestinal milieu. Most of these markers are associated with the innate immune system of the gut, apart from the more novel M2-pyruvate kinase (M2-PK. The innate immunity of the gut plays a role in maintaining a fine balance between tolerance to commensal bacteria and immune response to potential pathogens. It is a complex system, which comprises of multiple elements, including antimicrobial peptides (e.g. defensins, cathelicidins, lactoferrin and osteoprotegerin, inflammatory proteins (e.g. calprotectin and S100A12, and microbial products (e.g. short-chain fatty acids. Dysfunction of any component can lead to the development of intestinal disease, and different diseases have been associated with different faecal levels of these biomarkers. Stool quantification of these biomarkers therefore provides a non- invasive method that can assist in the assessment and diagnosis of various gastrointestinal conditions. This can potentially reduce the need for invasive procedures such as endoscopy. The abovementioned faecal biomarkers and their role in intestinal health and disease will be reviewed in this paper with a paediatric focus.

  15. Faecal calprotectin in the diagnosis of inflammatory bowel disease.

    Science.gov (United States)

    Burri, Emanuel; Beglinger, Christoph

    2011-01-01

    Suspicion of inflammatory bowel disease should be raised in any patient with chronic or recurrent abdominal pain and diarrhoea. However, symptoms of inflammatory bowel disease (IBD) overlap with functional gastrointestinal disorders and those patients may not need endoscopy. Currently, colonoscopy with multiple biopsies is considered the gold standard to establish the diagnosis of IBD. Unfortunately, patient selection for endoscopy based on symptoms is not reliable. The use of guidelines of appropriateness for endoscopy yields significantly more significant findings but the selection criteria suffer from low specificity. Calprotectin is a calcium binding protein of neutrophil granulocytes that correlates well with neutrophil infiltration of the intestinal mucosa when measured in faeces. In the last decade, a large body of evidence on the diagnostic value of faecal calprotectin has accumulated and measurement of calprotectin in faeces has been suggested as a surrogate marker of intestinal inflammation. Testing of faecal calprotectin has been highly useful to distinguish organic from functional intestinal disorders in patients with abdominal complaints. Additionally, faecal calprotectin has reliably identified colonic inflammation in patients with suspected IBD. The use of this inexpensive and widely available test in the evaluation and risk stratification in patients with abdominal complaints is likely to increase in the future.

  16. Isolation of Bacteroides from fish and human fecal samples for identification of unique molecular markers.

    Science.gov (United States)

    Kabiri, Leila; Alum, Absar; Rock, Channah; McLain, Jean E; Abbaszadegan, Morteza

    2013-12-01

    Bacteroides molecular markers have been used to identify human fecal contamination in natural waters, but recent work in our laboratory confirmed cross-amplification of several human-specific Bacteroides spp. assays with fecal DNA from fish. For identification of unique molecular markers, Bacteroides from human (n = 4) and fish (n = 7) fecal samples were cultured and their identities were further confirmed using Rapid ID 32A API strips. The 16S rDNA from multiple isolates from each sample was PCR amplified, cloned, and sequenced to identify unique markers for development of more stringent human-specific assays. In human feces, Bacteroides vulgatus was the dominant species (75% of isolates), whereas in tilapia feces, Bacteroides eggerthii was dominant (66%). Bacteroides from grass carp, channel catfish, and blue catfish may include Bacteroides uniformis, Bacteroides ovatus, or Bacteroides stercoris. Phylogenic analyses of the 16S rRNA gene sequences showed distinct Bacteroides groupings from each fish species, while human sequences clustered with known B. vulgatus. None of the fish isolates showed significant similarity to Bacteroides sequences currently deposited in NCBI (National Center for Biotechnology Information). This study expands the current sequence database of cultured fish Bacteroides. Such data are essential for identification of unique molecular markers in human Bacteroides that can be utilized in differentiating fish and human fecal contamination in water samples.

  17. Measurement of concentrations of Faecal Glucocorticoid Metabolites in free-ranging African Elephants within the Kruger National Park

    Directory of Open Access Journals (Sweden)

    Jozua J. Viljoen

    2008-05-01

    Full Text Available During the past several years, non-invasive monitoring of steroid metabolites in faeces of elephants has become an increasingly popular technique to generate more information about the causal relationship between hormones and behaviour in both living elephant species. This is important knowledge which can be used to optimise local conservation and wildlife management by finding new strategies for better elephant population management and control. In this context, however, information about an actual involvement of the hypothalamic-pituitary-adrenal axis during assumable stressful events is still limited, especially for wildlife populations. One difficulty in discovering such information is often the lack of reliable data for hormone baseline levels. Therefore, the aim of this study was to determine baseline concentrations of faecal glucocorticoid metabolites that could be expected within age classes and between seasons in African elephants (Loxodonta africana in the Kruger National Park (KNP . A total of 374 faecal samples were collected from randomly located family herds in the southern KNP between May 2002 and August 2005. The samples were analysed for immunoreactive concentrations of faecal glucocorticoid metabolites using a validated enzyme immunoassay for 3α,11oxo-cortisol metabolites(3α,11oxo-CM. All samples were grouped according to the estimated age class of the subject using a field method based on bolus diameter, and regarding the ecological season collected. No significant differences in faecal 3α,11oxo-CM concentrations were found across age classes (H3 = 7.54; p = 0.057, but the mean 3α,11oxo-CM concentration of samples collected in the dry season (n = 196 was significantly higher than in the wet season (n = 178 (u = 15206.50; p = 0.032, which indicates a possible physiological stress situation due to a decline in food quantity and quality. The information generated in this study represents a reliable data set for baseline

  18. 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

  19. Genotyping of cystic echinococcosis isolates from clinical samples of human and domestic animals

    Directory of Open Access Journals (Sweden)

    S.A. Fadhil

    2016-12-01

    Full Text Available Cystic hydatid disease is a cosmopolitan important disease in both human and animals. Many strains were investigated in this parasite. The aim of study was to characterize genotype variations of Echinococcus granulosus isolates collected from human and domestic animals in Al-Qadisiyah province/ Iraq based on sequencing of nad1 mitochondrial gene. Eighty hydatid cysts of human (12, sheep (15, cattle (36, and camels (17 were collected from hospital and slaughter house of the province, during October 2014 to June 2015; microscopic examination was made for cysts fluid to determine the fertility. DNAs extraction was done for each sample in addition to purify and concentrate of extracted DNA samples was performed to determine nad1 (400bp gene used conventional PCR method. Phylogenetic analysis was performed using NCBI-Blast Alignment identification and Unweighted Pair Group Method with Arithmetic Mean. Twenty five (10 from human and 5 from each studied animals samples were chosen due to their fertility and high DNA purity, in which three strains (genotypes were investigated including sheep strain (G1 40%, buffalo strain (G3 48% and camel strain (G6 12%, where human samples related to G1(20% and G3(80%; sheep samples related to G1(80% and G3(20%; cattle samples related to G1(60%, G3 (20% and G6 (20%; camels samples related to G1(20%, G3(40% and G6(40%. The dominant strain is a buffalo strain (G3; both of buffalo strain (G3 and sheep strain (G1 represented the actual source of human infection. There is no host specificity of detected genotypes.

  20. 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.

  1. Effect of high fibre diets formulated with different fibrous ingredients on performance, nutrient digestibility and faecal microbiota of weaned piglets.

    Science.gov (United States)

    Yu, Cangyou; Zhang, Shihai; Yang, Qing; Peng, Qian; Zhu, Jinlong; Zeng, Xiangfang; Qiao, Shiyan

    2016-08-01

    The aim of the experiment on 180 weaned piglets (8.9 kg body weight) was to investigate the influence of high fibre diets formulated with different fibrous ingredients on performance, nutrient digestibility, diarrhoea incidence and numbers of faecal microbiota. The dietary treatments included a Control diet and five high fibre diets formulated with different fibre sources including wheat bran, soybean hulls, naked oat hulls, palm kernel expeller and bamboo fibre. The high fibre diets averaged 14.6% neutral detergent fibre with different non-starch polysaccharides (NSP) components and were fed ad libitum for 28 d. Faecal samples were collected during the last 3 d of the experiment and the apparent total tract digestibility of nutrients and fibre components were determined. Pigs fed the Control and wheat bran diets had a higher (p ≤ 0.05) average daily gain (ADG) than pigs fed the palm kernel expeller and bamboo meal diets. The reduced ADG for pigs appeared to be related to reductions in the digestibility of gross energy and dry matter, respectively. The feed-to-gain ratio was significantly higher (p ≤ 0.05) for pigs fed the fibre diets. The digestibility of NSP components was different among the treatments. The diarrhoea incidence was not affected by treatments. The abundance of faecal bifidobacteria was significantly higher (p ≤ 0.05) for pigs fed the wheat bran diet than for pigs fed the bamboo meal diet. It was concluded that the diets formulated with different fibre sources when fed to weaned piglets have different effects on pig performance, nutrient digestibility and numbers of faecal microbiota. The wheat bran diet rich in arabinoxylans enabled a better performance than the other tested diets with fibre addition.

  2. 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.

  3. Short-chain fructo-oligosaccharides modulate intestinal microbiota and metabolic parameters of humanized gnotobiotic diet induced obesity mice.

    Science.gov (United States)

    Respondek, Frederique; Gerard, Philippe; Bossis, Mathilde; Boschat, Laura; Bruneau, Aurélia; Rabot, Sylvie; Wagner, Anne; Martin, Jean-Charles

    2013-01-01

    Prebiotic fibres like short-chain fructo-oligosaccharides (scFOS) are known to selectively modulate the composition of the intestinal microbiota and especially to stimulate Bifidobacteria. In parallel, the involvement of intestinal microbiota in host metabolic regulation has been recently highlighted. The objective of the study was to evaluate the effect of scFOS on the composition of the faecal microbiota and on metabolic parameters in an animal model of diet-induced obesity harbouring a human-type microbiota. Forty eight axenic C57BL/6J mice were inoculated with a sample of faecal human microbiota and randomly assigned to one of 3 diets for 7 weeks: a control diet, a high fat diet (HF, 60% of energy derived from fat)) or an isocaloric HF diet containing 10% of scFOS (HF-scFOS). Mice fed with the two HF gained at least 21% more weight than mice from the control group. Addition of scFOS partially abolished the deposition of fat mass but significantly increased the weight of the caecum. The analysis of the taxonomic composition of the faecal microbiota by FISH technique revealed that the addition of scFOS induced a significant increase of faecal Bifidobacteria and the Clostridium coccoides group whereas it decreased the Clostridium leptum group. In addition to modifying the composition of the faecal microbiota, scFOS most prominently affected the faecal metabolome (e.g. bile acids derivatives, hydroxyl monoenoic fatty acids) as well as urine, plasma hydrophilic and plasma lipid metabolomes. The increase in C. coccoides and the decrease in C. leptum, were highly correlated to these metabolic changes, including insulinaemia, as well as to the weight of the caecum (empty and full) but not the increase in Bifidobacteria. In conclusion scFOS induce profound metabolic changes by modulating the composition and the activity of the intestinal microbiota, that may partly explain their effect on the reduction of insulinaemia.

  4. Short-chain fructo-oligosaccharides modulate intestinal microbiota and metabolic parameters of humanized gnotobiotic diet induced obesity mice.

    Directory of Open Access Journals (Sweden)

    Frederique Respondek

    Full Text Available Prebiotic fibres like short-chain fructo-oligosaccharides (scFOS are known to selectively modulate the composition of the intestinal microbiota and especially to stimulate Bifidobacteria. In parallel, the involvement of intestinal microbiota in host metabolic regulation has been recently highlighted. The objective of the study was to evaluate the effect of scFOS on the composition of the faecal microbiota and on metabolic parameters in an animal model of diet-induced obesity harbouring a human-type microbiota. Forty eight axenic C57BL/6J mice were inoculated with a sample of faecal human microbiota and randomly assigned to one of 3 diets for 7 weeks: a control diet, a high fat diet (HF, 60% of energy derived from fat or an isocaloric HF diet containing 10% of scFOS (HF-scFOS. Mice fed with the two HF gained at least 21% more weight than mice from the control group. Addition of scFOS partially abolished the deposition of fat mass but significantly increased the weight of the caecum. The analysis of the taxonomic composition of the faecal microbiota by FISH technique revealed that the addition of scFOS induced a significant increase of faecal Bifidobacteria and the Clostridium coccoides group whereas it decreased the Clostridium leptum group. In addition to modifying the composition of the faecal microbiota, scFOS most prominently affected the faecal metabolome (e.g. bile acids derivatives, hydroxyl monoenoic fatty acids as well as urine, plasma hydrophilic and plasma lipid metabolomes. The increase in C. coccoides and the decrease in C. leptum, were highly correlated to these metabolic changes, including insulinaemia, as well as to the weight of the caecum (empty and full but not the increase in Bifidobacteria. In conclusion scFOS induce profound metabolic changes by modulating the composition and the activity of the intestinal microbiota, that may partly explain their effect on the reduction of insulinaemia.

  5. A Longitudinal Study of the Feline Faecal Microbiome Identifies Changes into Early Adulthood Irrespective of Sexual Development.

    Directory of Open Access Journals (Sweden)

    Oliver Deusch

    Full Text Available Companion animals provide an excellent model for studies of the gut microbiome because potential confounders such as diet and environment can be more readily controlled for than in humans. Additionally, domestic cats and dogs are typically neutered early in life, enabling an investigation into the potential effect of sex hormones on the microbiome. In a longitudinal study to investigate the potential effects of neutering, neutering age and gender on the gut microbiome during growth, the faeces of kittens (16 male, 14 female were sampled at 18, 30 and 42 weeks of age. DNA was shotgun sequenced on the Illumina platform and sequence reads were annotated for taxonomy and function by comparison to a database of protein coding genes. In a statistical analysis of diversity, taxonomy and functional potential of the microbiomes, age was identified as the only factor with significant associations. No significant effects were detected for gender, neutering, or age when neutered (19 or 31 weeks. At 18 weeks of age the microbiome was dominated by the genera Lactobacillus and Bifidobacterium (35% and 20% average abundance. Structural and functional diversity was significantly increased by week 30 but there was no further significant increase. At 42 weeks of age the most abundant genera were Bacteroides (16%, Prevotella (14% and Megasphaera (8%. Significant differences in functional potential included an enrichment for genes in energy metabolism (carbon metabolism and oxidative phosphorylation and depletion in cell motility (flagella and chemotaxis. We conclude that the feline faecal microbiome is predominantly determined by age when diet and environment are controlled for. We suggest this finding may also be informative for studies of the human microbiome, where control over such factors is usually limited.

  6. Biogas potential from anaerobic co-digestion of faecal sludge with food waste and garden waste

    Science.gov (United States)

    Afifah, Ukhtiy; Priadi, Cindy Rianti

    2017-03-01

    The limited faecal sludge management can be optimized by converting the sludge into biogas. This study purposed to optimize the biogas potential of faecal sludge with food waste and garden waste. The system using Anaerobic Co-digestion on the variation 25% and 50% concentration of faecal sludge based on Volatile Solids (VS). Inoculum used was cow's rumen. The study was operated using lab-scale batch reactor 51 L for 42 days. Biogas produced at 25% concentration of faecal sludge is 0,30 m3CH4/kg with 71,93% VS and 72,42% COD destruction. Meanwhile, at 50% concentration of faecal sludge produce 0,56 m3CH4/kg VS biogas with 92,43% VS and 87,55% COD destruction. This study concludes that biogas potential of 50% concentration greater than 25% concentration of faecal sludge.

  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. Determination of cadmium and lead in human biological samples by spectrometric techniques: a review.

    Science.gov (United States)

    Lemos, Valfredo Azevedo; de Carvalho, Anaildes Lago

    2010-12-01

    The analysis of human biological samples, such as blood, urine, nails, and hair, is generally used for the verification of human exposure to toxic metals. In this review, various spectrometric methods for the determination of cadmium and lead in biological samples are discussed and compared. Several spectrometric techniques are presented and discussed with respect to various characteristics such as sensitivity, selectivity, and cost. Special attention is drawn to the procedures for digestion prior to the determination of cadmium and lead in hair, nails, blood, and urine.

  9. Proteomic biomarker discovery in 1000 human plasma samples with mass spectrometry

    DEFF Research Database (Denmark)

    Cominetti, Ornella; Núñez Galindo, Antonio; Corthésy, John

    2016-01-01

    the quality of the MS data and provided descriptive statistics. The data set was interrogated for proteins with most stable expression levels in that set of plasma samples. We evaluated standard clinical variables that typically impact forthcoming results and assessed body mass index-associated and gender......-specific proteins at two time points. We demonstrate that analyzing a large number of human plasma samples for biomarker discovery with MS using isobaric tagging is feasible, providing robust and consistent biological results....

  10. Comparison of faecal microbial community of lantang, bama, erhualian, meishan, xiaomeishan, duroc, landrace, and yorkshire sows.

    Science.gov (United States)

    Yang, Lina; Bian, Gaorui; Su, Yong; Zhu, Weiyun

    2014-06-01

    The objective of this study was to investigate differences in the faecal microbial composition among Lantang, Bama, Erhualian, Meishan, Xiaomeishan, Duroc, Landrace, and Yorkshire sows and to explore the possible link of the pig breed with the gut microbial community. Among the sows, the Meishan, Landrace, Duroc, and Yorkshire sows were from the same breeding farm with the same feed. Fresh faeces were collected from three sows of each purebred breed for microbiota analysis and volatile fatty acid (VFA) determination. Denaturing gradient gel electrophoresis (DGGE) analysis revealed that samples from Bama, Erhualian, and Xiaomeishan sows, which from different farms, were generally grouped in one cluster, with similarity higher than 67.2%, and those from Duroc, Landrace, and Yorkshire sows were grouped in another cluster. Principal component analysis of the DGGE profile showed that samples from the foreign breeds and the samples from the Chinese indigenous breeds were scattered in two different groups, irrespective of the farm origin. Faecal VFA concentrations were significantly affected by the pig breed. The proportion of acetate was higher in the Bama sows than in the other breeds. The real-time PCR analysis showed that 16S rRNA gene copies of total bacteria, Firmicutes and Bacteroidetes were significantly higher in the Bama sows compared to Xiaomeishan and Duroc sows. Both Meishan and Erhualian sows had higher numbers of total bacteria, Firmicutes, Bacteroidetes and sulphate-reducing bacteria as compared to Duroc sows. The results suggest that the pig breed affects the composition of gut microbiota. The microbial composition is different with different breeds, especially between overseas breeds (lean type) and Chinese breeds (relatively obese type).

  11. Quantitative assessment of faecal shedding of β-lactam-resistant Escherichia coli and enterococci in dogs

    DEFF Research Database (Denmark)

    Gongora, Carmen Espinosa; Shah, Syed Qaswar Ali; Jessen, Lisbeth Rem

    2015-01-01

    Quantitative data on faecal shedding of antimicrobial resistant bacteria are crucial to assess the risk of transmission from dogs to other animals as well as humans. In this study we investigated prevalence and concentrations of β-lactam-resistant Escherichia coli and enterococci in the faeces...... of 108 dogs presenting at a veterinary hospital in Denmark. The dogs had not been treated with antimicrobials for 4 weeks prior to the study. Total E. coli and enterococci were quantified by counts on MacConkey and Slanetz-Bartley, respectively. Resistant E. coli and enterococci were counted on the same...... media containing relevant antibiotic concentrations, followed by species identification using MALDI-TOF. Ampicillin- and cefotaxime-resistant E. coli were detected in 40% and 8% of the dogs, respectively, whereas approximately 15% carried ampicillin-resistant enterococci, mainly Enterococcus faecium...

  12. Intestinal microbiota and faecal transplantation as treatment modality for insulin resistance and type 2 diabetes mellitus.

    Science.gov (United States)

    Udayappan, S D; Hartstra, A V; Dallinga-Thie, G M; Nieuwdorp, M

    2014-07-01

    The prevalence of obesity and diabetes mellitus type 2 is increasing rapidly around the globe. Recent insights have generated an entirely new perspective that the intestinal microbiota may play a significant role in the development of these metabolic disorders. Alterations in the intestinal microbiota composition promote systemic inflammation that is a hallmark of obesity and subsequent insulin resistance. Thus, it is important to understand the reciprocal relationship between intestinal microbiota composition and metabolic health in order to eventually prevent disease progression. In this respect, faecal transplantation studies have implicated that butyrate-producing intestinal bacteria are crucial in this process and be considered as key players in regulating diverse signalling cascades associated with human glucose and lipid metabolism.

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

    Directory of Open Access Journals (Sweden)

    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.

  14. Novel Bacteroides host strains for detection of human- and animal-specific bacteriophages in water.

    Science.gov (United States)

    Wicki, Melanie; Auckenthaler, Adrian; Felleisen, Richard; Tanner, Marcel; Baumgartner, Andreas

    2011-03-01

    Bacteriophages active against specific Bacteroides host strains were shown to be suitable for detection of human faecal pollution. However, the practical application of this finding is limited because some specific host strains were restricted to certain geographic regions. In this study, novel Bacteroides host strains were isolated that discriminate human and animal faecal pollution in Switzerland. Two strains specific for bacteriophages present in human faecal contamination and three strains specific for bacteriophages indicating animal faecal contamination were evaluated. Bacteriophages infecting human strains were exclusively found in human wastewater, whereas animal strains detected bacteriophages only in animal waste. The newly isolated host strains could be used to determine the source of surface and spring water faecal contamination in field situations. Applying the newly isolated host Bacteroides thetaiotaomicron ARABA 84 for detection of bacteriophages allowed the detection of human faecal contamination in spring water.

  15. China's human resources for maternal and child health: a national sampling survey.

    Science.gov (United States)

    Ren, Zhenghong; Song, Peige; Theodoratou, Evropi; Guo, Sufang; An, Lin

    2015-12-16

    In order to achieve the Millennium Development Goals (MDG) 4 and 5, the Chinese Government has invested greatly in improving maternal and child health (MCH) with impressive results. However, one of the most important barriers for further improvement is the uneven distribution of MCH human resources. There is little information about the distribution, quantity and capacity of the Chinese MCH human resources and we sought to investigate this. Cities at prefectural level were selected by random cluster sampling. All medical and health institutions providing MCH-related services in the sampled areas were investigated using a structured questionnaire. The data were weighted based on the proportion of the sampled districts/cities. Amount, proportions and numbers per 10,000 population of MCH human resources were estimated in order to reveal the quantity of the Chinese MCH human resources. The capacity of MCH human resources was evaluated by analyzing data on the education level and professional skills of the staff. There were 77,248 MCH workers in China in 2010. In general, 67.6% and 71.9% of the women's and children's health care professionals had an associate degree or higher, whereas around 30% had only high-school or lower degrees. More than 40% of the women's health workers were capable of providing skilled birth attendance, but these proportions varied between different institutions and locations. Evidence from this study highlights that Chinese MCH human resources are not in shortage in the national level. However, the quantity and capacity of MCH human resources are not evenly distributed among different institutions and locations. Finally there is a need in the improvement of the MCH services by improving the quality of MCH human resources.

  16. Efficient discrimination and removal of phospholipids during electromembrane extraction from human plasma samples

    DEFF Research Database (Denmark)

    Vårdal, Linda; Gjelstad, Astrid; Huang, Chuixiu

    2017-01-01

    AIM: For the first time, extracts obtained from human plasma samples by electromembrane extraction (EME) were investigated comprehensively with particular respect to phospholipids using ultra-high-performance liquid chromatography tandem mass spectrometry (UHPLC-MS/MS). Thhe purpose was to invest...

  17. Imitation of Tongue Protrusion in Human Neonates: Specificity of the Response in a Large Sample

    Science.gov (United States)

    Nagy, Emese; Pilling, Karen; Orvos, Hajnalka; Molnar, Peter

    2013-01-01

    Although a large body of evidence has accumulated on the young human infant's ability to imitate, the phenomenon has failed to gain unanimous acceptance. Imitation of tongue protrusion, the most tested gesture to date, was examined in a sample of 115 newborns in the first 5 days of life in 3 seating positions. An ethologically based…

  18. Analyses of human colonic mucus obtained by an in vivo sampling technique

    NARCIS (Netherlands)

    Hamer, H.M.; Jonkers, D.M.A.E.; Loof, A.; Houtvin, S.A.L.W. van; Troost, F.J.; Venema, K.; Kodde, A.; Koek, G.H.; Schipper, R.G.; Heerde, W.L. van; Brummer, R.J.

    2009-01-01

    Background: The mucus layer is an important dynamic component of the epithelial barrier. It contains mucin glycoproteins and other compounds secreted by the intestinal epithelium, such as secretory IgA. However, a standardized in vivo sampling technique of mucus in humans is not yet available. Aim:

  19. Groundwater sampling methods using glass wool filtration to trace human enteric viruses in Madison, Wisconsin

    Science.gov (United States)

    Human enteric viruses have been detected in the Madison, Wisconsin deep municipal well system. Earlier projects by the Wisconsin Geological and Natural History Survey (WGNHS) have used glass wool filters to sample groundwater for these viruses directly from the deep municipal wells. Polymerase chain...

  20. Elimination of bioweapons agents from forensic samples during extraction of human DNA.

    Science.gov (United States)

    Timbers, Jason; Wilkinson, Della; Hause, Christine C; Smith, Myron L; Zaidi, Mohsin A; Laframboise, Denis; Wright, Kathryn E

    2014-11-01

    Collection of DNA for genetic profiling is a powerful means for the identification of individuals responsible for crimes and terrorist acts. Biologic hazards, such as bacteria, endospores, toxins, and viruses, could contaminate sites of terrorist activities and thus could be present in samples collected for profiling. The fate of these hazards during DNA isolation has not been thoroughly examined. Our goals were to determine whether the DNA extraction process used by the Royal Canadian Mounted Police eliminates or neutralizes these agents and if not, to establish methods that render samples safe without compromising the human DNA. Our results show that bacteria, viruses, and toxins were reduced to undetectable levels during DNA extraction, but endospores remained viable. Filtration of samples after DNA isolation eliminated viable spores from the samples but left DNA intact. We also demonstrated that contamination of samples with some bacteria, endospores, and toxins for longer than 1 h compromised the ability to complete genetic profiling.

  1. Long-term performance and stability of molecular shotgun lipidomic analysis of human plasma samples.

    Science.gov (United States)

    Heiskanen, Laura A; Suoniemi, Matti; Ta, Hung Xuan; Tarasov, Kirill; Ekroos, Kim

    2013-09-17

    The stability of the lipid concentration levels in shotgun lipidomics analysis was tracked over a period of 3.5 years. Concentration levels in several lipid classes, such as phospholipids, were determined in human plasma lipid extracts. Impact of the following factors on the analysis was investigated: sample amount, internal standard amount, and sample dilution factor. Moreover, the reproducibility of lipid profiles obtained in both polarity modes was evaluated. Total number of samples analyzed was approximately 6800 and 7300 samples in negative and positive ion modes, respectively, out of which 610 and 639 instrument control samples were used in stability calculations. The assessed shotgun lipidomics approach showed to be remarkably robust and reproducible, requiring no batch corrections. Coefficients of variation (CVs) of lipid mean concentration measured with optimized analytical parameters were typically less than 15%. The high reproducibility indicated that no lipid degradation occurred during the monitored time period.

  2. A tool kit for quantifying eukaryotic rRNA gene sequences from human microbiome samples.

    Science.gov (United States)

    Dollive, Serena; Peterfreund, Gregory L; Sherrill-Mix, Scott; Bittinger, Kyle; Sinha, Rohini; Hoffmann, Christian; Nabel, Christopher S; Hill, David A; Artis, David; Bachman, Michael A; Custers-Allen, Rebecca; Grunberg, Stephanie; Wu, Gary D; Lewis, James D; Bushman, Frederic D

    2012-07-03

    Eukaryotic microorganisms are important but understudied components of the human microbiome. Here we present a pipeline for analysis of deep sequencing data on single cell eukaryotes. We designed a new 18S rRNA gene-specific PCR primer set and compared a published rRNA gene internal transcribed spacer (ITS) gene primer set. Amplicons were tested against 24 specimens from defined eukaryotes and eight well-characterized human stool samples. A software pipeline https://sourceforge.net/projects/brocc/ was developed for taxonomic attribution, validated against simulated data, and tested on pyrosequence data. This study provides a well-characterized tool kit for sequence-based enumeration of eukaryotic organisms in human microbiome samples.

  3. A human gut metaproteomic dataset from stool samples pretreated or not by differential centrifugation

    Directory of Open Access Journals (Sweden)

    Alessandro Tanca

    2015-09-01

    Full Text Available We present a human gut metaproteomic dataset deposited in the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD001573. Ten aliquots of a single stool sample collected from a healthy human volunteer were either pretreated by differential centrifugation (DC; N=5 or not centrifuged (NC; N=5. Protein extracts were then processed by filter-aided sample preparation, single-run liquid chromatography and high-resolution mass spectrometry, and peptide identification was carried out using Sequest-HT as search engine within the Proteome Discoverer informatic platform. The dataset described here is also related to the research article entitled “Enrichment or depletion? The impact of stool pretreatment on metaproteomic characterization of the human gut microbiota” published in Proteomics (Tanca et al., 2015, [1].

