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Sample records for bovine fecal swabs

  1. Development of an ELISA for evaluation of swab recovery efficiencies of bovine serum albumin.

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    Nadja Sparding

    Full Text Available After a potential biological incident the sampling strategy and sample analysis are crucial for the outcome of the investigation and identification. In this study, we have developed a simple sandwich ELISA based on commercial components to quantify BSA (used as a surrogate for ricin with a detection range of 1.32-80 ng/mL. We used the ELISA to evaluate different protein swabbing procedures (swabbing techniques and after-swabbing treatments for two swab types: a cotton gauze swab and a flocked nylon swab. The optimal swabbing procedure for each swab type was used to obtain recovery efficiencies from different surface materials. The surface recoveries using the optimal swabbing procedure ranged from 0-60% and were significantly higher from nonporous surfaces compared to porous surfaces. In conclusion, this study presents a swabbing procedure evaluation and a simple BSA ELISA based on commercial components, which are easy to perform in a laboratory with basic facilities. The data indicate that different swabbing procedures were optimal for each of the tested swab types, and the particular swab preference depends on the surface material to be swabbed.

  2. Comparison of culture and a multiplex probe PCR for identifying Mycoplasma species in bovine milk, semen and swab samples

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    Parker, Alysia M.; House, John K.; Hazelton, Mark S.; Bosward, Katrina L.; Sheehy, Paul A.

    2017-01-01

    Mycoplasma spp. are a major cause of mastitis, arthritis and pneumonia in cattle, and have been associated with reproductive disorders in cows. While culture is the traditional method of identification the use of PCR has become more common. Several investigators have developed PCR protocols to detect M. bovis in milk, yet few studies have evaluated other sample types or other important Mycoplasma species. Therefore the objective of this study was to develop a multiplex PCR assay to detect M. bovis, M. californicum and M. bovigenitalium, and evaluate its analytical performance against traditional culture of bovine milk, semen and swab samples. The PCR specificity was determined and the limit of detection evaluated in spiked milk, semen and swabs. The PCR was then compared to culture on 474 field samples from individual milk, bulk tank milk (BTM), semen and swab (vaginal, preputial, nose and eye) samples. Specificity analysis produced appropriate amplification for all M. bovis, M. californicum and M. bovigenitalium isolates. Amplification was not seen for any of the other Mollicutes or eubacterial isolates. The limit of detection of the PCR was best in milk, followed by semen and swabs. When all three Mycoplasma species were present in a sample, the limit of detection increased. When comparing culture and PCR, overall there was no significant difference in the proportion of culture and PCR positive samples. Culture could detect significantly more positive swab samples. No significant differences were identified for semen, individual milk or BTM samples. PCR identified five samples with two species present. Culture followed by 16S-23S rRNA sequencing did not enable identification of more than one species. Therefore, the superior method for identification of M. bovis, M. californicum and M. bovigenitalium may be dependent on the sample type being analysed, and whether the identification of multiple target species is required. PMID:28264012

  3. Distinguishing bovine fecal matter on spinach leaves using field spectroscopy

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    Detection of fecal contaminants on leafy greens in the field will allow for decreasing cross-contamination of produce during and post-harvest. Fecal contamination of leafy greens has been associated with E.coli O157:H7 outbreaks and foodbourne illnesses. In this study passive field spectroscopy, mea...

  4. Quantitative PCR for Detection and Enumeration of Genetic Markers of Bovine Fecal Pollution

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    Accurate assessment of health risks associated with bovine (cattle) fecal pollution requires a reliable host-specific genetic marker and a rapid quantification method. We report the development of quantitative PCR assays for the detection of two recently described cow feces-spec...

  5. Human-, Ovine-, and Bovine-Specific Viral Source Tracking Tools to Discriminate Between the Major Fecal Sources in Agricultural Waters.

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    Rusiñol, Marta; Moriarty, Elaine; Lin, Susan; Bofill-Mas, Sílvia; Gilpin, Brent

    2016-03-01

    This study evaluated the sources of fecal contamination in different river catchments, using a combination of microbial source tracking tools, for human, ruminant, ovine and bovine livestock, in order to define appropriate water management strategies. Every source of waterway pollution was evaluated in river water samples from one urban river catchment and two important farming regions in New Zealand. Fecal pollution was initially measured by testing Escherichia coli and evaluating the presence of human- and ruminant-associated DNA markers of Bacteroidales (BiAdo, BacHum-UCD, BacH, and BacR) and human and ruminant fecal sterols/stanols ratios. Then specific fecal pollution sources were assessed with previously reported quantitative PCR assays targeting human-, bovine-, and ovine-specific viruses: human adenoviruses (HAdV), human JC polyomaviruses, bovine polyomaviruses (BPyV), and ovine polyomaviruses (OPyV). High level of ruminant fecal contamination was detected all over the farming areas, whereas no ruminant sources were identified in the urban river sampling sites. BacR was the most frequently observed ruminant marker and OPyV and BPyV allowed the identification of ovine and bovine fecal sources. The human fecal viral marker (HAdV) was the most frequently observed human marker, highly abundant in the urban sites, and also present in farming areas. This is the first study using simultaneously the ovine and the bovine viral markers to identify and quantify both bovine and ovine fecal pollution.

  6. Distinguishing Bovine Fecal Matter on Spinach Leaves Using Field Spectroscopy

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    Colm D. Everard

    2016-08-01

    Full Text Available Detection of fecal contaminants on leafy greens in the field will allow for decreasing cross-contamination of produce during and post-harvest. Fecal contamination of leafy greens has been associated with Escherichia coli (E. coli O157:H7 outbreaks and foodborne illnesses. In this study, passive field spectroscopy measuring reflectance and fluorescence created by the sun’s light, coupled with numerical normalization techniques, are used to distinguish fecal contaminants on spinach leaves from soil on spinach leaves and uncontaminated spinach leaf portions. A Savitzky-Golay first derivative transformation and a waveband ratio of 710:688 nm as normalizing techniques were assessed. A soft independent modelling of class analogies (SIMCA procedure with a 216 sample training set successfully predicted all 54 test set sample types using the spectral region of 600–800 nm. The ratio of 710:688 nm along with set thresholds separated all 270 samples by type. Application of these techniques in-field to avoid harvesting of fecal contaminated leafy greens may lead to a reduction in foodborne illnesses as well as reduced produce waste.

  7. Isolation of bacterial strains from bovine fecal microflora capable of degradation of ceftiofur.

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    Rafii, Fatemeh; Williams, Anna J; Park, Miseon; Sims, Lillie M; Heinze, Thomas M; Cerniglia, Carl E; Sutherland, John B

    2009-10-20

    Ceftiofur, a third-generation cephalosporin used to treat bacterial infections in animals, is degraded in bovine feces but the specific bacteria involved are unknown. To find the bacteria involved in ceftiofur metabolism, the bovine fecal microflora was screened. Twenty-one nonidentical strains of bovine fecal bacteria were isolated on media containing 1-32 microg ml(-1) of ceftiofur. The cultures were incubated with 5 microg ml(-1) ceftiofur for different times, then centrifuged and analyzed by high-performance liquid chromatography. Three strains of Bacillus spp., two strains of Roseomonas spp., and one strain of Azospirillum sp. metabolized 5 microg ml(-1) ceftiofur in broth cultures in less than 24h; ten other strains of Roseomonas and one strain of Bacillus pumilus had metabolized it by 120 h. After the ceftiofur had been metabolized by these bacteria, the filter-sterilized supernatants of centrifuged cultures no longer inhibited the growth of a ceftiofur-sensitive strain of Kocuria rhizophila, which indicated that ceftiofur had been transformed to compounds without bactericidal activity. Each isolate was also found to be able to grow in the presence of other beta-lactams, and a nitrocefin assay showed beta-lactamase activity in the 17 strains that metabolized ceftiofur. The results show that some beta-lactamase-producing bacteria from the bovine fecal microflora are capable of transforming ceftiofur to metabolites lacking bactericidal activity.

  8. Molecular analysis of the bovine coronavirus S1 gene by direct sequencing of diarrheic fecal specimens

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    E. Takiuchi

    2008-04-01

    Full Text Available Bovine coronavirus (BCoV causes severe diarrhea in newborn calves, is associated with winter dysentery in adult cattle and respiratory infections in calves and feedlot cattle. The BCoV S protein plays a fundamental role in viral attachment and entry into the host cell, and is cleaved into two subunits termed S1 (amino terminal and S2 (carboxy terminal. The present study describes a strategy for the sequencing of the BCoV S1 gene directly from fecal diarrheic specimens that were previously identified as BCoV positive by RT-PCR assay for N gene detection. A consensus sequence of 2681 nucleotides was obtained through direct sequencing of seven overlapping PCR fragments of the S gene. The samples did not undergo cell culture passage prior to PCR amplification and sequencing. The structural analysis was based on the genomic differences between Brazilian strains and other known BCoV from different geographical regions. The phylogenetic analysis of the entire S1 gene showed that the BCoV Brazilian strains were more distant from the Mebus strain (97.8% identity for nucleotides and 96.8% identity for amino acids and more similar to the BCoV-ENT strain (98.7% for nucleotides and 98.7% for amino acids. Based on the phylogenetic analysis of the hypervariable region of the S1 subunit, these strains clustered with the American (BCoV-ENT, 182NS and Canadian (BCQ20, BCQ2070, BCQ9, BCQ571, BCQ1523 calf diarrhea and the Canadian winter dysentery (BCQ7373, BCQ2590 strains, but clustered on a separate branch of the Korean and respiratory BCoV strains. The BCoV strains of the present study were not clustered in the same branch of previously published Brazilian strains (AY606193, AY606194. These data agree with the genealogical construction and suggest that at least two different BCoV strains are circulating in Brazil.

  9. Full genome analysis of bovine astrovirus from fecal samples of cattle in Japan: identification of possible interspecies transmission of bovine astrovirus.

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    Nagai, Makoto; Omatsu, Tsutomu; Aoki, Hiroshi; Otomaru, Konosuke; Uto, Takehiko; Koizumi, Motoya; Minami-Fukuda, Fujiko; Takai, Hikaru; Murakami, Toshiaki; Masuda, Tsuneyuki; Yamasato, Hiroshi; Shiokawa, Mai; Tsuchiaka, Shinobu; Naoi, Yuki; Sano, Kaori; Okazaki, Sachiko; Katayama, Yukie; Oba, Mami; Furuya, Tetsuya; Shirai, Junsuke; Mizutani, Tetsuya

    2015-10-01

    A viral metagenomics approach was used to investigate fecal samples of Japanese calves with and without diarrhea. Of the different viral pathogens detected, read counts gave nearly complete astrovirus-related RNA sequences in 15 of the 146 fecal samples collected in three distinct areas (Hokkaido, Ishikawa, and Kagoshima Prefectures) between 2009 and 2015. Due to the lack of genetic information about bovine astroviruses (BoAstVs) in Japan, these sequences were analyzed in this study. Nine of the 15 Japanese BoAstVs were closely related to Chinese BoAstVs and clustered into a lineage (tentatively named lineage 1) in all phylogenetic trees. Three of 15 strains were phylogenetically separate from lineage 1, showing low sequence identities, and clustered instead with an American strain isolated from cattle with respiratory disease (tentatively named lineage 2). Interestingly, two of 15 strains clustered with lineage 1 in the open reading frame (ORF)1a and ORF1b regions, while they clustered with lineage 2 in the ORF2 region. Remarkably, one of 15 strains exhibited low amino acid sequence similarity to other BoAstVs and was clustered separately with porcine astrovirus type 5 in all trees, and ovine astrovirus in the ORF2 region, suggesting past interspecies transmission.

  10. Novel real-time PCR assays using TaqMan minor groove binder probes for identification of fecal carriage of Streptococcus bovis/Streptococcus equinus complex from rectal swab specimens.

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    Lopes, Paulo Guilherme Markus; Cantarelli, Vlademir Vicente; Agnes, Grasiela; Costabeber, Ane Micheli; d'Azevedo, Pedro Alves

    2014-03-01

    Real-time PCR based on the recN and gyrB genes was developed to detect four Streptococcus bovis/Streptococcus equinus complex (SBEC) subspecies from rectal swab specimens. The overall prevalence was 35.2%: Streptococcus gallolyticus subsp. gallolyticus (11.1%), S. gallolyticus subsp. pasteurianus (13%), Streptococcus infantarius subsp. coli (20.4%), and S. infantarius subsp. infantarius (11.1%). To conclude, these real-time PCR assays provide a reliable molecular method to detect SBEC pathogenic subspecies from rectal swab specimens.

  11. Development of Bacteroides 16S rRNA Gene TaqMan-Based Real-Time PCR Assays for Estimation of Total, Human, and Bovine Fecal Pollution in Water

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    Layton, Alice; McKay, Larry; Williams, Dan; Garrett, Victoria; Gentry, Randall; Sayler, Gary

    2006-01-01

    Bacteroides species are promising indicators for differentiating livestock and human fecal contamination in water because of their high concentration in feces and potential host specificity. In this study, a real-time PCR assay was designed to target Bacteroides species (AllBac) present in human, cattle, and equine feces. Direct PCR amplification (without DNA extraction) using the AllBac assay was tested on feces diluted in water. Fecal concentrations and threshold cycle were linearly correlated, indicating that the AllBac assay can be used to estimate the total amount of fecal contamination in water. Real-time PCR assays were also designed for bovine-associated (BoBac) and human-associated (HuBac) Bacteroides 16S rRNA genes. Assay specificities were tested using human, bovine, swine, canine, and equine fecal samples. The BoBac assay was specific for bovine fecal samples (100% true-positive identification; 0% false-positive identification). The HuBac assay had a 100% true-positive identification, but it also had a 32% false-positive rate with potential for cross-amplification with swine feces. The assays were tested using creek water samples from three different watersheds. Creek water did not inhibit PCR, and results from the AllBac assay were correlated with those from Escherichia coli concentrations (r2 = 0.85). The percentage of feces attributable to bovine and human sources was determined for each sample by comparing the values obtained from the BoBac and HuBac assays with that from the AllBac assay. These results suggest that real-time PCR assays without DNA extraction can be used to quantify fecal concentrations and provide preliminary fecal source identification in watersheds. PMID:16751534

  12. Swabs and other sampling techniques.

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    Lawrence, J C; Ameen, H

    1998-05-01

    This study explores the absorptive capacity of standard cotton wool-tipped swabs in vitro and in vivo. An alternative wound exudate sampling technique using small filter paper discs is also briefly examined. Results showed a poor uniformity of fluid absorption by swabs and a limited correlation of wound exudate quantities in relation to visual estimates and size of wound. It was found, however, that swabs reliably removed material from a wound surface. The filter paper technique appeared to offer no advantages.