  4. Easily-handled method to isolate mesenchymal stem cells from coagulated human bone marrow samples

    Institute of Scientific and Technical Information of China (English)

    Heng-Xiang; Wang; Zhi-Yong; Li; Zhi-Kun; Guo; Zi-Kuan; Guo

    2015-01-01

    AIM:To establish an easily-handled method to isolate mesenchymal stem cells(MSCs) from coagulated human bone marrow samples. METHODS: Thrombin was added to aliquots of seven heparinized human bone marrow samples to mimic marrow coagulation. The clots were untreated,treated with urokinase or mechanically cut into pieces before culture for MSCs. The un-coagulated samples and the clots were also stored at 4 ℃ for 8 or 16 h before the treatment. The numbers of colony-forming unit-fibroblast(CFU-F) in the different samples were determined. The adherent cells from different groups were passaged and their surface profile was analyzed with flow cytometry. Their capacities of in vitro osteogenesis and adipogenesis were observed after the cells were exposed to specific inductive agents.RESULTS: The average CFU-F number of urokinasetreated samples(16.85 ± 11.77/106) was comparable to that of un-coagulated control samples(20.22 ± 10.65/106,P = 0.293),which was significantly higher than those of mechanically-cut clots(6.5 ± 5.32/106,P < 0.01) and untreated clots(1.95 ± 1.86/106,P < 0.01). The CFU-F numbers decreased after samples were stored,but those of control and urokinase-treated clots remained higher than the other two groups. Consistently,the numbers of the attached cells at passage 0 were higher in control and urokinase-treated clots than those of mechanically-cut clots and untreated clots.The attached cells were fibroblast-like in morphology and homogenously positive for CD44,CD73 and CD90,and negative for CD31 and CD45. Also,they could be induced to differentiate into osteoblasts and adipocytes in vitro. CONCLUSION: Urokinase pretreatment is an optimal strategy to isolate MSCs from human bone marrow samples that are poorly aspirated and clotted.

  5. Rigorous Training of Dogs Leads to High Accuracy in Human Scent Matching-To-Sample Performance.

    Directory of Open Access Journals (Sweden)

    Sophie Marchal

    Full Text Available Human scent identification is based on a matching-to-sample task in which trained dogs are required to compare a scent sample collected from an object found at a crime scene to that of a suspect. Based on dogs' greater olfactory ability to detect and process odours, this method has been used in forensic investigations to identify the odour of a suspect at a crime scene. The excellent reliability and reproducibility of the method largely depend on rigor in dog training. The present study describes the various steps of training that lead to high sensitivity scores, with dogs matching samples with 90% efficiency when the complexity of the scents presented during the task in the sample is similar to that presented in the in lineups, and specificity reaching a ceiling, with no false alarms in human scent matching-to-sample tasks. This high level of accuracy ensures reliable results in judicial human scent identification tests. Also, our data should convince law enforcement authorities to use these results as official forensic evidence when dogs are trained appropriately.

  6. Evaluation of radiometric faecal culture and direct PCR on pooled faeces for detection of Mycobacterium avium subsp. paratuberculosis in cattle.

    Science.gov (United States)

    Eamens, Graeme J; Whittington, Richard J; Turner, Mark J; Austin, Susan L; Fell, Shayne A; Marsh, Ian B

    2007-11-15

    Dilution rates for pooled faecal culture (PFC) and direct IS900 polymerase chain reaction (D-PCR) tests were evaluated on faecal samples from infected cows mixed with uninfected faeces in dilutions from 1 in 5 to 1 in 50. PFC was performed by radiometric culture, with confirmation by IS900 PCR and restriction endonuclease analysis (PCR/REA) on growth, and by mycobactin dependency testing on solid medium. Using 37 culture positive faecal samples from 12 subclinical cows, 83.8% and 94.6% of samples were confirmed positive in the PFC assay at dilutions of 1 in 50 and 1 in 30, respectively. Lower dilutions (1 in 5 to 1 in 20) provided only marginally better sensitivity, and confirmation of PFC growth by PCR/REA was significantly more sensitive than mycobactin dependency. D-PCR had significantly lower sensitivity than PFC confirmed by PCR/REA, with pools of 1 in 50, 30, 10 and 5 yielding positive results in 64.9%, 70.3%, 78.4% and 83.8% of samples, respectively. Cattle considered to be shedding 1.5 x 10(6) viable M. avium subsp. paratuberculosis (Map)/g faeces (on the basis of estimated losses in processing and growth rates in radiometric broth) were positive at dilutions up to 1 in 50 in the PFC and D-PCR. Those shedding 5 x 10(5) viable Map/g were positive in the PFC at dilutions up to 1 in 40, but required a 1 in 10 dilution or less for D-PCR. The results suggest that for cattle shedding relatively high concentrations of Map in faeces (>2 x 10(5) viable Map/g), maximal dilutions of 1 in 30 for PFC and 1 in 10 for D-PCR would be applicable.

  7. Faecal contamination of drinking water during collection and household storage: the need to extend protection to the point of use.

    Science.gov (United States)

    Clasen, Thomas F; Bastable, Andrew

    2003-09-01

    Paired water samples were collected and analysed for thermotolerant coliforms (TTC) from 20 sources (17 developed or rehabilitated by Oxfam and 3 others) and from the stored household water supplies of 100 households (5 from each source) in 13 towns and villages in the Kailahun District of Sierra Leone. In addition, the female head of the 85 households drawing water from Oxfam improved sources was interviewed and information recorded on demographics, hygiene instruction and practices, sanitation facilities and water collection and storage practices. At the non-improved sources, the arithmetic mean TTC load was 407/100 ml at the point of distribution, rising to a mean count of 882/100 ml at the household level. Water from the improved sources met WHO guidelines, with no faecal contamination. At the household level, however, even this safe water was subject to frequent and extensive faecal contamination; 92.9% of stored household samples contained some level of TTC, 76.5% contained more than the 10 TTC per 100 ml threshold set by the Sphere Project for emergency conditions. The arithmetic mean TTC count for all samples from the sampled households was 244 TTC per 100 ml (geometric mean was 77). These results are consistent with other studies that demonstrate substantial levels of faecal contamination of even safe water during collection, storage and access in the home. They point to the need to extend drinking water quality beyond the point of distribution to the point of consumption. The options for such extended protection, including improved collection and storage methods and household-based water treatment, are discussed.

  8. Sequence space coverage, entropy of genomes and the potential to detect non-human DNA in human samples

    Directory of Open Access Journals (Sweden)

    Maley Carlo C

    2008-10-01

    Full Text Available Abstract Background Genomes store information for building and maintaining organisms. Complete sequencing of many genomes provides the opportunity to study and compare global information properties of those genomes. Results We have analyzed aspects of the information content of Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans, Arabidopsis thaliana, Saccharomyces cerevisiae, and Escherichia coli (K-12 genomes. Virtually all possible (> 98% 12 bp oligomers appear in vertebrate genomes while 98% to D. melanogaster (12–17 bp, C. elegans (11–17 bp, A. thaliana (11–17 bp, S. cerevisiae (10–16 bp and E. coli (9–15 bp. Frequencies of unique oligomers in the genomes follow similar patterns. We identified a set of 2.6 M 15-mers that are more than 1 nucleotide different from all 15-mers in the human genome and so could be used as probes to detect microbes in human samples. In a human sample, these probes would detect 100% of the 433 currently fully sequenced prokaryotes and 75% of the 3065 fully sequenced viruses. The human genome is significantly more compact in sequence space than a random genome. We identified the most frequent 5- to 20-mers in the human genome, which may prove useful as PCR primers. We also identified a bacterium, Anaeromyxobacter dehalogenans, which has an exceptionally low diversity of oligomers given the size of its genome and its GC content. The entropy of coding regions in the human genome is significantly higher than non-coding regions and chromosomes. However chromosomes 1, 2, 9, 12 and 14 have a relatively high proportion of coding DNA without high entropy, and chromosome 20 is the opposite with a low frequency of coding regions but relatively high entropy. Conclusion Measures of the frequency of oligomers are useful for designing PCR assays and for identifying chromosomes and organisms with hidden structure that had not been previously recognized. This information may be used to detect

  9. SAMPLING INTENSITY WITH FIXED PRECISION WHEN ESTIMATING VOLUME OF HUMAN BRAIN COMPARTMENTS

    Directory of Open Access Journals (Sweden)

    Rhiannon Maudsley

    2011-05-01

    Full Text Available Cavalieri sampling and point counting are frequently applied in combination with magnetic resonance (MR imaging to estimate the volume of human brain compartments. Current practice involves arbitrarily choosing the number of sections and sampling intensity within each section, and subsequently applying error prediction formulae to estimate the precision. The aim of this study is to derive a reference table for researchers who are interested in estimating the volume of brain regions, namely grey matter, white matter, and their union, to a given precision. In particular, this table, which is based on subsampling of a large brain data set obtained from coronal MR images, offers a recommendation for the minimum number of sections and mean number of points per section that are required to achieve a pre-defined coefficient of error of the volume estimator. Further analysis onMR brain data from a second human brain shows that the sampling intensity recommended is appropriate.

  10. Determination of cholesterol concentration in human milk samples using attenuated total reflectance Fourier transform infrared spectroscopy

    Science.gov (United States)

    Kamelska, A. M.; Pietrzak-Fiećko, R.; Bryl, K.

    2013-03-01

    Results of an inexpensive and rapid evaluation of the cholesterol concentration in human milk using ATR-FTIR techniques are presented. The FTIR spectrum of pure cholesterol was characterized and quantitatively estimated in the region between 2800 and 3200 cm-1. 125 samples at different stages of lactation were analyzed. There were no differences between the cholesterol concentrations in the samples of early (1-3 months), medium (4-6 months), and late (> 6 months) lactation stages ( p = 0.096968). The cholesterol concentration ranged from 4.30 to 21.77 mg/100 cm3. Such a broad range was due to the differences between the samples from different women ( p = 0.000184). The results indicate that ATR-FTIR has potential for rapid estimation of cholesterol concentration in human milk.

  11. The spectral absorption coefficient at 254 nm as a real-time early warning proxy for detecting faecal pollution events at alpine karst water resources.

    Science.gov (United States)

    Stadler, H; Klock, E; Skritek, P; Mach, R L; Zerobin, W; Farnleitner, A H

    2010-01-01

    Because spring water quality from alpine karst aquifers can change very rapidly during event situations, water abstraction management has to be performed in near real-time. Four summer events (2005-2008) at alpine karst springs were investigated in detail in order to evaluate the spectral absorption coefficient at 254 nm (SAC254) as a real-time early warning proxy for faecal pollution. For the investigation Low-Earth-Orbit (LEO) Satellite-based data communication between portable hydrometeorological measuring stations and an automated microbiological sampling device was used. The method for event triggered microbial sampling and analyzing was already established and described in a previous paper. Data analysis including on-line event characterisation (i.e. precipitation, discharge, turbidity, SAC254) and comprehensive E. coli determination (n>800) indicated that SAC254 is a useful early warning proxy. Irrespective of the studied event situations SAC254 always increased 3 to 6 hours earlier than the onset of faecal pollution, featuring different correlation phases. Furthermore, it seems also possible to use SAC254 as a real-time proxy parameter for estimating the extent of faecal pollution after establishing specific spring and event-type calibrations that take into consideration the variability of the occurrence and the transferability of faecal material It should be highlighted that diffuse faecal pollution from wildlife and live stock sources was responsible for spring water contamination at the investigated catchments. In this respect, the SAC254 can also provide useful information to support microbial source tracking efforts where different situations of infiltration have to be investigated.

  12. The spectral absorption coefficient at 254nm as a real-time early warning proxy for detecting faecal pollution events at alpine karst water resources

    Science.gov (United States)

    Stadler, H.; Klock, E.; Skritek, P.; Mach, R.L.; Zerobin, W.; Farnleitner, A.H.

    2011-01-01

    Because spring water quality from alpine karst aquifers can change very rapidly during event situations, water abstraction management has to be performed in near real-time. Four summer events (2005-2008) at alpine karst springs were investigated in detail in order to evaluate the spectral absorption coefficient at 254nm (SAC254) as a real-time early warning proxy for faecal pollution. For the investigation Low-Earth-Orbit (LEO) Satellite-based data communication between portable hydrometeorological measuring stations and an automated microbiological sampling device was used. The method for event triggered microbial sampling and analyzing was already established and described in a previous paper (Stadler et al., Wat. Sci. Technol. 58(4): 899-909, 2008). Data analysis including on-line event characterisation (i.e. precipitation, discharge, turbidity, SAC254) and comprehensive E. coli determination (n > 800) indicated that SAC254 is a useful early warning proxy. Irrespective of the studied event situations SAC254 always increased 3 to 6 hours earlier than the onset of faecal pollution, featuring different correlation phases. Furthermore, it seems also possible to use SAC254 as a real-time proxy parameter for estimating the extent of faecal pollution after establishing specific spring and event-type calibrations that take into consideration the variability of the occurrence and the transferability of faecal material It should be highlighted that diffuse faecal pollution from wildlife and live stock sources was responsible for spring water contamination at the investigated catchments. In this respect, the SAC254 can also provide useful information to support microbial source tracking efforts where different situations of infiltration have to be investigated. PMID:20962406

  13. Faecal calprotectin as a novel biomarker for differentiating between inflammatory bowel disease and irritable bowel syndrome.

    Science.gov (United States)

    Chang, Ming-Hui; Chou, Jen-Wei; Chen, Shan-Ming; Tsai, Ming-Chang; Sun, Yu-Shu; Lin, Chun-Che; Lin, Ching-Pin

    2014-07-01

    The present study aimed to investigate faecal calprotectin as a diagnostic marker to differentiate between patients with inflammatory bowel disease (IBD) and those with irritable bowel syndrome (IBS). A total of 20 healthy control subjects, 26 patients with IBS and 58 patients with IBD, including 22 with ulcerative colitis (UC) and 36 with Crohn's disease (CD), were recruited for the present study. Calprotectin was analysed in stool samples, and C-reactive protein (CRP) and the erythrocyte sedimentation rate (ESR) were assessed in blood samples. CRP and calprotectin levels, and the ESR were observed to be significantly higher in patients with CD and UC compared with those of the healthy control subjects (Pcalprotectin and CRP levels were observed (694.8±685.0 µg/g in IBD vs. 85.8±136.1 µg/g in IBS and 0.851±1.200 mg/dl in IBD vs. 0.16±0.23 mg/dl in IBS, respectively; Pcalprotectin [0.931±0.029; 95% confidence interval (CI), 0.874‑0.987] were significantly higher than that of CRP (0.865±0.041; 95% CI, 0.785‑0.946) and the ESR (0.869±0.042; 95% CI, 0.786‑0.952). These findings indicate that faecal calprotectin may represent a novel biomarker for diagnosing IBD and may be effective in distinguishing between IBD and IBS.

  14. 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.

  15. Post-weaning diet affects faecal microbial composition but not selected adipose gene expression in the cat (Felis catus.

    Directory of Open Access Journals (Sweden)

    Emma N Bermingham

    Full Text Available The effects of pre- (i.e., gestation and during lactation and post-weaning diet on the composition of faecal bacterial communities and adipose expression of key genes in the glucose and insulin pathways were investigated in the cat. Queens were maintained on a moderate protein:fat:carbohydrate kibbled ("Diet A"; 35:20:28% DM; n  =  4 or high protein:fat:carbohydrate canned ("Diet B"; 45:37:2% DM; n = 3 diet throughout pregnancy and lactation. Offspring were weaned onto these diets in a nested design (n  =  5 per treatment. Faecal samples were collected at wk 8 and 17 of age. DNA was isolated from faeces and bacterial 16S rRNA gene amplicons were analysed by pyrosequencing. RNA was extracted from blood (wk 18 and adipose tissue and ovarian/testicular tissues (wk 24 and gene expression levels determined using RT-qPCR. Differences (P<0.05 in composition of faecal bacteria were observed between pregnant queens fed Diet A or B. However, pre-weaning diet had little effect on faecal bacterial composition in weaned kittens. In contrast, post-weaning diet altered bacterial population profiles in the kittens. Increased (P<0.05 abundance of Firmicutes (77% vs 52% of total reads and Actinobacteria (0.8% vs 0.2% of total reads, and decreased (P<0.05 abundance of Fusobacteria (1.6% vs 18.4% of total reads were observed for kittens fed the Diet A compared to those fed Diet B post-weaning. Feeding Diet B pre-weaning increased (P<0.05 the expression levels of INRS, LEPT, PAI-1 and tended to increase GLUT1, while the expression levels of IRS-1 in blood increased in kittens fed Diet A pre-weaning. Post-weaning diet had no effect on expression levels of target genes. Correlations between the expression levels of genes involved in glucose and insulin pathways and faecal Bacteriodetes and Firmicutes phyla were identified. The reasons for why post-weaning diet affects microbial populations and not gene expression levels are of interest.

  16. Identification of human Norovirus (HNoV in domestic pig stool samples

    Directory of Open Access Journals (Sweden)

    María F. Gutiérrez

    2011-08-01

    Full Text Available To determine the presence of NoVs as a possible causal zoonotic agent of acute diarrhea in pigs and humans. Materialsand methods. We collected a total of 77 samples from diarrheal children under 5 years and pigs under 2 months from La Chambatown in Tolima, Colombia. These samples were transported to the Laboratory of Virology of the Pontificia Universidad Javerianain Bogotá, and extraction with Trizol-reagent was done following the manufacturer’s instructions. After obtaining the RNA, thenext step was to perform RT-PCR for obtaining the expected amplification product of 213- bp NoVs. Finally, the positive samplesobtained in the RT-PCR were sequenced and analyzed by bioinformatics methods. Results. Six positive diarrheic samples fromchildren and a positive diarrheic sample from pigs were detected by a band of 231 bp. Five of the six positive samples in childrenand the positive pig sample were sequenced and analyzed. Conclusion. Given the close genetic relationship between pig andhuman sequences, this could be an indication of the potential existence of a common animal acting as a reservoir for human orother animal strains.

  17. Total reflection X-ray fluorescence as a fast multielemental technique for human placenta sample analysis

    Science.gov (United States)

    Marguí, E.; Ricketts, P.; Fletcher, H.; Karydas, A. G.; Migliori, A.; Leani, J. J.; Hidalgo, M.; Queralt, I.; Voutchkov, M.

    2017-04-01

    In the present contribution, benchtop total reflection X-ray fluorescence spectrometry (TXRF) has been evaluated as a cost-effective multielemental analytical technique for human placenta analysis. An easy and rapid sample preparation consisting of suspending 50 mg of sample in 1 mL of a Triton 1% solution in deionized water showed to be the most suitable for this kind of samples. However, for comparison purposes, an acidic microwave acidic digestion procedure was also applied. For both sample treatment methodologies, limits of detection for most elements were in the low mg/kg level. Accurate and precise results were obtained using internal standardization as quantification approach and applying a correction factor to compensate for absorption effects. The correction factor was based on the proportional ratio between the slurry preparation results and those obtained for the analysis of a set of human placenta samples analysed by microwave acidic digestion and ICP-AES analysis. As a study case, the developed TXRF methodology was applied for multielemental analysis (K, Ca, Fe, Cu, Zn, As, Se, Br, Rb and Sr) of several healthy women's placenta samples from two regions in Jamaica.

  18. Residues of PCDDs and PCDFs in human milk samples in Ahmedabad, India

    Energy Technology Data Exchange (ETDEWEB)

    Kashyap, R.; Bhatnagar, V.; Sadhu, H.; Jhamb, N.; Karanjkar, R.; Saiyed, H. [National Inst. of Occupational Health, Ahmedabad (India)

    2004-09-15

    Polychlorinated dibenzo-p-dioxins (PCDDs) and Polychlorinated dibenzo furans (PCDFs) represent a class of organic environmental pollutants. They are unwanted byproduct of incineration, uncontrolled burning and certain industrial processes. They are persistent in nature and bioaccumulates through food chain. These are hazardous to human health and environment. The residues of these toxicants have been detected in human adipose tissue, blood and milk. WHO has coordinated two rounds of follow up studies on levels of PCDD/Fs and PCBs in human milk and the data shows a decreasing trend during the last 30 years. However, in India there is no data available on the exposure and residues of these contaminants. This study presents first time the levels of dioxin and furans in human milk samples collected from the Ahmedabad city in India.

  19. The impact of baseline faecal egg counts on the efficacy of single-dose albendazole against Trichuris trichiura.

    Science.gov (United States)

    Levecke, B; Mekonnen, Z; Albonico, M; Vercruysse, J

    2012-02-01

    There is considerable variation in the efficacy of single-dose albendazole (400mg) against Trichuris trichiura across human trials. Factors contributing to this variation have not yet been identified. We assessed the impact of mean baseline faecal egg counts (FEC) on the efficacy of single-dose albendazole against T. trichiura in five previously conducted trials. Our results suggest that efficacy measured by reduction in mean FECs decreased significantly (p<0.0001) when mean baseline FECs increased, highlighting that this parameter should be considered as an important confounding factor for drug efficacy.

  20. Sensitive Procedure for Rapid Detection of Human Brucellosis, Based on PCR Method in Contaminated Serum Samples

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    Eslam Ghezelsofla

    2013-07-01

    Full Text Available AbstractBackground and objective: Brucellosis is a zoonosis transmittable to humans poses a significant public health problem in many developing countries and requires rapid and accurate diagnostic methods. Here, our aim was to develop a diagnostic polymerase chain reaction (PCR assay in artificially contaminated serum samples as a model for rapid and accurate laboratory confirmation of human brucellosis. Material and methods: In this study, initially the standard Brucella abortus strain (2308 were cultured on Brucella agar medium and then colonies were inactivated by formalin 10 %. Genomic DNA was extracted from inactivated bacterial colonies. Serial dilutions of bacterial-DNA were prepared in fetal bovine serum (FBS and water and subsequently DNA extraction were repeated on these artificially contaminated samples. The two pairs of primers amplified two different fragments included in: a gene encoding an outer membrane protein (omp-2 (primers JPF/JPR and a sequence 16S rRNA of B. abortus (primers F4/R2. Results: The two primers assayed showed a difference in sensitivity for detecting Brucella DNA, ranging between 5 pg and 50 pg for artificially contaminated serum samples and 50Fg and 5 pg for contaminated control samples. Therefore, the sensitivity of PCR using F4/R2 primers was greater than the PCR using JPF/JPR primers.Conclusion: Although the sensitivity of PCR using these primers was affected by serum inhibitors, they are still the most sensitive and they could provide a useful tool for the diagnosis of human brucellosis.

  1. A new rapid home test for faecal calprotectin in ulcerative colitis

    DEFF Research Database (Denmark)

    Elkjaer, M; Burisch, Johan; Hansen, V Voxen

    2010-01-01

    Enzyme-linked immunosorbent assay (ELISA) is a time-consuming method for the measurement of faecal calprotectin. Two new quantitative rapid tests have been developed.......Enzyme-linked immunosorbent assay (ELISA) is a time-consuming method for the measurement of faecal calprotectin. Two new quantitative rapid tests have been developed....

  2. A new rapid home test for faecal calprotectin in ulcerative colitis

    DEFF Research Database (Denmark)

    Elkjaer, M; Burisch, Johan; Hansen, V Voxen

    2010-01-01

    Enzyme-linked immunosorbent assay (ELISA) is a time-consuming method for the measurement of faecal calprotectin. Two new quantitative rapid tests have been developed.......Enzyme-linked immunosorbent assay (ELISA) is a time-consuming method for the measurement of faecal calprotectin. Two new quantitative rapid tests have been developed....

  3. 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...

  4. A percutaneous needle biopsy technique for sampling the supraclavicular brown adipose tissue depot of humans.

    Science.gov (United States)

    Chondronikola, M; Annamalai, P; Chao, T; Porter, C; Saraf, M K; Cesani, F; Sidossis, L S

    2015-10-01

    Brown adipose tissue (BAT) has been proposed as a potential target tissue against obesity and its related metabolic complications. Although the molecular and functional characteristics of BAT have been intensively studied in rodents, only a few studies have used human BAT specimens due to the difficulty of sampling human BAT deposits. We established a novel positron emission tomography and computed tomography-guided Bergström needle biopsy technique to acquire human BAT specimens from the supraclavicular area in human subjects. Forty-three biopsies were performed on 23 participants. The procedure was tolerated well by the majority of participants. No major complications were noted. Numbness (9.6%) and hematoma (2.3%) were the two minor complications noted, which fully resolved. Thus, the proposed biopsy technique can be considered safe with only minimal risk of adverse events. Adoption of the proposed method is expected to increase the sampling of the supraclavicular BAT depot for research purposes so as to augment the scientific knowledge of the biology of human BAT.

  5. 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 indi

  6. [Detection of human parvovirus B19, human bocavirus and human parvovirus 4 infections in blood samples among 95 patients with liver disease in Nanjing by nested PCR].

    Science.gov (United States)

    Tong, Rui; Zhou, Wei-Min; Liu, Xi-Jun; Wang, Yue; Lou, Yong-Liang; Tan, Wen-Jie

    2013-04-01

    To analyze the infection of human parvovirus B19, human bocavirus (HBoV) and human parvovirus 4 (PARV4) in blood samples among patients with liver disease in Nanjing by molecular detection. Nested PCR assays were designed and validated to detect B19, HBoV and PARV4, respectively. The assays were used to screen three parvoviruses in blood samples from 95 patients with different liver disease in Nanjing. The parvovirus infection was analyzed statistically. The detection limits were 10 copies of genomic DNA equivalents per reaction for each assays and the good specificity were observed. The frequency of B19 and HBoV were 2/95 (2.1%) and 9/95 (9.5%) in blood samples respectively. No PARV4 was detected. HBoV was detected in 3/5 patients with drug-induced hepatitis. Both B19 and HBoV infection were detected in blood from patients with liver disease.

  7. The effectiveness of sewage treatment processes to remove faecal pathogens and antibiotic residues

    Science.gov (United States)

    Hendricks, Rahzia; Pool, Edmund John

    2012-01-01

    Pathogens and antibiotics enter the aquatic environment via sewage effluents and may pose a health risk to wild life and humans. The aim of this study was to determine the levels of faecal bacteria, and selected antibiotic residues in raw wastewater and treated sewage effluents from three different sewage treatment plants in the Western Cape, South Africa. Sewage treatment plant 1 and 2 use older technologies, while sewage treatment plant 3 has been upgraded and membrane technologies were incorporated in the treatment processes. Coliforms and Escherichia coli (E. coli) were used as bioindicators for faecal bacteria. A chromogenic test was used to screen for coliforms and E. coli. Fluoroquinolones and sulfamethoxazole are commonly used antibiotics and were selected to monitor the efficiency of sewage treatment processes for antibiotic removal. Enzyme Linked Immunosorbent Assays (ELISAs) were used to quantitate antibiotic residues in raw and treated sewage. Raw intake water at all treatment plants contained total coliforms and E. coli. High removal of E. coli by treatment processes was evident for treatment plant 2 and 3 only. Fluoroquinolones and sulfamethoxazole were detected in raw wastewater from all sewage treatment plants. Treatment processes at plant 1 did not reduce the fluoroquinolone concentration in treated sewage effluents. Treatment processes at plant 2 and 3 reduced the fluoroquinolone concentration by 21% and 31%, respectively. Treatment processes at plant 1 did not reduce the sulfamethoxazole concentration in treated sewage effluents. Treatment processes at plant 2 and 3 reduced sulfamethoxazole by 34% and 56%, respectively. This study showed that bacteria and antibiotic residues are still discharged into the environment. Further research needs to be undertaken to improve sewage treatment technologies, thereby producing a better quality treated sewage effluent. PMID:22242882

  8. Antigenic typing of brazilian rabies virus samples isolated from animals and humans, 1989-2000

    Directory of Open Access Journals (Sweden)

    FAVORETTO Silvana Regina

    2002-01-01

    Full Text Available Animal and human rabies samples isolated between 1989 and 2000 were typified by means of a monoclonal antibody panel against the viral nucleoprotein. The panel had been previously established to study the molecular epidemiology of rabies virus in the Americas. Samples were isolated in the Diagnostic Laboratory of the Pasteur Institute and in other rabies diagnostic centers in Brazil. In addition to the fixed virus samples CVS-31/96-IP, preserved in mouse brain, and PV-BHK/97, preserved in cell culture, a total of 330 rabies virus samples were isolated from dogs, cats, cattle, horses, bats, sheep, goat, swine, foxes, marmosets, coati and humans. Six antigenic variants that were compatible with the pre-established monoclonal antibodies panel were defined: numbers 2 (dog, 3 (Desmodus rotundus, 4 (Tadarida brasiliensis, 5 (vampire bat from Venezuela, 6 (Lasiurus cinereus and Lab (reacted to all used antibodies. Six unknown profiles, not compatible with the panel, were also found. Samples isolated from insectivore bats showed the greatest variability and the most commonly isolated variant was variant-3 (Desmodus rotundus. These findings may be related to the existence of multiple independent transmission cycles, involving different bat species.

  9. Comparison of chlorzoxazone one-sample methods to estimate CYP2E1 activity in humans

    DEFF Research Database (Denmark)

    Kramer, Iza; Dalhoff, Kim; Clemmesen, Jens O

    2003-01-01

    OBJECTIVE: Comparison of a one-sample with a multi-sample method (the metabolic fractional clearance) to estimate CYP2E1 activity in humans. METHODS: Healthy, male Caucasians ( n=19) were included. The multi-sample fractional clearance (Cl(fe)) of chlorzoxazone was compared with one...... estimates, Cl(est) at 3 h or 6 h, and MR at 3 h, can serve as reliable markers of CYP2E1 activity. The one-sample clearance method is an accurate, renal function-independent measure of the intrinsic activity; it is simple to use and easily applicable to humans.......-time-point clearance estimation (Cl(est)) at 3, 4, 5 and 6 h. Furthermore, the metabolite/drug ratios (MRs) estimated from one-time-point samples at 1, 2, 3, 4, 5 and 6 h were compared with Cl(fe). RESULTS: The concordance between Cl(est) and Cl(fe) was highest at 6 h. The minimal mean prediction error (MPE) of Cl...

  10. Selection of Candidate Housekeeping Genes for Normalization in Human Postmortem Brain Samples

    Directory of Open Access Journals (Sweden)

    Aldo Pagano

    2011-08-01

    Full Text Available The most frequently used technique to study the expression profile of genes involved in common neurological disorders is quantitative real-time RT-PCR, which allows the indirect detection of very low amounts of selected mRNAs in tissue samples. Expression analysis by RT-qPCR requires an appropriate normalization to the expression level of genes characterized by a stable, constitutive transcription. However, the identification of a gene transcribed at a very stable level is difficult if not impossible, since significant fluctuations of the level of mRNA synthesis often accompanies changes of cell behavior. The aim of this study is to identify the most stable genes in postmortem human brain samples of patients affected by Alzheimer’s disease (AD suitable as reference genes. The experiments analyzed 12 commonly used reference genes in brain samples from eight individuals with AD and seven controls. After a careful analysis of the results calculated by geNorm and NormFinder algorithms, we found that CYC1 and EIF4A2 are the best reference genes. We remark on the importance of the determination of the best reference genes for each sample to be analyzed and suggest a practical combination of reference genes to be used in the analysis of human postmortem samples.

  11. Modelling the fate and transport of faecal bacteria in estuarine and coastal waters.

    Science.gov (United States)

    Gao, Guanghai; Falconer, Roger A; Lin, Binliang

    2015-11-15

    This paper details a numerical model developed to predict the fate and transport of faecal bacteria in receiving surface waters. The model was first validated by comparing model predicted faecal bacteria concentrations with available field measurements. The model simulations agreed well with the observation data. After calibration, the model was applied to investigate the effects of different parameters, including: tidal processes, river discharges from the upstream boundaries and bacteria inputs from the upstream boundaries, wastewater treatment works (WwTWs), rivers and combined sewer overflows (CSO), on the concentrations of faecal bacteria in the Ribble Estuary. The results revealed that the tide and upstream boundary bacteria inputs were the primary factors controlling the distribution of faecal bacteria. The bacteria inputs from the WwTWs in the model domain were generally found not to have a significant impact on distribution of faecal bacteria in the estuary.

  12. Quality assesment for the analysis of PCDDs/PCDFs in individual human serum samples

    Energy Technology Data Exchange (ETDEWEB)

    Perez, F. [IIQAB-CSIC, Barcelona (Spain). Dept. of Ecotechnologies, Lab. of Dioxins; Abad, E.; Llerena, J.J.; Caixach, J.; Rivera, J.

    2004-09-15

    The aim of this work was to optimise a relevant methodology for the ultratrace analysis of PCDDs/PCDFs in individual human serum samples. In order to carry out the study, different strategies including the elaboration of quality control samples, parallel sample analysis, control blanks and a number of quality assurance measures were implemented as analytical current practices. Some of the main drawbacks in the analysis of PCDDs/PCDFs in these kind of samples come from two conflicting aspects: the small sample size and the low levels expected to be found. Taking this into account, an unavoidable compromise between the sample amount and the minimum analytical requirements, mainly the detection limit (LOD), is mandatory. To reach this goal C{sub 18} solid phase extraction was used to remove the analytes from the matrix. Clean up was performed by solid-liquid adsorption chromatography using a variety of adsorbents. Instrumental analysis was achieved by high-resolution gas chromatography coupled to high-resolution mass spectrometry (HRGC/HRMS). Finally, the optimised methodology was applied to evaluate the potential impact in general population living in the surroundings of an obsolete municipal waste incinerator plant (MWI). Thus, more than 400 individuals serum samples potentially exposed to the emission of the incinerator and people not exposed were considered in this study.

  13. Diets supplemented with chickpea or its main oligosaccharide component raffinose modify faecal microbial composition in healthy adults.

    Science.gov (United States)

    Fernando, W M U; Hill, J E; Zello, G A; Tyler, R T; Dahl, W J; Van Kessel, A G

    2010-06-01

    The effects of diets supplemented with either chickpea or its main oligosaccharide raffinose on the composition of the faecal microbial community were examined in 12 healthy adults (18-65 years) in a randomised crossover intervention study. Subjects consumed their usual diet supplemented with soups and desserts that were unfortified, or fortified with either 200 g/d of canned chickpeas or 5 g/d of raffinose for 3 week periods. Changes in faecal bacterial populations of subjects were examined using 16S rRNA-based terminal restriction fragment length polymorphisms (T-RFLP) and clone libraries generated from the diet pools. Classification of the clone libraries and T-RFLP analysis revealed that Faecalibacterium prausnitzii, reported to be an efficient butyrate producer and a highly metabolically active bacterium in the human intestinal microbiota, was more abundant in the raffinose diet and the chickpea diet compared to the control diet. However, no significant difference was observed in the faecal total short chain fatty acid concentration or in the levels of the components (butyrate, acetate and propionate) with the chickpea diet or the raffinose diet compared to the control diet. Bifidobacterium species were detected by T-RFLP in all three diet groups and quantitative real-time PCR (qPCR) analysis showed a marginal increase in 16S rRNA gene copies of Bifidobacterium with the raffinose diet compared to control (P>0.05). The number of individuals showing TRFs for the Clostridium histolyticum - Clostridum lituseburense groups, which include pathogenic bacteria species and putrefactive bacteria, were lower in the chickpea diet compared to the other two treatments. Diet appeared to affect colonisation by a high ammonia-producing bacterial isolate which was detected in 83%, 92% and 42% of individuals in the control, raffinose and chickpea groups, respectively. Our results indicate that chickpea and raffinose have the potential to modulate the intestinal microbial

  14. Barriers to acceptance of self-sampling for human papillomavirus across ethnolinguistic groups of women.

    Science.gov (United States)

    Howard, Michelle; Lytwyn, Alice; Lohfeld, Lynne; Redwood-Campbell, Lynda; Fowler, Nancy; Karwalajtys, Tina

    2009-01-01

    Immigrant and low socio-economic (SES) women in North America underutilize Papanicolaou screening. Vaginal swab self-sampling for oncogenic human papillomavirus (HPV) has the potential to increase cervical cancer screening participation. The purpose of this qualitative study was to understand the perceptions of lower SES and immigrant women regarding self-sampling for HPV. Eleven focus-group interviews were conducted: one with Canadian-born English-speaking lower SES women, and two groups each with Arabic, Cantonese, Dari (Afghani), Somali and Spanish (Latino)-speaking women (one group conducted in English, the other in the native language) recently immigrated to Canada. Five to nine women aged 35 to 65 years and married with children participated in each group. Themes included 1) who might use self-sampling and why; 2) aversion to self-sampling and reasons to prefer physician; 3) ways to improve the appeal of self-sampling. Women generally perceived benefits of self-sampling and a small number felt they might use the method, but all groups had some reservations. Reasons included: uncertainty over performing the sampling correctly; fear of hurting themselves; concern about obtaining appropriate material; and concerns about test accuracy. Women preferred testing by a health care professional because they were accustomed to pelvic examinations, it was more convenient, or they trusted the results. Perceptions of self-sampling for HPV were similar across cultures and pertained to issues of confidence in self-sampling and need for physician involvement in care. These findings can inform programs and studies planning to employ self-sampling as a screening modality for cervical cancer.

  15. A human gut microbial gene catalogue established by metagenomic sequencing

    DEFF Research Database (Denmark)

    dos Santos, Marcelo Bertalan Quintanilha; Sicheritz-Pontén, Thomas; Nielsen, Henrik Bjørn

    2010-01-01

    , from faecal samples of 124 European individuals. The gene set, ,150 times larger than the human gene complement, contains an overwhelming majority of the prevalent (more frequent) microbial genes of the cohort and probably includes a large proportion of the prevalent human intestinal microbial genes......To understand the impact of gut microbes on human health and well-being it is crucial to assess their genetic potential. Here we describe the Illumina-based metagenomic sequencing, assembly and characterization of 3.3 million non-redundant microbial genes, derived from 576.7 gigabases of sequence...

  16. Genomic studies of envelope gene sequences from mosquito and human samples from Bangkok, Thailand.

    Science.gov (United States)

    Pitaksajjakul, Pannamthip; Benjathummarak, Surachet; Son, Hyun Ngoc; Thongrungkiat, Supatra; Ramasoota, Pongrama

    2016-01-01

    Dengue virus (DENV) is an RNA virus showing a high degree of genetic variation as a consequence of its proofreading inability. This variation plays an important role in virus evolution and pathogenesis. Although levels of within-host genetic variation are similar following equilibrium, variation among different hosts is frequently different. To identify dengue quasispecies present among two hosts, we collected patient samples from six acute DENV cases and two pools of Aedes aegypti mosquitoes and analyzed the genetic variation of regions of the viral envelope gene. Among human and mosquito samples, we found three major clusters originating from two subpopulations. Although several shared lineages were observed in the two hosts, only one lineage showing evidence of neutral selection was observed among two hosts. Taken together, our data provide evidence for the existence of a DENV quasispecies, with less genetic variation observed in mosquitoes than humans and with circulating lineages found in both host types.

  17. Load and failure behavior of human muscle samples in the context of proximal femur replacement

    OpenAIRE

    Schleifenbaum, Stefan; Schmidt, Michael; Möbius, Robert; Wolfskämpf, Thomas; Schröder, Christian; Grunert, Ronny; Hammer, Niels; Prietzel, Torsten

    2016-01-01

    Background: To ensure adequate function after orthopedic tumor reconstruction, it is important to reattach the remaining soft tissue to the implant. This study aimed at obtaining mechanical properties of textile muscle-implant and muscle-bone connections in a preliminary test. Methods: Two groups of soft-tissue attachment were mechanically tested and compared: Native bone-muscle samples obtained from human femora and muscles attached to a prosthetic implant by means of Trevira® attachment tu...

  18. Dioxin-like activity of environmental compounds in human blood and environmental samples

    DEFF Research Database (Denmark)

    Long, Manhai; Bonefeld-Jørgensen, Eva Cecilie

    2012-01-01

    R transactivation bioassay is utilized in an array of projects to study the AhR-mediated activities of individual chemicals and mixtures and for epidemiological purposes. This review summarizes a series of studies regarding the DL-activity of single compounds and complex compound mixtures in the environment...... a cost-effective and integrated screening tool for measurement of the DL-activity in human, environmental and commercial samples....

  19. Separation of proteins from human plasma by sample displacement chromatography in hydrophobic interaction mode

    OpenAIRE

    Josic, Djuro; Breen, Lucas; Clifton, James; Gajdosik, Martina Srajer; Gaso-Sokac, Dajana; Rucevic, Marijana; Müller, Egbert

    2012-01-01

    Sample displacement chromatography (SDC) in reversed-phase and ion-exchange modes was introduced approximately twenty years ago. This method was first used for the preparative purification of peptides and proteins. Recently, SDC in ion-exchange mode was also successfully used for enrichment of low abundance proteins from human plasma. In this paper, the use of SDC for the separation of plasma proteins in hydrophobic interaction mode is demonstrated. By use of two or more columns coupled in se...

  20. Dioxin-like activity of environmental compounds in human blood and environmental samples

    DEFF Research Database (Denmark)

    Long, Manhai; Bonefeld-Jørgensen, Eva Cecilie

    2012-01-01

    and humans. We found that some pesticides, plasticizers and phytoestrogens can activate the AhR, and the combined effect of compounds with no or weak AhR potency cannot be ignored. The significant DL-activity in the wastewater effluent indicates the treatment is not sufficient to prevent contamination...... of surface waters with dioxins. Our results from human studies suggest that the serum DL-activity reflect the complex mixture of persistent organic pollutants (POPs). Greenlandic Inuit had lower serum DL-activity level compared to Europeans, probably due to long distance from the dioxin sources and UV...... a cost-effective and integrated screening tool for measurement of the DL-activity in human, environmental and commercial samples....

  1. Dioxin-like activity in environmental and human samples from Greenland and Denmark

    DEFF Research Database (Denmark)

    Long, Manhai; Bonefeld-Jørgensen, Eva Cecilie

    2012-01-01

    and humans. We found that some pesticides, plasticizers and phytoestrogens can activate the AhR, and the combined effect of compounds with no or weak AhR potency cannot be ignored. The significant DL-activity in the wastewater effluent indicates the treatment is not sufficient to prevent contamination...... of surface waters with dioxins. Our results from human studies suggest that the serum DL-activity reflect the complex mixture of persistent organic pollutants (POPs). Greenlandic Inuit had lower serum DL-activity level compared to Europeans, probably due to long distance from the dioxin sources and UV...... a cost-effective and integrated screening tool for measurement of the DL-activity in human, environmental and commercial samples....

  2. Five-week dietary exposure to dry diets alters the faecal bacterial populations in the domestic cat (Felis catus).

    Science.gov (United States)

    Bermingham, Emma N; Kittelmann, Sandra; Henderson, Gemma; Young, Wayne; Roy, Nicole C; Thomas, David G

    2011-10-01

    The effects of wet (canned) or dry (kibbled) diets on faecal bacterial populations in the cat were investigated in eight domestic short-haired cats (four males and four females; averaging 6 years of age and 3.4 kg) in a nested design. The cats were fed ad libitum a commercially available wet diet (moisture 82.0 %, crude protein 51.7 %, fat 28.9 %, carbohydrate (CHO) 8.9 % and ash 10.6 % DM) for 5 weeks. On the fifth week, individual feed intakes and faecal outputs were determined. Fresh faecal samples were collected twice daily, mixed for homogeneity, subsampled and stored at - 85 °C until analysis. The cats were then switched to a commercially available dry diet (moisture 8.5 %, crude protein 33.0 %, fat 11.0 %, CHO 49.4 % and ash 6.6 % DM) for 5 weeks, and fresh faeces were sampled as described previously. Energy intake tended to be higher in cats fed dry diets (P 0.05). Denaturing gradient gel electrophoresis (DGGE) of bacterial 16S rRNA genes amplified from DNA extracted from faeces was performed. The unweighted pair group method with arithmetic mean cluster analysis of bacterial community profiles using Pearson's correlation revealed diet-specific clustering when the same cats were fed on either a dry or a wet diet (dissimilarity between the groups, 88.6 %; P Pelomonas and Fusobacteriaceae were influenced by a short-term change in diet format. This suggests that 5-week dietary exposure is sufficient to alter gastrointestinal microflora.

  3. 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

    2017-07-17

    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.

  4. Least destructive sampling of human remains using laser drilling for Sr isotope analysis by TIMS

    Science.gov (United States)

    Willmes, Malte; Moffat, Ian; Grün, Rainer; Armstrong, Richard; Kinsley, Les; McMorrow, Linda

    2013-04-01

    Strontium isotope ratios (87Sr/86Sr) measured in ancient human remains can be used to reconstruct migration patterns of ancient human populations. This application is based on the fact that different geologic regions have distinct Sr isotope signatures that are cycled through the soils, plants and rivers, and eventually enter the food cycle. Sr isotope ratios measured in skeletal remains (bones and teeth) reflect the average of dietary Sr that was consumed when the tissue was formed, allowing the investigation of human migration between geologically distinct terrains. The analysis of human remains is always a sensitive topic requiring minimal damage to the sample, while at the same time providing highly precise and accurate results. Samples can be analysed either by solution methods like thermal ionisation mass spectrometry (TIMS), or by in-situ laser ablation MC-ICP-MS. For TIMS a drill is used to extract a small amount of sample, which is then digested in acid and Sr is separated out using ion exchange chromatography. This technique provides highly precise and accurate results, because any isobaric interferences are removed during chemical separation. The drawback is that drilling may cause visible damage to the sample, restricting access to precious human remains. LA-MC-ICP-MS analysis is very fast and nearly destruction free. However, the accuracy and precision of LA-MC-ICP-MS is limited by a number of factors including large instrumental mass discrimination, laser-induced isotopic and elemental fractionations and molecular interferences on 87Sr. Its application thus requires rigorous data reduction, which can introduce significant uncertainties into the analysis. This is especially true for samples with relatively low Sr concentrations such as human teeth (e.g., Woodhead et al., 2005; Horstwood et al., 2008; Vroon et al., 2008). In addition, LA-MC-ICP-MS has traditionally required a flat sample surface, thus an unbroken tooth needs to be cut, which is rather

  5. Laser induced breakdown spectroscopy of human liver samples with Wilson's disease

    Science.gov (United States)

    Grolmusová, Zuzana; Horňáčková, Michaela; Plavčan, Jozef; Kopáni, Martin; Babál, Pavel; Veis, Pavel

    2013-08-01

    Laser induced breakdown spectroscopy (LIBS) is an elemental analytical technique with various applications. The paper demonstrates the first LIBS measurements of human liver samples for the purpose of detecting the higher copper content related with the advanced stage of Wilson's disease. These measurements were implemented using a Nd:YAG laser working at the wavelength of 532 nm and an echelle type spectrometer equipped with an intensified CCD camera allowing for a wide spectral range coverage (200-950 nm) and rapid camera gating (minimum gating time of 5 ns). Seven liver samples with suspected Wilson's disease and five reference samples were investigated. The main parameter of interest was the Cu/C ratio obtained at first from spectra and secondly directly from an iCCD image. Our experiment is a pilot study, which shows LIBS analysis of human liver samples for the purpose of detecting the normal and higher copper content for the first time. The method proved to be a quick and a low-cost approach for the detection of pathological accumulation of copper in the affected tissue.

  6. DNA purification from crude samples for human identification using gradient elution isotachophoresis.

    Science.gov (United States)

    Strychalski, Elizabeth A; Konek, Christopher; Butts, Erica L R; Vallone, Peter M; Henry, Alyssa C; Ross, David

    2013-09-01

    Gradient elution isotachophoresis (GEITP) was demonstrated for DNA purification, concentration, and quantification from crude samples, represented here by soiled buccal swabs, with minimal sample preparation prior to human identification using STR analysis. During GEITP, an electric field applied across leading and trailing electrolyte solutions resulted in isotachophoretic focusing of DNA at the interface between these solutions, while a pressure-driven counterflow controlled the movement of the interface from the sample reservoir into a microfluidic capillary. This counterflow also prevented particulates from fouling or clogging the capillary and reduced or eliminated contamination of the delivered DNA by PCR inhibitors. On-line DNA quantification using laser-induced fluorescence compared favorably with quantitative PCR measurements and potentially eliminates the need for quantitative PCR prior to STR analysis. GEITP promises to address the need for a rapid and robust method to deliver DNA from crude samples to aid the forensic community in human identification. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. Detection of Streptococcus mutans Genomic DNA in Human DNA Samples Extracted from Saliva and Blood

    Science.gov (United States)

    Vieira, Alexandre R.; Deeley, Kathleen B.; Callahan, Nicholas F.; Noel, Jacqueline B.; Anjomshoaa, Ida; Carricato, Wendy M.; Schulhof, Louise P.; DeSensi, Rebecca S.; Gandhi, Pooja; Resick, Judith M.; Brandon, Carla A.; Rozhon, Christopher; Patir, Asli; Yildirim, Mine; Poletta, Fernando A.; Mereb, Juan C.; Letra, Ariadne; Menezes, Renato; Wendell, Steven; Lopez-Camelo, Jorge S.; Castilla, Eduardo E.; Orioli, Iêda M.; Seymen, Figen; Weyant, Robert J.; Crout, Richard; McNeil, Daniel W.; Modesto, Adriana; Marazita, Mary L.

    2011-01-01

    Caries is a multifactorial disease, and studies aiming to unravel the factors modulating its etiology must consider all known predisposing factors. One major factor is bacterial colonization, and Streptococcus mutans is the main microorganism associated with the initiation of the disease. In our studies, we have access to DNA samples extracted from human saliva and blood. In this report, we tested a real-time PCR assay developed to detect copies of genomic DNA from Streptococcus mutans in 1,424 DNA samples from humans. Our results suggest that we can determine the presence of genomic DNA copies of Streptococcus mutans in both DNA samples from caries-free and caries-affected individuals. However, we were not able to detect the presence of genomic DNA copies of Streptococcus mutans in any DNA samples extracted from peripheral blood, which suggests the assay may not be sensitive enough for this goal. Values of the threshold cycle of the real-time PCR reaction correlate with higher levels of caries experience in children, but this correlation could not be detected for adults. PMID:21731912

  8. 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.

  9. Pathogenic Vibrio Strains Isolated from Human Stool and Water Samples from Western Kenya

    Directory of Open Access Journals (Sweden)

    Roselida Achieng Owuor

    2016-03-01

    Full Text Available Objective: Investigate the type of pathogenic Vibrio strains from water and stool samples collected from Migori, SonduMiriu, Nyando and Yala regions in Western Kenya. Methods: A total of 811 samples (596 water and 215 stool samples were collected during the study periods of May to December 2013 and August to September 2014. Pathogenic Vibrio strains were identified through culturing in TCBS Agar, followed by oxidation, string and serological (polyvalent tests, respectively. The PCR analysis was done using combined primers targeting Vibrionaceae 16SrRNA and species specific primers for V. vulnificus and V. cholerae. Results: The results showed the presence of V. vulnificus and V. cholerae. However, V. parahaemolyticus was not found in any of the samples. The PCR results for 16SrRNA, Vib 1, and Vib 2 showed polymorphism in the genes, this was an indication of cross combination of genes from more than one strain in one isolate. Conclusion: The study showed the presence of V. cholerae (Ogawa and Inaba in water and human stool samples. Type B V. vulnificus was detected in the water sample collected from River Migori. This information is of essence in controlling and managing cholera in the western part of Kenya. J Microbiol Infect Dis 2016;6(1: 1-7

  10. Isolation and clinical sample typing of human leptospirosis cases in Argentina.

    Science.gov (United States)

    Chiani, Yosena; Jacob, Paulina; Varni, Vanina; Landolt, Noelia; Schmeling, María Fernanda; Pujato, Nazarena; Caimi, Karina; Vanasco, Bibiana

    2016-01-01

    Leptospira typing is carried out using isolated strains. Because of difficulties in obtaining them, direct identification of infective Leptospira in clinical samples is a high priority. Multilocus sequence typing (MLST) proved highly discriminatory for seven pathogenic species of Leptospira, allowing isolate characterization and robust assignment to species, in addition to phylogenetic evidence for the relatedness between species. In this study we characterized Leptospira strains circulating in Argentina, using typing methods applied to human clinical samples and isolates. Phylogenetic studies based on 16S ribosomal RNA gene sequences enabled typing of 8 isolates (6 Leptospira interrogans, one Leptospira wolffii and one Leptospira broomii) and 58 out of 85 (68.2%) clinical samples (55 L. interrogans, 2 Leptospira meyeri, and one Leptospira kirschneri). MLST results for the L. interrogans isolates indicated that five were probably Canicola serogroup (ST37) and one was probably Icterohaemorrhagiae serogroup (ST17). Eleven clinical samples (21.6%), provided MLST interpretable data: five were probably Pyrogenes serogroup (ST13), four Sejroe (ST20), one Autumnalis (ST22) and one Canicola (ST37). To the best of our knowledge this study is the first report of the use of an MLST typing scheme with seven loci to identify Leptospira directly from clinical samples in Argentina. The use of clinical samples presents the advantage of the possibility of knowing the infecting strain without resorting to isolates. This study also allowed, for the first time, the characterization of isolates of intermediate pathogenicity species (L. wolffii and L. broomii) from symptomatic patients.

  11. Detailed faecal fat analysis using Fourier transform infrared spectroscopy: Exploring the possibilities.

    Science.gov (United States)

    De Koninck, Anne-Sophie; Nys, Karen; Vandenheede, Brent; Van Biervliet, Stephanie; Speeckaert, Marijn M; Delanghe, Joris R

    2016-11-01

    Fourier transform infrared (FTIR) spectroscopic determination of faecal fat is a simple and elegant alternative for the classical Van De Kamer approach. Besides quantification of the total amount of fat, analysis of the lipase hydrolysis efficiency (fatty acid/triglyceride ratio), fatty acid chain length and trans-unsaturated fatty acids could provide a better monitoring of dietary treatment. Stool samples (26 routine samples and 36 cystic fibrosis patients) were analysed with the Perkin Elmer Spectrum Two® spectrometer (3500-450cm(-1)). Fatty acid/triglyceride ratio was calculated using the absorbance ratio at 2855:1746cm(-1). To estimate lipase hydrolysis efficiency, sample ratios were compared with the ratio of butter and pure free fatty acids. Mean fatty acid chain length was calculated using the absorbance ratio at 2855:1709cm(-1). The absorbance at 966cm(-1) was used to trace the presence of trans-type unsaturated fatty acids. Butter showed a low fatty acid/triglyceride ratio (1.21) and pure free fatty acids a high fatty acid/triglyceride ratio (6.76). Mean fatty acid/triglyceride ratio of routine stool samples was 4.16±1.01. The applicability of fatty acid/triglyceride ratios was also tested in cystic fibrosis patients under treatment with a mean of 4.92±0.98. Relative absorbance contribution per carbon atom was 0.06 (ratio 1.06 for C18 standard, 0.91 for C16 standard). The mean ratio of the stool samples was 1.12 (mean acyl chain length of C19), with values ranging from 0.73 (C12) to 1.68 (C28). The presence of traceable amounts of trans-unsaturated fatty acids was also demonstrated. For the analysis of faecal material, FTIR provides unique information, difficult to obtain using other techniques. These findings offer perspectives for diet monitoring in patients with (non-)pancreatic malabsorption. Copyright © 2016 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

  12. Occurrence of pathogenic and faecal Escherichia coli in layer hens

    Directory of Open Access Journals (Sweden)

    Silvia Tagliabue

    2010-01-01

    Full Text Available A total of 117 Escherichia coli from colibacillosis affected (APEC and clinically healthy birds (AFEC were serotyped and tested for the presence of virulence genes: iss, tsh, cva. A total of 54.5% E. Coli were typeable and 15 different serogroups were identified. The most common serogroups among APEC strains were O78, O2 and O128, whereas O139 was predominant in faecal strains from healthy birds. Iss, tsh e cva were more frequently detected among the septicaemic E. coli strains. The association of virulence genes was observed. Particularly, the pathotype iss-tsh-cva was present in 46.5% of APEC strains. Referring to serogroups, E. coli O78 and O2 originating from colibacillosis affected birds were always isstsh- cva positive but did not share virulence genes when they came from healthy birds.

  13. Near infrared reflectance measurement of nitrogen faecal losses.

    Science.gov (United States)

    Benini, L; Caliari, S; Bonfante, F; Guidi, G C; Brentegani, M T; Castellani, G; Sembenini, C; Bardelli, E; Vantini, I

    1992-06-01

    Chemical methods of measuring nitrogen in stools are complex, unpleasant, and therefore rarely performed. Recently, near infrared reflectance (NIRA) has been suggested for stool analysis. The aim of this study was to evaluate the possible application of this method in routine faecal nitrogen measurement. Nitrogen concentration and daily output were measured in the stools of 83 patients using NIRA and, for comparison, the Kjeldahl method. Nitrogen concentration and output ranged between 0.4-2.72 g% and 0.45-8.96 g/day respectively. Correlation coefficients (r), of 0.89 and 0.97 were found between the two methods for concentration and output respectively, and similar values were found in patients on enteral nutrition. Repeated measurements from the same stool collection, requiring only a few minutes, allowed homogenisation to be avoided. NIRA seems to be an easy, fast, and reliable alternative to chemical assays of nitrogen measurement in the management of patients with digestive disorders.

  14. 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.

  15. Dioxin and PCB levels in human samples from the Greek population

    Energy Technology Data Exchange (ETDEWEB)

    Leondiadis, L.; Vassiliadou, I.; Costopoulou, D.; Papadopoulos, A. [Mass Spectrometry and Dioxin Analysis Lab. - NCSR Demokritos, Athens (Greece)

    2004-09-15

    Polychlorinated biphenyls (PCBs) are commercial chemical substances produced in a large scale since 1930, with a wide range of applications in industry, such as for coolant fluids in transformers and dielectric fluids in capacitors. After their health effects became apparent, PCB production was banned in the late 1970s. However, humans are still exposed through PCB leakage of old capacitors and transformers and disposal of contaminated materials. Dioxins (polychlorinated dibenzo-p-dioxins (PCDDs) and polychlorinated dibenzo-furans (PCDFs)), are formed as undesirable by-products mainly during the production of chlorinated chemicals and during the combustion of municipal and hazardous waste. Due to potential health hazard (dermal toxicity, immunotoxicity, reproductive effects, teratogenicity, endocrine disruption and carcinogenicity), their monitoring in humans is of high general concern. Enough information on POP presence in human tissues from industrialized countries is available to suggest that the concentration of these compounds has decreased during the last 10 years. Monitoring of human exposure to PCBs and dioxins, contaminants that accumulate in lipid tissue, is most conveniently performed by analysis of blood plasma or blood serum. Monitoring of dioxins in human milk is of also great importance, since it is especially feared that lactational exposure to dioxins and related compounds may adversely affect brain development and the immune system of infants and children. The present study includes the analyses of non-ortho, mono-ortho, indicator PCBs, and PCDD/Fs in human blood and human milk samples collected between November 2002 and February 2004 and is the first study of this kind to be undertaken in Greece.

  16. Genetic identification of missing persons: DNA analysis of human remains and compromised samples.

    Science.gov (United States)

    Alvarez-Cubero, M J; Saiz, M; Martinez-Gonzalez, L J; Alvarez, J C; Eisenberg, A J; Budowle, B; Lorente, J A

    2012-01-01

    Human identification has made great strides over the past 2 decades due to the advent of DNA typing. Forensic DNA typing provides genetic data from a variety of materials and individuals, and is applied to many important issues that confront society. Part of the success of DNA typing is the generation of DNA databases to help identify missing persons and to develop investigative leads to assist law enforcement. DNA databases house DNA profiles from convicted felons (and in some jurisdictions arrestees), forensic evidence, human remains, and direct and family reference samples of missing persons. These databases are essential tools, which are becoming quite large (for example the US Database contains 10 million profiles). The scientific, governmental and private communities continue to work together to standardize genetic markers for more effective worldwide data sharing, to develop and validate robust DNA typing kits that contain the reagents necessary to type core identity genetic markers, to develop technologies that facilitate a number of analytical processes and to develop policies to make human identity testing more effective. Indeed, DNA typing is integral to resolving a number of serious criminal and civil concerns, such as solving missing person cases and identifying victims of mass disasters and children who may have been victims of human trafficking, and provides information for historical studies. As more refined capabilities are still required, novel approaches are being sought, such as genetic testing by next-generation sequencing, mass spectrometry, chip arrays and pyrosequencing. Single nucleotide polymorphisms offer the potential to analyze severely compromised biological samples, to determine the facial phenotype of decomposed human remains and to predict the bioancestry of individuals, a new focus in analyzing this type of markers.