  13. Double swab technique for collecting touched evidence.

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    Pang, B C M; Cheung, B K K

    2007-07-01

    Touched evidence is often submitted to forensic laboratories for DNA analysis. Classical stain recovery technique, involving one wet cotton swab, is commonly used for recovering the touched evidence. Double swab technique, using a wet cotton swab followed by a dry cotton swab, was compared with the classical technique for recovering the touched evidence. The wet cotton swabs and the dry cotton swabs were individually extracted. DNA extracts were quantified and amplified at 15 polymorphic loci. DNA recovered in some of the second dry swabs contained sufficient amount of DNA to yield a DNA profile. This study shows that the double swab technique improves the quality of the resulting DNA profiles. The double swab technique for recovering touched evidence at crime scenes is recommended.

  14. Streptococcus agalactiae in the environment of bovine dairy herds--rewriting the textbooks?

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    Jørgensen, H J; Nordstoga, A B; Sviland, S; Zadoks, R N; Sølverød, L; Kvitle, B; Mørk, T

    2016-02-29

    Many free-stall bovine dairy herds in Norway fail to eradicate Streptococcus agalactiae despite long-term control measures. In a longitudinal study of 4 free-stall herds with automatic milking systems (AMS), milk and extramammary sites were sampled 4 times with 1-2 month intervals. Composite milk, rectal- and vaginal swabs were collected from dairy cows; rectal swabs from heifers and young stock; rectal- and tonsillar swabs from calves; and environmental swabs from the AMS, the floors, cow beds, watering and feeding equipment. A cross sectional study of 37 herds was also conducted, with 1 visit for environmental sampling. Fifteen of the herds were known to be infected with S. agalactiae while the remaining 22 had not had evidence of S. agalactiae mastitis in the preceding 2 years. All samples were cultured for S. agalactiae, and selected isolates (n=54) from positive herds were genotyped by Multi Locus Sequence Typing (MLST). Results show that the bovine gastrointestinal tract and the dairy cow environment are reservoirs of S. agalactiae, and point to the existence of 2 transmission cycles; a contagious transmission cycle via the milking machine and an oro-fecal transmission cycle, with drinking water as the most likely vehicle for transmission. Ten sequence types were identified, and results suggest that strains differ in their ability to survive in the environment and transmit within dairy herds. Measures to eradicate S. agalactiae from bovine dairy herds should take into account the extra-mammary reservoirs and the potential for environmental transmission of this supposedly exclusively contagious pathogen.

  15. Identifying fecal matter contamination in produce fields using multispectral reflectance imaging under ambient solar illumination

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    An imaging device to detect fecal contamination in fresh produce fields could allow the producer to avoid harvesting fecal-contaminated produce. E.coli O157:H7 outbreaks have been associated with fecal-contaminated leafy greens. In this study, in-field spectral profiles of bovine fecal matter, soil,...

  16. MICROBIOLOGICAL PROFILE OF VAGINAL SWABS.

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    Sevitha

    2012-10-01

    Full Text Available ABSTRACT: BACKGROUND/OBJECTIVES: Bacterial vaginosis (BV, an alteration of vaginal flora involving a decrease in Lactobacilli and predo minance of anaerobic bacteria, is the most common cause of vaginal complaints for women of chil dbearing age .Causative agents include Gardnerella vaginalis, facultative lactobacilli, My coplasma hominis, Viridans streptococci & anaerobic bacteria. The most frequent manifestation s of genitourinary candidiasis is vulvovaginal candidiasis & is diagnosed in 40 % of women with vaginal complaints. The present study was undertaken to study the occurrence of Bac terial vaginosis & Vulvovaginal candidiasis in women with vaginal complaints. MATERIALS AND METHODS: The study included 100 High vaginal swabs with H/O white discharge per vaginum f or a period of 6 months from June 2011.Swabs were stained by Grams method & were cult ured. RESULTS: Out of 100 samples, in 35(35%Gram smear findings were normal & no growth in culture. 26(26%samples had polymorphs with Gardnerella morphotype, gram negative c urved rods, fusiforms & Lactobacilli were absent/present in low numbers(1 to 2+, the sme ar was interpreted as consistent with BV. 15 samples (15% had the growth of Candida spp. In the remaining 24 samples, the Gram stain findings had only vaginal epithelial cells with Lactobacilli, but the culture had the growth o f Group B Streptococcus 10(10%, E. coli & coliforms 10(10%,Enterococcus spp 14(14%which could just be colonisers. CONCLUSION: Bacterial vaginosis is the predominant cause of leuc orrhoea (26% followed by vulvovaginal candidiasis accounting for 15 % of the cases. Detection of intrapartum vaginal colonisation of Group B Streptococci, E. coli & colif orms & Enterococcus spp. in pregnant women is of significance as it can get transmitted to the neonate & cause sepsis

  17. Detection and characterization of viruses as field and vaccine strains in feedlot cattle with bovine respiratory disease

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    This study investigated viruses in bovine respiratory disease (BRD) cases in feedlots, including bovine herpesvirus-1 (BoHV-1), bovine viral diarrhea virus (BVDV), bovine respiratory syncytial virus (BRSV), bovine coronaviruses (BoCV) and parainfluenza-3 virus (PI3V). Nasal swabs were collected fro...

  18. Swabbing for respiratory viral infections in older patients: a comparison of rayon and nylon flocked swabs.

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    Hernes, S S; Quarsten, H; Hagen, E; Lyngroth, A L; Pripp, A H; Bjorvatn, B; Bakke, P S

    2011-02-01

    The purpose of this study was to compare the sampling efficacy of rayon swabs and nylon flocked swabs, and of oropharyngeal and nasopharyngeal specimens for the detection of respiratory viruses in elderly patients. Samples were obtained from patients 60 years of age or above who were newly admitted to Sorlandet Hospital Arendal, Norway. The patients were interviewed for current symptoms of a respiratory tract infection. Using rayon swabs and nylon flocked swabs, comparable sets of mucosal samples were harvested from the nasopharynx and the oropharynx. The samples were analysed using real-time polymerase chain reaction (PCR) methods. A total of 223 patients (mean age 74.9 years, standard deviation [SD] 9.0 years) were swabbed and a virus was recovered from 11% of the symptomatic patients. Regardless of the sampling site, a calculated 4.8 times higher viral load (95% confidence interval [CI] 1.3-17, p = 0.017) was obtained using the nylon flocked swabs as compared to the rayon swabs. Also, regardless of the type of swab, a calculated 19 times higher viral load was found in the samples from the nasopharynx as compared to the oropharynx (95% CI 5.4-67.4, p Nylon flocked swabs appear to be more efficient than rayon swabs.

  19. The effect of sampling and storage on the fecal microbiota composition in healthy and diseased subjects.

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    Danyta I Tedjo

    Full Text Available Large-scale cohort studies are currently being designed to investigate the human microbiome in health and disease. Adequate sampling strategies are required to limit bias due to shifts in microbial communities during sampling and storage. Therefore, we examined the impact of different sampling and storage conditions on the stability of fecal microbial communities in healthy and diseased subjects. Fecal samples from 10 healthy controls, 10 irritable bowel syndrome and 8 inflammatory bowel disease patients were collected on site, aliquoted immediately after defecation and stored at -80 °C, -20 °C for 1 week, at +4°C or room temperature for 24 hours. Fecal transport swabs (FecalSwab, Copan were collected and stored for 48-72 hours at room temperature. We used pyrosequencing of the 16S gene to investigate the stability of microbial communities. Alpha diversity did not differ between all storage methods and -80 °C, except for the fecal swabs. UPGMA clustering and principal coordinate analysis showed significant clustering by test subject (p < 0.001 but not by storage method. Bray-Curtis dissimilarity and (unweighted UniFrac showed a significant higher distance between fecal swabs and -80 °C versus the other methods and -80 °C samples (p < 0.009. The relative abundance of Ruminococcus and Enterobacteriaceae did not differ between the storage methods versus -80 °C, but was higher in fecal swabs (p < 0.05. Storage up to 24 hours (at +4 °C or room temperature or freezing at -20 °C did not significantly alter the fecal microbial community structure compared to direct freezing of samples from healthy subjects and patients with gastrointestinal disorders.

  20. An integratable microfluidic cartridge for forensic swab samples lysis.

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    Yang, Jianing; Brooks, Carla; Estes, Matthew D; Hurth, Cedric M; Zenhausern, Frederic

    2014-01-01

    Fully automated rapid forensic DNA analysis requires integrating several multistep processes onto a single microfluidic platform, including substrate lysis, extraction of DNA from the released lysate solution, multiplexed PCR amplification of STR loci, separation of PCR products by capillary electrophoresis, and analysis for allelic peak calling. Over the past several years, most of the rapid DNA analysis systems developed started with the reference swab sample lysate and involved an off-chip lysis of collected substrates. As a result of advancement in technology and chemistry, addition of a microfluidic module for swab sample lysis has been achieved in a few of the rapid DNA analysis systems. However, recent reports on integrated rapid DNA analysis systems with swab-in and answer-out capability lack any quantitative and qualitative characterization of the swab-in sample lysis module, which is important for downstream forensic sample processing. Maximal collection and subsequent recovery of the biological material from the crime scene is one of the first and critical steps in forensic DNA technology. Herein we present the design, fabrication and characterization of an integratable swab lysis cartridge module and the test results obtained from different types of commonly used forensic swab samples, including buccal, saliva, and blood swab samples, demonstrating the compatibility with different downstream DNA extraction chemistries. This swab lysis cartridge module is easy to operate, compatible with both forensic and microfluidic requirements, and ready to be integrated with our existing automated rapid forensic DNA analysis system. Following the characterization of the swab lysis module, an integrated run from buccal swab sample-in to the microchip CE electropherogram-out was demonstrated on the integrated prototype instrument. Therefore, in this study, we demonstrate that this swab lysis cartridge module is: (1) functionally, comparable with routine benchtop lysis

  1. Nylon flocked swab severely reduces Hexagon Obti sensibility.

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    Frippiat, Christophe; De Roy, Gilbert; Fontaine, Louis-Marie; Dognaux, Sophie; Noel, Fabrice; Heudt, Laeticia; Lepot, Laurent

    2015-02-01

    Hexagon Obti immunological blood test and flocked swab are widely used in forensic laboratories. Nevertheless, up to now, no compatibility tests have been published between sampling with the ethylene oxide treated flocked swab and the Hexagon Obti blood detection strip. In this study, we investigated this compatibility. Our work shows that sampling with ethylene oxide treated flocked swab reduces by a factor of at least 100 the detection threshold of blood using the Hexagon Obti immunological test.

  2. Comparing non-woven, filmateci and woven gauze swabs.

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    Thomas, S; Loveless, P; Hay, N P; Toyick, N

    1993-01-02

    The physical characteristics and performance of seven non-woven swabs intended for topical use were compared with those of filmated swabs and woven cotton gauze in a series of laboratory tests. The results of this study suggest that the non-woven swabs have significant advantages over the other type examined. Based upon current pricing structures they represent a highly cost-effective alternative to the more traditional products for routine wound management procedures. As the various non-wovens have very different handling characteristics, it should be possible to select a swab to suit most requirements from the range of products available.

  3. Nondestructive Biological Evidence Collection with Alternative Swabs and Adhesive Lifters.

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    Plaza, Dane T; Mealy, Jamia L; Lane, J Nicholas; Parsons, M Neal; Bathrick, Abigail S; Slack, Donia P

    2016-03-01

    In forensic science, biological material is typically collected from evidence via wet/dry double swabbing with cotton swabs, which is effective but can visibly damage an item's surface. When an item's appearance must be maintained, dry swabbing and tape-lifting may be employed as collection techniques that are visually nondestructive to substrates' surfaces. This study examined the efficacy of alternative swab matrices and adhesive lifters when collecting blood and fingerprints from glass, painted drywall, 100% cotton, and copy paper. Data were evaluated by determining the percent profile and quality score for each STR profile generated. Hydraflock(®) swabs, BVDA Gellifters(®) , and Scenesafe FAST™ tape performed as well as or better than cotton swabs when collecting fingerprints from painted drywall and 100% cotton. Collection success was also dependent on the type of biological material sampled and the substrate on which it was deposited. These results demonstrated that alternative swabs and adhesive lifters can be effective for nondestructive DNA collection from various substrates.

  4. The fecal bacteria

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    Sadowsky, Michael J.; Whitman, Richard L.