  17. A simple sample preparation method for measuring amoxicillin in human plasma by hollow fiber centrifugal ultrafiltration.

    Science.gov (United States)

    Dong, Wei-Chong; Hou, Zi-Li; Jiang, Xin-Hui; Jiang, Ye

    2013-02-01

    A simple sample preparation method has been developed for the determination of amoxicillin in human plasma by hollow fiber centrifugal ultrafiltration (HF-CF-UF). A 400-μL plasma sample was placed directly into the HF-CF-UF device, which consisited of a slim glass tube and a U-shaped hollow fiber. After centrifugation at 1.25 × 10(3) g for 10 min, the filtrate was withdrawn from the hollow fiber and 20 µL was directly injected into the high-performance liquid chromatography (HPLC) for analysis. The calibration curve was linear over the range of 0.1-20 µg/mL (r = 0.9996) and the limit of detection was as low as 0.025 µg/mL. The average recovery and absolute recovery were 99.9% and 84.5%, respectively. Both the intra-day and inter-day precisions (relative standard deviation) were less than 3.1% for three concentrations (0.25, 2.5 and 10 µg/mL). The sample preparation process was simplified. Only after a single centrifugal ultrafiltration can the filtrate be injected directly into HPLC. The present method is simple, sensitive and accurate. It could be effective for the analysis of biological samples with high protein contents, especially for the biopharmaceutical analysis of drugs that use traditional isolation techniques for sample preparation such as the protein precipitation method.

  18. Small Sample Kernel Association Tests for Human Genetic and Microbiome Association Studies.

    Science.gov (United States)

    Chen, Jun; Chen, Wenan; Zhao, Ni; Wu, Michael C; Schaid, Daniel J

    2016-01-01

    Kernel machine based association tests (KAT) have been increasingly used in testing the association between an outcome and a set of biological measurements due to its power to combine multiple weak signals of complex relationship with the outcome through the specification of a relevant kernel. Human genetic and microbiome association studies are two important applications of KAT. However, the classic KAT framework relies on large sample theory, and conservativeness has been observed for small sample studies, especially for microbiome association studies. The common approach for addressing the small sample problem relies on computationally intensive resampling methods. Here, we derive an exact test for KAT with continuous traits, which resolve the small sample conservatism of KAT without the need for resampling. The exact test has significantly improved power to detect association for microbiome studies. For binary traits, we propose a similar approximate test, and we show that the approximate test is very powerful for a wide range of kernels including common variant- and microbiome-based kernels, and the approximate test controls the type I error well for these kernels. In contrast, the sequence kernel association tests have slightly inflated genomic inflation factors after small sample adjustment. Extensive simulations and application to a real microbiome association study are used to demonstrate the utility of our method. © 2015 WILEY PERIODICALS, INC.

  19. A salting out and resin procedure for extracting Schistosoma mansoni DNA from human urine samples

    Directory of Open Access Journals (Sweden)

    Rodrigues Nilton B

    2010-04-01

    Full Text Available Abstract Background In this paper a simple and cheap salting out and resin (InstaGene matrix® resin - BioRad DNA extraction method from urine for PCR assays is introduced. The DNA of the fluke Schistosoma mansoni was chosen as the target since schistosomiasis lacks a suitable diagnostic tool which is sensitive enough to detect low worm burden. It is well known that the PCR technique provides high sensitivity and specificity in detecting parasite DNA. Therefore it is of paramount importance to take advantage of its excellent performance by providing a simple to handle and reliable DNA extraction procedure, which permits the diagnosis of the disease in easily obtainable urine samples. Findings The description of the extraction procedure is given. This extraction procedure was tested for reproducibility and efficiency in artificially contaminated human urine samples. The reproducibility reached 100%, showing positive results in 5 assay repetitions of 5 tested samples each containing 20 ng DNA/5 ml. The efficiency of the extraction procedure was also evaluated in a serial dilution of the original 20 ng DNA/5 ml sample. Detectable DNA was extracted when it was at a concentration of 1.28 pg DNA/mL, revealing the high efficiency of this procedure. Conclusions This methodology represents a promising tool for schistosomiasis diagnosis utilizing a bio-molecular technique in urine samples which is now ready to be tested under field conditions and may be applicable to the diagnosis of other parasitic diseases.

  20. Recognition of serous ovarian tumors in human samples by multimodal nonlinear optical microscopy

    Science.gov (United States)

    Adur, Javier; Pelegati, Vitor B.; Costa, Leverson F. L.; Pietro, Luciana; de Thomaz, Andre A.; Almeida, Diogo B.; Bottcher-Luiz, Fatima; Andrade, Liliana A. L. A.; Cesar, Carlos L.

    2011-09-01

    We used a multimodal nonlinear optics microscopy, specifically two-photon excited fluorescence (TPEF), second and third harmonic generation (SHG/THG) microscopies, to observe pathological conditions of ovarian tissues obtained from human samples. We show that strong TPEF + SHG + THG signals can be obtained in fixed samples stained with hematoxylin and eosin (H&E) stored for a very long time, and that H&E staining enhanced the THG signal. We then used the multimodal TPEF-SHG-THG microscopies in a stored file of H&E stained samples of human ovarian cancer to obtain complementary information about the epithelium/stromal interface, such as the transformation of epithelium surface (THG) and the overall fibrillary tissue architecture (SHG). This multicontrast nonlinear optics microscopy is able to not only differentiate between cancerous and healthy tissue, but can also distinguish between normal, benign, borderline, and malignant specimens according to their collagen disposition and compression levels within the extracellular matrix. The dimensions of the layers of epithelia can also be measured precisely and automatically. Our data demonstrate that optical techniques can detect pathological changes associated with ovarian cancer.

  1. Exploring the acceptability of human papillomavirus self-sampling among Muslim immigrant women.

    Science.gov (United States)

    Lofters, Aisha K; Vahabi, Mandana; Fardad, Mitra; Raza, Afrah

    2017-01-01

    With appropriate screening (ie, the Papanicolaou [Pap] test), cervical cancer is highly preventable, and high-income countries, including Canada, have observed significant decreases in cervical cancer mortality. However, certain subgroups, including immigrants from countries with large Muslim populations, experience disparities in cervical cancer screening. Little is known about the acceptability of human papillomavirus (HPV) self-sampling as a screening strategy among Muslim immigrant women in Canada. This study assessed cervical cancer screening practices, knowledge and attitudes, and acceptability of HPV self-sampling among Muslim immigrant women. A convenience sample of 30 women was recruited over a 3-month period (June-August 2015) in the Greater Toronto Area. All women were between 21 and 69 years old, foreign-born, and self-identified as Muslim, and had good knowledge of English. Data were collected through a self-completed questionnaire. More than half of the participants falsely indicated that Pap tests may cause cervical infection, and 46.7% indicated that the test is an intrusion on privacy. The majority of women reported that they would be willing to try HPV self-sampling, and more than half would prefer this method to provider-administered sampling methods. Barriers to self-sampling included confidence in the ability to perform the test and perceived cost, and facilitators included convenience and privacy being preserved. The results demonstrate that HPV self-sampling may provide a favorable alternative model of care to the traditional provider-administered Pap testing. These findings add important information to the literature related to promoting cancer screening among women who are under or never screened for cervical cancer.

  2. Human-parathormone assay for use in dogs: validation, sample handling studies, and parathyroid function testing.

    Science.gov (United States)

    Torrance, A G; Nachreiner, R

    1989-07-01

    Ten commercially available parathormone (PTH) assays were competitively validated, using dilutional parallelism, intra-assay and interassay coefficients of variation, and sensitivity and measured responses of 2 dogs to calcium and EDTA infusions. A 2-site immunoradiometric assay for intact human-PTH was superior to the others for estimating canine-PTH, met the criteria for validity, and was further investigated. A series of sample-handling studies was performed. Serum and plasma samples stored at 24 C lost 15% (n = 5; P less than 0.05) of PTH between 2 and 24 hours. This did not occur at 6 C. The mean PTH concentration of sera from blood samples clotted at 24 C was 6% (P less than 0.05) higher than equivalent EDTA samples. Serum samples stored at 6 and 37 C deteriorated 35% and 100% (n = 5; P less than 0.05), respectively, after 1 week, whereas samples stored at -20 and -70 C for 4 weeks did not deteriorate. There was no significant deterioration of PTH in samples frozen (-40 C) and thawed up to 7 times (n = 5). Parathyroid function testing was investigated by use of 2-hour infusions of disodium EDTA (25 mg/kg/h), 10-minute infusions of calcium gluconate (3 mg of elemental calcium/kg/10 min), and physiologic saline controls (n = 8). Renal function was monitored before and after EDTA infusion by exogenous creatinine clearance. Infusion of disodium EDTA increased mean PTH concentration from 67 (time 0) to 317 and 235 pg/ml at 90 and 180 minutes, respectively (P less than 0.001). Infusion of calcium gluconate decreased mean PTH concentration from 84 (time 0) to 14 and 12 pg/ml at 15 and 60 minutes, respectively (P less than 0.005). There were no observable side effects of the infusions in normal conscious dogs and no differences in exogenous creatinine clearance after EDTA infusion.

  3. Freezing adversely affects measurement of vascular endothelial growth factor levels in human aqueous samples

    Directory of Open Access Journals (Sweden)

    Sankarathi Balaiya

    2011-01-01

    Full Text Available Sankarathi Balaiya Sandeep Grover Ravi K Murthy Kakarla V ChalamDepartment of Ophthalmology, University of Florida College of Medicine, Jacksonville, FL, USAPurpose: Aqueous levels of vascular endothelial growth factor (VEGF can be a surrogate marker of intraocular VEGF activity and a measure of efficacy of anti-VEGF treatment in a variety of vasoproliferative retinal disorders, including diabetic retinopathy, age-related macular degeneration, and central retinal vein occlusion. Measurement of the VEGF level may be adversely affected by premeasurement variables, such as freezing and delay, in sample analysis. We aim to evaluate the effect of storage and delayed measurement of human aqueous VEGF levels in these conditions.Methods: Aqueous samples collected from patients receiving intravitreal injection of bevacizumab for various retinal diseases were divided into two groups. In Group 1, the VEGF levels were analyzed on the same day; in Group 2, the VEGF levels were analyzed after 21 days of freezer storage (-80°C using immunobead assay. Statistical comparison using a paired t-test was performed between the two groups.Results: Thirty-one aqueous humor samples were collected, and the VEGF concentration for fresh samples was 7.8 ± 5.9 pg/mL (mean ± SD compared to 6.5 ± 6.0 pg/mL in frozen samples, resulting in a statistically significant difference (P = 0.03.Conclusions: Accurate measurement of the VEGF level is a vital component of clinical decision-making. Delayed analysis of VEGF levels in aqueous samples may result in significant sample degradation and lower levels of measured VEGF.Keywords: VEGF level, aqueous humor, immunobead assay, VEGF storage

  4. Study of microtip-based extraction and purification of DNA from human samples for portable devices

    Science.gov (United States)

    Fotouhi, Gareth

    DNA sample preparation is essential for genetic analysis. However, rapid and easy-to-use methods are a major challenge to obtaining genetic information. Furthermore, DNA sample preparation technology must follow the growing need for point-of-care (POC) diagnostics. The current use of centrifuges, large robots, and laboratory-intensive protocols has to be minimized to meet the global challenge of limited access healthcare by bringing the lab to patients through POC devices. To address these challenges, a novel extraction method of genomic DNA from human samples is presented by using heat-cured polyethyleneimine-coated microtips generating a high electric field. The microtip extraction method is based on recent work using an electric field and capillary action integrated into an automated device. The main challenges to the method are: (1) to obtain a stable microtip surface for the controlled capture and release of DNA and (2) to improve the recovery of DNA from samples with a high concentration of inhibitors, such as human samples. The present study addresses these challenges by investigating the heat curing of polyethyleneimine (PEI) coated on the surface of the microtip. Heat-cured PEI-coated microtips are shown to control the capture and release of DNA. Protocols are developed for the extraction and purification of DNA from human samples. Heat-cured PEI-coated microtip methods of DNA sample preparation are used to extract genomic DNA from human samples. It is discovered through experiment that heat curing of a PEI layer on a gold-coated surface below 150°C could inhibit the signal of polymerase chain reaction (PCR). Below 150°C, the PEI layer is not completely cured and dissolved off the gold-coated surface. Dissolved PEI binds with DNA to inhibit PCR. Heat curing of a PEI layer above 150°C on a gold-coated surface prevents inhibition to PCR and gel electrophoresis. In comparison to gold-coated microtips, the 225°C-cured PEI-coated microtips improve the

  5. Faecal sterols as sewage markers in the Langat River, Malaysia: Integration of biomarker and multivariate statistical approaches

    Institute of Scientific and Technical Information of China (English)

    Nur Hazirah Adnan; Mohamad Pauzi Zakaria; Hafizan Juahir; Masni Mohd Ali

    2012-01-01

    The Langat River in Malaysia has been experiencing anthropogenic input from urban,rural and industrial activities for many years.Sewage contamination,possibly originating from the greater than three million inhabitants of the Langat River Basin,were examined.Sediment samples from 22 stations (SL01-SL22) along the Langat River were collected,extracted and analysed by GC-MS.Six different sterols were identified and quantified.The highest sterol concentration was found at station SL02 (618.29 ng/g dry weight),which situated in the Balak River whereas the other sediment samples ranged between 11.60 and 446.52 ng/g dry weight.Sterol ratios were used to identify sources,occurrence and partitioning of faecal matter in sediments and majority of the ratios clearly demonstrated that sewage contamination was occurring at most stations in the Langat River.A multivariate statistical analysis was used in conjunction with a combination of biomarkers to better understand the data that clearly separated the compounds.Most sediments of the Langat River were found to contain low to mid-range sewage contamination with some containing ‘significant' levels of contamination.This is the first report on sewage pollution in the Langat River based on a combination of biomarker and multivariate statistical approaches that will establish a new standard for sewage detection using faecal sterols.

  6. A faecal analysis of helminth infections in wild and captive wolves, Canis lupus L., in Poland.

    Science.gov (United States)

    Szafrańska, E; Wasielewski, O; Bereszyński, A

    2010-12-01

    One hundred and three samples of faeces of reared grey wolves from four locations (Stobnica Park and Zoological Gardens in Bydgoszcz, Wrocław and Cracow) and twenty-six samples of faeces from two free-roaming packs of grey wolf (Canis lupus L.) in Piła (Forest Divisions: Borne Sulinowo, Czarnobór, Jastrowo) and Zielona Góra (Forest Divisions: Torzym, Krosno Odrzańskie) were collected between 2005 and 2007. Helminth eggs were detected in 78.6% of faecal samples of reared grey wolves and in 88.4% of those of free-roaming wolves. The trematode Alaria alata (80.1%) and nematodes Eucoleus aerophilus (23.1%) and Spirocerca lupi (11.5%) were only detected from wild packs of wolves and the nematodes Ancylostoma caninum (35.9%), Trichuris vulpis (15.5%) and Toxocara canis (3.9%) were only detected from reared wolves. Differences were observed in the prevalence and composition of helminth fauna between reared and wild grey wolves and our results are compared with those from studies within Poland and elsewhere in Europe.

  7. Persistence of Bacillus thuringiensis bioinsecticides in the gut of human-flora-associated rats.

    Science.gov (United States)

    Wilcks, Andrea; Hansen, Bjarne Munk; Hendriksen, Niels Bohse; Licht, Tine Rask

    2006-12-01

    The capability of two bioinsecticide strains of Bacillus thuringiensis (ssp. israelensis and ssp. kurstaki) to germinate and persist in vivo in the gastrointestinal tract of human-flora-associated rats was studied. Rats were dosed either with vegetative cells or spores of the bacteria for 4 consecutive days. In animals fed spores, B. thuringiensis cells were detected in faecal and intestinal samples of all animals, whereas vegetative cells only poorly survived the gastric passage. Heat-treatment of intestinal samples, which kills vegetative cells, revealed that B. thuringiensis spores were capable of germination in the gastrointestinal tract. In one animal fed spores of B. thuringiensis ssp. kurstaki, these bacteria were detected at high density (10(3)-10(4) CFU g(-1) faecal and intestinal samples) even 2 weeks after the last dosage. In the same animal, passage of B. thuringiensis ssp. kurstaki to the spleen was observed; however, no other adverse effects were observed. Denaturing gradient gel electrophoresis of PCR-amplified bacterial 16S rRNA genes in faecal samples revealed no major effect of B. thuringiensis on the composition of the indigenous gut bacteria. Additionally, no cytotoxic effect was detectable in gut samples by Vero cell assay.

  8. Paenibacillus spp. isolated from human and environmental samples in Spain: detection of 11 new species

    Directory of Open Access Journals (Sweden)

    J.A. Sáez-Nieto

    2017-09-01

    Full Text Available One hundred thirty-six isolates, 88 human and 48 environmental, that met the requirements to belong to the genus Paenibacillus were identified using a polyphasic taxonomic approach known as 16S rRNA plus phenotypic traits. Thirty-seven Paenibacillus species were identified; some had not been previously reported from clinical samples. The main species were P. pabuli (13 isolates, P. provencensis (11, P. phoenicis (9 and P. lautus (8. P. pabuli (11/13 and P. provencensis (8/11 were mainly environmental isolates, while P. phoenicis (9/9 and P. lautus (6/8 were mainly human isolates. Despite the difficulties in assigning to human Paenibacillus isolates a role as a pathogen or contaminant, here 25% of the isolates were involved in true infections, especially in those cases that affected abscesses, wound exudates, ocular infections and diverse fluids. In addition, 15 isolates were identified as 11 ‘Candidatus’ to a new species, all of them from human specimens except one that was obtained from laboratory air. The antimicrobial susceptibility testing showed 95.6% of isolates were resistant to ampicillin, 44% were resistant to cotrimoxazole, 20 to 30% were resistant to cefotaxime and vancomycin and 13% were resistant to rifampicin and erythromycin.

  9. Applicability of the CALUX bioassay for screening of dioxin levels in human milk samples

    DEFF Research Database (Denmark)

    Laier, P.; Cederberg, Tommy Licht; Larsen, John Christian;

    2003-01-01

    . The results obtained with the bioassay when testing milk extracts fractionated into dioxins/furans, non-ortho PCB and mono/di-ortho PCB fractions indicated that the correlation between the bioassay and the chemical analyses depends primarily on the A receptor activity observed in the mono/di-ortho PCB......The CALUX (chemically activated luciferase expression) bioassay based on rat hepatoma (H4IIE) cells is a sensitive assay for the detection of Ah receptor agonists like 2,3,7,8-substituted chlorinated dibenzo-p-dioxins and dibenzofurans and related PCBs. In this paper, the assay was optimized...... and applied for monitoring levels of dioxins in human milk samples. Combination effects of dioxin-like compounds were evaluated by testing potential mechanisms of interaction between seven of the major dioxin-like compounds in human milk using the isobole method. Results showed that the compounds acted...

  10. Dioxin-like activity in environmental and human samples from Greenland and Denmark

    DEFF Research Database (Denmark)

    Long, Manhai; Bonefeld-Jørgensen, Eva Cecilie

    2012-01-01

    of surface waters with dioxins. Our results from human studies suggest that the serum DL-activity reflect the complex mixture of persistent organic pollutants (POPs). Greenlandic Inuit had lower serum DL-activity level compared to Europeans, probably due to long distance from the dioxin sources and UV...... degradation of the high potent dioxin and/or the inhibitory effect of the high level of non-DL POPs. Selective bioaccumulation of PCBs in the food chain may contribute to the negative correlation between serum POPs and DL-activity observed in Greenlandic Inuit. Hence the AhR transactivation bioassay provides...... a cost-effective and integrated screening tool for measurement of the DL-activity in human, environmental and commercial samples....

  11. Nondestructive sampling of human skeletal remains yields ancient nuclear and mitochondrial DNA.

    Science.gov (United States)

    Bolnick, Deborah A; Bonine, Holly M; Mata-Míguez, Jaime; Kemp, Brian M; Snow, Meradeth H; LeBlanc, Steven A

    2012-02-01

    Museum curators and living communities are sometimes reluctant to permit ancient DNA (aDNA) studies of human skeletal remains because the extraction of aDNA usually requires the destruction of at least some skeletal material. Whether these views stem from a desire to conserve precious materials or an objection to destroying ancestral remains, they limit the potential of aDNA research. To help address concerns about destructive analysis and to minimize damage to valuable specimens, we describe a nondestructive method for extracting DNA from ancient human remains. This method can be used with both teeth and bone, but it preserves the structural integrity of teeth much more effectively than that of bone. Using this method, we demonstrate that it is possible to extract both mitochondrial and nuclear DNA from human remains dating between 300 BC and 1600 AD. Importantly, the method does not expose the remains to hazardous chemicals, allowing them to be safely returned to curators, custodians, and/or owners of the samples. We successfully amplified mitochondrial DNA from 90% of the individuals tested, and we were able to analyze 1-9 nuclear loci in 70% of individuals. We also show that repeated nondestructive extractions from the same tooth can yield amplifiable mitochondrial and nuclear DNA. The high success rate of this method and its ability to yield DNA from samples spanning a wide geographic and temporal range without destroying the structural integrity of the sampled material may make possible the genetic study of skeletal collections that are not available for destructive analysis. Copyright © 2011 Wiley Periodicals, Inc.

  12. An Improved Method for High Quality Metagenomics DNA Extraction from Human and Environmental Samples

    DEFF Research Database (Denmark)

    Bag, Satyabrata; Saha, Bipasa; Mehta, Ojasvi

    2016-01-01

    and human origin samples. We introduced a combination of physical, chemical and mechanical lysis methods for proper lysis of microbial inhabitants. The community microbial DNA was precipitated by using salt and organic solvent. Both the quality and quantity of isolated DNA was compared with the existing...... methodologies and the supremacy of our method was confirmed. Maximum recovery of genomic DNA in the absence of substantial amount of impurities made the method convenient for nucleic acid extraction. The nucleic acids obtained using this method are suitable for different downstream applications. This improved...

  13. Modular Sampling and Analysis Techniques for the Real-Time Analysis of Human Breath

    Energy Technology Data Exchange (ETDEWEB)

    Frank, M; Farquar, G; Adams, K; Bogan, M; Martin, A; Benner, H; Spadaccini, C; Steele, P; Davis, C; Loyola, B; Morgan, J; Sankaran, S

    2007-07-09

    At LLNL and UC Davis, we are developing several techniques for the real-time sampling and analysis of trace gases, aerosols and exhaled breath that could be useful for a modular, integrated system for breath analysis. Those techniques include single-particle bioaerosol mass spectrometry (BAMS) for the analysis of exhaled aerosol particles or droplets as well as breath samplers integrated with gas chromatography mass spectrometry (GC-MS) or MEMS-based differential mobility spectrometry (DMS). We describe these techniques and present recent data obtained from human breath or breath condensate, in particular, addressing the question of how environmental exposure influences the composition of breath.

  14. Genetic Characterization of Atypical Mansonella (Mansonella) ozzardi Microfilariae in Human Blood Samples from Northeastern Peru

    Science.gov (United States)

    Marcos, Luis A.; Arrospide, Nancy; Recuenco, Sergio; Cabezas, Cesar; Weil, Gary J.; Fischer, Peter U.

    2012-01-01

    DNA sequence comparisons are useful for characterizing proposed new parasite species or strains. Microfilariae with an atypical arrangement of nuclei behind the cephalic space have been recently described in human blood samples from the Amazon region of Peru. Three blood specimens containing atypical microfilariae were genetically characterized using three DNA markers (5S ribosomal DNA, 12S ribosomal DNA, and cytochrome oxidase I). All atypical microfilariae were clustered into the Mansonella group and indistinguishable from M. ozzardi based on these DNA markers. PMID:22826497

  15. [The quality control of preanalytical variations for the determination of lead in samples of human origin].

    Science.gov (United States)

    Zhong, Kun; Wang, Wei; He, Falin; Wang, Zhiguo

    2015-02-01

    The aims of this article was to provide the quality control requirements of preanalytical variation for the determination of lead in samples of human origin, reduce the influence of preanalytical variation on the test results. According to the Clinical and Laboratory Standards Institute documents, control of preanalytical variation in trace element determinations, analytical procedures for the determination of lead in blood and urine and other references and guidelines, the methods of quality control of lead determination had been made, including: the factors needed to be considered before collection, preservation, transportation and other preanalytical factors, the abilities and considerations of laboratory staff, etc.

  16. Antibiotic resistance genes in the bacteriophage DNA fraction of human fecal samples.

    Science.gov (United States)

    Quirós, Pablo; Colomer-Lluch, Marta; Martínez-Castillo, Alexandre; Miró, Elisenda; Argente, Marc; Jofre, Juan; Navarro, Ferran; Muniesa, Maite

    2014-01-01

    A group of antibiotic resistance genes (ARGs) (blaTEM, blaCTX-M-1, mecA, armA, qnrA, and qnrS) were analyzed by real-time quantitative PCR (qPCR) in bacteriophage DNA isolated from feces from 80 healthy humans. Seventy-seven percent of the samples were positive in phage DNA for one or more ARGs. blaTEM, qnrA, and, blaCTX-M-1 were the most abundant, and armA, qnrS, and mecA were less prevalent. Free bacteriophages carrying ARGs may contribute to the mobilization of ARGs in intra- and extraintestinal environments.

  17. Calcium isolation from large-volume human urine samples for 41Ca analysis by accelerator mass spectrometry.

    Science.gov (United States)

    Miller, James J; Hui, Susanta K; Jackson, George S; Clark, Sara P; Einstein, Jane; Weaver, Connie M; Bhattacharyya, Maryka H

    2013-08-01

    Calcium oxalate precipitation is the first step in preparation of biological samples for (41)Ca analysis by accelerator mass spectrometry. A simplified protocol for large-volume human urine samples was characterized, with statistically significant increases in ion current and decreases in interference. This large-volume assay minimizes cost and effort and maximizes time after (41)Ca administration during which human samples, collected over a lifetime, provide (41)Ca:Ca ratios that are significantly above background.

  18. Calcium Isolation from Large-Volume Human Urine Samples for 41Ca Analysis by Accelerator Mass Spectrometry

    Science.gov (United States)

    Miller, James J; Hui, Susanta K; Jackson, George S; Clark, Sara P; Einstein, Jane; Weaver, Connie M; Bhattacharyya, Maryka H

    2013-01-01

    Calcium oxalate precipitation is the first step in preparation of biological samples for 41Ca analysis by accelerator mass spectrometry. A simplified protocol for large-volume human urine samples was characterized, with statistically significant increases in ion current and decreases in interference. This large-volume assay minimizes cost and effort and maximizes time after 41Ca administration during which human samples, collected over a lifetime, provide 41Ca:Ca ratios that are significantly above background. PMID:23672965

  19. Human Cytomegalovirus and Human Umbilical Vein Endothelial Cells: Restriction of Primary Isolation to Blood Samples and Susceptibilities of Clinical Isolates from Other Sources to Adaptation

    OpenAIRE

    2002-01-01

    In immunocompromised patients with disseminated infection, human cytomegalovirus (HCMV) is widespread in the microvascular endothelium of multiple organs. Human umbilical vein endothelial cells (HUVEC) were used in parallel to human embryonic lung fibroblasts (HELF) to recover HCMV from blood samples of immunocompromised patients. Using the shell vial technique, comparable median numbers of p72-positive HUVEC and HELF cells were found with the 26 HCMV-positive buffy coat samples out of 150 ex...

  20. Optimization of a Pre-MEKC Separation SPE Procedure for Steroid Molecules in Human Urine Samples

    Directory of Open Access Journals (Sweden)

    Ilona Olędzka

    2013-11-01

    Full Text Available Many steroid hormones can be considered as potential biomarkers and their determination in body fluids can create opportunities for the rapid diagnosis of many diseases and disorders of the human body. Most existing methods for the determination of steroids are usually time- and labor-consuming and quite costly. Therefore, the aim of analytical laboratories is to develop a new, relatively low-cost and rapid implementation methodology for their determination in biological samples. Due to the fact that there is little literature data on concentrations of steroid hormones in urine samples, we have made attempts at the electrophoretic determination of these compounds. For this purpose, an extraction procedure for the optimized separation and simultaneous determination of seven steroid hormones in urine samples has been investigated. The isolation of analytes from biological samples was performed by liquid-liquid extraction (LLE with dichloromethane and compared to solid phase extraction (SPE with C18 and hydrophilic-lipophilic balance (HLB columns. To separate all the analytes a micellar electrokinetic capillary chromatography (MECK technique was employed. For full separation of all the analytes a running buffer (pH 9.2, composed of 10 mM sodium tetraborate decahydrate (borax, 50 mM sodium dodecyl sulfate (SDS, and 10% methanol was selected. The methodology developed in this work for the determination of steroid hormones meets all the requirements of analytical methods. The applicability of the method has been confirmed for the analysis of urine samples collected from volunteers—both men and women (students, amateur bodybuilders, using and not applying steroid doping. The data obtained during this work can be successfully used for further research on the determination of steroid hormones in urine samples.