    2011-01-01

    The Fecal Bacteria offers a balanced, integrated discussion of fecal bacteria and their presence and ecology in the intestinal tract of mammals, in the environment, and in the food supply. This volume covers their use in examining and assessing water quality in order to offer protection from illnesses related to swimming in or ingesting contaminated water, in addition to discussing their use in engineering considerations of water quality, modeling, monitoring, and regulations. Fecal bacteria are additionally used as indicators of contamination of ready-to-eat foods and fresh produce. The intestinal environment, the microbial community structure of the gut microbiota, and the physiology and genomics of this broad group of microorganisms are explored in the book. With contributions from an internationally recognized group of experts, the book integrates medicine, public health, environmental, and microbiological topics in order to provide a unique, holistic understanding of fecal bacteria. Moreover, it shows how the latest basic science and applied research findings are helping to solve problems and develop effective management strategies. For example, readers will discover how the latest tools and molecular approaches have led to our current understanding of fecal bacteria and enabled us to improve human health and water quality. The Fecal Bacteria is recommended for microbiologists, clinicians, animal scientists, engineers, environmental scientists, food safety experts, water quality managers, and students. It will help them better understand fecal bacteria and use their knowledge to protect human and environmental health. They can also apply many of the techniques and molecular tools discussed in this book to the study of a broad range of microorganisms in a variety of habitats.

  5. Mycoplasmas associated with bovine conjunctivitis and keratoconjunctivitis.

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    Naglić, T; Sanković, F; Madić, J; Hajsig, D; Seol, B; Busch, K

    1996-01-01

    In two separate herds of fattening calves a sudden-onset outbreak of ocular disease with profuse lacrimation occurred. The disease resembled the early stage of infectious bovine keratoconjunctivitis but after a few days the clinical signs of bronchopneumonia appeared. From conjunctival swabs Mycoplasma (M.) bovigenitalium, M. bovirhinis and infectious bovine rhinotracheitis (IBR) virus were isolated. Moraxella bovis infection was not established. In one of the herds M. bovigenitalium was also found in the pneumonic lungs of dead calves. In one herd M. bovoculi was isolated from a cow with chronic keratoconjunctivitis, housed together with affected calves. Mycoplasmas were not isolated from ocular swabs of six bulls originating from a Reproductive Centre with temporary occurrence of unilateral serous conjunctivitis resistant to antibiotic therapy.

  6. Fecal Occult Blood Test and Fecal Immunochemical Test

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    ... Visit Global Sites Search Help? Fecal Occult Blood Test and Fecal Immunochemical Test Share this page: Was this page helpful? Also ... Test Common Questions Ask Us Related Pages The Test How is it used? When is it ordered? ...

  7. [Fecal microbiota transplantation].

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    Šturdík, Igor; Hlavatý, Tibor; Payer, Juraj

    2016-02-01

    Fecal microbiota transplantation (FMT) is a therapeutic method, in which the fecal microflora from healthy donors is transmitted to the patient to restore the healthy microbial composition of the gut. In the recent years, there is a growing interest in the therapeutic potential of FMT in various diseases. The standard FMT protocols do not exist. Procedures of FMT vary in several aspects such as donor selection, preparation of fecal material, preparation of the recipient and administration way. FMT appears to be the most successful in the treatment of recurrent Clostridium difficile infection (CDI), randomized controlled studies reported 90 % success rate. There is a limited evidence for FMT as a treatment of ulcerative colitis. FMT has been also studied as treatment of diseases with impaired gut microbiota, such as cardiovascular, autoimmune and metabolic diseases. Many unanswered questions with regard to FMT remain and further research is needed.

  8. Evaluation of the MicroWorks, Inc. Swab Sampling System (MSSSTM) for Use in Performing Quantitative Swab Sampling.

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    Rubio, Sandy; McIver, Dawn; Behm, Natalie; Fisher, Madeline; Fleming, William

    2010-01-01

    The purpose of this study was to qualify the MicroWorks, Inc. Swab Sampling System (MSSS™) swab kit for use in sampling cleanroom surfaces for bioburden. A six-part study was performed to demonstrate the suitability of the swab materials, the recovery of bioburden from typical cleanroom surfaces, the neutralization of typical disinfectants used in cleanrooms, the removal of diluents from the swabbed surface, and the hold time for test samples. A total of 13 challenge organisms were used: six National Collection of Type Cultures/American Type Culture Collection (NCTC/ATCC) standard culture organisms and seven environmental isolates, which were recovered from different MedImmune manufacturing facilities. Based on the results of the study it was shown that 12 of the challenge organisms were recovered from the calcium alginate swab materials and 13 of the challenge organisms were recovered from the sodium citrate diluent at ≥70%. Eleven organisms, including the six NCTC/ATCC organisms and five of the environmental organisms, were recovered from stainless steel, glass, polyvinylchloride curtain material, latex glove material, and neoprene at a rate of ≥70%. Effective neutralization was shown for LpH (an acid phenolic compound manufactured by Steris Corporation, Mentor, OH), Vesphene II, Spor-Klenz, 70% isopropyl alcohol (IPA), and Biocides B, X, and Y when utilizing the filtration/rinsing process. Recovery of six NCTC/ATCC organisms was demonstrated at ≥70%. The study also demonstrated that the diluents could easily be removed from the swabbed surface by following the swab with a 70% IPA wipe. A hold time of at least 24 h was demonstrated when samples were stored at 2-8 °C. The results of this study demonstrated that the MSSS™ swab kit and qualified test method recover ≥70% of surface bioburden from common cleanroom surfaces in the presence of a wide variety of disinfectants.

  9. Rectal swabs for analysis of the intestinal microbiota.

    Science.gov (United States)

    Budding, Andries E; Grasman, Matthijs E; Eck, Anat; Bogaards, Johannes A; Vandenbroucke-Grauls, Christina M J E; van Bodegraven, Adriaan A; Savelkoul, Paul H M

    2014-01-01

    The composition of the gut microbiota is associated with various disease states, most notably inflammatory bowel disease, obesity and malnutrition. This underlines that analysis of intestinal microbiota is potentially an interesting target for clinical diagnostics. Currently, the most commonly used sample types are feces and mucosal biopsy specimens. Because sampling method, storage and processing of samples impact microbiota analysis, each sample type has its own limitations. An ideal sample type for use in routine diagnostics should be easy to obtain in a standardized fashion without perturbation of the microbiota. Rectal swabs may satisfy these criteria, but little is known about microbiota analysis on these sample types. In this study we investigated the characteristics and applicability of rectal swabs for gut microbiota profiling in a clinical routine setting in patients presenting with various gastro-intestinal disorders. We found that rectal swabs appeared to be a convenient means of sampling the human gut microbiota. Swabs can be performed on demand, whenever a patient presents; swab-derived microbiota profiles are reproducible, whether they are gathered at home by patients or by medical professionals in an outpatient setting and may be ideally suited for clinical diagnostics and large-scale studies.

  10. Rectal swabs for analysis of the intestinal microbiota.

    Directory of Open Access Journals (Sweden)

    Andries E Budding

    Full Text Available The composition of the gut microbiota is associated with various disease states, most notably inflammatory bowel disease, obesity and malnutrition. This underlines that analysis of intestinal microbiota is potentially an interesting target for clinical diagnostics. Currently, the most commonly used sample types are feces and mucosal biopsy specimens. Because sampling method, storage and processing of samples impact microbiota analysis, each sample type has its own limitations. An ideal sample type for use in routine diagnostics should be easy to obtain in a standardized fashion without perturbation of the microbiota. Rectal swabs may satisfy these criteria, but little is known about microbiota analysis on these sample types. In this study we investigated the characteristics and applicability of rectal swabs for gut microbiota profiling in a clinical routine setting in patients presenting with various gastro-intestinal disorders. We found that rectal swabs appeared to be a convenient means of sampling the human gut microbiota. Swabs can be performed on demand, whenever a patient presents; swab-derived microbiota profiles are reproducible, whether they are gathered at home by patients or by medical professionals in an outpatient setting and may be ideally suited for clinical diagnostics and large-scale studies.

  11. Imaging fecal incontinence

    Energy Technology Data Exchange (ETDEWEB)

    Fuchsjaeger, Michael H. E-mail: michael.fuchsjaeger@univie.ac.at; Maier, Andrea G

    2003-08-01

    Fecal incontinence is the inability to defer release of gas or stool from the anus and rectum by mechanisms of voluntary control. It is an important medical disorder affecting the quality of life of up to 20% of the population above 65 years. The most common contributing factors include previous vaginal deliveries, pelvic or perineal trauma, previous anorectal surgery, and rectal prolapse. Many physicians lack experience and knowledge related to pelvic floor incontinence disorders, but advancing technology has improved this knowledge. Increased experience with endoanal ultrasound and endoanal magnetic resonance imaging have given us a better understanding not only of the anatomy of the anal canal but also of the underlying morphological defects in fecal incontinence. Current imaging methods are emphasized and recent literature is reviewed.

  12. Experiences with the Dutch Working Party on antibiotic policy (SWAB).

    NARCIS (Netherlands)

    Prins, J.M.; Degener, J.E.; Neeling, A.J. de; Gyssens, I.C.J.

    2008-01-01

    The Dutch Working Party on Antibiotic Policy (Stichting Werkgroep AntibioticaBeleid, SWAB) was founded in 1996 as an initiative of the Society for Infectious Diseases, the Dutch Society for Medical Microbiology, and the Dutch Association of Hospital Pharmacists. Its primary goal is to contribute to

  13. Detecting Rickettsia parkeri infection from eschar swab specimens.

    Science.gov (United States)

    Myers, Todd; Lalani, Tahaniyat; Dent, Mike; Jiang, Ju; Daly, Patrick L; Maguire, Jason D; Richards, Allen L

    2013-05-01

    The typical clinical presentation of several spotted fever group Rickettsia infections includes eschars. Clinical diagnosis of the condition is usually made by analysis of blood samples. We describe a more sensitive, noninvasive means of obtaining a sample for diagnosis by using an eschar swab specimen from patients infected with Rickettsia parkeri.

  14. Decay of Fecal Indicator Bacteria and Microbial Source Tracking Markers in Cattle Feces

    Science.gov (United States)

    The survival of fecal indicator bacteria (FIB) and microbial source tracking (MST) markers in water microcosms and manure amended soils has been well documented; however, little is known about the survival of MST markers in bovine feces deposited on pastures. We conducted a study...

  15. A comparison of DNA collection and retrieval from two swab types (cotton and nylon flocked swab) when processed using three QIAGEN extraction methods.

    Science.gov (United States)

    Brownlow, Robert J; Dagnall, Kathryn E; Ames, Carole E

    2012-05-01

    The Metropolitan Police Service currently uses cotton swabs to retrieve DNA for forensic profiling. Recently, a new nylon flocked swab type has become available from Copan (MicroRheologics, Brescia, Italy) that it is claimed, offers increased sample recovery and release yields. If true, the flocked swab may have important applications in DNA evidence retrieval. This study examines the DNA retrieval capability of cotton and nylon flocked swabs when extracted using three common extraction platforms (QIAcube, BioRobot EZ1 and manually processed QIAamp DNA investigator kit). Results indicate that both swab types are capable of recovering high percentages of DNA (>50%); however, the extraction platform selected was shown to have a significant effect upon DNA retrieval. Across all experiments, the cotton swab combined with the spin-column extractions was shown to be most effective, with the nylon swab and BioRobot EZ1 combination being the least effective. These findings illustrate the importance of extraction method selection.

  16. Comparison of air samples, nasal swabs, ear-skin swabs and environmental dust samples for detection of Methicillin Resistant Staphylococcus aureus (MRSA) in pig herds

    DEFF Research Database (Denmark)

    Agersø, Yvonne; Vigre, Håkan; Cavaco, Lina;

    2014-01-01

    To identify a cost-effective and practical method for detection of methicillin-resistant Staphylococcus aureus (MRSA) in pig herds, the relative sensitivity of four sample types: nasal swabs, ear-skin (skin behind the ears) swabs, environmental dust swabs and air was compared. Moreover, dependency...... detection by air sampling is easy to perform, reduces costs and analytical time compared to existing methods, and is recommended for initial testing of herds. Ear-skin swab sampling may be more sensitive for MRSA detection than air sampling or nasal swab sampling.......-herd prevalence ⩾25%]. The results indicate that taking swabs of skin behind the ears (ten pools of five) was even more sensitive than taking nasal swabs (ten pools of five) at the herd level and detected significantly more positive samples. spa types t011, t034 and t4208 were observed. In conclusion, MRSA...

  17. [Fecal microbiota transplantation: review].

    Science.gov (United States)

    Barbut, F; Collignon, A; Butel, M-J; Bourlioux, P

    2015-01-01

    Fecal microbiota transplantation (FMT) has gained an increasing medical interest, since the recognition of the role of disturbed microbiota in the development of various diseases. To date, FMT is an established treatment modality for multiple recurrent Clostridium difficile infection (RCDI), despite lack of standardization of the procedure. Persisting normalization of the disturbed colonic microbiota associated with RCDI seems to be responsible for the therapeutic effect of FMT. For other diseases, FMT should be considered strictly experimental, only offered to patients in an investigational clinical setting. Although the concept of FMT is appealing, current expectations should be damped until future evidence arises.

  18. [Fecal microbiota transplantation].

    Science.gov (United States)

    García-García-de-Paredes, Ana; Rodríguez-de-Santiago, Enrique; Aguilera-Castro, Lara; Ferre-Aracil, Carlos; López-Sanromán, Antonio

    2015-03-01

    Bacteria can no longer be seen as an enemy. Nowadays, there is enough evidence to place the microbiota as a key element in human homeostasis. Despite initial skepticism, fecal microbiota transplantation (FMT) is a real therapeutic alternative for patients with recurrent Clostridium difficile infection. Moreover, this procedure has shown promising results in ulcerative colitis and other non-gastrointestinal disorders. There is still a lack of knowledge and clinical trials with long- term follow-up. Therefore, the available data should be interpreted with caution. In this document we provide a detailed review of the literature on the intestinal microbiota and FMT.