  1. Three dimensional imaging of paraffin embedded human lung tissue samples by micro-computed tomography.

    Directory of Open Access Journals (Sweden)

    Anna E Scott

    Full Text Available Understanding the three-dimensional (3-D micro-architecture of lung tissue can provide insights into the pathology of lung disease. Micro computed tomography (µCT has previously been used to elucidate lung 3D histology and morphometry in fixed samples that have been stained with contrast agents or air inflated and dried. However, non-destructive microstructural 3D imaging of formalin-fixed paraffin embedded (FFPE tissues would facilitate retrospective analysis of extensive tissue archives of lung FFPE lung samples with linked clinical data.FFPE human lung tissue samples (n = 4 were scanned using a Nikon metrology µCT scanner. Semi-automatic techniques were used to segment the 3D structure of airways and blood vessels. Airspace size (mean linear intercept, Lm was measured on µCT images and on matched histological sections from the same FFPE samples imaged by light microscopy to validate µCT imaging.The µCT imaging protocol provided contrast between tissue and paraffin in FFPE samples (15 mm x 7 mm. Resolution (voxel size 6.7 µm in the reconstructed images was sufficient for semi-automatic image segmentation of airways and blood vessels as well as quantitative airspace analysis. The scans were also used to scout for regions of interest, enabling time-efficient preparation of conventional histological sections. The Lm measurements from µCT images were not significantly different to those from matched histological sections.We demonstrated how non-destructive imaging of routinely prepared FFPE samples by laboratory µCT can be used to visualize and assess the 3D morphology of the lung including by morphometric analysis.

  2. High-throughput miRNA profiling of human melanoma blood samples

    Directory of Open Access Journals (Sweden)

    Rass Knuth

    2010-06-01

    Full Text Available Abstract Background MicroRNA (miRNA signatures are not only found in cancer tissue but also in blood of cancer patients. Specifically, miRNA detection in blood offers the prospect of a non-invasive analysis tool. Methods Using a microarray based approach we screened almost 900 human miRNAs to detect miRNAs that are deregulated in their expression in blood cells of melanoma patients. We analyzed 55 blood samples, including 20 samples of healthy individuals, 24 samples of melanoma patients as test set, and 11 samples of melanoma patients as independent validation set. Results A hypothesis test based approch detected 51 differentially regulated miRNAs, including 21 miRNAs that were downregulated in blood cells of melanoma patients and 30 miRNAs that were upregulated in blood cells of melanoma patients as compared to blood cells of healthy controls. The tets set and the independent validation set of the melanoma samples showed a high correlation of fold changes (0.81. Applying hierarchical clustering and principal component analysis we found that blood samples of melanoma patients and healthy individuals can be well differentiated from each other based on miRNA expression analysis. Using a subset of 16 significant deregulated miRNAs, we were able to reach a classification accuracy of 97.4%, a specificity of 95% and a sensitivity of 98.9% by supervised analysis. MiRNA microarray data were validated by qRT-PCR. Conclusions Our study provides strong evidence for miRNA expression signatures of blood cells as useful biomarkers for melanoma.

  3. Detection of Human Papillomavirus 18 in Cervical Cancer Samples Using PCR-ELISA (DIAPOPS

    Directory of Open Access Journals (Sweden)

    KN Tafreshi

    2011-12-01

    Full Text Available Background and Objectives: Human Papillomavirus (HPV infection is a major risk factor for adenocarcinoma of the cervix. The high-risk types of the virus such as HPV16 and HPV18, which possess the E6 and E7 oncogenes, are responsible for approximately 50% of all cervical cancers. A rapid, sensitive and specific test has been proposed for detection of HPV to improve cervical cancer screening programs.Objectives: The aim of this study was to develop a fast PCR-ELISA assay designated as DIAPOPS (Detection of Immobilized Amplified Products in a One Phase Systemfor detection of HPV16 and HPV18 types in SCC samples and Pap smears. The type specific primers and probes were designed for PCR and PCR-ELISA. The amplified products were hybridized with a specific biotin-labeled probe for HPV18 inner amplicons. The hybrids were detected with peroxidase conjugated avidin. The test was performed on the paraffin block and Pap smear samples from the cervical cancer patients, and the results of DIAPOPS were compared with conventional PCR assay.Results: The 70 samples (SCC and Pap smear samples were collected from Imam Khomeini and Mirzakoochak Khan Hospitals in Tehran. The PCR-based method detected six HPV16 positive, three HPV18 positive and Two HPV33 positive samples. DIAPOPS results were compared with the conventional PCR results and they showed an increase in sensitivity of the DIAPOPS test. Not only all of them were confirmed by PCR-ELISA but also three samples that conventional PCR showed negative for HPV18, were demonstrated positive by the PCR-ELISA method.Conclusion: The results of the study show that modified PCR-ELISA assay is more sensitive to detect HPV types and can be used for diagnostic purposes.

  4. Wheat bran extract alters colonic fermentation and microbial composition, but does not affect faecal water toxicity: a randomised controlled trial in healthy subjects.

    Science.gov (United States)

    Windey, Karen; De Preter, Vicky; Huys, Geert; Broekaert, Willem F; Delcour, Jan A; Louat, Thierry; Herman, Jean; Verbeke, Kristin

    2015-01-28

    Wheat bran extract (WBE), containing arabinoxylan-oligosaccharides that are potential prebiotic substrates, has been shown to modify bacterial colonic fermentation in human subjects and to beneficially affect the development of colorectal cancer (CRC) in rats. However, it is unclear whether these changes in fermentation are able to reduce the risk of developing CRC in humans. The aim of the present study was to evaluate the effects of WBE on the markers of CRC risk in healthy volunteers, and to correlate these effects with colonic fermentation. A total of twenty healthy subjects were enrolled in a double-blind, cross-over, randomised, controlled trial in which the subjects ingested WBE (10 g/d) or placebo (maltodextrin, 10 g/d) for 3 weeks, separated by a 3-week washout period. At the end of each study period, colonic handling of NH3 was evaluated using the biomarker lactose[15N, 15N']ureide, colonic fermentation was characterised through a metabolomics approach, and the predominant microbial composition was analysed using denaturing gradient gel electrophoresis. As markers of CRC risk, faecal water genotoxicity was determined using the comet assay and faecal water cytotoxicity using a colorimetric cell viability assay. Intake of WBE induced a shift from urinary to faecal 15N excretion, indicating a stimulation of colonic bacterial activity and/or growth. Microbial analysis revealed a selective stimulation of Bifidobacterium adolescentis. In addition, WBE altered the colonic fermentation pattern and significantly reduced colonic protein fermentation compared with the run-in period. However, faecal water cytotoxicity and genotoxicity were not affected. Although intake of WBE clearly affected colonic fermentation and changed the composition of the microbiota, these changes were not associated with the changes in the markers of CRC risk.

  5. Multi-elemental imaging of paraffin-embedded human samples by laser-induced breakdown spectroscopy

    Science.gov (United States)

    Moncayo, S.; Trichard, F.; Busser, B.; Sabatier-Vincent, M.; Pelascini, F.; Pinel, N.; Templier, I.; Charles, J.; Sancey, L.; Motto-Ros, V.

    2017-07-01

    Chemical elements play central roles for physiological homeostasis in human cells, and their dysregulation might lead to a certain number of pathologies. Novel imaging techniques that improve the work of pathologists for tissue analysis and diagnostics are continuously sought. We report the use of Laser-Induced Breakdown Spectroscopy (LIBS) to perform multi-elemental images of human paraffin-embedded skin samples on the entire biopsy scale in a complementary and compatible way with microscope histopathological examination. A specific instrumental configuration is proposed in order to detect most of the elements of medical interest (i.e. P, Al, Mg, Na, Zn, Si, Fe, and Cu). As an example of medical application, we selected and analysed skin biopsies, including healthy skin tissue, cutaneous metastasis of melanoma, Merkel-cell carcinoma and squamous cell carcinoma. Clear distinctions in the distribution of chemical elements are observed from the different samples investigated. This study demonstrates the high complementarity of LIBS elemental imaging with conventional histopathology, opening new opportunities for any medical application involving metals.

  6. Quantitative second-harmonic generation imaging to detect osteogenesis imperfecta in human skin samples

    Science.gov (United States)

    Adur, J.; Ferreira, A. E.; D'Souza-Li, L.; Pelegati, V. B.; de Thomaz, A. A.; Almeida, D. B.; Baratti, M. O.; Carvalho, H. F.; Cesar, C. L.

    2012-03-01

    Osteogenesis Imperfecta (OI) is a genetic disorder that leads to bone fractures due to mutations in the Col1A1 or Col1A2 genes that affect the primary structure of the collagen I chain with the ultimate outcome in collagen I fibrils that are either reduced in quantity or abnormally organized in the whole body. A quick test screening of the patients would largely reduce the sample number to be studied by the time consuming molecular genetics techniques. For this reason an assessment of the human skin collagen structure by Second Harmonic Generation (SHG) can be used as a screening technique to speed up the correlation of genetics/phenotype/OI types understanding. In the present work we have used quantitative second harmonic generation (SHG) imaging microscopy to investigate the collagen matrix organization of the OI human skin samples comparing with normal control patients. By comparing fibril collagen distribution and spatial organization, we calculated the anisotropy and texture patterns of this structural protein. The analysis of the anisotropy was performed by means of the two-dimensional Discrete Fourier Transform and image pattern analysis with Gray-Level Co-occurrence Matrix (GLCM). From these results, we show that statistically different results are obtained for the normal and disease states of OI.

  7. Goblet cells of the normal human bulbar conjunctiva and their assessment by impression cytology sampling.

    Science.gov (United States)

    Doughty, Michael J

    2012-07-01

    Goblet cells of the conjunctiva are the main source of mucus for the ocular surface. The objectives of this review are to consider the goblet cells as assessed by various histological, cytological and electron microscopy methods, and to assess the consistency of published reports (over more than 25 years) of goblet cell density (GCD) from impression cytology specimens from nominally healthy human subjects. Reported GCD values have been notably variable, with a range from 24 to 2226 cells/mm² for average values. Data analysis suggests that a high density of goblet cells should be expected for the healthy human conjunctiva, with a tendency toward higher values in samples taken from normally covered locations (inferior and superior bulbar conjunctiva) of the open eye (at 973 +/- 789 cells/ mm²) than in samples taken from exposed (interpalpebral) locations (at 427 +/- 376 cells/mm²). No obvious change in GCD was found with respect to age, perhaps because the variability of the data did not allow detection of any age-related decline in GCD. Analyses of published data from 33 other sources indicated a trend for GCD to be lower than normal across a spectrum of ocular surface diseases.

  8. Deep RNA sequencing analysis of readthrough gene fusions in human prostate adenocarcinoma and reference samples

    Directory of Open Access Journals (Sweden)

    Nacu Serban

    2011-01-01

    Full Text Available Abstract Background Readthrough fusions across adjacent genes in the genome, or transcription-induced chimeras (TICs, have been estimated using expressed sequence tag (EST libraries to involve 4-6% of all genes. Deep transcriptional sequencing (RNA-Seq now makes it possible to study the occurrence and expression levels of TICs in individual samples across the genome. Methods We performed single-end RNA-Seq on three human prostate adenocarcinoma samples and their corresponding normal tissues, as well as brain and universal reference samples. We developed two bioinformatics methods to specifically identify TIC events: a targeted alignment method using artificial exon-exon junctions within 200,000 bp from adjacent genes, and genomic alignment allowing splicing within individual reads. We performed further experimental verification and characterization of selected TIC and fusion events using quantitative RT-PCR and comparative genomic hybridization microarrays. Results Targeted alignment against artificial exon-exon junctions yielded 339 distinct TIC events, including 32 gene pairs with multiple isoforms. The false discovery rate was estimated to be 1.5%. Spliced alignment to the genome was less sensitive, finding only 18% of those found by targeted alignment in 33-nt reads and 59% of those in 50-nt reads. However, spliced alignment revealed 30 cases of TICs with intervening exons, in addition to distant inversions, scrambled genes, and translocations. Our findings increase the catalog of observed TIC gene pairs by 66%. We verified 6 of 6 predicted TICs in all prostate samples, and 2 of 5 predicted novel distant gene fusions, both private events among 54 prostate tumor samples tested. Expression of TICs correlates with that of the upstream gene, which can explain the prostate-specific pattern of some TIC events and the restriction of the SLC45A3-ELK4 e4-e2 TIC to ERG-negative prostate samples, as confirmed in 20 matched prostate tumor and normal

  9. Exploring the acceptability of human papillomavirus self-sampling among Muslim immigrant women

    Directory of Open Access Journals (Sweden)

    Lofters AK

    2017-07-01

    Full Text Available Aisha K Lofters,1–4 Mandana Vahabi,5,6 Mitra Fardad,7 Afrah Raza8 1Centre for Urban Health Solutions, Li Ka Shing Knowledge Institute, St. Michael’s Hospital, 2Department of Family and Community Medicine, University of Toronto, 3Department of Family and Community Medicine, St. Michael’s Hospital, 4Institute for Clinical Evaluative Sciences, 5Faculty of Community Services, Daphne Cockwell School of Nursing, 6Graduate Program in Immigration and Settlement Studies, Ryerson University, 7Faculty of Community Service, Daphne Cockwell School of Nursing, Ryerson University, Toronto, ON, Canada; 8University of Michigan Medical School, Ann Arbor, MI, USA Background: With appropriate screening (ie, the Papanicolaou [Pap] test, cervical cancer is highly preventable, and high-income countries, including Canada, have observed significant decreases in cervical cancer mortality. However, certain subgroups, including immigrants from countries with large Muslim populations, experience disparities in cervical cancer screening. Little is known about the acceptability of human papillomavirus (HPV self-sampling as a screening strategy among Muslim immigrant women in Canada. This study assessed cervical cancer screening practices, knowledge and attitudes, and acceptability of HPV self-sampling among Muslim immigrant women. Methods: A convenience sample of 30 women was recruited over a 3-month period (June–August 2015 in the Greater Toronto Area. All women were between 21 and 69 years old, foreign-born, and self-identified as Muslim, and had good knowledge of English. Data were collected through a self-completed questionnaire. Results: More than half of the participants falsely indicated that Pap tests may cause cervical infection, and 46.7% indicated that the test is an intrusion on privacy. The majority of women reported that they would be willing to try HPV self-sampling, and more than half would prefer this method to provider-administered sampling methods

  10. Microbial water quality and sedimentary faecal sterols as markers of sewage contamination in Kuwait.

    Science.gov (United States)

    Lyons, B P; Devlin, M J; Abdul Hamid, S A; Al-Otiabi, A F; Al-Enezi, M; Massoud, M S; Al-Zaidan, A S; Smith, A J; Morris, S; Bersuder, P; Barber, J L; Papachlimitzou, A; Al-Sarawi, H A

    2015-11-30

    Microbial water quality and concentrations of faecal sterols in sediment have been used to assess the degree of sewage contamination in Kuwait's marine environment. A review of microbial (faecal coliform, faecal streptococci and Escherichia coli) water quality data identified temporal and spatial sources of pollution around the coastline. Results indicated that bacterial counts regularly breach regional water quality guidelines. Sediments collected from a total of 29 sites contained detectable levels of coprostanol with values ranging from 29 to 2420 ng g(-1) (dry weight). Hot spots based on faecal sterol sediment contamination were identified in Doha Bay and Sulaibikhat Bay, which are both smaller embayments of Kuwait Bay. The ratio of epicoprostanol/coprostanol indicates that a proportion of the contamination was from raw or partially treated sewage. Sewage pollution in these areas are thought to result from illegal connections and discharges from storm drains, such as that sited at Al-Ghazali.

  11. Reset of a critically disturbed microbial ecosystem: faecal transplant in recurrent Clostridium difficile infection

    NARCIS (Netherlands)

    Fuentes Enriquez de Salamanca, S.; Nood, van E.; Tims, S.; Heikamp-de Jong, I.; Braak, ter C.J.F.; Keller, J.J.; Zoetendal, E.G.; Vos, de W.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

  12. Prevalence of human papillomavirus infection in a clinic sample of transsexuals in Italy.

    Science.gov (United States)

    Loverro, Giuseppe; Di Naro, Edoardo; Caringella, Anna Maria; De Robertis, Anna Lisa; Loconsole, Daniela; Chironna, Maria

    2016-02-01

    Detectable human papillomavirus (HPV) DNA is the most common sexually transmitted infection. Reports on the prevalence of detectable HPV DNA among transsexuals (not sex workers) are scarce. The objective of the study was to determine the prevalence of detectable HPV DNA in a clinic sample of transsexuals and to assess the relationship between detectable HPV DNA and cytological outcomes. Clinical samples (oral, anal, vaginal, cervicovaginal and penile scraped cells) from 35 transsexuals (surgically treated and surgically untreated) who attended the outpatient Clinic of Gender Identity Dysphoria of the Department of Obstetrics and Gynecology of Policlinico Hospital (Bari, Italy) were collected for cytological analysis and HPV DNA detection and typing. All enrolled subjects answered an anonymous structured questionnaire about their sexual habits. Serological status for other sexually transmitted diseases (hepatitis B virus (HBV), hepatitis C virus (HCV), HIV and syphilis) was also evaluated. HPV DNA was detected in 14 of 35 patients (40.0%). The prevalence of detectable HPV DNA was 38.2% (13/34) in tested anal samples, 9.1% (2/22) in vaginal samples and 8.3% (1/12) in penile samples. Oncogenic HPV genotypes have been detected in 93% of HPV-positive transsexuals. More than one-third (35.7%) of HPV-positive transsexuals were infected with at least one of the four vaccine-preventable genotypes, 6, 11, 16 and 18. The high rate of detectable HPV DNA by oncogenic types suggests that periodic cytological screening and clinical evaluation may be necessary since transsexuals are at high risk of anogenital cancer. Also promoting HPV vaccination in younger subjects may be advisable. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

  13. Comparison of sequencing platforms for single nucleotide variant calls in a human sample.

    Science.gov (United States)

    Ratan, Aakrosh; Miller, Webb; Guillory, Joseph; Stinson, Jeremy; Seshagiri, Somasekar; Schuster, Stephan C

    2013-01-01

    Next-generation sequencings platforms coupled with advanced bioinformatic tools enable re-sequencing of the human genome at high-speed and large cost savings. We compare sequencing platforms from Roche/454(GS FLX), Illumina/HiSeq (HiSeq 2000), and Life Technologies/SOLiD (SOLiD 3 ECC) for their ability to identify single nucleotide substitutions in whole genome sequences from the same human sample. We report on significant GC-related bias observed in the data sequenced on Illumina and SOLiD platforms. The differences in the variant calls were investigated with regards to coverage, and sequencing error. Some of the variants called by only one or two of the platforms were experimentally tested using mass spectrometry; a method that is independent of DNA sequencing. We establish several causes why variants remained unreported, specific to each platform. We report the indel called using the three sequencing technologies and from the obtained results we conclude that sequencing human genomes with more than a single platform and multiple libraries is beneficial when high level of accuracy is required.

  14. Accumulation levels and characteristics of some pesticides in human adipose tissue samples from Southeast China.

    Science.gov (United States)

    Wang, Na; Shi, Lili; Kong, Deyang; Cai, Daoji; Cao, Yanzhong; Liu, Yongming; Pang, Guofang; Yu, Rongbin

    2011-08-01

    This paper presents a comprehensive study of pesticide levels and bio-accumulation characteristics in human adipose tissues among residents of Southeast China. A large number of adipose samples (n=633) were selected for 58 pesticides and were analyzed by high sensitive Gas Chromatography-Tandem Mass Spectrometry (GC-MS/MS). The results showed that POPs pesticides were frequently detected, including 2,4'-DDD, 2,4'-DDE, 2,4'-DDT, 4,4'-DDD, 4,4'-DDE, 4,4'-DDT, α-HCH, β-HCH, γ-HCH, δ-HCH, hexachlorobenzene (HCB), and mirex. Other detected pesticide species were dicofol, methamidophos and chlordimeform, which have rarely been reported. Comparing to different countries, the concentrations of total DDT and HCH in these three Chinese southeastern sites were in the middle range, whereas the HCB and mirex were in the lower end. A significant correlation was observed between region as well as age and POPs pesticide levels. Some pesticide residue levels were also found significantly correlated to occupation. However, there was no significant correlation between gender and pesticides. Meanwhile, it is interesting to find that mortality of malignant tumors tends to associate with the pesticides levels in human adipose tissue. More importantly, the measured data presented in this study provide realistic information which is useful for assessing human exposure to pesticides in the general population of Southeast China. Copyright © 2011 Elsevier Ltd. All rights reserved.

  15. Tracking human footprints in Antarctica through passive sampling of polycyclic aromatic hydrocarbons in inland lakes.

    Science.gov (United States)

    Yao, Yao; Meng, Xiang-Zhou; Wu, Chen-Chou; Bao, Lian-Jun; Wang, Feng; Wu, Feng-Chang; Zeng, Eddy Y

    2016-06-01

    Freely dissolved polycyclic aromatic hydrocarbons (PAHs) were monitored in seven inland lakes of Antarctica by a polyethylene (PE)-based passive sampling technique, with the objective of tracking human footprints. The measured concentrations of PAHs were in the range of 14-360 ng L(-1) with the highest values concentrated around the Russian Progress II Station, indicating the significance of human activities to the loading of PAHs in Antarctica. The concentrations of PAHs in the inland lakes were in the upper part of the PAHs levels in aquatic environments from remote and background regions across the globe. The composition profiles of PAHs indicated that PAHs in the inland lakes were derived mainly from local oil spills, which was corroborated by a large number of fuel spillage reports from ship and plane crash incidents in Antarctica during recent years. Clearly, local human activities, rather than long-range transport, are the dominant sources of PAH contamination to the inland lakes. Finally, the present study demonstrates the efficacy of PE-based passive samplers for investigating PAHs in the aquatic environment of Antarctica under complex field conditions.

  16. Effect of environmental parameters on pathogen and faecal indicator organism concentrations within an urban estuary

    Science.gov (United States)

    Henry, Rebekah; Schang, Christelle; Kolotelo, Peter; Coleman, Rhys; Rooney, Graham; Schmidt, Jonathan; Deletic, Ana; McCarthy, David T.

    2016-06-01

    Current World Health Organisation figures estimate that ∼2.5 million deaths per year result from recreational contact with contaminated water sources. Concerns about quantitative risk assessments of waterways using faecal indicator organisms (FIOs) as surrogates to infer pathogenic risk currently exist. In Melbourne, Australia, the Yarra River has come under public scrutiny due to perceived public health risks associated with aquatic recreation; a characteristic shared with urban estuaries worldwide. A 10-month study of the Yarra estuary investigated the processes that affect FIOs and pathogens within this system. A total of 74 samples were collected from three estuarine and two upstream, freshwater, locations under different climatic and hydrological conditions, and the levels of Escherichia coli, enterococci, Clostridium perfringens, fRNA coliphages, Campylobacter spp. Cryptosporidium oocysts, Giardia cysts, adenoviruses, and enteroviruses were monitored. Reference pathogenic bacteria, protozoa, and viruses were detected in 81%, 19%, and 8% of samples, respectively. Variations in FIO concentrations were found to be associated with changes in specific climatic and hydrological variables including: temperature, flow, humidity and rainfall. In contrast, pathogen levels remained unaffected by all variables investigated. Limitations of current national and international culture-based standard methods may have played a significant role in limiting the identification of correlative relationships The data demonstrate the differences between FIOs and microbial pathogens in terms of sources, sinks, and survival processes within an urban estuary and provide further evidence of the inadequacy of FIO inclusion in the development of worldwide regulatory water quality criteria and risk assessment models.

  17. Detection of Mycobacterium tuberculosis and Mycobacterium bovis from human sputum samples through multiplex PCR.

    Science.gov (United States)

    Jabbar, Abdul; Khan, Jafar; Ullah, Aman; Rehman, Hazir; Ali, Ijaz

    2015-07-01

    Tuberculosis (TB) has a long history and being present even before the start of recording history. It has left detrimental effects on all aspect of the life and geared the developments in the science of health. TB is caused by Mycobacterium tuberculosis complex (MTBC) including five species M. tuberculosis, M. bovis, M. africanum, M. canetti, and M. microti. M. tuberculosis and M. bovis infect both animals and humans. Therefore, differentiation of these two closely related species is very important for epidemiological and management purpose. We undertook the present study to characterize mycobacteria isolated from sputum of known TB patients by conventional methods and further, by multiplex PCR (mPCR) to detect the prevalence of Zoonotic TB (TB caused by M. bovis). Sputum samples from TB patient were collected from two tertiary care hospitals in Peshawar i.e. Lady Reading Hospital and Hayatabad Medical Complex. All the samples were subjected to Ziehl Neelsen (ZN) stain, culture on Lowenstein Jensen (LJ) and Stone Brink medium, Nitrate reduction test and multiplex PCR. A total of hundred mycobacterial strains were isolated from these samples on the basis of ZN staining, cultural and biochemical methods. Later on, these isolates were subjected to multiplex PCR by using pncATB-1.2 and pncAMT-2 primers specific to M. tuberculosis and JB21, JB22 primers specific to M. bovis. By means of conventional method, these hundred cultures isolates were differentiated into M. tuberculosis (ninety six) and M. bovis (four). Furthermore, by mPCR, it was determined that out of hundred isolates, ninety-eight were identified as M. tuberculosis and two isolates as M. bovis. This molecular method enables to differentiate M. bovis from M. tuberculosis in human sputum.

  18. Faecal corticosterone levels of dogs relinquished to a shelter in Japan

    OpenAIRE

    2015-01-01

    This study investigated the baseline level of faecal corticosterone in dogs relinquished to a shelter and compared changes in it caused by social events that dogs experienced. Faecal corticosterone was measured to assess the average stress levels of dogs that depend on the actual conditions of the shelter. One category of subject animals was dogs relinquished by their owner or stray dogs who were penned in a group (group RG) or caged individually due to their incompatibility (group RI), and t...

  19. Effect of disturbance of the gastrointestinal microflora on the faecal excretion of Fusobacterium necrophorum biovar A.

    OpenAIRE

    Smith, G. R.; Thornton, E. A.

    1993-01-01

    Oral pretreatment of mice with either a mixture of kanamycin and erythromycin or metronidazole to modify the gut microflora greatly enhanced the faecal excretion of Fusobacterium necrophorum biovar A given by mouth. This lends support to the suggestion that disturbance of the gastrointestinal microflora in animals such as cattle, which often carry the organism in the rumen, may lead to intestinal multiplication and faecal excretion, thereby providing a source of infection that may lead to nec...

  20. Taenia saginata: an unusual cause of post-appendectomy faecal fistula

    Science.gov (United States)

    Najih, Mohammed; Laraqui, Hicham; Njoumi, Nouredine; Mouhafid, Faycel; Moujahid, Mountassir; Ehirchiou, Abdelkader; Zentar, Aziz

    2016-01-01

    Post-appendectomy faecal fistula is a rare surgical complication, associated with significant morbidity. Taenia saginata infestation is one of the most common cestode infestation in the gastrointestinal tract. It makes many complications as obstruction, perforation, anastomotic leakage or appendicular stump dehiscence. The objective of our study is to report a very rare case of post appendectomy faecal fistula caused by taenia saginata infestation and was successfully treated conservatively. PMID:28292157

  1. Human genomic DNA analysis using a semi-automated sample preparation, amplification, and electrophoresis separation platform.

    Science.gov (United States)

    Raisi, Fariba; Blizard, Benjamin A; Raissi Shabari, Akbar; Ching, Jesus; Kintz, Gregory J; Mitchell, Jim; Lemoff, Asuncion; Taylor, Mike T; Weir, Fred; Western, Linda; Wong, Wendy; Joshi, Rekha; Howland, Pamela; Chauhan, Avinash; Nguyen, Peter; Petersen, Kurt E

    2004-03-01

    The growing importance of analyzing the human genome to detect hereditary and infectious diseases associated with specific DNA sequences has motivated us to develop automated devices to integrate sample preparation, real-time PCR, and microchannel electrophoresis (MCE). In this report, we present results from an optimized compact system capable of processing a raw sample of blood, extracting the DNA, and performing a multiplexed PCR reaction. Finally, an innovative electrophoretic separation was performed on the post-PCR products using a unique MCE system. The sample preparation system extracted and lysed white blood cells (WBC) from whole blood, producing DNA of sufficient quantity and quality for a polymerase chain reaction (PCR). Separation of multiple amplicons was achieved in a microfabricated channel 30 microm x 100 microm in cross section and 85 mm in length filled with a replaceable methyl cellulose matrix operated under denaturing conditions at 50 degrees C. By incorporating fluorescent-labeled primers in the PCR, the amplicons were identified by a two-color (multiplexed) fluorescence detection system. Two base-pair resolution of single-stranded DNA (PCR products) was achieved. We believe that this integrated system provides a unique solution for DNA analysis.

  2. [Phenotypic characterization and distribution of Yersinia in human and environmental samples].

    Science.gov (United States)

    Javier Castillo, F; Larraz, V; Asunción Lafarga, M; Navarro, M; Gómez-Lus, R

    1994-01-01

    The distribution of species and phenotypes of Yersinia isolated from environmental samples over an eight year period are compared to that of stool cultures obtained from patients of the same geographical location (Zaragoza, Spain). The number of samples and the percentage contamination were as follows: wastewater 362, 67.4%, freshwater 523, 13.4%, raw food 607, 24.5% and cooked food 1134, 7.9%. Yersinia enterocolitica was isolated significantly more frequently than other species in wastewater, while Yersinia intermedia was the most significant species found in freshwater. Significant differences between the percentage isolates of identified species in raw and cooked foods were not found. Fifteen different serogroups were identified from faeces, thirteen of which were also isolated from environmental samples. Three serogroups of Y. enterocolitica associated with human disease were isolated from the patients faeces as follows: O:3, 145 cases; O:8, 3 cases and O:5,27, 1 case. A low proportion were isolated from food: O:3, 3 strains; O:8, 2 strains and O:5,27, 5 strains. Only one isolate from serogroup O:3 was obtained from freshwater.

  3. [Detection and typing by molecular biology of human papillomavirus in genital samples].