  19. Incontinencia fecal del adulto

    OpenAIRE

    2011-01-01

    El propósito de esta revisión es actualizar los conocimientos sobre esta patología, destacando su evolución clínica, estudio y tratamiento, aspectos que ameritan un enfoque multidisciplinario, ya que, además de su compleja fisiopatología, puede asociarse a incontinencia urinaria y prolapso de los tres compartimentos de la pelvis. La incontinencia fecal (IF) constituye una patología altamente prevalente que afecta al menos un 2% de la población y hasta el 45% de los pacientes en casas de repos...

  20. Fecal microbiota composition and frailty

    NARCIS (Netherlands)

    van Tongeren, SP; Slaets, JPJ; Harmsen, HJM; Welling, GW

    2005-01-01

    The relationship between fecal microbiota composition and frailty in the elderly was studied. Fecal samples from volunteers with high frailty scores showed a significant reduction in the number of lactobacilli (26-fold). At much higher population levels, both the Bacteroides/Prevotella (threefold) a

  1. CERVICO-VAGINAL SWABS TO PREDICT PROM: A CASE STUDY

    Directory of Open Access Journals (Sweden)

    Boricha

    2013-04-01

    Full Text Available ABSTRACT: BACKGROUND: The presence of lower genital tract infections poses a threat to the health of a woman. During pregnancy, these infection s may also have a direct effect on the fetus or may indirectly predispose to fetal damage secondar y to premature labour or premature rupture of membranes. Early detection is thus import ant because maternal physiological alterations and the presence of a fetus may hamper the diagnosis and the management of such infections. Antepartum treatment of lower genital tr act infections or bacterial colonization has been found to reduce the incidence of preterm births . OBJECTIVES: To study the impact of education and socio-economic background, to assess diagnostic efficacy in pregnancy, to study the effect of intervention on the outcome of pregnan cy and finally, to study the appropriate trimester for taking a cervicovaginal swab in pregna nt women. MATERIALS AND METHODS - Our case study was a prospective study involving 100 pregnant women following up in the outpatient department of a community hospital from 200 8-2010 with respect to their cervicovaginal microbial growth in each trimester. Patients were divided into culture positive and negative groups and treated accordingly RESULTS – In our study, we found that streptococcus, candida and staphylococcus were the mo st commonly prevalent among all the microorganisms isolated. Out of 100 women, 27 were swab positive in the 1 st trimester with an increasing trend of 1% in swab positivity in subsequ ent trimesters. Among swab positive cases, 51.85%(1 st , 50%(2 nd and 51.72%(3 rd landed up in preterm labour with or without PROM. CONCLUSION – There was a very high positive correlation between the incidence of a positive swab culture and preterm events. We found that the best time for a cervicovaginal swab was during the 3 rd trimester. Our study had a high negative predictiv e value i.e. absence of growth were best in predicting that cases would not go in t o

  2. Absence of Streptococcus pneumoniae in pharyngeal swabs of geriatric inpatients.

    Science.gov (United States)

    Jomrich, Nina; Kellner, Silvia; Djukic, Marija; Eiffert, Helmut; Nau, Roland

    2015-07-01

    Colonization of the pharynx by Streptococcus pneumoniae was studied in 185 in-hospital geriatric patients (median age 81 years) from 29 March 2011 to 22 June 2011. Swabs were plated on blood agar plates. Colonies with a morphology suggesting S. pneumoniae were further analyzed. Surprisingly, pneumococci were not found in any of the samples. Pneumococci chronically colonizing the pharynx of elderly people may be much rarer than previously thought and probably are not the source of pneumococcal pneumonia in old age.

  3. Contact dermatitis to alcohol swabs masquerading as vaccine allergy.

    Science.gov (United States)

    Storer, Emma; Marshman, Gillian; Kupa, Ann

    2004-05-01

    A 14-year-old girl developed an eruption on her upper arm of pruritic, follicular papules each time she received a vaccination. This was initially thought to be a local reaction to the vaccines. After a similar rash appeared at a venepuncture site, a contact allergy to the alcohol swabs used before the procedures was postulated. A repeated open application test clarified this observation.

  4. Fecal pollution source tracking in waters intended for human supply based on archaeal and bacterial genetic markers.

    Science.gov (United States)

    Bianco, Kayo; Barreto, Camila; Oliveira, Samara Sant'Anna; Pinto, Leonardo Henriques; Albano, Rodolpho Mattos; Miranda, Catia Chaia; Clementino, Maysa Mandetta

    2015-12-01

    The determination of fecal pollution sources in aquatic ecosystems is essential to estimate associated health risks. In this study, we evaluate eight microbial source tracking (MST) markers including host-specific Bacteroidales and Methanobrevibacter spp. for discrimination between human, bovine, equine, and swine fecal contamination in waters intended for human supply. Overall, the novel host-specific archaeal and bacterial primers proposed in this study demonstrated high sensitivity and specificity. Markers for the Archaea domain were more prevalent in the fecal and water samples studied. We conclude that the investigations regarding the sources of fecal pollution in public water supplies can contribute to improve the quality of human health. To our knowledge, this is the first analysis using both archaeal and bacterial fecal MST markers on tropical water bodies of Rio de Janeiro city, Brazil.

  5. Infectious bovine keratoconjunctivitis: a review of cases in clinical practice.

    Science.gov (United States)

    Alexander, Dominic

    2010-11-01

    Infectious bovine keratoconjunctivitis (IBK) is a painful ocular disease affecting cattle worldwide. The publications documenting this condition focus on what is the accepted cause of IBK--Moraxella bovis. This article draws on experience and recorded data made at the time of the initial examination and follow-up visits. Laboratory culture of ocular swabs was undertaken where appropriate. Diagnosis of IBK is usually based on clinical signs, environment, and history. Misdiagnosis of the organisms involved is a genuine possibility. This article focuses on recent outbreaks of bovine ocular disease in the United Kingdom in three counties over a 12-month period.

  6. Specific probiotics or 'fecal transplantation'.

    Science.gov (United States)

    Kruis, Wolfgang

    2012-01-01

    The intestinal ecosystem consists mainly of the enteric flora and to a large extent determines intestinal but also extraintestinal health and disease. General alterations and specific molecular changes of intestinal bacteria cause local as well as systemic immune reactions. Nonantibiotic treatment of the enteric flora has a long tradition and spans a range of different interventions from nutrition to specific probiotics and complete fecal transplantation. When comparing therapy to specific probiotics and fecal transplantation, several aspects need to be considered, like biological consequences, safety and therapeutic evidence. The introduction of probiotics into therapy occurred more than hundred years ago. In contrast, experiences with fecal transplantation are more recent and more limited. Safety issues have not been definitively clarified. Because of the different biological activities of probiotics and fecal transplantation, it can be hypothesized that they may play different roles in the treatment of various diseases. More research is needed before the details, safety and therapeutic effects of bacteriotherapy for IBD become sufficiently clear.

  7. Tracking the Sources of Fecal Contaminations: an Interdisciplinary Toolbox

    Science.gov (United States)

    Jeanneau, L.; Jarde, E.; Derrien, M.; Gruau, G.; Solecki, O.; Pourcher, A.; Marti, R.; Wéry, N.; Caprais, M.; Gourmelon, M.; Mieszkin, S.; Jadas-Hécart, A.; Communal, P.

    2011-12-01

    Fecal contaminations of inland and coastal waters induce risks to human health and economic losses. In order to improve water management, it is necessary to identify the sources of contamination, which implies the development of specific markers. In order to be considered as a valuable host-specific marker, one must (1) be source specific, (2) occur in high concentration in polluting matrices, (3) exhibit extra-intestinal persistence similar to fecal indicator bacteria (FIB) and (4) not grow out of the host. However, up to day no single marker has fulfilled all those criteria. Thus, it has been suggested to use a combination of markers in order to generate more reliable data. This has lead to the development of a Microbial Source Tracking (MST) toolbox including FIB and microbial and chemical specific markers in order to differentiate between human, bovine and porcine fecal contaminations. Those specific markers are, (1) genotypes of F-specific RNA bacteriophages, (2) bacterial markers belonging to the Bacteroidales (human-specific HF183, ruminant-specific Rum-2-Bac and pig-specific Pig-2-Bac markers), to the Bifidobacterium (Bifidobacterium adolescentis) and pig-specific Lactobacillus amylovorus, (3) fecal stanols and (4) caffeine. The development of this MST toolbox was composed of four steps, from the molecular scale to the watershed scale. At the molecular scale, the specificity and the concentration of those markers were studied in cattle and pig manures and in waste water treatment plant (WWTP) effluents and influents. At the microcosm scale, the transfer of bovine and porcine specific markers was investigated by rainfall simulations on agricultural plots amended with cattle or pig manure. Moreover, the relative persistence of FIB and human, porcine and bovine specific markers was investigated in freshwater and seawater microcosms inoculated with a WWTP influent, pig manure and cow manure. Finally, the aforementioned MST toolbox has been validated at the

  8. Development of a non invasion real-time PCR assay for the quantitation of chicken parvovirus in fecal swabs

    Science.gov (United States)

    The present study describes the development of a real time Taqman polymerase chain reaction (PCR) assay using a fluorescent labeled probe for the detection and quantitation of chicken parvovirus (ChPV) in feces. The primers and probes were designed based on the nucleotide sequence of the non struct...

  9. Characterization of sources and loadings of fecal pollutants using microbial source tracking assays in urban and rural areas of the Grand River Watershed, Southwestern Ontario.

    Science.gov (United States)

    Lee, Dae-Young; Lee, Hung; Trevors, Jack T; Weir, Susan C; Thomas, Janis L; Habash, Marc

    2014-04-15

    Sources of fecal water pollution were assessed in the Grand River and two of its tributaries (Ontario, Canada) using total and host-specific (human and bovine) Bacteroidales genetic markers in conjunction with reference information, such as land use and weather. In-stream levels of the markers and culturable Escherichia coli were also monitored during multiple rain events to gain information on fecal loadings to catchment from diffuse sources. Elevated human-specific marker levels were accurately identified in river water impacted by a municipal wastewater treatment plant (WWTP) effluent and at a downstream site in the Grand River. In contrast, the bovine-specific marker showed high levels of cattle fecal pollution in two tributaries, both of which are characterized as intensely farmed areas. The bovine-specific Bacteroidales marker increased with rainfall in the agricultural tributaries, indicating enhanced loading of cattle-derived fecal pollutants to river from non-point sources following rain events. However, rain-triggered fecal loading was not substantiated in urban settings, indicating continuous inputs of human-originated fecal pollutants from point sources, such as WWTP effluent. This study demonstrated that the Bacteroidales source tracking assays, in combination with land use information and hydrological data, may provide additional insight into the spatial and temporal distribution of source-specific fecal contamination in streams impacted by varying land uses. Using the approach described in this study may help to characterize impacted water sources and to design targeted land use management plans in other watersheds in the future.

  10. Detection of Campylobacter spp. in chicken fecal samples by real-time PCR

    DEFF Research Database (Denmark)

    Lund, Marianne; Nordentoft, Steen; Pedersen, Karl

    2004-01-01

    and compared to conventional culturing using selective enrichment. There was no statistically significant difference in performance between real-time PCR and culture by selective enrichment, and the diagnostic specificity was 0.96 with an agreement of 0.92. Therefore, the assay should be useful for screening......A real-time PCR assay for detecting thermophilic Campylobacter spp. directly in chicken feces has been developed. DNA was isolated from fecal material by using magnetic beads followed by PCR with a prealiquoted PCR mixture, which had been stored at -18degreesC. Campylobacter could be detected...... in less than 4 h, with a detection limit of 100 to 150 CFU/ml, in a fecal suspension. A bacterial internal control was added before DNA extraction to control both DNA isolation and the presence of PCR inhibitors in the samples. The assay was performed on 111 swab samples from a Danish surveillance program...

  11. Surface, Water, and Air Biocharacterization (SWAB) Flight Experiment

    Science.gov (United States)

    Castro, V. A.; Ott, C. M.; Pierson, D. L.