    Science.gov (United States)

    Suárez Moya, A; Esquivias Gómez, J I; Vidart Aragón, J A; Picazo de la Garza, J J

    2006-06-01

    Recently, there has been a marked increase in human papillomavirus (HPV) infection, and the etiological relationship between some HPV genotypes and genital cancer has been confirmed. Therefore, we used current molecular biology techniques to evaluate the prevalence of these viruses and their genotype in genital samples. We processed 401 genital samples from 281 women and 120 men, all with a diagnosis compatible with HPV infection. Virus was detected using PCR, and positive samples were typed using an array technique which enabled us to detect the 35 most common types of mucous-associated HPV. Of the 401 patients studied, 185 (46.1%) were positive, and only one type of HPV was detected in 133 cases. We found that 41.6% of the women and 56.7% of the men were positive. A total of 260 HPVs were typed; 154 were high oncogenic risk. They infected 16 men (23.5%) and 88 women (75.2%). The difference was statistically significant (pHVP 16 in 52 cases. We found a 46% prevalence of HPV infection. More than half of these patients were infected by high-risk HPV. The presence of high-risk HPV was significantly higher in women.

  4. Polychlorinated biphenyls and organochlorine pesticides in human milk samples from two regions in Croatia.

    Science.gov (United States)

    Klinčić, D; Herceg Romanić, S; Matek Sarić, M; Grzunov, J; Dukić, B

    2014-03-01

    We analyzed 20 polychlorinated biphenyls (PCBs) and seven organochlorine pesticides (OCPs) in milk samples collected during 2009-2011 from primiparae living in two different regions in Croatia. p,p'-DDE is the dominant organochlorine pesticide. α-HCH/γ-HCH and p,p'-DDE/p,p'-DDT ratios indicate that there is fresh input of γ-HCH in investigated population on both locations, while this is not applicable to p,p'-DDT. The PCB profile was dominated by higher chlorinated congeners. Non-ortho PCB congeners which have the highest TEF values were not detected in any of individual samples. Toxic equivalents for mono-ortho substituted PCB congeners indicated higher exposure to toxic PCBs in Zadar, but estimated daily intakes for both locations indicate that infants consuming mother's milk are not at risk of adverse effects caused by PCBs and OCPs. Our study builds on the previous research of human milk samples collected in Zagreb and reveals that over 10-year period, levels of investigated organochlorine compounds decreased significantly. Copyright © 2014 Elsevier B.V. All rights reserved.

  5. Analysis of inflammatory response in human plasma samples by an automated multicapillary electrophoresis system.

    Science.gov (United States)

    Larsson, Anders; Hansson, Lars-Olof

    2004-01-01

    A new automated multicapillary zone electrophoresis instrument with a new high-resolution (HR) buffer (Capillarys with HR buffer) for analysis of human plasma proteins was evaluated. Albumin, alpha(1)-antitrypsin, alpha(1)-acid glycoprotein, haptoglobin, fibrinogen, immunoglobulin (Ig)A, IgG and IgM were determined nephelometrically in 200 patient plasma samples. The same samples were then analyzed on the Capillarys system (Sebia, Paris, France). The albumin concentration from the nephelometric determination was used for quantification of the individual peaks in the capillary electrophoresis (CE) electropherogram. There was strong linear correlation between the nephelometric and electrophoretic determination of alpha(1)-antitrypsin (R(2) = 0.906), alpha(1)-acid glycoprotein (R(2) =0.894) and haptoglobin (R(2) = 0.913). There was also good correlation between the two determinations of gamma-globulins (R(2) = 0.883), while the correlation was weaker for fibrinogen (R(2) = 0.377). The Capillarys instrument is a reliable system for plasma protein analysis, combining the advantages of full automation, good analytical performance and high throughput. The HR buffer in combination with albumin quantification allows the simultaneous quantification of inflammatory markers in plasma samples without the need for nephelometric determination of these proteins.

  6. PERT: a method for expression deconvolution of human blood samples from varied microenvironmental and developmental conditions.

    Directory of Open Access Journals (Sweden)

    Wenlian Qiao

    Full Text Available The cellular composition of heterogeneous samples can be predicted using an expression deconvolution algorithm to decompose their gene expression profiles based on pre-defined, reference gene expression profiles of the constituent populations in these samples. However, the expression profiles of the actual constituent populations are often perturbed from those of the reference profiles due to gene expression changes in cells associated with microenvironmental or developmental effects. Existing deconvolution algorithms do not account for these changes and give incorrect results when benchmarked against those measured by well-established flow cytometry, even after batch correction was applied. We introduce PERT, a new probabilistic expression deconvolution method that detects and accounts for a shared, multiplicative perturbation in the reference profiles when performing expression deconvolution. We applied PERT and three other state-of-the-art expression deconvolution methods to predict cell frequencies within heterogeneous human blood samples that were collected under several conditions (uncultured mono-nucleated and lineage-depleted cells, and culture-derived lineage-depleted cells. Only PERT's predicted proportions of the constituent populations matched those assigned by flow cytometry. Genes associated with cell cycle processes were highly enriched among those with the largest predicted expression changes between the cultured and uncultured conditions. We anticipate that PERT will be widely applicable to expression deconvolution strategies that use profiles from reference populations that vary from the corresponding constituent populations in cellular state but not cellular phenotypic identity.

  7. PERT: a method for expression deconvolution of human blood samples from varied microenvironmental and developmental conditions.

    Science.gov (United States)

    Qiao, Wenlian; Quon, Gerald; Csaszar, Elizabeth; Yu, Mei; Morris, Quaid; Zandstra, Peter W

    2012-01-01

    The cellular composition of heterogeneous samples can be predicted using an expression deconvolution algorithm to decompose their gene expression profiles based on pre-defined, reference gene expression profiles of the constituent populations in these samples. However, the expression profiles of the actual constituent populations are often perturbed from those of the reference profiles due to gene expression changes in cells associated with microenvironmental or developmental effects. Existing deconvolution algorithms do not account for these changes and give incorrect results when benchmarked against those measured by well-established flow cytometry, even after batch correction was applied. We introduce PERT, a new probabilistic expression deconvolution method that detects and accounts for a shared, multiplicative perturbation in the reference profiles when performing expression deconvolution. We applied PERT and three other state-of-the-art expression deconvolution methods to predict cell frequencies within heterogeneous human blood samples that were collected under several conditions (uncultured mono-nucleated and lineage-depleted cells, and culture-derived lineage-depleted cells). Only PERT's predicted proportions of the constituent populations matched those assigned by flow cytometry. Genes associated with cell cycle processes were highly enriched among those with the largest predicted expression changes between the cultured and uncultured conditions. We anticipate that PERT will be widely applicable to expression deconvolution strategies that use profiles from reference populations that vary from the corresponding constituent populations in cellular state but not cellular phenotypic identity.

  8. 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

  9. Probiotic preparation reduces faecal water genotoxicity and cytotoxicity in chickens fed ochratoxin A contaminated feed (in vivo study).

    Science.gov (United States)

    Śliżewska, Katarzyna; Nowak, Adriana; Smulikowska, Stefania

    2016-01-01

    The aim of the present study was to assess the genotoxicity and cytotoxicity of the faecal water of chickens fed ochratoxin A (OTA) contaminated feed with and without probiotic preparation. The study was performed on 20 healthy female Ross broiler chickens divided into 4 groups: control chickens - fed with non-supplemented feed; PP chickens - fed feed supplemented with the probiotic preparation; OTA chickens - fed feed contaminated with 1 mg per kg of OTA; OTA + PP chickens - fed feed contaminated with 1 mg per kg of OTA and supplemented with the probiotic preparation. Faecal water samples were collected on the 35(th) day of life of chickens from each group. Genotoxicity was measured using the comet assay, and cytotoxicity by means of MTT tests. Mean DNA damage, measured as the percentage of DNA in the tails of the comets, was 8.50 ± 1.10 for chickens fed OTA at 1 mg/kg and 6.41 ± 0.67 in the controls. The supplementation of feed with the probiotic preparation decreased the extent of DNA damage to 4.74 ± 0.78. In the control group of chickens the average cytotoxicity was 38.5 ± 0.5 (in MTT), while in the probiotic preparation group (PP group) it was 31.8 ± 0.7 (in MTT). After supplementation of the feed with the probiotic preparation, the genotoxicity and cytotoxicity were decreased in a statistically significant manner.

  10. Modulation of the faecal microbiome of healthy adult dogs by inclusion of potato fibre in the diet.

    Science.gov (United States)

    Panasevich, Matthew R; Kerr, Katherine R; Dilger, Ryan N; Fahey, George C; Guérin-Deremaux, Laetitia; Lynch, Gary L; Wils, Daniel; Suchodolski, Jan S; Steer, Jörg M; Dowd, Scot E; Swanson, Kelly S

    2015-01-14

    Inclusion of fermentable fibres in the diet can have an impact on the hindgut microbiome and provide numerous health benefits to the host. Potato fibre (PF), a co-product of potato starch isolation, has a favourable chemical composition of pectins, resistant and digestible starch, cellulose, and hemicelluloses. The objective of the present study was to evaluate the effect of increasing dietary PF concentrations on the faecal microbiome of healthy adult dogs. Fresh faecal samples were collected from ten female dogs with hound bloodlines (6·13 (SEM 0·17) years; 22·0 (SEM 2·1) kg) fed five test diets containing graded concentrations of PF (0, 1·5, 3, 4·5 or 6% as-fed; Roquette Frères) in a replicated 5 × 5 Latin square design. Extraction of DNA was followed by amplification of the V4-V6 variable region of the 16S rRNA gene using barcoded primers. Sequences were classified into taxonomic levels using Basic Local Alignment Search Tool (BLASTn) against a curated GreenGenes database. Inclusion of PF increased (Pprebiotic fibre.

  11. Assessment of zoonotic transmission of Giardia and Cryptosporidium between cattle and humans in rural villages in Bangladesh.

    Science.gov (United States)

    Ehsan, Amimul M; Geurden, Thomas; Casaert, Stijn; Parvin, Sonia M; Islam, Taohidul M; Ahmed, Uddin M; Levecke, Bruno; Vercruysse, Jozef; Claerebout, Edwin

    2015-01-01

    Giardia and Cryptosporidium are important causes of diarrhoea in Bangladesh. The high prevalence of both parasites in humans and cattle in rural Bangladesh and the common use of water ponds by village inhabitants and their animals suggest a potential for zoonotic transmission. Direct transmission of Giardia and Cryptosporidium between cattle and their handlers and indirect transmission through water ponds was investigated. Faecal/stool samples were collected from 623 calves and 125 calf handlers in a cross-sectional survey. In two villages, water samples were collected monthly from water ponds and faecal/stool samples were collected monthly from inhabitants and their cattle. Giardia cysts and Cryptosporidium oocysts were detected in water samples and in faecal/stool samples and positive samples were genotyped, to determine their human or animal origin. The prevalence of Giardia and Cryptosporidium in calves was 22% and 5% respectively. In calf handlers, the prevalence of Giardia and Cryptosporidium was 11.2% and 3.2% respectively. Both in the cross-sectional survey and in the longitudinal study in the villages, G. duodenalis assemblage E was most prevalent in calves, while in humans assemblage AII, BIII and BIV were found. In cattle, Cryptosporidium parvum, C. bovis and C. andersoni were identified, but no Cryptosporidium sequences were obtained from humans. Giardia and Cryptosporidium were detected in 14/24 and 12/24 water samples respectively. G. duodenalis assemblage E and BIV (-like), as well as C. andersoni and C. hominis were identified. Although the presence of Giardia and Cryptosporidium in both water ponds suggests that water-borne transmission of Giardia and Cryptosporidium is possible, the genotyping results indicate that there is no significant direct or indirect (water-borne) transmission of Giardia between cattle and people in this area of rural Bangladesh. No conclusions could be drawn for Cryptosporidium, because of the low number of sequences that

  12. Analysis of persistence of human papillomavirus infection in men evaluated by sampling multiple genital sites.

    Science.gov (United States)

    Capra, G; Nyitray, A G; Lu, B; Perino, A; Marci, R; Schillaci, R; Matranga, D; Firenze, A; Caleca, M; Bellavia, C; Guarneri, F; Giuliano, A; Giovannelli, L

    2015-11-01

    Although human papillomavirus (HPV) infection has been studied extensively in women, data on male infection are limited. The purpose of this study was to investigate persistence of HPV infection at multiple genital sites in men and to define potential associations with socio-behavioural characteristics. Penile, urethral and seminal specimens were tested by the INNO-LiPA HPV system (Innogenetics) and a PCR assay. Persistence was defined as the detection of same HPV type at ≥ 2 consecutive visits. The Kaplan-Meier method and the log-rank test were applied to estimate the likelihood of persistence. A total of 50 men (median age: 33 years) were followed for a median of 14.7 months. Altogether, 49%, 36%, 26% and 11% of baseline HPV-positive men had 6-, 12-, 18- and 24-month persistent infection with any HPV type, respectively. The 6-, 12- and 18- month persistence was more common for oncogenic HPV infections; 24-month persistence was similar. The median duration of persistence was 21.7 months for any HPV. The median duration of persistence for any HPV type was significantly longer in the penile sample (22.5 months, 95% CI: 18.3-26.7) than the semen sample (15.3 months, 95% CI: 14.5-16.1). Over a third of type-specific HPV infections in men remained persistent over a 24-month period. The median duration of HPV infection was longer in penile samples compared to seminal samples. As being increasing the attention of HPV vaccination as a potential preventive approach also for men, it is imperative to obtain additional insight on natural history of HPV infection in men, particularly as far as incidence and duration are concerned.

  13. Comparison of two adult mosquito sampling methods with human landing catches in south-central Ethiopia.

    Science.gov (United States)

    Kenea, Oljira; Balkew, Meshesha; Tekie, Habte; Gebre-Michael, Teshome; Deressa, Wakgari; Loha, Eskindir; Lindtjørn, Bernt; Overgaard, Hans J

    2017-01-13

    The human landing catch (HLC) is the standard reference method for measuring human exposure to mosquito bites. However, HLC is labour-intensive, exposes collectors to infectious mosquito bites and is subjected to collector bias. These necessitate local calibration and application of alternative methods. This study was undertaken to determine the relative sampling efficiency (RSE) of light traps with or without yeast-produced carbon dioxide bait vs. HLC in south-central Ethiopia. The experiment was conducted for 39 nights in a 3 × 3 Latin square randomized design with Anopheles arabiensis as the target species in the period between July and November 2014 in Edo Kontola village, south-central Ethiopia. Center for Disease Control and Prevention light trap catches (LTC) and yeast-generated carbon dioxide-baited light trap catches (CB-LTC) were each evaluated against HLC. The total nightly mosquito catches for each Anopheles species in either method was compared with HLC by Pearson correlation and simple linear regression analysis on log-transformed [log10(x + 1)] values. To test if the RSE of each alternative method was affected by mosquito density, the ratio of the number of mosquitoes in each method to the number of mosquitoes in HLC was plotted against the average mosquito abundance. Overall, 7606 Anopheles females were collected by the three sampling methods. Among these 5228 (68.7%) were Anopheles ziemanni, 1153 (15.2%) An. arabiensis, 883 (11.6%) Anopheles funestus s.l., and 342 (4.5%) Anopheles pharoensis. HLC yielded 3392 (44.6%), CB-LTC 2150 (28.3%), and LTC 2064 (27.1%) Anopheles females. The RSEs of LTC and HLC for An. arabiensis were significantly correlated (p method for sampling An. arabiensis. LTC can be used for large-scale indoor An. arabiensis surveillance and monitoring when it is difficult to use HLC. CB-LTC does not substantially improve sampling of this major vector compared to LTC in this setting. Trial registration PACTR201411000882128

  14. Altered defaecatory behaviour and faecal incontinence in a video-tracked animal model of pudendal neuropathy.

    Science.gov (United States)

    Devane, L A; Lucking, E; Evers, J; Buffini, M; Scott, S M; Knowles, C H; O'Connell, P R; Jones, J F X

    2017-05-01

    The aim was to develop a behavioural animal model of faecal continence and assess the effect of retro-uterine balloon inflation (RBI) injury. RBI in the rat causes pudendal neuropathy, a risk factor for obstetric related faecal incontinence in humans. Video-tracking of healthy rats (n = 12) in a cage containing a latrine box was used to monitor their defaecatory behaviour index (DBI) over 2 weeks. The DBI (range 0-1) was devised by dividing the defaecation rate (pellets per hour) outside the latrine by that of the whole cage. A score of 0 indicates all pellets were deposited in the latrine. Subsequently, the effects of RBI (n = 19), sham surgery (n = 4) and colostomy (n = 2) were determined by monitoring the DBI for 2 weeks preoperatively and 3 weeks postoperatively. The DBI for healthy rats was 0.1 ± 0.03 with no significant change over 2 weeks (P = 0.71). In the RBI group, 13 of 19 rats (68%) showed no significant change in DBI postoperatively (0.08 ±  -0.05 vs 0.11 ±  -0.07) while in six rats the DBI increased from 0.16 ±  -0.09 to 0.46 ± 0.23. The negative control, sham surgery, did not significantly affect the DBI (0.09 ± 0.06 vs 0.08 ± 0.04, P = 0.14). The positive control, colostomy, increased the DBI from 0.26 ± 0.03 to 0.86 ± 0.08. This is the first study showing a quantifiable change in defaecatory behaviour following injury in an animal model. This model of pudendal neuropathy affects continence in 32% of rats and provides a basis for research on interventions for incontinence. Colorectal Disease © 2017 The Association of Coloproctology of Great Britain and Ireland.

  15. Sedimentary records of sewage pollution using faecal markers in contrasting peri-urban shallow lakes

    Energy Technology Data Exchange (ETDEWEB)

    Vane, C.H., E-mail: chv@bgs.ac.uk [British Geological Survey, Keyworth, Nottingham, NG12 5GG (United Kingdom); Kim, A.W. [British Geological Survey, Keyworth, Nottingham, NG12 5GG (United Kingdom); McGowan, S. [School of Geography, University of Nottingham, University Park, Nottingham, NG7 2RD (United Kingdom); Leng, M.J.; Heaton, T.H.E.; Kendrick, C.P. [NERC Isotope Geosciences Laboratory, British Geological Survey, Keyworth, Nottingham, NG12 5GG (United Kingdom); Coombs, P. [British Geological Survey, Keyworth, Nottingham, NG12 5GG (United Kingdom); Yang, H. [Environmental Change Research Centre, University College London, WC1 6BT (United Kingdom); Swann, G.E.A. [NERC Isotope Geosciences Laboratory, British Geological Survey, Keyworth, Nottingham, NG12 5GG (United Kingdom)

    2010-12-15

    Sewage contamination in shallow lake sediments is of concern because the pathogens, organic matter and nutrients contribute to the deterioration of the water-bodies' health and ecology. Sediment cores from three shallow lakes (Coneries, Church and Clifton Ponds) within Attenborough nature reserve located downstream of sewage treatment works were analysed for TOC, C/N, {delta}{sup 13}C, {delta}{sup 15}N, bacterial coliforms and faecal sterols. {sup 210}Pb and {sup 137}Cs activities were used to date the sediments. Elemental analysis suggests that the source of organic matter was algal and down profile changes in {delta}{sup 13}C indicate a possible decrease in productivity with time which could be due to improvements in sewage treatment. {delta}{sup 15}N for Coneries Pond are slightly higher than those observed in Church or Clifton and are consistent with a sewage-derived nitrate source which has been diluted by non-sewage sources of N. The similarity in {delta}{sup 15}N values (+ 12 per mille to + 10 per mille ) indicates that the three ponds were not entirely hydrologically isolated. Analysis by gas chromatography/mass spectrometry (GC/MS) reveals that Coneries Pond had sterol concentrations in the range 20 to 30 {mu}g/g (dry wt.), whereas, those from Clifton and Church Ponds were lower. The highest concentrations of the human-sourced sewage marker 5{beta}-coprostanol were observed in the top 40 cm of Coneries Pond with values up to 2.2 {mu}g/g. In contrast, Church and Clifton Pond sediments contain only trace amounts throughout. Down-profile comparison of 5{beta}-coprostanol/cholesterol, 5{beta}-coprostanol/(5{beta}-coprostanol + 5{alpha}-cholestanol) and 5{beta}-epicoprostanol/coprostanol as well as 5{alpha}-cholestanol/cholesterol suggests that Coneries Pond has received appreciable amounts of faecal contamination. Examination of 5{beta}-stigmastanol (marker for herbivorous/ruminant animals) down core concentrations suggests a recent decrease in manure

  16. In Vitro Efficient Expansion of Tumor Cells Deriving from Different Types of Human Tumor Samples

    Directory of Open Access Journals (Sweden)

    Ilaria Turin

    2014-03-01

    Full Text Available Obtaining human tumor cell lines from fresh tumors is essential to advance our understanding of antitumor immune surveillance mechanisms and to develop new ex vivo strategies to generate an efficient anti-tumor response. The present study delineates a simple and rapid method for efficiently establishing primary cultures starting from tumor samples of different types, while maintaining the immuno-histochemical characteristics of the original tumor. We compared two different strategies to disaggregate tumor specimens. After short or long term in vitro expansion, cells analyzed for the presence of malignant cells demonstrated their neoplastic origin. Considering that tumor cells may be isolated in a closed system with high efficiency, we propose this methodology for the ex vivo expansion of tumor cells to be used to evaluate suitable new drugs or to generate tumor-specific cytotoxic T lymphocytes or vaccines.

  17. Determination of Human Chorionic Gonadotropin in Postmortem Samples in Ectopic Pregnancies.

    Science.gov (United States)

    Palmiere, Cristian; Lesta, Maria del Mar; Fanton, Laurent; Ventura, Francesco; Bonsignore, Alessandro; Reggiani Bonetti, Luca

    2016-01-01

    Increased human chorionic gonadotropin levels (HCG) can be detected in femoral blood, bile, and vitreous humor collected during autopsy of pregnant women using a standard kit designed for living patients. In the study herein, the concentrations of HCG were measured in postmortem serum, vitreous, bile, cerebrospinal, and pericardial fluids in 4 cases of fatal ectopic pregnancy and 40 controls using a quantitative electrochemiluminescence immunoassay designed for living patients. No false-negative cases were identified in any of the analyzed samples in any of the ectopic pregnancy cases. No correlations were found between total HCG levels in postmortem serum and the other tested specimens. The results of this study would suggest that higher HCG in bile, vitreous, pericardial, and cerebrospinal fluids may confirm the existence of ectopic pregnancy and therefore identify other situations in which this hormone is increased, although gestational age cannot be reliably estimated using these values. © 2015 American Academy of Forensic Sciences.

  18. Ultrasensitive PCR and real-time detection from human genomic samples using a bidirectional flow microreactor.

    Science.gov (United States)

    Chen, Lin; West, Jonathan; Auroux, Pierre-Alain; Manz, Andreas; Day, Philip J R

    2007-12-01

    In this paper we present a reliable bidirectional flow DNA amplification microreactor for processing real-world genomic samples. This system shares the low-power thermal responsiveness of a continuous flow reactor with the low surface area to volume ratio character of stationary reactors for reducing surface inhibitory effects. Silanization with dimethyldichlorosilane in combination with dynamic surface passivation was used to enhance PCR compatibility and enable efficient amplification. For real-time fragment amplification monitoring we have implemented an epimodal fluorescent detection capability. The passivated bidirectional flow system was ultrasensitive, achieving an RNase P gene detection limit of 24 human genome copies with a reaction efficiency of 77%. This starts to rival the performance of a conventional real-time PCR instrument with a reaction efficiency of 93% and revitalizes flow-through PCR as a viable component of lab on a chip DNA analysis formats.

  19. Analyses of robotic traverses and sample sites in the Schrödinger basin for the HERACLES human-assisted sample return mission concept

    Science.gov (United States)

    Steenstra, Edgar S.; Martin, Dayl J. P.; McDonald, Francesca E.; Paisarnsombat, Sarinya; Venturino, Christian; O'Hara, Sean; Calzada-Diaz, Abigail; Bottoms, Shelby; Leader, Mark K.; Klaus, Kurt K.; van Westrenen, Wim; Needham, Debra H.; Kring, David A.

    2016-09-01

    The International Space Exploration Coordination Group (ISECG) developed an integrated Global Exploration Roadmap (GER) that outlines plans for human-assisted sample return from the lunar surface in ∼2024 and for human presence on the lunar surface in ∼2028. Previous studies have identified the Schrödinger basin, situated on the far side of the Moon, as a prime target for lunar science and exploration where a significant number of the scientific concepts reviewed by the National Research Council (NRC, 2007) can be addressed. In this study, two robotic mission traverses within the Schrödinger basin are proposed based on a 3 year mission plan in support of the HERACLES human-assisted sample return mission concept. A comprehensive set of modern remote sensing data (LROC imagery, LOLA topography, M3 and Clementine spectral data) has been integrated to provide high-resolution coverage of the traverses and to facilitate identification of specific sample localities. We also present a preliminary Concept of Operations (ConOps) study based on a set of notional rover capabilities and instrumental payload. An extended robotic mission to the Schrödinger basin will allow for significant sample return opportunities from multiple distinct geologic terrains and will address multiple high-priority NRC (2007) scientific objectives. Both traverses will offer the first opportunity to (i) sample pyroclastic material from the lunar farside, (ii) sample Schrödinger impact melt and test the lunar cataclysm hypothesis, (iii) sample deep crustal lithologies in an uplifted peak ring and test the lunar magma ocean hypothesis and (iv) explore the top of an impact melt sheet, enhancing our ability to interpret Apollo samples. The shorter traverse will provide the first opportunity to sample farside mare deposits, whereas the longer traverse has significant potential to collect SPA impact melt, which can be used to constrain the basin-forming epoch. These robotic missions will revalidate

  20. Trace samples of human blood in mosquitoes as a forensic investigation tool.

    Science.gov (United States)

    Rabêlo, K C N; Albuquerque, C M R; Tavares, V B; Santos, S M; Souza, C A; Oliveira, T C; Oliveira, N C L; Crovella, S

    2015-11-23

    Investigations of any type of crime invariably starts at the crime scene by collecting evidence. Thus, the purpose of this research was to collect and analyze an entomological trace from an environment that is similar to those of indoor crime scenes. Hematophagous mosquitoes were collected from two residential units; saliva of volunteers that were residents in the units was also collected for genetic analysis as reference samples. We examined the allele frequencies of 15 short tandem repeat loci (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818, and FGA) and amelogenin. A total of 26 female hematophagous mosquitoes were identified as Aedes aegypti, Aedes albopictus, and Culex quinquefasciatus; we were able to obtain 11 forensically valid genetic profiles, with a minimum of 0.028203 ng/μL of human DNA. Thus, the results of this study showed that it was possible to correlate human genetic information from mosquitoes with the volunteer reference samples, which validates the use of this information as forensic evidence. Furthermore, we observed mixed genetic profiles from one mosquito. Therefore, it is clearly important to collect these insects indoors where crimes were committed, because it may be possible to find intact genetic profiles of suspects in the blood found in the digestive tract of hematophagous mosquitoes for later comparison to identify an offender and/or exclude suspects.

  1. Effect of a synbiotic food consumption on human gut metabolic profiles evaluated by (1)H Nuclear Magnetic Resonance spectroscopy.

    Science.gov (United States)

    Ndagijimana, Maurice; Laghi, Luca; Vitali, Beatrice; Placucci, Giuseppe; Brigidi, Patrizia; Guerzoni, M Elisabetta

    2009-08-31

    The capacity of human lactobacilli and bifidobacteria to produce metabolites under conditions that may prevail in the human intestine has been studied "in vitro". However, the effect of systematic probiotic consumption on human metabolic phenotype has not been investigated in faeces. This paper shows the potential for the use of (1)H Nuclear Magnetic Resonance ((1)H NMR) spectroscopy for studying the changes of the metabolic profiles of human faecal slurries. Faeces of 16 subjects, characterized by different natural levels of lactobacilli and bifidobacteria were recovered before and after 1 month of supplementation with a synbiotic food based on Lactobacillus acidophilus, Bifidobacterium longum and fructooligosaccharides, and analyzed by (1)H NMR. Multivariate statistical approach has been applied to the data obtained and particularly Canonical Discriminant Analysis of Principal Coordinates (CAP). More than 150 molecules belonging to short chain fatty acids, organic acids, esters, alcohols and amino acids were detected and quantified in the samples considered. The number and the extent of these molecules in faecal slurries were strongly affected by the synbiotic food consumption and gave rise to characteristic metabolic signature. In particular, the short chain fatty acid concentrations significantly increased while the amino acids contents decreased. The comparison of the data indicated that the intake of the synbiotic food alters the host metabolism in a measure dependent on the initial level of lactobacilli and bifidobacteria detected in the faecal specimens. The analysis of (1)H NMR profiles with CAP allowed a separation of faecal samples of the subjects on the basis of the synbiotic food intake. The multivariate statistical approach used demonstrated the potential of NMR metabolic profiles to provide biomarkers of the gut-microbial activity related to dietary supplementation of probiotics.

  2. Effects of obesity, energy restriction and neutering on the faecal microbiota of cats.

    Science.gov (United States)

    Fischer, Manuela M; Kessler, Alexandre M; Kieffer, Dorothy A; Knotts, Trina A; Kim, Kyoungmi; Wei, Alfreda; Ramsey, Jon J; Fascetti, Andrea J

    2017-09-29

    Surveys report that 25-57 % of cats are overweight or obese. The most evinced cause is neutering. Weight loss often fails; thus, new strategies are needed. Obesity has been associated with altered gut bacterial populations and increases in microbial dietary energy extraction, body weight and adiposity. This study aimed to determine whether alterations in intestinal bacteria were associated with obesity, energy restriction and neutering by characterising faecal microbiota using 16S rRNA gene sequencing in eight lean intact, eight lean neutered and eight obese neutered cats before and after 6 weeks of energy restriction. Lean neutered cats had a bacterial profile similar to obese rodents and humans, with a greater abundance (Penergy restriction (PEnergy reduction was concurrent with significant shifts in two low-abundance bacterial genera and trends in four additional genera. The greatest change was a reduction in the Firmicutes genus, Sarcina, from 4·54 to 0·65 % abundance after energy restriction. The short duration of energy restriction may explain why few bacterial changes were observed in the obese cats. Additional work is needed to understand how neutering, obesity and weight loss are related to changes in feline microbiota and how these microbial shifts affect host physiology.