    2012-01-01

    The determination of risk from infectious disease during spaceflight missions is composed of several factors including both the concentration and characteristics of the microorganisms to which the crew are exposed. Thus, having a good understanding of the microbial ecology aboard spacecraft provides the necessary information to mitigate health risks to the crew. While preventive measures are taken to minimize the presence of pathogens on spacecraft, medically significant organisms have been isolated from both the Mir and International Space Station (ISS). Historically, the method for isolation and identification of microorganisms from spacecraft environmental samples depended upon their growth on culture media. Unfortunately, only a fraction of the organisms may grow on a specific culture medium, potentially omitting those microorganisms whose nutritional and physical requirements for growth are not met. To address this bias in our understanding of the ISS environment, the Surface, Water, and Air Biocharacterization (SWAB) Flight Experiment was designed to investigate and develop monitoring technology to provide better microbial characterization. For the SWAB flight experiment, we hypothesized that environmental analysis using non-culture-based technologies would reveal microorganisms, allergens, and microbial toxins not previously reported in spacecraft, allowing for a more complete health assessment. Key findings during this experiment included: a) Generally, advanced molecular techniques were able to reveal a few organisms not recovered using culture-based methods; however, there is no indication that current monitoring is "missing" any medically significant bacteria or fungi. b) Molecular techniques have tremendous potential for microbial monitoring, however, sample preparation and data analysis present challenges for spaceflight hardware. c) Analytical results indicate that some molecular techniques, such as denaturing gradient gel electrophoresis (DGGE), can

  12. Evaluation of the Recovery Rate of Different Swabs for Microbial Environmental Monitoring.

    Science.gov (United States)

    Goverde, Marcel; Willrodt, Julian; Staerk, Alexandra

    Contact plates, dipslides, and swabs are used for the microbiological monitoring of surfaces in controlled environments such as pharmaceutical clean rooms. In the present study, three different swab types using two different methods (direct streaking on agar versus elution followed by membrane filtration) were evaluated. In a first study, representative surfaces in pharmaceutical clean rooms were artificially inoculated using three different environmental strains (in vitro study). In a second study, a naturally inoculated floor was swabbed with the same three swab types, again using the two different recovery methods (in situ study). With the in vitro study, clear differences were found between the three swab types as well as between the two recovery methods. In addition, recovery rate of the swab type was dependent on the recovery method (interactive effect). One swab type showed a higher recovery rate with direct streaking on agar, while the other swab type showed better results using the elution/membrane filtration method. This difference can be explained by the fact that both swabs were each developed for their specific application. The type of surface also had a highly significant effect on the recovery rates. Recovery on stainless steel was better than for the other surfaces, while lexan had the lowest recovery rate. From the three different strains applied in the in vitro study, Micrococcus luteus had significantly higher recovery results compared to the other two strains (Bacillus thuringiensis, Aspergillus brasiliensis). The differences in recovery between the swab type and recovery method were less pronounced in the in situ study. In particular, the recovery of the swab type depending on the recovery method was not found. In conclusion, if swabs are to be used for environmental monitoring, their suitability should first be evaluated. This can be approached with artificially inoculated surfaces. However, naturally inoculated surfaces might be more

  13. Fecal microbiota transplantation: in perspective.

    Science.gov (United States)

    Gupta, Shaan; Allen-Vercoe, Emma; Petrof, Elaine O

    2016-03-01

    There has been increasing interest in understanding the role of the human gut microbiome to elucidate the therapeutic potential of its manipulation. Fecal microbiota transplantation (FMT) is the administration of a solution of fecal matter from a donor into the intestinal tract of a recipient in order to directly change the recipient's gut microbial composition and confer a health benefit. FMT has been used to successfully treat recurrent Clostridium difficile infection. There are preliminary indications to suggest that it may also carry therapeutic potential for other conditions such as inflammatory bowel disease, obesity, metabolic syndrome, and functional gastrointestinal disorders.

  14. Bovine rhinitis viruses are common in U.S. cattle with bovine respiratory disease.

    Science.gov (United States)

    Hause, Ben M; Collin, Emily A; Anderson, Joe; Hesse, Richard A; Anderson, Gary

    2015-01-01

    Bovine rhinitis viruses (BRV) are established etiological agents of bovine respiratory disease complex however little research into their epidemiology and ecology has been published for several decades. In the U.S., only bovine rhinitis A virus 1 (BRAV1) has been identified while bovine rhinitis A virus 2 (BRAV2) and bovine rhinitis B virus (BRBV) were previously only identified in England and Japan, respectively. Metagenomic sequencing of a nasal swab from a bovine respiratory disease (BRD) diagnostic submission from Kansas identified contigs with approximately 90% nucleotide similarity to BRAV2 and BRBV. A combination of de novo and templated assemblies using reference genomes yielded near complete BRAV2 and BRBV genomes. The near complete genome of bovine rhinitis A virus 1 (BRAV1) was also determined from a historical isolate to enable further molecular epidemiological studies. A 5'-nuclease reverse transcription PCR assay targeting the 3D polymerase gene was designed and used to screen 204 archived BRD clinical specimens. Thirteen (6.4%) were positive. Metagenomic sequencing of six positive samples identified mixed BRAV1/BRAV2, BRAV1/BRBV and BRAV2/BRBV infections for five samples. One sample showed infection only with BRAV1. Seroprevalence studies using a cell culture adapted BRBV found immunofluorescence assay-reactive antibodies were common in the herds analyzed. Altogether, these results demonstrate that BRV infections are common in cattle with respiratory disease and that BRAV1, BRAV2 and BRBV co-circulate in U.S. cattle and have high similarity to viruses isolated more than 30 years ago from diverse locations.

  15. Bovine rhinitis viruses are common in U.S. cattle with bovine respiratory disease.

    Directory of Open Access Journals (Sweden)

    Ben M Hause

    Full Text Available Bovine rhinitis viruses (BRV are established etiological agents of bovine respiratory disease complex however little research into their epidemiology and ecology has been published for several decades. In the U.S., only bovine rhinitis A virus 1 (BRAV1 has been identified while bovine rhinitis A virus 2 (BRAV2 and bovine rhinitis B virus (BRBV were previously only identified in England and Japan, respectively. Metagenomic sequencing of a nasal swab from a bovine respiratory disease (BRD diagnostic submission from Kansas identified contigs with approximately 90% nucleotide similarity to BRAV2 and BRBV. A combination of de novo and templated assemblies using reference genomes yielded near complete BRAV2 and BRBV genomes. The near complete genome of bovine rhinitis A virus 1 (BRAV1 was also determined from a historical isolate to enable further molecular epidemiological studies. A 5'-nuclease reverse transcription PCR assay targeting the 3D polymerase gene was designed and used to screen 204 archived BRD clinical specimens. Thirteen (6.4% were positive. Metagenomic sequencing of six positive samples identified mixed BRAV1/BRAV2, BRAV1/BRBV and BRAV2/BRBV infections for five samples. One sample showed infection only with BRAV1. Seroprevalence studies using a cell culture adapted BRBV found immunofluorescence assay-reactive antibodies were common in the herds analyzed. Altogether, these results demonstrate that BRV infections are common in cattle with respiratory disease and that BRAV1, BRAV2 and BRBV co-circulate in U.S. cattle and have high similarity to viruses isolated more than 30 years ago from diverse locations.

  16. Equivalence of self- and staff-collected nasal swabs for the detection of viral respiratory pathogens.

    Directory of Open Access Journals (Sweden)

    Manas K Akmatov

    Full Text Available BACKGROUND: The need for the timely collection of diagnostic biosamples during symptomatic episodes represents a major obstacle to large-scale studies on acute respiratory infection (ARI epidemiology. This may be circumvented by having the participants collect their own nasal swabs. We compared self- and staff-collected swabs in terms of swabbing quality and detection of viral respiratory pathogens. METHODOLOGY/PRINCIPAL FINDINGS: We conducted a prospective study among employees of our institution during the ARI season 2010/2011 (December-March. Weekly emails were sent to the participants (n = 84, reminding them to come to the study center in case of new symptoms. The participants self-collected an anterior nasal swab from one nostril, and trained study personnel collected one from the other nostril. The participants self-collected another two swabs (one from each nostril on a subsequent day. Human β-actin DNA concentration was determined in the swabs as a quality control. Viral respiratory pathogens were detected by multiplex RT-PCR (Seeplex RV15 kit, Seegene, Eschborn, Germany. Of 84 participants, 56 (67% reported at least one ARI episode, 18 participants two, and one participant three. Self-swabbing was highly accepted by the participants. The amount of β-actin DNA per swab was higher in the self- than in the staff-collected swabs (p = 0.008. β-actin concentration was lower in the self-swabs collected on day 1 than in those collected on a subsequent day (p<0.0001. A respiratory viral pathogen was detected in 31% (23/75 of staff- and in 35% (26/75 of self-collected swabs (p = 0.36. With both approaches, the most frequently identified pathogens were human rhinoviruses A/B/C (12/75 swabs, 16% and human coronavirus OC43 (4/75 swabs, 5%. There was almost perfect agreement between self- and staff-collected swabs in terms of pathogen detection (agreement = 93%, kappa = 0.85, p<0.0001. CONCLUSIONS/SIGNIFICANCE: Nasal self-swabbing

  17. Salmonella fecal excretion control in broiler chickens by organic acids and essential oils blend feed added

    Directory of Open Access Journals (Sweden)

    A Borsoi

    2011-03-01

    Full Text Available Salmonellosis is an important disease with economic impact as it may affect animal performance and may result in foodborne disease in humans through the eggs and carcass contamination. Regarding the Salmonella control, it is possible to decrease its fecal excretion and the contamination of chicken carcasses by adding organic acids to the feed or drinking water at appropriate times. The aim of this study was to test a blend of organic acids and essential oils in broilers challenged with Salmonella Enteritidis (SE, and to verify the fecal excretion of Salmonella. Sixty broilers were placed in four groups. One group was the negative control. Another group was orally inoculated at 1 day-old with 10(5 CFU/mL of SE as a positive SE control. Two groups (T3 and T4 were orally inoculated at 1 day-old with 10(5 CFU/mL of SE and their feed was separately treated with 0.5 and 1% of organic acids and essential oils, respectively. To assess the fecal excretion of SE, cloacal swabs were collected from all birds at 2, 6, 13 and 20 days after inoculation. The T3 and T4 groups showed a reduction in fecal excretion of SE at 6 and 20 days after inoculation.

  18. Bowel Control Problems (Fecal Incontinence)

    Science.gov (United States)

    ... medical test results. In addition to a general medical history, the health care provider may ask the following questions: When did fecal ... delivery hemorrhoids and rectal prolapse rectocele inactivity ... on a person’s medical history, physical exam, and medical test results. Treatment ...

  19. Contamination of Bovine, Sheep and Goat Meat with Brucella Spp.

    Science.gov (United States)

    Casalinuovo, Francesco; Ciambrone, Lucia; Cacia, Antonio; Rippa, Paola

    2016-01-01

    A study was conducted in order to evaluate the contamination by Brucella spp. of meat from animals slaughtered because they had resulted positive for brucellosis at some time during their life. After slaughter and before delivery to market outlets, swab samples were taken from 307 carcasses of infected animals: 40 cattle, 60 sheep and 207 goats. The swabs were subsequently analysed by means of polymerase chain reaction (PCR) tests. In addition, bacteriological tests were carried out on the lymph nodes and internal organs of the same animals. Brucella spp. was detected by means of PCR in 25/307 carcasses (8%): 1 bovine (2.5%), 9 sheep (15%) and 15 goats (7.2%) and was isolated by means of a cultural method in 136/307 carcasses (44%). Moreover, additional analysis, performed on lymph nodes from the same carcasses that had proved positive by PCR, allowed highlighting type 3 Brucella abortus in the bovine carcass and type 3 Brucella melitensis in the sheep and goat carcasses. The study shows that cattle, sheep and goats meat of animals slaughtered because they had tested positive for brucellosis may be contaminated by Brucella spp. As this could constitute a real risk of transmission to both butchery personnel and consumers, the meat of animals infected by Brucella spp. should be analysed before being marketed. In this respect, PCR technique performed on swabs proved to be more useful, practical and faster than the traditional bacteriological method. PMID:27853716

  20. Contamination of Bovine, Sheep and Goat Meat with Brucella Spp.

    Science.gov (United States)

    Casalinuovo, Francesco; Ciambrone, Lucia; Cacia, Antonio; Rippa, Paola

    2016-06-03

    A study was conducted in order to evaluate the contamination by Brucella spp. of meat from animals slaughtered because they had resulted positive for brucellosis at some time during their life. After slaughter and before delivery to market outlets, swab samples were taken from 307 carcasses of infected animals: 40 cattle, 60 sheep and 207 goats. The swabs were subsequently analysed by means of polymerase chain reaction (PCR) tests. In addition, bacteriological tests were carried out on the lymph nodes and internal organs of the same animals. Brucella spp. was detected by means of PCR in 25/307 carcasses (8%): 1 bovine (2.5%), 9 sheep (15%) and 15 goats (7.2%) and was isolated by means of a cultural method in 136/307 carcasses (44%). Moreover, additional analysis, performed on lymph nodes from the same carcasses that had proved positive by PCR, allowed highlighting type 3 Brucella abortus in the bovine carcass and type 3 Brucella melitensis in the sheep and goat carcasses. The study shows that cattle, sheep and goats meat of animals slaughtered because they had tested positive for brucellosis may be contaminated by Brucella spp. As this could constitute a real risk of transmission to both butchery personnel and consumers, the meat of animals infected by Brucella spp. should be analysed before being marketed. In this respect, PCR technique performed on swabs proved to be more useful, practical and faster than the traditional bacteriological method.

  1. Contamination of bovine, sheep and goat meat with Brucella spp.

    Directory of Open Access Journals (Sweden)

    Francesco Casalinuovo

    2016-06-01

    Full Text Available A study was conducted in order to evaluate the contamination by Brucella spp. of meat from animals slaughtered because they had resulted positive for brucellosis at some time during their life. After slaughter and before delivery to market outlets, swab samples were taken from 307 carcasses of infected animals: 40 cattle, 60 sheep and 207 goats. The swabs were subsequently analysed by means of polymerase chain reaction (PCR tests. In addition, bacteriological tests were carried out on the lymph nodes and internal organs of the same animals. Brucella spp. was detected by means of PCR in 25/307 carcasses (8%: 1 bovine (2.5%, 9 sheep (15% and 15 goats (7.2% and was isolated by means of a cultural method in 136/307 carcasses (44%. Moreover, additional analysis, performed on lymph nodes from the same carcasses that had proved positive by PCR, allowed highlighting type 3 Brucella abortus in the bovine carcass and type 3 Brucella melitensis in the sheep and goat carcasses. The study shows that cattle, sheep and goats meat of animals slaughtered because they had tested positive for brucellosis may be contaminated by Brucella spp. As this could constitute a real risk of transmission to both butchery personnel and consumers, the meat of animals infected by Brucella spp. should be analysed before being marketed. In this respect, PCR technique performed on swabs proved to be more useful, practical and faster than the traditional bacteriological method.

  2. 77 FR 29914 - Bovine Spongiform Encephalopathy; Importation of Bovines and Bovine Products

    Science.gov (United States)

    2012-05-21

    ... RIN 0579-AC68 Bovine Spongiform Encephalopathy; Importation of Bovines and Bovine Products AGENCY... live bovines and products derived from bovines with regard to bovine spongiform encephalopathy. This... with regard to bovine spongiform encephalopathy. Comments on the proposed rule were required to......

  3. Owner-collected swabs of pets: a method fit for the purpose of zoonoses research.

    Science.gov (United States)

    Möbius, N; Hille, K; Verspohl, J; Wefstaedt, P; Kreienbrock, L

    2013-09-01

    As part of the preparation of a large cohort study in the entire German population, this study examined the feasibility of cat and dog owners collecting nasal and oral swabs of their animals at home as a method of assessing exposure to zoonoses. In veterinary clinics in Hannover, Germany, 100 pet owners were recruited. Nasal and oral swabs of pets were taken by a veterinarian at the clinic and owners took swabs at home. Swabs were analysed regarding bacterial growth and compared (owner vs. vet) using Cohen's kappa and McNemar's test. The return rate of kits was 92%, and 77% of owners thought it unnecessary to have veterinarian assistance to swab the mouth. McNemar's test results: oral swabs 78% agreement with Gram-positive bacterial growth, 87% agreement with Gram-negative bacterial growth; with similar results for nasal swabs. Although sample quality differed, this method allowed the receipt of swabs from pets in order to obtain information about colonization with zoonotic pathogens.

  4. Revised SWAB guidelines for antimicrobial therapy of community-acquired pneumonia

    NARCIS (Netherlands)

    Schouten, JA; Prins, JM; Bonten, MJ; Degener, J; Janknegt, RE; Hollander, JMR; Jonkers, RE; Wijnands, WJ; Verheij, TJ; Sachs, APE; Kullberg, BJ

    2005-01-01

    The Dutch Working Party on Antibiotic Policy (SWAB) develops evidence-based guidelines, aimed at optimalisation of antibiotic use and limitation of the spread of antimicrobial resistance. A revision of the SWAB guideline for the treatment of community-acquired pneumonia (CAP), published in 1998, was

  5. Mannheimiose pulmonar experimental em bezerros: swab nasal e nasofaringeano como auxílio diagnóstico Experimental pneumonic mannheimiosis in calves: nasal and nasopharingeal swabs for diagnostic

    Directory of Open Access Journals (Sweden)

    Adriana de Souza Coutinho

    2009-01-01

    Full Text Available Um modelo experimental de mannheimiosepneumônica bovina (MPB foi utilizado com o objetivo de avaliar as espécies bacterianas das cavidades nasais e nasofaringeanas em diferentes momentos do curso da doença, bem como verificar a eficiência diagnóstica do exame microbiológico dos swabs nasais (SN e nasofaringeanos (SNF. Um total de 28 bezerros foi distribuído aleatoriamente em quatro grupos experimentais (G1 a G4. SN e SNF foram colhidos sete dias antes e 12 (G1, 24 (G2, 48 (G3 e 72 (G4 horas após a inoculação intrabronquial de Mannheimia haemolytica. Após a indução da MPB, a bactéria M. haemolytica biotipo A foi predominante nos SN e SNF, sendo isolada em todos os momentos avaliados, com exceção de um SN colhido 24 horas após a indução da infecção. Não houve diferença significativa nas taxas de isolamento de Pasteurella multocida nos SN ou SNF, colhidos antes e após a indução da MPB. Contudo, esta bactéria passou a ser isolada mais freqüentemente após a indução da MPB, principalmente no SNF. Portanto, pode-se concluir que o exame microbiológico de SN e SNF é um teste auxiliar no diagnóstico da MPB.An experimental model of bovine pneumonic mannheimiosis (BPM was used to evaluate the nasal and nasopharynx bacterial species of calves during the course of the disease and for checking the diagnostic efficiency of nasal swab (NS and nasopharingeal swab (NPS microbiological exams. A total of 28 calves were randomized into four experimental groups (G1-G4. NS and NPS were obtained 7 days before and 12 (G1, 24 (G2, 48 (G3 e 72 (G4 hours after intrabronchial inoculation of Mannheimia haemolytica. After the induction of BPM, M. haemolytica biotype A was the predominant isolated bacterium in NS and NPS in all evaluated sampling times, except for one NS (harvested 24 hours. There were no significant statistical differences for the rates of Pasteurella multocida isolation in NS and NPS, harvested before and after the induction

  6. Detection of Streptococcus pneumoniae from Different Types of Nasopharyngeal Swabs in Children.

    Directory of Open Access Journals (Sweden)

    Felix S Dube

    Full Text Available A better understanding of the epidemiology of nasopharyngeal carriage of Streptococcus pneumoniae is important to assess the impact of vaccination and the pathogenesis of pneumococcal disease. We compared the recovery of S. pneumoniae from nylon flocked, Dacron and rayon swabs.The recovery of S. pneumoniae from mocked specimens using flocked, Dacron and rayon swabs were compared by culture. The yield from paired nasopharyngeal (NP samples obtained from healthy children sampled with flocked and Dacron swabs was also determined using culture and lytA-targeted real-time polymerase chain reaction (qPCR.Using mock specimen, the percentage recovery of S. pneumoniae ATCC 49619 (serotype 19F strain from the flocked swabs was 100%, while it was 41% from Dacron swabs and 7% from rayon swabs. Similar results were observed for S. pneumoniae serotypes 1 and 5. S. pneumoniae was cultured from 18 of 42 (43% paired NP samples from the healthy children (median age 8 [interquartile range (IQR 5-16] months. The median number of colony-forming units (CFU recovered from flocked swabs was two-fold higher (8.8×10(4 CFU/mL [IQR, 2.0×10(2 - 4.0×10(5 CFU/mL] than Dacron swabs (3.7×10(4 CFU/mL [IQR, 4.0×10(2-3.2×10(5 CFU/mL], p = 0.17. Using lytA-targeted qPCR from paired NP samples, the median copy number of S. pneumoniae detected from flocked swabs was significantly higher than from Dacron swabs (3.0×10(5 genome copies/mL [IQR, 1.3×10(2-1.8×10(6] vs. 9.3×10(4 genome copies/mL [IQR, 7.0×10(1-1.1×10(6]; p = 0.005.Flocked swabs released more S. pneumoniae compared to both Dacron and rayon swabs from mock specimens. Similarly, higher bacterial loads were detected by qPCR from flocked swabs compared with Dacron swabs from healthy children.

  7. Fecal transplant policy and legislation.

    Science.gov (United States)

    Vyas, Dinesh; Aekka, Apoorva; Vyas, Arpita

    2015-01-07

    Fecal microbiota transplantation (FMT) has garnered significant attention in recent years in the face of a reemerging Clostridium difficile (C. difficile) epidemic. Positive results from the first randomized control trial evaluating FMT have encouraged the medical community to explore the process further and expand its application beyond C. difficile infections and even the gastrointestinal domain. However promising and numerous the prospects of FMT appear, the method remains limited in scope today due to several important barriers, most notably a poorly defined federal regulatory policy. The Food and Drug Administration has found it difficult to standardize and regulate the administration of inherently variable, metabolically active, and ubiquitously available fecal material. The current cumbersome policy, which classifies human feces as a drug, has prevented physicians from providing FMT and deserving patients from accessing FMT in a timely fashion, and subsequent modifications seem only to be temporary. The argument for reclassifying fecal material as human tissue is well supported. Essentially, this would allow for a regulatory framework that is sufficiently flexible to expand access to care and facilitate research, but also appropriately restrictive and centralized to ensure patient safety. Such an approach can facilitate the advancement of FMT to a more refined, controlled, and aesthetic process, perhaps in the form of a customized and well-characterized stool substitute therapy.

  8. Detection of novel polyomaviruses, TSPyV, HPyV6, HPyV7, HPyV9 and MWPyV in feces, urine, blood, respiratory swabs and cerebrospinal fluid.

    Directory of Open Access Journals (Sweden)

    Rebecca J Rockett

    Full Text Available Eight novel human polyomaviruses have been discovered since 2007. Prevalence rates and tissue tropism for the most recent members HPyV 6, 7, 9, TSPyV and MWPyV are largely unknown. We used real-time PCR to determine the presence of HPyV 6, 7, 9, TSPyV and MWPyV in feces (n = 263, urine (n = 189, blood (n = 161, respiratory swabs (n = 1385 and cerebrospinal fluid (n = 171 from both healthy control children and children and adults undergoing diagnostic testing. Whole genome sequencing was able to be performed on 9 MWPyV positive specimens. Novel polyomaviruses were only detected in respiratory swabs and feces, with no detections of HPyV 9 in any sample type. MWPyV was found to be the most prevalent novel polyomavirus, being detected in 18 (1.5% respiratory specimens from symptomatic patients, 16 (9.8% respiratory sample from healthy control children, 11 (5.9% fecal specimens from patient suffering gastrointestinal illness, and in 13 (15.3% of feces from healthy control children. MWPyV was found only in respiratory and fecal specimens from children, the oldest being 9 years old. HPyV 6, 7, 9 and TSPyV were also detected in respiratory specimens and fecal specimens at low prevalence (<1.3%. The majority of these detections were found in immunocompromised patients. Our findings suggest that MWPyV can result in a subclinical infection, persistent or intermittent shedding, particularly in young children. The other novel polyomaviruses were also found in respiratory and fecal specimens, but at lower prevalence and most commonly in immunocompromised individuals.

  9. Broth versus solid agar culture of swab samples of cadaveric allograft musculoskeletal tissue.

    Science.gov (United States)

    Varettas, Kerry

    2013-12-01

    As part of the donor assessment protocol, bioburden assessment must be performed on allograft musculoskeletal tissue samples collected at the time of tissue retrieval. Swab samples of musculoskeletal tissue allografts from cadaveric donors are received at the microbiology department of the South Eastern Area Laboratory Services (Australia) to determine the presence of bacteria and fungi. This study will review the isolation rate of organisms from solid agar and broth culture of swab samples of cadaveric allograft musculoskeletal tissue over a 6-year period, 2006-2011. Swabs were inoculated onto horse blood agar (anaerobic, 35 °C) and chocolate agar (CO2, 35 °C) and then placed into a cooked meat broth (aerobic, 35 °C). A total of 1,912 swabs from 389 donors were received during the study period. 557 (29.1 %) swabs were culture positive with the isolation of 713 organisms, 249 (34.9 %) from solid agar culture and an additional 464 (65.1 %) from broth culture only. This study has shown that the broth culture of cadaveric allograft musculoskeletal swab samples recovered a greater amount of organisms than solid agar culture. Isolates such as Clostridium species and Staphylococcus aureus would not have been isolated from solid agar culture alone. Broth culture is an essential part of the bioburden assessment protocol of swab samples of cadaveric allograft musculoskeletal tissue in this laboratory.

  10. A Comparison of Tissue versus Swab Culturing of Infected Diabetic Foot Wounds

    Directory of Open Access Journals (Sweden)

    Ying Huang

    2016-01-01

    Full Text Available Objective. To compare the efficacy of swabbing versus tissue biopsy for microbiological diagnosis of diabetic foot infection. Methods. This was a prospective trial. Fifty-six patients with diabetic foot infection were divided into the following 3 groups according to the PEDIS grading system: grade 2 (n=10, grade 3 (n=29, and grade 4 (n=17. Two specimens were collected from each wound for microbial culturing after debridement, including a superficial swab and a deep tissue punch biopsy specimen. Results. Swab culturing identified all of the microorganisms isolated from the corresponding deep tissue specimens in 9/10 of grade 2 wounds (90.0%, and this proportion decreased to 12/29 (41.4% and 7/17 (41.2% for grades 3 and 4 wounds, respectively (p=0.02. Moreover, the sensitivity for identifying Gram-negative bacteria, such as E. coli and Citrobacter, by swabbing was low (33.3%. In addition, some Gram-negative bacteria, such as Serratia and Ralstonia pickettii, were isolated from deep tissues but not from swabs. Conclusions. Swab culturing may be reliable for identification of pathogens in diabetic foot wounds classified as grade 2. However, it is advisable to culture deep tissue specimens for wounds of grade ≥3 because swab culturing is associated with a high risk of missing pathogens, especially Gram-negative bacteria.

  11. Utilizing Moist or Dry Swabs for the Sampling of Nasal MRSA Carriers? An In Vivo and In Vitro Study

    Science.gov (United States)

    Warnke, Philipp; Devide, Annette; Weise, Mirjam; Frickmann, Hagen; Schwarz, Norbert Georg; Schäffler, Holger; Ottl, Peter; Podbielski, Andreas

    2016-01-01

    This study investigates the quantitative bacterial recovery of Methicillin-resistant Staphylococcus aureus (MRSA) in nasal screenings by utilizing dry or moistened swabs within an in vivo and an in vitro experimental setting. 135 nasal MRSA carriers were each swabbed in one nostril with a dry and in the other one with a moistened rayon swab. Quantitative bacterial recovery was measured by standard viable count techniques. Furthermore, an anatomically correct artificial nose model was inoculated with a numerically defined suspension of MRSA and swabbed with dry and moistened rayon, polyurethane-foam and nylon-flocked swabs to test these different settings and swab-materials under identical laboratory conditions. In vivo, quantities of MRSA per nostril in carriers varied between 107 colony forming units, with a median of 2.15x104 CFU. However, no statistically significant differences could be detected for the recovery of MRSA quantities when swabbing nasal carriers with moist or dry rayon swabs. In vitro testing confirmed the in vivo data for swabs with rayon, polyurethane and nylon-flocked tips, since pre-moistening of swabs did not significantly affect the quantities of retrieved bacteria. Therefore, pre-moistening of swabs prior to nasal MRSA sampling provides no advantage in terms of recovering greater bacterial quantities and therefore can be omitted. In addition, this situation can be mimicked in an in vitro model, thereby providing a useful basis for future in vitro testings of new swab types or target organisms for screening approaches. PMID:27626801

  12. Dynamic changes of the respiratory microbiota and its relationship to fecal and blood microbiota in healthy young cats.