  3. Characterization of quinolone resistance in Salmonella spp. isolates from food products and human samples in Brazil

    Science.gov (United States)

    Pribul, Bruno Rocha; Festivo, Marcia Lima; de Souza, Miliane Moreira Soares; dos Prazeres Rodrigues, Dalia

    2016-01-01

    Non-typhoidal salmonellosis is an important zoonotic disease caused by Salmonella enterica. The aim of this study was to investigate the prevalence of plasmid-mediated quinolone resistance in Salmonella spp. and its association with fluoroquinolone susceptibility in Brazil. A total of 129 NTS isolates (samples from human origin, food from animal origin, environmental, and animal) grouped as from animal (n = 62) and human (n = 67) food were evaluated between 2009 and 2013. These isolates were investigated through serotyping, antimicrobial susceptibility testing, and the presence of plasmid-mediated quinolone resistance (PMQR) genes (qnr, aac(6′)-Ib) and associated integron genes (integrase, and conserved integron region). Resistance to quinolones and/or fluoroquinolones, from first to third generations, was observed. Fifteen isolates were positive for the presence of qnr genes (8 qnrS, 6 qnrB, and 1 qnrD) and twenty three of aac(6′)-Ib. The conserved integron region was detected in 67 isolates as variable regions, from ±600 to >1000 pb. The spread of NTS involving PMQR carriers is of serious concern and should be carefully monitored. PMID:26887245

  4. Assessment of malathion and its effects on leukocytes in human blood samples

    Science.gov (United States)

    Sharma, Amit Kumar; Tiwari, Udita; Gaur, Mulayam Singh; Tiwari, Rajeev Kumar

    2016-01-01

    Abstract In the present paper, we report a reproducible, cost effective, fast response method for detection of malathion and its effects on leukocytes in different human blood groups. Spectroscopic methods (UV-Vis spectrometry) and Fourier transform infrared coupled with solid phase extraction were applied for analyzing malathion content in human blood plasma. The spiking levels of malathion in the range of 0.1-1.7 µg/mL were extracted from blood plasma samples using SPE. The present active functional groups (C = O; P-O-C; -OH; P = S) were also characterized. The recovery rate of malathion was 80%±4.5%. The calculated correlation coefficient was 0.9799, indicating the linearity of the results. The limit of detection (LOD) and limit of quantification (LOQ) were (0.1-1.7) µg/mL and (0.3-1.5) µg/mL, respectively. Malathion <1.0 µg/mL showed no significant change while higher levels of malathion exposure (1.5 µg/mL and 3.0 µg/mL) reduced the number of white blood cells. In conclusion, the spectroscopic results may be useful to understand the mechanism of other pesticides such as methyl parathion and parathion.

  5. Characterization of quinolone resistance in Salmonella spp. isolates from food products and human samples in Brazil.

    Science.gov (United States)

    Pribul, Bruno Rocha; Festivo, Marcia Lima; de Souza, Miliane Moreira Soares; Rodrigues, Dalia dos Prazeres

    2016-01-01

    Non-typhoidal salmonellosis is an important zoonotic disease caused by Salmonella enterica. The aim of this study was to investigate the prevalence of plasmid-mediated quinolone resistance in Salmonella spp. and its association with fluoroquinolone susceptibility in Brazil. A total of 129 NTS isolates (samples from human origin, food from animal origin, environmental, and animal) grouped as from animal (n=62) and human (n=67) food were evaluated between 2009 and 2013. These isolates were investigated through serotyping, antimicrobial susceptibility testing, and the presence of plasmid-mediated quinolone resistance (PMQR) genes (qnr, aac(6')-Ib) and associated integron genes (integrase, and conserved integron region). Resistance to quinolones and/or fluoroquinolones, from first to third generations, was observed. Fifteen isolates were positive for the presence of qnr genes (8 qnrS, 6 qnrB, and 1 qnrD) and twenty three of aac(6')-Ib. The conserved integron region was detected in 67 isolates as variable regions, from ±600 to >1000pb. The spread of NTS involving PMQR carriers is of serious concern and should be carefully monitored.

  6. Determination of human albumin in serum and urine samples by constant-energy synchronous fluorescence method.

    Science.gov (United States)

    Madrakian, Tayyebeh; Bagheri, Habibollah; Afkhami, Abbas

    2015-08-01

    A sensitive spectrofluorimetric method using constant-energy synchronous fluorescence technique is proposed for the determination of human albumin without separation. In this method, no reagent was used for enhancement of the fluorescence signal of albumin in the solution. Effects of some parameters, such as energy difference between excitation and emission monochromators (ΔE), emission and excitation slit widths and scan rate of wavelength were studied and the optimum conditions were established. For this purpose factorial design and response surface method were employed for optimization of the effective parameters on the fluorescence signal. The results showed that the scan rate of the wavelength has no significant effect on the analytical signal. The calibration curve was linear in the range 0.1-220.0 µg mL(-1) of albumin with a detection limit of 7.0 × 10(-3)  µg mL(-1). The relative standard deviations (RSD) for six replicate measurements of albumin were calculated as 2.2%, 1.7% and 1.3% for 0.5, 10.0 and 100.0 µg mL(-1) albumin, respectively. Furthermore the proposed method has been employed for the determination of albumin in human serum and urine samples.

  7. 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

  8. Proof of concept of faecal egg nematode counting as a practical means of veterinary engagement with planned livestock health management in a lower income country.

    Science.gov (United States)

    Leahy, Eithne; Bronsvoort, Barend; Gamble, Luke; Gibson, Andrew; Kaponda, Henderson; Mayer, Dagmar; Mazeri, Stella; Shervell, Kate; Sargison, Neil

    2017-01-01

    The wellbeing and livelihood of farmers in impoverished regions of the world is intrinsically linked to the health and welfare of their livestock; hence improved animal health is a pragmatic component of poverty alleviation. Prerequisite knowledge and understanding of the animal health challenges facing cattle keepers in Malawi is constrained by the lack of veterinary infrastructure, which inevitably accompanies under-resourced rural development in a poor country. We collaborated with public and private paraveterinary services to locate 62 village Zebu calves and 60 dairy co-operative calves dispersed over a wide geographical area. All calves were visited twice about 2 to 3 weeks apart, when they were clinically examined and faecal samples were collected. The calves were treated with 7.5 mg/kg of a locally-available albendazole drench on the first visit, and pre- and post- treatment trichostrongyle and Toxocara faecal egg counts were performed using a modified McMaster method. Our clinical findings point towards a generally poor level of animal health, implying a role of ticks and tick-transmitted diseases in village calves and need for improvement in neonatal calf husbandry in the dairy co-operative holdings. High faecal trichostrongyle egg counts were not intuitive, based on our interpretation of the animal management information that was provided. This shows the need for better understanding of nematode parasite epidemiology within the context of local husbandry and environmental conditions. The albendazole anthelmintic was effective against Toxocara, while efficacy against trichostrongyle nematodes was poor in both village and dairy co-operative calves, demonstrating the need for further research to inform sustainable drug use. Here we describe the potential value of faecal nematode egg counting as a platform for communicating with and gaining access to cattle keepers and their animals, respectively, in southern Malawi, with the aim of providing informative

  9. Characterization of a Hemoglobin Adduct from Ethyl Vinyl Ketone Detected in Human Blood Samples.

    Science.gov (United States)

    Carlsson, Henrik; Motwani, Hitesh V; Osterman Golkar, Siv; Törnqvist, Margareta

    2015-11-16

    Electrophiles have the ability to form adducts to nucleophilic sites in proteins and DNA. Internal exposure to such compounds thus constitutes a risk for toxic effects. Screening of adducts using mass spectrometric methods by adductomic approaches offers possibilities to detect unknown electrophiles present in tissues. Previously, we employed untargeted adductomics to detect 19 unknown adducts to N-terminal valine in hemoglobin (Hb) in human blood. This article describes the characterization of one of these adducts, which was identified as the adduct from ethyl vinyl ketone (EVK). The mean adduct level was 40 ± 12 pmol/g Hb in 12 human blood samples; adduct levels from acrylamide (AA) and methyl vinyl ketone (MVK) were quantified for comparison. Using l-valine p-nitroanilide (Val-pNA), introduced as a model of the N-terminal valine, the rate of formation of the EVK adduct was studied, and the rate constant determined to 200 M(-1)h(-1) at 37 °C. In blood, the reaction rate was too fast to be feasibly measured, EVK showing a half-life adduct was found to be unstable, with a half-life of 7.6 h. From the mean adduct level measured in human blood, a daily dose (area under the concentration-time-curve, AUC) of 7 nMh EVK was estimated. The AUC of AA from intake via food is about 20 times higher. EVK is naturally present in a wide range of foods and is also used as a food additive. Most probably, naturally formed EVK is a major source to observed adducts. Evaluation of available toxicological data and information on occurrence of EVK indicate that further studies of EVK are motivated. This study illustrates a quantitative strategy in the initial evaluation of the significance of an adduct detected through adduct screening.

  10. Inactivation of human immunodeficiency virus type 1 in blood samples stored as high-salt lysates.

    Science.gov (United States)

    Zolg, J W; Lanciotti, R S; Wendlinger, M; Meyer, W A

    1990-09-01

    Blood samples to be tested for the presence of parasite DNA by using specific DNA probes are routinely stored in our laboratory as high-salt lysates (HSL). To safeguard against the risk of accidental infection with etiological agents such as the human immunodeficiency virus type 1 (HIV-1) while manipulating large numbers of blood samples in preparation for DNA probing, we determined the residual infectivity of HIV-1 after exposure to HSL components. Both high-titer virus stocks or provirus-carrying cells, suspended either in tissue culture medium or freshly drawn blood, were completely inactivated upon contact with the HSL components. This was verified by the absence of any detectable HIV-1-specific antigen in the supernatants of long-term cultures and the absence of virus-specific DNA fragments after amplification by polymerase chain reaction with DNA from such cultures as target DNA. These results support the conclusion that the virus is in fact completely inactivated by contact with the HSL components, rendering blood specimens stored as HSL noninfectious in regard to HIV-1.

  11. Aqueous two phase system based on ionic liquid for isolation of quinine from human plasma sample.

    Science.gov (United States)

    Flieger, J; Czajkowska-Żelazko, A

    2015-01-01

    Aqueous two phase system was applied for selective extraction of quinine from human plasma. Bi-phase was constructed from ionic liquid: butyl-methyl-imidazolium chloride after addition kosmotropic salts K₃PO₄ or KH₂PO₄. Quinine was determined in plasma samples after drinking of tonic containing quinine. Determination was performed by HPLC on 5-μm Zorbax SB-CN column and eluent containing 40% acetonitrile (v/v), 20 mM phosphate buffer at pH 3 and 40 mM NaPF₆ using external standard method. The spectrophotometric detection was set λ=214 nm. Selective fluorescence detection was performed at excitation of 325 nm and emission of 375 nm. Proposed strategy provides suitable sample purification and gives extraction yields in the range of 89-106%. The determination coefficient (R(2)) has a value ≥0.997 in the range of 50-800 ng/ml quinine concentration. The limit of quantification was set at 27.9 ng/ml and the detection limit was found to be 8.4 ng/ml under fluorescence detection.

  12. Analysis of Fluconazole in Human Urine Sample by High Performance Liquid Chromatography Method

    Science.gov (United States)

    Hermawan, D.; Ali, N. A. Md; Ibrahim, W. A. Wan; Sanagi, M. M.

    2013-04-01

    A method for determination of fluconazole, antifungal drug in human urine by using reversed-phased high performance liquid chromatography (RP-HPLC) with ultraviolet (UV) detector was developed. Optimization HPLC conditions were carried out by changing the flow rate and composition of mobile phase. The optimum separation conditions at a flow rate 0.85 mL/min with a composition of mobile phase containing methanol:water (70:30, v/v) with UV detection at a wavelength 254 nm was able to analyze fluconazole within 3 min. The excellent linearity was obtained in the range of concentration 1 to 10 μg/mL with r2 = 0.998. The limit of detection (LOD) and limit of quantitation (LOQ) were 0.39 μg/mL and 1.28 μg/mL, respectively. Solid phase extraction (SPE) method using octadecylsilane (C18) as a sorbent was used to clean-up and pre-concentrated of the urine sample prior to HPLC analysis. The average recoveries of fluconazole in spiked urine sample was 72.4% with RSD of 3.21% (n=3).

  13. Proteomic and oxidative stress analysis in human brain samples of Huntington disease.

    Science.gov (United States)

    Sorolla, Ma Alba; Reverter-Branchat, Gemma; Tamarit, Jordi; Ferrer, Isidre; Ros, Joaquim; Cabiscol, Elisa

    2008-09-01

    Huntington disease (HD) is a neurodegenerative disorder caused by expansion of CAG repeats in exon 1 of the huntingtin gene, affecting initially the striatum and progressively the cortex. This work reports a proteomic analysis of human brain postmortem samples obtained from striatum and cortex of patients with HD compared to samples of age- and sex-matched controls. Antioxidant defense proteins that were strongly induced in striatum, but also detectable in cortex, were identified as peroxiredoxins 1, 2, and 6, as well as glutathione peroxidases 1 and 6. The activities of other antioxidant enzymes such as mitochondrial superoxide dismutase and catalase were also increased in HD. Aconitase, a protein involved in energy metabolism, showed decreased activities in striatum of HD patients. Protein carbonyls, used as markers of oxidative stress, were increased in HD, and glial fibrillary acidic protein, aconitase, gamma-enolase, and creatine kinase B were identified as the main targets. Taken together, these results indicate that oxidative stress and damage to specific macromolecules would participate in the disease progression. Also, these data support the rationale for therapeutic strategies that either potentiate antioxidant defenses or avoid oxidative stress generation to delay disease progression.

  14. Prevalence and genotyping of high risk human papillomavirus in cervical cancer samples from Punjab, Pakistan.

    Science.gov (United States)

    Siddiqa, Abida; Zainab, Maidah; Qadri, Ishtiaq; Bhatti, Muhammad Faraz; Parish, Joanna L

    2014-07-17

    Cervical cancer is the third most common cause of cancer-related death in women worldwide. Infection with high-risk human papillomavirus (HPV) is established as the cause of cervical carcinoma, therefore, high risk HPV detection may have prognostic significance for the women who are at increased risk of disease progression. The paucity of data on the incidence of cervical cancer in Pakistan makes it difficult to determine disease burden. Even less information is available regarding the prevalent HPV strains in cervical specimens collected from this region. Cervical cancer is a neglected disease in Pakistan in terms of screening, prevention, and vaccination. Identification and accurate genotyping of the virus burden in cancer specimens is important to inform intervention policies for future management of HPV associated disease and to potentially stratify patients dependent on HPV status. In this study, detection and genotyping of HPV types 16 and 18 from 77 cervical specimens were carried out. Consensus primers GP5+/GP6+, which detect 44 genital HPV types, and type specific primers (TS16 and TS18) were used in conjunction with newly designed type specific primers. Using a combination of these methods of detection, a total of 94.81% (95% CI ±4.95) of cervical lesions were positive for HPV. Single infections of HPV16 were detected in 24.68% (95% CI ±9.63) of total samples and HPV18 was found in 25.97% (95% CI ±9.79) samples. Interestingly, a high proportion of samples (40.26%, 95% CI ±10.95) was positive for both HPV16 and 18, indicating a higher incidence of co-infection than previously reported for similar ethnic regions. The HPV genotype of 3.90% of HPV positive samples remained undetected, although these samples were positive with the GP5+/GP6+ primer set indicating infection with an HPV type other than 16 or 18. These data indicate that the overall incidence of high risk HPV infection in cervical cancer and intraepithelial neoplasia specimens in Punjab

  15. 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 influenc

  16. Origin and spatial-temporal distribution of faecal bacteria in a bay of Lake Geneva, Switzerland.

    Science.gov (United States)

    Poté, John; Goldscheider, Nico; Haller, Laurence; Zopfi, Jakob; Khajehnouri, Fereidoun; Wildi, Walter

    2009-07-01

    The origin and distribution of microbial contamination in Lake Geneva's most polluted bay were assessed using faecal indicator bacteria (FIB). The lake is used as drinking water, for recreation and fishing. During 1 year, water samples were taken at 23 points in the bay and three contamination sources: a wastewater treatment plant (WWTP), a river and a storm water outlet. Analyses included Escherichia coli, enterococci (ENT), total coliforms (TC), and heterotrophic plate counts (HPC). E. coli input flux rates from the WWTP can reach 2.5 x 10(10) CFU/s; those from the river are one to three orders of magnitude lower. Different pathogenic Salmonella serotypes were identified in water from these sources. FIB levels in the bay are highly variable. Results demonstrate that (1) the WWTP outlet at 30 m depth impacts near-surface water quality during holomixis in winter; (2) when the lake is stratified, the effluent water is generally trapped below the thermocline; (3) during major floods, upwelling across the thermocline may occur; (4) the river permanently contributes to contamination, mainly near the river mouth and during floods, when the storm water outlet contributes additionally; (5) the lowest FIB levels in the near-surface water occur during low-flow periods in the bathing season.

  17. Unusual sub-genus associations of faecal Prevotella and Bacteroides with specific dietary patterns.

    Science.gov (United States)

    De Filippis, Francesca; Pellegrini, Nicoletta; Laghi, Luca; Gobbetti, Marco; Ercolini, Danilo

    2016-10-21

    Diet has a recognized effect in shaping gut microbiota. Many studies link an increase in Prevotella to high-fibre diet, while Bacteroides abundance is usually associated with the consumption of animal fat and protein-rich diets. Nevertheless, closely related species and strains may harbour different genetic pools; therefore, further studies should aim to understand whether species of the same genus are consistently linked to dietary patterns or equally responsive to diet variations. Here, we used oligotyping of 16S rRNA gene sequencing data to exploit the diversity within Prevotella and Bacteroides genera in faecal samples of omnivore and non-omnivore subjects from a previously studied cohort. A great heterogeneity was found in oligotype composition. Nevertheless, different oligotypes within the same genus showed distinctive correlation patterns with dietary components and metabolome. We found that some Prevotella oligotypes are significantly associated with the plant-based diet but some are associated with animal-based nutrients, and the same applies to Bacteroides. Therefore, an indiscriminate association of Bacteroidetes genera with specific dietary patterns may lead to an oversimplified vision that does not take into account sub-genus diversity and the different possible responses to dietary components. We demonstrated that Prevotella and Bacteroides oligotypes show distinctive correlation patterns with dietary components and metabolome. These results substantiate a current oversimplification of diet-dependent microbe-host associations and highlighted that sub-genus differences must be taken into account when planning gut microbiota modulation for health benefits.

  18. Microwave treatment of faecal sludge from intensively used toilets in the slums of Nairobi, Kenya.

    Science.gov (United States)

    Mawioo, Peter M; Hooijmans, Christine M; Garcia, Hector A; Brdjanovic, Damir

    2016-12-15

    Toilet facilities in highly dense areas such as the slum and emergency settlements fill up rapidly; thus, requiring frequent emptying. Consequently, big quantities of fresh faecal sludge (FS) containing large amounts of pathogens are generated. Fast and efficient FS treatment technologies are therefore required for safe treatment and disposal of the FS in such conditions. This study explores the applicability of a microwave (MW) technology for the treatment of fresh FS obtained from urine-diverting dry toilets placed in slum settlements in Nairobi, Kenya. Two sample fractions containing 100 g and 200 g of FS were exposed to MW irradiation at three input MW power levels of 465, 1085 and 1550 W at different exposure times ranging from 0.5 to 14 min. The variation in the FS temperature, pathogen reduction via the destruction of E. coli and Ascaris lumbricoides eggs, and vol/wt reduction were measured during the MW treatment. It was demonstrated that the MW technology can rapidly and efficiently achieve complete reduction of E. coli and Ascaris lumbricoides eggs, and over 70% vol/wt reduction in the fresh FS. Furthermore, the successful evaluation of the MW technology under real field conditions demonstrated that MW irradiation can be applied for rapid treatment of fresh FS in situations such as urban slum and emergency conditions.

  19. SEROTYPING AND ANTIMICROBIAL DRUG RESISTANCE OF SALMONELLA ISOLATED FROM LETTUCE AND HUMAN DIARRHEA SAMPLES IN BURKINA FASO.

    Science.gov (United States)

    Siourimè, Somda Namwin; Isidore, Bonkoungou Ouindgueta Juste; Oumar, Traoré; Nestor, Bassolé Ismael Henri; Yves, Traoré; Nicolas, Barro; Aly, Savadogo

    2017-01-01

    Background: In Burkina Faso dirty water in particular those of the stoppings and the gutter ones are used for vegetables irrigation in the gardens. The aim of this study was to determine the prevalence and antibiotic susceptibility of Salmonella serotypes from humans and lettuce samples inBurkina Faso. Materials and Methods:Salmonella strains isolated from patients in 2009 to 2015 and lettuce samples in 2014 in Burkina Faso were serotyped using specific antisera. All strains were subjected to a set of 14 antibiotics to study their antibiogram by using Baeur–Kirby disk diffusion method. Results: Out of 154 Salmonella isolated, 60 were from human and 94 from lettuce samples. Serotyping revealed four different serotypes and 39% (60) untypeable strains from human and lettuce (14 and 46 strains). Salmonella serotypes from human and lettuce samples were: Paratyphi A (10% and 22%), Paratyphi B (34% and 8%), Paratyphi C (14% and 18%) and Typhi (21% and 1%). A high resistance of Salmonella Paratyphi B and Salmonella spp to tetracycline were 70% from human and 35 % from lettuce samples. Multiresistance was observed to tetracycline, chloramphenicol and amoxicillin/clavulanic-acid or ampicillin with Salmonella ParatyphiB 35% and Salmonella Typhi 33% from human samples and Salmonella spp 4% from lettuce samples. Conclusion: This study showed the diversity of Salmonella serotypes from both clinical and environmental samples and emergence of multiresistant Salmonella to antibiotics in Burkina Faso. A lettuce is a potential source of transmission of Salmonella causing diarrhea among human in Burkina Faso. List of non-standard Abbreviations : HDB: Hôpital du District de Bogodogo, LNSP: Laboratoire National de Santé Publique, DSG : District Sanitaire de Gourcy, DSB : District Sanitaire de Boromo PMID:28670637

  20. Locally produced natural conditioners for dewatering of faecal sludge

    Science.gov (United States)

    Gold, Moritz; Dayer, Pauline; Faye, Marie Christine Amie Sene; Clair, Guillaume; Seck, Alsane; Niang, Seydou; Morgenroth, Eberhard; Strande, Linda

    2016-01-01

    ABSTRACT In urban areas of low-income countries, treatment of faecal sludge (FS) is insufficient or non-existent. This results in large amounts of FS being dumped into the environment. Existing treatment technologies for FS, such as settling-thickening tanks and drying beds, are land intensive which is limiting in urban areas. Enhanced settling and dewatering by conditioning was evaluated in order to reduce the treatment footprint (or increase treatment capacity). Conventional wastewater conditioners, such as commercially available lime and polymers, are expensive, and commonly rely on complex supply chains for use in low-income countries. Therefore, the treatment performance of five conditioners which could be produced locally was evaluated: Moringa oleifera seeds and press cake, Jatropha curcas seeds, Jatropha Calotropis leaves and chitosan. M. oleifera seeds and press cake, and chitosan improved settling and dewatering and had a similar performance compared to lime and polymers. Optimal dosages were 400–500 kg M. oleifera/t TS, 300–800 kg lime/t TS and 25–50 kg polymer solution/t TS. In comparison, chitosan required 1.5–3.75 kg/t TS. These dosages are comparable to those recommended for wastewater (sludge). The results indicate that conditioning of FS can reduce total suspended solids (TSS) in the effluent of settling-thickening tanks by 22–81% and reduce dewatering time with drying beds by 59–97%. This means that the area of drying beds could be reduced by 59–97% with end-use as soil conditioner, or 9–26% as solid fuel. Least expensive options and availability will depend on the local context. In Dakar, Senegal, chitosan produced from shrimp waste appears to be most promising. PMID:26984372

  1. 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

  2. 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

    in an increase in faecal fat of 5.2 (1.6-8.8) g day(-1). In conclusion, dietary calcium has the potential to increase faecal fat excretion to an extent that could be relevant for prevention of weight (re-)gain. Long-term studies are required to establish its potential contribution.......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...

  3. Assessment of adrenocortical activity by non-invasive measurement of faecal cortisol metabolites in dromedary camels (Camelus dromedarius).

    Science.gov (United States)

    Sid-Ahmed, Omer-Elfaroug; Sanhouri, Ahmed; Elwaseela, Badr-Eldin; Fadllalah, Imad; Mohammed, Galal-Eldin Elazhari; Möstl, Erich

    2013-08-01

    The aim of this study was to determine whether glucocorticoid production could be monitored non-invasively in dromedary camels by measuring faecal cortisol metabolites (FCMs). Five Sudanese dromedaries, two males and three females, were injected with a synthetic adrenocorticotropic hormone (ACTH) analogue. Blood samples were collected pre- and post-ACTH injection. Faeces were sampled after spontaneous defecation for five consecutive days (2 days before and 3 days after ACTH injection). Baseline plasma cortisol values ranged from 0.6 to 10.8 ng/ml in males and from 1.1 to 16.6 ng/ml in females, while peak values after ACTH injection were 10.9-41.9 in males and 10-42.2 ng/ml in females. Peak blood cortisol values were reached between 1.5 and 2.0 h after ACTH injection. The concentration of FCMs increased after ACTH injection in the faeces of both sexes, although steroid levels peaked earlier in males [24 h; (286.7-2,559.7 ng/g faeces)] than in females [36-48 h; (1,182.6-5,169.1 ng/g faeces)], reflecting increases of 3.1-8.3- and 4.3-8-fold above baseline levels. To detect chromatographic patterns of immunoreactive FCMs, faecal samples with high FCM concentrations from both sexes were pooled and subjected to reverse phase high performance liquid chromatography (RP-HPLC). RP-HPLC analysis revealed sex differences in the polarity of FCMs, with females showing more polar FCMs than males. We concluded that stimulation of adrenocortical activity by ACTH injection resulted in a measurable increase in blood cortisol that was reliably paralleled by increases in FCM levels. Thus, measurement of FCMs is a powerful tool for monitoring the adrenocortical responses of dromedaries to stressors in field conditions.

  4. Suitability of faecal near-infrared reflectance spectroscopy (NIRS) predictions for estimating gross calorific value

    Energy Technology Data Exchange (ETDEWEB)

    De la Roza-Delgado, B.; Modroño, S.; Vicente, F.; Martínez-Fernández, A.; Soldado, A.

    2015-07-01

    A total of 220 faecal pig and poultry samples, collected from different experimental trials were employed with the aim to demonstrate the suitability of Near Infrared Reflectance Spectroscopy (NIRS) technology for estimation of gross calorific value on faeces as output products in energy balances studies. NIR spectra from dried and grounded faeces samples were analyzed using a Foss NIRSystem 6500 instrument, scanning over the wavelength range 400-2500 nm. Validation studies for quantitative analytical models were carried out to estimate the relevance of method performance associated to reference values to obtain an appropriate, accuracy and precision. The results for prediction of gross calorific value (GCV) of NIRS calibrations obtained for individual species showed high correlation coefficients comparing chemical analysis and NIRS predictions, ranged from 0.92 to 0.97 for poultry and pig. For external validation, the ratio between the standard error of cross validation (SECV) and the standard error of prediction (SEP) varied between 0.73 and 0.86 for poultry and pig respectively, indicating a sufficiently precision of calibrations. In addition a global model to estimate GCV in both species was developed and externally validated. It showed correlation coefficients of 0.99 for calibration, 0.98 for cross-validation and 0.97 for external validation. Finally, relative uncertainty was calculated for NIRS developed prediction models with the final value when applying individual NIRS species model of 1.3% and 1.5% for NIRS global prediction. This study suggests that NIRS is a suitable and accurate method for the determination of GCV in faeces, decreasing cost, timeless and for convenient handling of unpleasant samples.. (Author)

  5. Tracking human activity and well-being in natural environments using wearable sensors and experience sampling.

    Science.gov (United States)

    Doherty, Sean T; Lemieux, Christopher J; Canally, Culum

    2014-04-01

    A growing range of studies have begun to document the health and well-being benefits associated with contact with nature. Most studies rely on generalized self-reports following engagement in the natural environment. The actual in-situ experience during contact with nature, and the environmental features and factors that evoke health benefits have remained relatively unexplored. Smartphones offer a new opportunity to monitor and interact with human subjects during everyday life using techniques such as Experience Sampling Methods (ESM) that involve repeated self-reports of experiences as they occur in-situ. Additionally, embedded sensors in smartphones such as Global Positioning Systems (GPS) and accelerometers can accurately trace human activities. This paper explores how these techniques can be combined to comprehensively explore the perceived health and well-being impacts of contact with nature. Custom software was developed to passively track GPS and accelerometer data, and actively prompt subjects to complete an ESM survey at regular intervals throughout their visit to a provincial park in Ontario, Canada. The ESM survey includes nine scale questions concerning moods and emotions, followed by a series of open-ended experiential questions that subjects provide recorded audio responses to. Pilot test results are used to illustrate the nature, quantity and quality of data obtained. Participant activities were clearly evident from GPS maps, including especially walking, cycling and sedate activities. From the ESM surveys, participants reported an average of 25 words per question, taking an average of 15 s to record them. Further qualitative analysis revealed that participants were willing to provide considerable insights into their experiences and perceived health impacts. The combination of passive and interactive techniques is sure to make larger studies of this type more affordable and less burdensome in the future, further enhancing the ability to understand

  6. Molecular epidemiology of human papillomavirus infections in cervical samples from cuban women older than 30 years.

    Science.gov (United States)

    Soto, Yudira; Torres, Griselda; Kourí, Vivian; Limia, Celia María; Goicolea, Adibel; Capó, Virginia; Pérez, Lissette; de la Torre, Ana Isabel; López, Ledy Xiomara; Govín, Anamays; Correa, Consuelo Beatriz; Alemán, Yoan; Alvarez, Alina Ana; Manzano, Blanca Rosa

    2014-07-01

    This study aimed to provide information about the molecular epidemiology of human papillomavirus (HPV) in a group of Cuban women. DNA from cervical samples was analyzed using a quantitative real-time polymerase chain reaction (PCR), which detects 6 of the clinically most relevant high-risk HPV types. Furthermore, end point PCR and sequencing were performed. Three hundred twenty-two women (211 with positive and 111 with negative cytologic results) aged between 30 and 69 years were enrolled. Risk factors associated with HPV infections and premalignant lesions were also investigated. HPV DNA was detected in 76.1% (245/322) of the studied population, and 34 different genotypes were found. There was an association between HPV infection and low educational level, history of oral contraceptives, menopausal stage, as well as cigarette and/or alcohol consumption. Besides, in a multivariate analysis, previous positive Pap test result and positive colposcopy finding were both predictor variables for HPV infections and for premalignant lesions. Human papillomavirus infection was found in 94.3% of women (199/211) with positive cytologic result and in 41.4% (46/111) of those with negative results, being more likely that the first group was infected with any HPV (odds ratio = 23.43; 95% CI = 11.70-46.92; p = .000). The most common genotypes were HPV types 16, 18, 31, 58, 33, and 45. All the cases with HPV positive findings had at least 1 high-risk HPV genotype. This is the first report of the molecular epidemiology of HPV in Cuban women, based on results from a DNA sequence and quantitative PCR. Most individuals were infected with high-risk HPV types. These findings support the inclusion of HPV vaccine in Cuba.