    Science.gov (United States)

    Vientós-Plotts, Aida I; Ericsson, Aaron C; Rindt, Hansjorg; Grobman, Megan E; Graham, Amber; Bishop, Kaitlin; Cohn, Leah A; Reinero, Carol R

    2017-01-01

    Advances in the field of metagenomics using culture-independent methods of microbial identification have allowed characterization of rich and diverse communities of bacteria in the lungs of healthy humans, mice, dogs, sheep and pigs. These data challenge the long held belief that the lungs are sterile and microbial colonization is synonymous with pathology. Studies in humans and animals demonstrate differences in the composition of airway microbiota in health versus disease suggesting respiratory dysbiosis occurs. Using 16S rRNA amplicon sequencing of DNA extracted from rectal and oropharyngeal (OP) swabs, bronchoalveolar lavage fluid (BALF), and blood, our objective was to characterize the fecal, OP, blood, and lower airway microbiota over time in healthy cats. This work in healthy cats, a species in which a respiratory microbiota has not yet been characterized, sets the stage for future studies in feline asthma in which cats serve as a comparative and translational model for humans. Fecal, OP and BALF samples were collected from six healthy research cats at day 0, week 2, and week 10; blood was collected at week 10. DNA was extracted, amplified via PCR, and sequenced using the Illumina MiSeq platform. Representative operational taxonomic units (OTUs) were identified and microbial richness and diversity were assessed. Principal component analysis (PCA) was used to visualize relatedness of samples and PERMANOVA was used to test for significant differences in microbial community composition. Fecal and OP swabs provided abundant DNA yielding a mean±SEM of 65,653±6,145 and 20,6323±4,360 sequences per sample, respectively while BALF and blood samples had lower coverage (1,489±430 and 269±18 sequences per sample, respectively). Oropharyngeal and fecal swabs were significantly richer than BALF (mean number OTUs 93, 88 and 36, respectively; p airways. In comparison, blood had an apparent compositional similarity with BALF with regard to a few dominant taxa, but

  13. Surgical swab counting: a qualitative analysis from the perspective of the scrub nurse.

    Science.gov (United States)

    D'Lima, D; Sacks, M; Blackman, W; Benn, J

    2014-05-01

    The aim of the study was to conduct a qualitative exploration of the sociotechnical processes underlying retained surgical swabs, and to explore the fundamental reasons why the swab count procedure and related protocols fail in practice. Data was collected through a set of 27 semistructured qualitative interviews with scrub nurses from a large, multi-site teaching hospital. Interview transcripts were analysed using established constant comparative methods, moving between inductive and deductive reasoning. Key findings were associated with interprofessional perspectives, team processes and climate and responsibility for the swab count. The analysis of risk factors revealed that perceived social and interprofessional issues played a significant role in the reliability of measures to prevent retained swabs. This work highlights the human, psychological and organisational factors that impact upon the reliability of the process and gives rise to recommendations to address contextual factors and improve perioperative practice and training.

  14. Efficacy of a Sonicating Swab for Removal and Capture of Listeria monocytogenes in Biofilm on Stainless Steel.

    Science.gov (United States)

    Branck, Tobyn A; Hurley, Matthew J; Prata, Gianna N; Crivello, Christina A; Marek, Patrick J

    2017-03-17

    Listeria monocytogenes is of great concern in food processing facilities because it persists in biofilms, potentiating biotransfer. Stainless steel is commonly used for food contact surfaces and transport containers. L. monocytogenes biofilm on stainless steel served as a model system for surface sampling to test the performance of a sonicating swab in comparison to a standard cotton swab. Swab performance and consistency were determined using total viable counts. Stainless steel coupons sampled with both swabs were examined with SEM to visualize biofilms and surface structures (i.e. polishing grooves and scratches). LSCM was used to image and quantitate the percent area of remaining biofilm after sampling with each swab type. The total viable count was significantly higher (P ≤ 0.05) for the sonicating swab in comparison to the standard swab within each trial. The sonicating swab was more consistent in cell recovery than standard swab having lower CVs ranging from 8.9% to 12.3% and 7.1% to 37.6% respectively. SEM imaging showed biofilm remaining in the polished grooves of the coupons sampled with the standard swab but were noticeably absent for the sonicating swab. Percent area measurement of biofilm remaining on stainless steel coupons showed significantly (P ≤ 0.05) less biofilm remained when using the sonicating swab (median 1.1%) in comparison to the standard swab (median 70.4%). The sonicating swab provided a higher recovery of cells with more consistency than the standard swab and is the first swabbing device to employ: sonication, suction, and scrubbing.IMPORTANCE Inadequate surface sampling can result in food borne illness outbreaks from biotransfer since verification of sanitization protocols relies on surface sampling and recovery of microorganisms for detection and enumeration. Swabbing is a standard method for microbiological sampling of surfaces. Although swabbing offers portability and ease of use, there are limitations, such as high user

  15. Simplicimonas-like DNA in vaginal swabs of cows and heifers cross-reacting in the real-time PCR for T. foetus.

    Science.gov (United States)

    Frey, Caroline F; Müller, Norbert; Stäuber, Norbert; Marreros, Nelson; Hofmann, Larissa; Hentrich, Brigitte; Hirsbrunner, Gaby

    2017-04-15

    Cows on an alpine pasture were presented with severe signs of vaginitis. To rule out infection with Tritrichomonas foetus, vaginal swabs were taken and real-time PCR based on detection via fluorescence resonance energy transfer (FRET) probes and targeting the first internal transcribed spacer (ITS-1) of nuclear ribosomal DNA (rDNA) was performed. PCR was positive in 25 of totally 34 assessed cows. However, the melting profiles of the probes targeting the diagnostic PCR products differed from the T. foetus positive control. Subsequent sequencing of the amplicons revealed 91% identity to Simplicimonas sp. sequences deposited in GenBank™. Furthermore, there was no clear association between positive PCR result and presence of vaginitis. To investigate the distribution of this Simplicimonas-like organism in cows, more herds grazing on the same alpine pastures as well as unrelated cows were tested. In total, 133 cows and 16 heifers were sampled, 53 cows and 6 heifers even twice. Vaginitis was evident in 43 cows and 4 heifers. All-over-positivity of PCR was 44%, including nine tests performed on heifers. Melting peak analysis indicated Simplicimonas-like organisms in all positive samples. Culture attempts in bovine InPouch ™ TF failed. No association between a positive PCR result and the presence of vaginitis was found. This is, to the best of our knowledge, the first report on Simplicimonas-like DNA in vaginal swabs of female cattle. Our data suggest that when testing vaginal swabs of cattle by means of T. foetus PCR, false positive reactions due to Simplicimonas-like organisms may occur.

  16. A Comparison of Tissue versus Swab Culturing of Infected Diabetic Foot Wounds

    OpenAIRE

    Ying Huang; Ying Cao; Mengchen Zou; Xiangrong Luo; Ya Jiang; Yaoming Xue; Fang Gao

    2016-01-01

    Objective. To compare the efficacy of swabbing versus tissue biopsy for microbiological diagnosis of diabetic foot infection. Methods. This was a prospective trial. Fifty-six patients with diabetic foot infection were divided into the following 3 groups according to the PEDIS grading system: grade 2 (n = 10), grade 3 (n = 29), and grade 4 (n = 17). Two specimens were collected from each wound for microbial culturing after debridement, including a superficial swab and a deep tissue punch biops...

  17. A polymerase chain reaction for detection of Brucella canis in vaginal swabs of naturally infected bitches.

    Science.gov (United States)

    Keid, L B; Soares, R M; Vasconcellos, S A; Chiebao, D P; Salgado, V R; Megid, J; Richtzenhain, L J

    2007-12-01

    A PCR assay for the detection of Brucella canis in canine vaginal swab samples was evaluated, comparing its performance with that of bacterial isolation, serological tests, and a blood PCR assay. One hundred and forty-four female dogs were clinically examined to detect reproductive problems and they were tested by the rapid slide agglutination test, with and without 2-mercaptoethanol (2ME-RSAT and RSAT, respectively). In addition, microbiological culture and PCR were performed on blood and vaginal swab samples. The results of the vaginal swab PCR were compared to those of the other tests using the Kappa coefficient and McNemar test. Of the 144 females that were examined, 66 (45.8%) were RSAT positive, 23 (15.9%) were 2ME-RSAT positive, 49 (34.02%) were blood culture positive, 6 (4.1%) were vaginal swab culture positive, 54 (37.5%) were blood PCR positive, 52 (36.2%) were vaginal swab PCR positive, and 50.69% (73/144) were positive by the combined PCR. The PCR was able to detect as few as 3.8 fg of B. canis DNA experimentally diluted in 54 ng of canine DNA, extracted from vaginal swab samples of non-infected bitches. In addition, the PCR assay amplified B. canis genetic sequences from vaginal swab samples containing 1.0 x 10(0) cfu/mL. In conclusion, vaginal swab PCR was a good candidate as a confirmatory test for brucellosis diagnosis in bitches suspected to be infected, especially those negative on blood culture or blood PCR; these animals may be important reservoirs of infection and could complicate attempts to eradicate the disease in confined populations.

  18. New technique to take samples from environmental surfaces using flocked nylon swabs.

    Science.gov (United States)

    Hedin, G; Rynbäck, J; Loré, B

    2010-08-01

    Environmental surfaces near infected and/or colonised patients in hospitals are commonly contaminated with potentially pathogenic micro-organisms. At present, however, there is no standardised method for taking samples from surfaces in order to perform quantitative cultures. Usually contact plates or swabs are used, but these methods may give different results. The recovery rate of traditional swabbing, e.g. cotton or rayon, is poor. With a new type of swab utilising flocked nylon, the recovery may be enhanced up to three times compared with a rayon swab. In this study, we inoculated reference strains of Staphylococcus aureus and Enterococcus hirae onto a bedside table and took samples 1h later when inocula were dry. Sequential samples were taken from the same surface. A new sampling technique using two sequential nylon swabs for each sample was validated. The efficiency of the sampling, percentage recovery of the inoculum and the variation of culture results obtained from repeated experiments are described. Enhanced efficiency and higher recovery of inoculum were demonstrated using two sequential flocked nylon swabs for sampling.

  19. Fabrication of SERS swab for direct detection of trace explosives in fingerprints.

    Science.gov (United States)

    Gong, Zhengjun; Du, Hongjie; Cheng, Fansheng; Wang, Cong; Wang, Canchen; Fan, Meikun

    2014-12-24

    Swab sampling is of great importance in surface contamination analysis. A cotton swab (cotton Q-tip) was successfully transformed into surface-enhanced Raman scattering (SERS) substrate (SERS Q-tip) through a bottom-up strategy, where Ag NPs were first self-assembled onto the Q-tip followed by in situ growing. The capability for direct swab detection of Raman probe Nile Blue A (NBA) and a primary explosive marker 2,4-dinitrotoluene (2,4-DNT) using the SERS Q-tip was explored. It was found that at optimum conditions, a femotogram of NBA on glass surface could be swab-detected. The lowest detectable amount for 2,4-DNT is only ∼1.2 ng/cm(2) (total amount of 5 ng) on glass surface, 2 orders of magnitude more sensitive than similar surface analysis achieved with infrared technique, and comparable even with that obtained by ion mobility spectrometry-mass spectrometry. Finally, 2,4-DNT left on fingerprints was also analyzed. It was found that SERS signal of 2,4-DNT from 27th fingerprint after touching 2,4-DNT powder can still be clearly identified by swabbing with the SERS Q-tip. We believe this is the first direct SERS swabbing test of explosives on fingerprint on glass. Considering its relative long shelf life (>30 d), the SERS Q-tip may find great potential in future homeland security applications when combined with portable Raman spectrometers.

  20. Comparison of sputum and nasopharyngeal swabs for detection of respiratory viruses.

    Science.gov (United States)

    Jeong, Ji Hun; Kim, Kyung Hee; Jeong, Sung Hwan; Park, Jeong Woong; Lee, Sang Min; Seo, Yiel Hea

    2014-12-01

    Diagnostic tests for respiratory viral infections use traditionally either nasopharyngeal washes or swabs. Sputum is representative of the lower respiratory tract but is used rarely for viral testing. The aim of this study was to compare the detection rates of respiratory viruses from nasopharyngeal swabs and sputum using a multiplex real-time reverse transcription-polymerase chain reaction (RT-PCR). Adults who were admitted or presented to the clinics of Gil Medical Center with acute respiratory symptoms were recruited from 1 November 2012 to 31 March 2013. Paired specimens of nasopharyngeal swabs and sputum were obtained from 154 subjects, and RNA was extracted and tested for 16 different respiratory viruses using the Anyplex II RV16 Detection kit (Seegene, Seoul, Korea). The positive rate was 53% (81/154) for nasopharyngeal swabs and 68% (105/154) for sputum (P viruses were identified for 107 illnesses. Influenza A virus, RSV A, HRV, coronavirus OC43, and adenovirus were detected more frequently in sputum samples than in nasopharyngeal swabs (P viruses from sputum samples were significantly higher than those from nasopharyngeal swabs in adults using real-time multiplex RT-PCR. These findings suggest that sputum would benefit for the detection of respiratory viruses by nucleic acid amplification tests (NAATs) in patients who produce sputum. Further studies are needed to establish standardized RNA extraction methods from sputum samples.

  1. Endoluminal magnetic resonance imaging in fecal incontinence

    NARCIS (Netherlands)

    E. Rociu (Elena)

    2000-01-01

    textabstractFecal incontinence is a chronic disability, has serious emotional impact and increased risk for social isolation. Imaging has become important in the diagnostic work-up of fecal incontinence. The research described in this thesis continues the line of efforts to improve the quality and t

  2. Utility of a fecal real-time PCR protocol for detection of Mycobacterium bovis infection in African buffalo (Syncerus caffer).