  7. A novel Chlamydiaceae-like bacterium found in faecal specimens from sea birds from the Bering Sea.

    Science.gov (United States)

    Christerson, Linus; Blomqvist, Maria; Grannas, Karin; Thollesson, Mikael; Laroucau, Karine; Waldenström, Jonas; Eliasson, Ingvar; Olsen, Björn; Herrmann, Björn

    2010-08-01

    The family Chlamydiaceae contains several bacterial pathogens of important human and veterinary medical concern, such as Chlamydia trachomatis and Chlamydophila psittaci. Within the order Chlamydiales there are also an increasing number of chlamydia-like bacteria whose biodiversity, host range and environmental spread seem to have been largely underestimated, and which are currently being investigated for their potential medical relevance. In this study we present 16S rRNA, rnpB and ompA gene sequence data congruently indicating a novel chlamydia-like bacterium found in faecal specimens from opportunistic fish-eating sea birds, belonging to the Laridae and Alcidae families, from the Bering Sea. This novel bacterium appears to be closer to the Chlamydiaceae than other chlamydia-like bacteria and is most likely a novel genus within the Chlamydiaceae family.

  8. Human papillomavirus testing by self-sampling: assessment of accuracy in an unsupervised clinical setting

    Science.gov (United States)

    Szarewski, Anne; Cadman, Louise; Mallett, Susan; Austin, Janet; Londesborough, Philip; Waller, Jo; Wardle, Jane; Altman, Douglas G; Cuzick, Jack

    2007-01-01

    Objectives: To compare the performance and acceptability of unsupervised self-sampling with clinician sampling for high-risk human papillomavirus (HPV) types for the first time in a UK screening setting. Setting: Nine hundred and twenty women, from two demographically different centres, attending for routine cervical smear testing Methods: Women performed an unsupervised HPV self-test. Immediately afterwards, a doctor or nurse took an HPV test and cervical smear. Women with an abnormality on any test were offered colposcopy. Results: Twenty-one high-grade and 39 low-grade cervical intraepithelial neoplasias (CINs) were detected. The sensitivity for high-grade disease (CIN2+) for the self HPV test was 81% (95% confidence interval [CI] 60–92), clinician HPV test 100% (95% CI 85–100), cytology 81% (95% CI 60–92). The sensitivity of both HPV tests to detect high- and low-grade cervical neoplasia was much higher than that of cytology (self-test 77% [95%CI 65–86], clinician test 80% [95% CI 68–88], cytology 48% [95% CI 36–61]). For both high-grade alone, and high and low grades together, the specificity was significantly higher for cytology (greater than 95%) than either HPV test (between 82% and 87%). The self-test proved highly acceptable to women and they reported that the instructions were easy to understand irrespective of educational level. Conclusions: Our results suggest that it would be reasonable to offer HPV self-testing to women who are reluctant to attend for cervical smears. This approach should now be directly evaluated among women who have been non-attenders in a cervical screening programme. PMID:17362570

  9. Levels and complexity of IgA antibody against oral bacteria in samples of human colostrum.

    Science.gov (United States)

    Petrechen, L N; Zago, F H; Sesso, M L T; Bertoldo, B B; Silva, C B; Azevedo, K P; de Lima Pereira, S A; Geraldo-Martins, V R; Ferriani, V P L; Nogueira, R D

    2015-01-01

    Streptococcus mutans (SM) have three main virulence antigens: glucan binding protein B (gbpB), glucosyltransferase (Gtf) and antigens I/II (Ag I/II) envolved in the capacity of those bacteria to adhere and accumulate in the dental biofilm. Also, the glycosyltransferases 153 kDa of Streptococcus gordonii (SGO) and 170kDa of Streptococcus sanguinis (SSA) were important antigens associated with the accumulation of those bacterias. Streptococcus mitis (SMI) present IgA1 protease of 202 kDa. We investigated the specificity and levels IgA against those antigens of virulence in samples of human colostrum. This study involved 77 samples of colostrum that were analyzed for levels of immunoglobulian A, M and G by Elisa. The specificity of IgA against extracts of SM and initials colonizators (SSA, SMI, SGO) were analyzed by the Western blot. The mean concentration of IgA was 2850.2 (±2567.2) mg/100 mL followed by IgM and IgG (respectively 321.8±90.3 and 88.3±51.5), statistically different (pbacteria antigens and theirs virulence antigens. To SM, the GbpB was significantly lower detected than others antigens of SM (p0.4). So, the breast milk from first hours after birth presented significant levels of IgA specific against important virulence of antigens those oral streptococci, which can disrupt the installation and accumulation process of these microorganisms in the oral cavity. Copyright © 2014 Elsevier GmbH. All rights reserved.

  10. Novel encapsulation improves recovery of probiotic strains in fecal samples of human volunteers.

    Science.gov (United States)

    Mai, Volker; Waugh, Sheldon; Byrd, Doratha; Simpson, Damion; Ukhanova, Maria

    2017-02-01

    Probiotic supplements can contribute to maintaining health and ameliorating various disease symptoms. Probiotics can be delivered in many forms with crucial differences in their survival during gastrointestinal (GI) passage. Previously, a novel encapsulation, Probiotic Pearls™ Acidophilus, Integrative Therapeutics, LLC, USA (Pearls), was shown to increase survival in vitro after exposure to gastric conditions. Here, we compare fecal recovery in human volunteers consuming Pearls or a conventional hard-shelled gelatin capsule. We performed a randomized double-blinded, two-armed trial, with six healthy subjects in each 12-day study arm. In fecal samples collected at baseline, twice during the intervention period, and after washout, we compared colony counts between the two encapsulation methods. The identity of the colonies was confirmed by colony morphology, strain-specific PCR, and 16S rRNA gene sequencing. We further performed a comprehensive 16S rRNA gene sequencing-based analysis to identify differential effects on overall microbiota composition. We detected an average log increase in bifidobacteria of 0.152 cfu/g with gelatin and 0.651 cfu/g with Pearls capsules (p > 0.05). Total lactobacilli counts increased in both groups with no difference between the groups. However, the supplemented Lactobacillus acidophilus NCFM decreased to baseline levels within 7 days after end of supplementation with gelatin capsules while 3.11 log cfu/g higher counts compared to baseline (p = 0.05) remained for Pearls. Targeted qPCR largely confirmed the trends observed by viable plate counts. Protecting the probiotic strains by Pearls encapsulation results in higher recovery rates of the supplemented lactobacilli and bifidobacteria in fecal samples and increased persistence, suggesting an improved survival and viability that might increase efficacy towards achieving desired health benefits.

  11. Detection of nandrolone, testosterone, and their esters in rat and human hair samples.

    Science.gov (United States)

    Höld, K M; Borges, C R; Wilkins, D G; Rollins, D E; Joseph, R E

    1999-10-01

    Nandrolone and testosterone are anabolic androgenic steroids occasionally abused by athletes. A sensitive, specific, and reproducible gas chromatography-mass spectrometry method for the quantitative determination of nandrolone, testosterone, and their esters in hair has been developed. The limits of quantitation of this method, based on 20 mg of hair, were 50 pg/mg for nandrolone and testosterone, 100 pg/mg for testosterone acetate, and 200 pg/mg for nandrolone-decanoate. Nandrolone-d3 and testosterone-d3 were used as internal standards. This method has been applied to the analysis of these compounds incorporated into rat and human hair. Male Long-Evans rats were given nandrolone decanoate 60 mg/kg intraperitoneally (i.p.) once daily for 10 days over a time period of 14 days. Two of the three rats contained nandrolone in the pigmented hair collected at day 21 at a concentration of 63 and 76 pg/mg, respectively. No drug was found in the corresponding nonpigmented hair. The rat hair samples that tested positive for nandrolone contained also nandrolone decanoate in concentrations of 0.9 and 1.2 ng/mg, respectively. In a separate experiment rats were given testosterone acetate 10 mg/kg i.p. once daily for five days. No testosterone or testosterone acetate was detected in the rat hair samples. Hair specimens were also obtained from four self-reported steroid users. The hair of two subjects were determined to be positive for testosterone in concentrations of 54 and 81 pg/mg. These data demonstrate that it is possible to detect the steroids nandrolone, testosterone, and nandrolone decanoate in hair after systemic administration.

  12. Impacts of infection with different toxigenic Clostridium difficile strains on faecal microbiota in children

    Science.gov (United States)

    Ling, Zongxin; Liu, Xia; Jia, Xiaoyun; Cheng, Yiwen; Luo, Yueqiu; Yuan, Li; Wang, Yuezhu; Zhao, Chunna; Guo, Shu; Li, Lanjuan; Xu, Xiwei; Xiang, Charlie

    2014-12-01

    Increasing evidence suggests that altered intestinal microbial composition and function result in an increased risk of Clostridium difficile-associated diarrhoea (CDAD); however, the specific changes of intestinal microbiota in children suffering from CDAD and their associations with C. difficile strain toxigenicity are poorly understood. High-throughput pyrosequencing showed that reduced faecal bacterial diversity and dramatic shifts of microbial composition were found in children with CDAD. The Firmicutes/Bacteroidetes ratio was increased significantly in patients with CDAD, which indicated that dysbiosis of faecal microbiota was closely associated with CDAD. C. difficile infection resulted in an increase in lactate-producing phylotypes, with a corresponding decrease in butyrate-producing bacteria. The decrease in butyrate and lactate buildup impaired intestinal colonisation resistance, which increased the susceptibility to C. difficile colonisation. Strains of C. difficile which were positive for both toxin A and toxin B reduced faecal bacterial diversity to a greater degree than strains that were only toxin B-positive, and were associated with unusually abundant Enterococcus, which implies that the C. difficile toxins have different impacts on the faecal microbiota of children. Greater understanding of the relationships between disruption of the normal faecal microbiota and colonisation with C. difficile that produces different toxins might lead to improved treatment.

  13. Sanitary inspection of wells using risk-of-contamination scoring indicates a high predictive ability for bacterial faecal pollution in the peri-urban tropical lowlands of Dar es Salaam, Tanzania.

    Science.gov (United States)

    Mushi, Douglas; Byamukama, Denis; Kirschner, Alexander K T; Mach, Robert L; Brunner, K; Farnleitner, Andreas H

    2012-06-01

    Sanitary inspection of wells was performed according to World Health Organization (WHO) procedures using risk-of-contamination (ROC) scoring in the peri-urban tropical lowlands of Dar es Salaam, Tanzania. The ROC was assessed for its capacity to predict bacterial faecal pollution in the investigated well water. The analysis was based on a selection of wells representing environments with low to high presumptive faecal pollution risk and a multi-parametric data set of bacterial indicators, generating a comprehensive picture of the level and characteristics of faecal pollution (such as vegetative Escherichia coli cells, Clostridium perfringens spores and human-associated sorbitol fermenting Bifidobacteria). ROC scoring demonstrated a remarkable ability to predict bacterial faecal pollution levels in the investigated well water (e.g. 87% of E. coli concentration variations were predicted by ROC scoring). Physicochemical characteristics of the wells were not reflected by the ROC scores. Our results indicate that ROC scoring is a useful tool for supporting health-related well water management in urban and suburban areas of tropical, developing countries. The outcome of this study is discussed in the context of previously published results, and future directions are suggested.

  14. Prevalence of Human Papillomavirus Infection in Unselected SurePath Samples Using the APTIMA HPV mRNA Assay

    DEFF Research Database (Denmark)

    Rebolj, Matejka; Preisler, Sarah; Ejegod, Ditte M;

    2013-01-01

    The APTIMA Human Papillomavirus (HPV) Assay detects E6/E7 mRNA from 14 human papillomavirus genotypes. Horizon was a population-based split-sample study among well-screened women, with an aim to compare APTIMA, Hybrid Capture 2 (HC2), and liquid-based cytology (LBC) using SurePath samples. APTIMA...... agreement between APTIMA and HC2. This is the first APTIMA study using SurePath samples on the PANTHER platform. The trends in positivity rates on SurePath samples for APTIMA, HC2, and LBC were consistent with studies based on PreservCyt samples, and the agreement between the two HPV assays was substantial....... The high proportions of women testing positive suggest that in countries with a high HPV prevalence, caution will be needed if HPV tests, including mRNA-based tests, are to replace LBC....

  15. Sensitivity of PCR assays for murine gammaretroviruses and mouse contamination in human blood samples.

    Directory of Open Access Journals (Sweden)

    Li Ling Lee

    Full Text Available Gammaretroviruses related to murine leukemia virus (MLV have variously been reported to be present or absent in blood from chronic fatigue syndrome/myalgic encephalomyelitis (CFS/ME patients and healthy controls. Using subjects from New York State, we have investigated by PCR methods whether MLV-related sequences can be identified in nucleic acids isolated from whole blood or from peripheral blood mononuclear cells (PBMCs or following PBMC culture. We have also passaged the prostate cancer cell line LNCaP following incubation with plasma from patients and controls and assayed nucleic acids for viral sequences. We have used 15 sets of primers that can effectively amplify conserved regions of murine endogenous and exogenous retrovirus sequences. We demonstrate that our PCR assays for MLV-related gag sequences and for mouse DNA contamination are extremely sensitive. While we have identified MLV-like gag sequences following PCR on human DNA preparations, we are unable to conclude that these sequences originated in the blood samples.

  16. Gene expression profiling of human breast tissue samples using SAGE-Seq.

    Science.gov (United States)

    Wu, Zhenhua Jeremy; Meyer, Clifford A; Choudhury, Sibgat; Shipitsin, Michail; Maruyama, Reo; Bessarabova, Marina; Nikolskaya, Tatiana; Sukumar, Saraswati; Schwartzman, Armin; Liu, Jun S; Polyak, Kornelia; Liu, X Shirley

    2010-12-01

    We present a powerful application of ultra high-throughput sequencing, SAGE-Seq, for the accurate quantification of normal and neoplastic mammary epithelial cell transcriptomes. We develop data analysis pipelines that allow the mapping of sense and antisense strands of mitochondrial and RefSeq genes, the normalization between libraries, and the identification of differentially expressed genes. We find that the diversity of cancer transcriptomes is significantly higher than that of normal cells. Our analysis indicates that transcript discovery plateaus at 10 million reads/sample, and suggests a minimum desired sequencing depth around five million reads. Comparison of SAGE-Seq and traditional SAGE on normal and cancerous breast tissues reveals higher sensitivity of SAGE-Seq to detect less-abundant genes, including those encoding for known breast cancer-related transcription factors and G protein-coupled receptors (GPCRs). SAGE-Seq is able to identify genes and pathways abnormally activated in breast cancer that traditional SAGE failed to call. SAGE-Seq is a powerful method for the identification of biomarkers and therapeutic targets in human disease.

  17. Haematospirillum jordaniae gen. nov., sp. nov., isolated from human blood samples.

    Science.gov (United States)

    Humrighouse, B W; Emery, B D; Kelly, A J; Metcalfe, M G; Mbizo, J; McQuiston, J R

    2016-04-01

    A Gram-negative, aerobic, motile, spiral-shaped bacterium, strain H5569(T), was isolated from a human blood sample. Phenotypic and molecular characteristics of the isolate were investigated. Optimal growth was found to occur at 35 °C under aerobic conditions on Heart Infusion Agar supplemented with 5 % rabbit blood. The major fatty acids present in the cells were identified as C16:0, C16:1ω7c and C18:1ω7c. The predominant respiratory quinone was found to be ubiquinone-Q10. The G+C content of genomic DNA for strain H5569(T) was found to be 49.9 %. Based on 16S rRNA gene sequence analysis results, 13 additional isolates were also analysed in this study. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the organism, represented by strain H5569(T), forms a distinct lineage within the family Rhodospirillaceae, closely related to two Novispirillum itersonii subspecies (93.9-94.1 %) and two Caenispirillum sp. (91.2-91.6 %). Based on these results, the isolate H5569(T) is concluded to represent a new genus and species for which the name Haematospirillum jordaniae gen. nov., sp. nov. is proposed. The type strain is H5569(T) (=DSM(T) 28903 = CCUG 66838(T)).

  18. Sources of technical variability in quantitative LC-MS proteomics: human brain tissue sample analysis.

    Science.gov (United States)

    Piehowski, Paul D; Petyuk, Vladislav A; Orton, Daniel J; Xie, Fang; Moore, Ronald J; Ramirez-Restrepo, Manuel; Engel, Anzhelika; Lieberman, Andrew P; Albin, Roger L; Camp, David G; Smith, Richard D; Myers, Amanda J

    2013-05-03

    To design a robust quantitative proteomics study, an understanding of both the inherent heterogeneity of the biological samples being studied as well as the technical variability of the proteomics methods and platform is needed. Additionally, accurately identifying the technical steps associated with the largest variability would provide valuable information for the improvement and design of future processing pipelines. We present an experimental strategy that allows for a detailed examination of the variability of the quantitative LC-MS proteomics measurements. By replicating analyses at different stages of processing, various technical components can be estimated and their individual contribution to technical variability can be dissected. This design can be easily adapted to other quantitative proteomics pipelines. Herein, we applied this methodology to our label-free workflow for the processing of human brain tissue. For this application, the pipeline was divided into four critical components: Tissue dissection and homogenization (extraction), protein denaturation followed by trypsin digestion and SPE cleanup (digestion), short-term run-to-run instrumental response fluctuation (instrumental variance), and long-term drift of the quantitative response of the LC-MS/MS platform over the 2 week period of continuous analysis (instrumental stability). From this analysis, we found the following contributions to variability: extraction (72%) > instrumental variance (16%) > instrumental stability (8.4%) > digestion (3.1%). Furthermore, the stability of the platform and its suitability for discovery proteomics studies is demonstrated.

  19. Sources of Technical Variability in Quantitative LC-MS Proteomics: Human Brain Tissue Sample Analysis.

    Energy Technology Data Exchange (ETDEWEB)

    Piehowski, Paul D.; Petyuk, Vladislav A.; Orton, Daniel J.; Xie, Fang; Moore, Ronald J.; Ramirez Restrepo, Manuel; Engel, Anzhelika; Lieberman, Andrew P.; Albin, Roger L.; Camp, David G.; Smith, Richard D.; Myers, Amanda J.

    2013-05-03

    To design a robust quantitative proteomics study, an understanding of both the inherent heterogeneity of the biological samples being studied as well as the technical variability of the proteomics methods and platform is needed. Additionally, accurately identifying the technical steps associated with the largest variability would provide valuable information for the improvement and design of future processing pipelines. We present an experimental strategy that allows for a detailed examination of the variability of the quantitative LC-MS proteomics measurements. By replicating analyses at different stages of processing, various technical components can be estimated and their individual contribution to technical variability can be dissected. This design can be easily adapted to other quantitative proteomics pipelines. Herein, we applied this methodology to our label-free workflow for the processing of human brain tissue. For this application, the pipeline was divided into four critical components: Tissue dissection and homogenization (extraction), protein denaturation followed by trypsin digestion and SPE clean-up (digestion), short-term run-to-run instrumental response fluctuation (instrumental variance), and long-term drift of the quantitative response of the LC-MS/MS platform over the 2 week period of continuous analysis (instrumental stability). From this analysis, we found the following contributions to variability: extraction (72%) >> instrumental variance (16%) > instrumental stability (8.4%) > digestion (3.1%). Furthermore, the stability of the platform and its’ suitability for discovery proteomics studies is demonstrated.

  20. Association of human papillomavirus and Chlamydia trachomatis with intraepithelial alterations in cervix samples

    Directory of Open Access Journals (Sweden)

    Denise Wohlmeister

    2016-02-01

    Full Text Available The influence of different infectious agents and their association with human papillomavirus (HPV in cervical carcinogenesis have not been completely elucidated. This study describes the association between cytological changes in cervical epithelium and the detection of the most relevant aetiological agents of sexually transmitted diseases. Samples collected from 169 patients were evaluated by conventional cytology followed by molecular analysis to detect HPV DNA, Chlamydia trachomatis, herpes simplex virus 1 and 2,Neisseria gonorrhoeae, Mycoplasma genitalium, Trichomonas vaginalis, andTreponema pallidum, besides genotyping for most common high-risk HPV. An association between cytological lesions and different behavioural habits such as smoking and sedentariness was observed. Intraepithelial lesions were also associated with HPV and C. trachomatis detection. An association was also found between both simple and multiple genotype infection and cytological changes. The investigation of HPV and C. trachomatisproved its importance and may be considered in the future for including in screening programs, since these factors are linked to the early diagnosis of patients with precursor lesions of cervical cancer.

  1. Health risk assessment along the wastewater and faecal sludge management and reuse chain of Kampala, Uganda: a visualization.

    Science.gov (United States)

    Fuhrimann, Samuel; Winkler, Mirko S; Schneeberger, Pierre H H; Niwagaba, Charles B; Buwule, Joseph; Babu, Mohammed; Medlicott, Kate; Utzinger, Jürg; Cissé, Guéladio

    2014-11-01

    Reuse of wastewater in agriculture is a common feature in the developing world. While this strategy might contribute to the livelihood of farming communities, there are health risks associated with the management and reuse of wastewater and faecal sludge. We visualise here an assessment of health risks along the major wastewater channel in Kampala, Uganda. The visualization brings to bear the context of wastewater reuse activities in the Nakivubo wetlands and emphasises interconnections to disease transmission pathways. The contextual features are complemented with findings from environmental sampling and a cross-sectional epidemiological survey in selected exposure groups. Our documentation can serve as a case study for a step-by-step implementation of risk assessment and management as described in the World Health Organization's 2006 guidelines for the safe use of wastewater, greywater and excreta in light of the forthcoming sanitation safety planning approach.

  2. Health risk assessment along the wastewater and faecal sludge management and reuse chain of Kampala, Uganda: a visualization

    Directory of Open Access Journals (Sweden)

    Samuel Fuhrimann

    2014-11-01

    Full Text Available Reuse of wastewater in agriculture is a common feature in the developing world. While this strategy might con- tribute to the livelihood of farming communities, there are health risks associated with the management and reuse of wastewater and faecal sludge. We visualise here an assessment of health risks along the major wastewater channel in Kampala, Uganda. The visualization brings to bear the context of wastewater reuse activities in the Nakivubo wetlands and emphasises interconnections to disease transmission pathways. The contextual features are complemented with findings from environmental sampling and a cross-sectional epidemiological survey in selected exposure groups. Our documentation can serve as a case study for a step-by-step implementation of risk assessment and management as described in the World Health Organization’s 2006 guidelines for the safe use of wastewater, greywater and excreta in light of the forthcoming san- itation safety planning approach.

  3. Human sexuality education in the middle grades classroom: A review of curricula in a sample of Florida school districts

    Science.gov (United States)

    Myrick, Melinda D.

    2007-12-01

    This study examined the extent to which human sexuality topics are covered in Florida middle school science classrooms and the process by which curricular decisions are made regarding human sexuality education on a county-wide basis. Primary data included interviews with county-level administrators who oversee curricular decisions related to the middle-grades science curriculum or health curriculum in twelve school districts within the state. These districts represented four geographic locations and districts of various sizes. Administrators from four of the twelve studies in the sample chose to provide information regarding their human sexuality education curriculum. In two cases, teacher leads were identified and were interviewed to understand the implementation of the curriculum within the classroom. Additional data were collected from the district curriculum guides for human sexuality education and the adopted middle-grades science textbook for each county. The interview and documentary data were analyzed by comparison to established criteria for a comprehensive human sexuality education curriculum. The analysis revealed that the scope of human sexuality education varied considerably within the sample and that much of the curricula in place failed to include topics and activities that have been identified as important in a successful human sexuality education program. These findings are limited because few counties chose to fully participate. Additional research is clearly needed to examine the effectiveness of existing human sexuality education curricula in Florida. In addition, research is needed to understand the characteristics, values, and beliefs of successful human sexuality education instructors across the state.

  4. Accurate measurement of circulating mitochondrial DNA content from human blood samples using real-time quantitative PCR.

    Science.gov (United States)

    Ajaz, Saima; Czajka, Anna; Malik, Afshan

    2015-01-01

    We describe a protocol to accurately measure the amount of human mitochondrial DNA (MtDNA) in peripheral blood samples which can be modified to quantify MtDNA from other body fluids, human cells, and tissues. This protocol is based on the use of real-time quantitative PCR (qPCR) to quantify the amount of MtDNA relative to nuclear DNA (designated the Mt/N ratio). In the last decade, there have been increasing numbers of studies describing altered MtDNA or Mt/N in circulation in common nongenetic diseases where mitochondrial dysfunction may play a role (for review see Malik and Czajka, Mitochondrion 13:481-492, 2013). These studies are distinct from those looking at genetic mitochondrial disease and are attempting to identify acquired changes in circulating MtDNA content as an indicator of mitochondrial function. However, the methodology being used is not always specific and reproducible. As more than 95 % of the human mitochondrial genome is duplicated in the human nuclear genome, it is important to avoid co-amplification of nuclear pseudogenes. Furthermore, template preparation protocols can also affect the results because of the size and structural differences between the mitochondrial and nuclear genomes. Here we describe how to (1) prepare DNA from blood samples; (2) pretreat the DNA to prevent dilution bias; (3) prepare dilution standards for absolute quantification using the unique primers human mitochondrial genome forward primer (hMitoF3) and human mitochondrial genome reverse primer(hMitoR3) for the mitochondrial genome, and human nuclear genome forward primer (hB2MF1) and human nuclear genome reverse primer (hB2MR1) primers for the human nuclear genome; (4) carry out qPCR for either relative or absolute quantification from test samples; (5) analyze qPCR data; and (6) calculate the sample size to adequately power studies. The protocol presented here is suitable for high-throughput use.

  5. Modular approach to customise sample preparation procedures for viral metagenomics: a reproducible protocol for virome analysis.

    Science.gov (United States)

    Conceição-Neto, Nádia; Zeller, Mark; Lefrère, Hanne; De Bruyn, Pieter; Beller, Leen; Deboutte, Ward; Yinda, Claude Kwe; Lavigne, Rob; Maes, Piet; Van Ranst, Marc; Heylen, Elisabeth; Matthijnssens, Jelle

    2015-11-12

    A major limitation for better understanding the role of the human gut virome in health and disease is the lack of validated methods that allow high throughput virome analysis. To overcome this, we evaluated the quantitative effect of homogenisation, centrifugation, filtration, chloroform treatment and random amplification on a mock-virome (containing nine highly diverse viruses) and a bacterial mock-community (containing four faecal bacterial species) using quantitative PCR and next-generation sequencing. This resulted in an optimised protocol that was able to recover all viruses present in the mock-virome and strongly alters the ratio of viral versus bacterial and 16S rRNA genetic material in favour of viruses (from 43.2% to 96.7% viral reads and from 47.6% to 0.19% bacterial reads). Furthermore, our study indicated that most of the currently used virome protocols, using small filter pores and/or stringent centrifugation conditions may have largely overlooked large viruses present in viromes. We propose NetoVIR (Novel enrichment technique of VIRomes), which allows for a fast, reproducible and high throughput sample preparation for viral metagenomics studies, introducing minimal bias. This procedure is optimised mainly for faecal samples, but with appropriate concentration steps can also be used for other sample types with lower initial viral loads.

  6. Interferon-λ4 (IFNL4 transcript expression in human liver tissue samples.

    Directory of Open Access Journals (Sweden)

    Ahmad Amanzada

    Full Text Available Eradication of hepatitis C virus (HCV infection, both spontaneous and treatment-induced, is marked by the wildtype allele C of a single nucleotide polymorphism upstream of the IL28B gene, rs12979860. This favorable allele was recently described to be in linkage disequilibrium with the wildtype allele TT of a dinucleotide polymorphism, ss469415590, located within a new protein-coding gene. While the TT allele introduces a frame-shift and disrupts the open reading frame, only the variant allele, ΔG, creates a novel type III interferon (IFN protein, IFN-λ4/IFNL4. Absence of IFNL4 is thus supposed to favor resolution of HCV infection. As to date IFNL4 mRNA transcription has only been investigated in polyI:C-stimulated primary human hepatocytes and not yet in HCV infection in vivo, this study analyzed IFNL4 mRNA expression in human liver biopsy specimens. Samples were obtained from patients with a broad panel of disorders including no liver disease, liver diseases of non-viral etiology, chronic hepatitis B and chronic hepatitis C. Hepatic IFNL4 transcripts were detectable exclusively in a subgrou