    Science.gov (United States)

    Roug, Annette; Geoghegan, Claire; Wellington, Elizabeth; Miller, Woutrina A; Travis, Emma; Porter, David; Cooper, David; Clifford, Deana L; Mazet, Jonna A K; Parsons, Sven

    2014-01-01

    A real-time PCR protocol for detecting Mycobacterium bovis in feces was evaluated in bovine tuberculosis-infected African buffalo (Syncerus caffer). Fecal samples spiked with 1.42 × 10(3) cells of M. bovis culture/g and Bacille Calmette-Guérin standards with 1.58 × 10(1) genome copies/well were positive by real-time PCR but all field samples were negative.

  3. Use of steam condensing at subatmospheric pressures to reduce Escherichia coli O157:H7 numbers on bovine hide.

    Science.gov (United States)

    McEvoy, J M; Doherty, A M; Sheridan, J J; Blair, I S; McDowell, D A

    2001-11-01

    This study used a laboratory-scale apparatus to apply subatmospheric steam to bovine hide pieces inoculated with Escherichia coli O157:H7 in maximum recovery diluent (MRD) and in high-liquid content and low-liquid content fecal suspensions (HLC fecal and LLC fecal, respectively). The survival of the organism in fecal clods, which were stored for 24 days in a desiccated state, was assessed. Inoculated fecal clods were also treated with subatmospheric steam. Steam treatment at 80 +/- 2 degrees C for 20 s reduced E. coli O157:H7 concentrations on hide inoculated to initial concentrations of approximately 7 log10 CFU/g by 5.46 (MRD inoculum), 4.17 (HLC fecal inoculum), and 5.99 (LLC fecal inoculum) log10 CFU/g. The reductions achieved in samples inoculated with LLC feces were larger than in samples inoculated with HLC feces (P Steam treatment (20 s) of 3-day-old clods reduced surviving E. coli O157:H7 numbers from 4.20 log10 CFU/g to below the limit of detection of the assay used (1.20 log10 CFU/g). This study shows that steam condensing at or below 80 +/- 2 degrees C can reduce E. coli O157:H7 when present on bovine hide, reducing the risk of cross contamination to the carcass during slaughter and dressing.

  4. Quantification of Human and Animal Viruses to Differentiate the Origin of the Fecal Contamination Present in Environmental Samples

    Directory of Open Access Journals (Sweden)

    Sílvia Bofill-Mas

    2013-01-01

    Full Text Available Many different viruses are excreted by humans and animals and are frequently detected in fecal contaminated waters causing public health concerns. Classical bacterial indicator such as E. coli and enterococci could fail to predict the risk for waterborne pathogens such as viruses. Moreover, the presence and levels of bacterial indicators do not always correlate with the presence and concentration of viruses, especially when these indicators are present in low concentrations. Our research group has proposed new viral indicators and methodologies for determining the presence of fecal pollution in environmental samples as well as for tracing the origin of this fecal contamination (microbial source tracking. In this paper, we examine to what extent have these indicators been applied by the scientific community. Recently, quantitative assays for quantification of poultry and ovine viruses have also been described. Overall, quantification by qPCR of human adenoviruses and human polyomavirus JC, porcine adenoviruses, bovine polyomaviruses, chicken/turkey parvoviruses, and ovine polyomaviruses is suggested as a toolbox for the identification of human, porcine, bovine, poultry, and ovine fecal pollution in environmental samples.

  5. Post-coital vaginal sampling with nylon flocked swabs improves DNA typing.

    Science.gov (United States)

    Benschop, Corina C G; Wiebosch, Danielle C; Kloosterman, Ate D; Sijen, Titia

    2010-02-01

    In the examination of sexual assault cases, DNA typing of vaginal samples mostly occurs after differential DNA extraction. Notwithstanding the differential extraction method, the DNA profiles from the seminal fraction often show the male alleles at low-level in combination with female alleles. This unfavorable ratio male to female DNA is due to a limited amount of sperm cells and an overwhelming quantity of female cells. In this study, we compared standard cotton and nylon flocked swabs for post-coital vaginal sampling. Twelve couples donated 88 vaginal swabs - 44 cotton, 44 nylon flocked - which were taken with a time since intercourse (TSI) up to 84 h. These vaginal swabs were sorted into categories on the basis of the TSI and submitted to (1) microscopic examination for the presence of male cells, (2) presumptive tests for the detection of seminal fluid and (3) DNA typing. Cellular elution was found to be 6-fold more efficient from the nylon flocked swabs. This makes microscopic analysis less time consuming as the higher cell yield and better cell morphology simplify detection of male cells. Both swab types reveal similar results regarding presumptive tests and male DNA typing. Positive presumptive tests (RSID-semen and PSA) were obtained up to 60 h TSI and male autosomal profiles up to 72 h TSI. Interestingly, over 50% of the samples negative for both presumptive tests resulted in informative male STR profiles. After differential extraction, less DNA was left on the nylon flocked swabs and more male DNA was isolated. Our results imply that the use of nylon flocked swabs for vaginal sampling will improve microscopic analysis and DNA typing in the medical forensic investigation of sexual assault cases.

  6. Biofeedback therapy for fecal incontinence.

    Science.gov (United States)

    Goldenberg, D A; Hodges, K; Hershe, T; Jinich, H

    1980-10-01

    Operant conditioning offers a new therapeutic modality for fecal incontinence. Our experience with biofeedback therapy in six male and six female patients (ages 12-78 years) is presented. Incontinence was associated with a surgical procedure in six patients and with a medical condition in six patients. Rectosphincteric manometry was performed using a three balloon technic, with one balloon positioned in the rectum as a distending stimulus and the others at the internal and external sphinchters. Pressure responses to measured volumes of rectal distention were displayed on a polygraph. Rectosphincteric reflexes and sensory thresholds for rectal distention were determined. Patients were then encouraged to elevate sphinchter pressures while observing their manometric responses. Follow-up of 10-96 weeks showed ten patients had good responses, with complete continence in six patients. Nine of 10 responders required only one treatment session. Operant conditioning is a valuable technic in properly selected patients with an 80% probability of success.

  7. Campylobacter sp in eggs from cloacal swab positive breeder hens Campylobacter sp em ovos provenientes de matrizes pesadas com swab cloacal positivo

    Directory of Open Access Journals (Sweden)

    Belchiolina Beatriz Fonseca

    2006-12-01

    Full Text Available Campylobacter sp is a microaerophilic, thermotolerating Gram negative bacterium, known to be one of the main causes of food-borne human infections. Among the foods that carry these microorganisms, the chicken is outstanding. In Brazil, a large chicken exporting country, few researches are conducted about their prevalence in breeder hens and the transmission through eggs. The aim of this research was to verify the presence of Campylobacter sp in the shells and within the eggs from positive cloacal swab breeder hens. Microbiological analyses were made on cloacal swabs of 140 weighed breeder hens. The positive breeder hens were set aside and in a total of 244 of their eggs, Campylobacter sp was present in macerated shells and yolk contents during 7 weeks. Out of the 140 researched breeder hens, 25 (17.8% were positive from cloacal swabs, however the eggs were not positive. The physiological characteristics of the birds, their eggs and Campylobacter sp favor the bacterium entering and surviving in the eggs, but in this study, no positive result was found in macerated shells or in the yolks, indicating that vertical transmission is probably an unusual event.Campylobacter sp é reconhecida como uma das principais causas de gastrenterite humana de origem alimentar. Dentre os alimentos veiculadores desses microrganismos, a carne de frango tem sido a mais implicada. Os estudos existentes sobre a transmissão vertical da Campylobacter são escassos e não conclusivos. O objetivo desse estudo foi verificar a presença de Campylobacter sp na casca e interior de ovos de matrizes positivas em swabs cloacais e a possibilidade de transmissão vertical. Foram analisados swabs cloacais de 140 matrizes pesadas e seus ovos colhidos para análise durante 7 semanas consecutivas. Dos 244 ovos colhidos, 129 foram fumigados e 115 analisados sem tratamento. Foram analisados o macerado da casca e a gema. Das 140 matrizes pesquisadas, 25 (17,8% foram positivas em swabs

  8. National validation study of a swab protocol for the recovery of Bacillus anthracis spores from surfaces.

    Science.gov (United States)

    Hodges, Lisa R; Rose, Laura J; O'Connell, Heather; Arduino, Matthew J

    2010-05-01

    Twelve Laboratory Response Network (LRN) affiliated laboratories participated in a validation study of a macrofoam swab protocol for the recovery, detection, and quantification of viable B. anthracis (BA) Sterne spores from steel surfaces. CDC personnel inoculated steel coupons (26cm(2)) with 1-4 log(10) BA spores and recovered them by sampling with pre-moistened macrofoam swabs. Phase 1 (P1) of the study evaluated swabs containing BA only, while dust and background organisms were added to swabs in Phase 2 (P2) to mimic environmental conditions. Laboratories processed swabs and enumerated spores by culturing eluted swab suspensions and counting colonies with morphology consistent with BA. Processed swabs were placed in enrichment broth, incubated 24h, and cultured by streaking for isolation. Real-time PCR was performed on selected colonies from P2 samples to confirm the identity of BA. Mean percent recovery (%R) of spores from the surface ranged from 15.8 to 31.0% (P1) and from 27.9 to 55.0% (P2). The highest mean percent recovery was 31.0% (sd 10.9%) for P1 (4 log(10) inoculum) and 55.0% (sd 27.6%) for P2 (1 log(10) inoculum). The overall %R was higher for P2 (44.6%) than P1 (24.1%), but the overall reproducibility (between-lab variability) was lower in P2 than in P1 (25.0 vs 16.5%CV, respectively). The overall precision (within-lab variability) was close to identical for P1 and P2 (44.0 and 44.1, respectively), but varied greatly between inoculum levels. The protocol demonstrated linearity in %R over the three inoculum levels and is able to detect between 26 and 5x10(6)spores/26cm(2). Sensitivity as determined by culture was >98.3% for both phases and all inocula, suggesting that the culture method maintains sensitivity in the presence of contaminants. The enrichment broth method alone was less sensitive for sampled swabs (66.4%) during P2, suggesting that the presence of background organisms inhibited growth or isolation of BA from the broth. The addition of

  9. Sensitive diagnosis of cutaneous leishmaniasis by lesion swab sampling coupled to qPCR

    Science.gov (United States)

    ADAMS, EMILY R.; GOMEZ, MARIA ADELAIDA; SCHESKE, LAURA; RIOS, RUBY; MARQUEZ, RICARDO; COSSIO, ALEXANDRA; ALBERTINI, AUDREY; SCHALLIG, HENK; SARAVIA, NANCY GORE

    2015-01-01

    SUMMARY Variation in clinical accuracy of molecular diagnostic methods for cutaneous leishmaniasis (CL) is commonly observed depending on the sample source, the method of DNA recovery and the molecular test. Few attempts have been made to compare these variables. Two swab and aspirate samples from lesions of patients with suspected CL (n = 105) were evaluated alongside standard diagnosis by microscopic detection of amastigotes or culture of parasites from lesion material. Three DNA extraction methods were compared: Qiagen on swab and aspirate specimens, Isohelix on swabs and Boil/Spin of lesion aspirates. Recovery of Leishmania DNA was evaluated for each sample type by real-time polymerase chain reaction detection of parasitic 18S rDNA, and the diagnostic accuracy of the molecular method determined. Swab sampling combined with Qiagen DNA extraction was the most efficient recovery method for Leishmania DNA, and was the most sensitive (98%; 95% CI: 91–100%) and specific (84%; 95% CI: 64–95%) approach. Aspirated material was less sensitive at 80% (95% CI: 70–88%) and 61% (95% CI: 50–72%) when coupled to Qiagen or Boil-Spin DNA extraction, respectively. Swab sampling of lesions was painless, simple to perform and coupled with standardized DNA extraction enhances the feasibility of molecular diagnosis of CL. PMID:25111885

  10. A Non-Invasive Strategy for Neonatal Alloimmune Thrombocytopenia Diagnosis: Newborn Platelet Genotyping with Buccal Swabs

    Directory of Open Access Journals (Sweden)

    Gérald Bertrand

    2016-07-01

    Full Text Available Neonatal alloimmune thrombocytopenia results from the maternal immune response against fetal-specific antigens inherited from the father. The diagnosis is ascertained only when the maternal alloantibody and the offending antigen present in the newborn are identified. Up until now most laboratories perform DNA extraction for neonatal genotyping from newborn blood samplings. In order to avoid such an invasive procedure, two protocols of DNA extraction from buccal swabs were developed: a manual protocol using the QIAamp mini blood kit (Qiagen, and an automated procedure with the MagNA Pure Compact instrument (Roche. Both EDTA-blood and buccal swabs from thrombocytopenic newborns were genotyped manually (14 samples, automatically (15 samples or both manually and automatically (two samples. Human Platelet Antigen (HPA genotyping was performed using the BeadChip assay (BioArray, Immucor. Concordant genotypings were obtained for all samples except for one swab with the manual method. The automated DNA extraction from newborn buccal swabs with the MagNA Pure Compact instrument was chosen as the first-line strategy, with a significant gain of time in processing buccal swabs.

  11. Moving fecal microbiota transplantation into the mainstream.

    Science.gov (United States)

    Orenstein, Robert; Griesbach, Cheryl L; DiBaise, John K

    2013-10-01

    In recent years, fecal microbiota transplantation (aka fecal transplantation, fecal bacteriotherapy, FMT) has become increasing utilized to treat recurrent and refractory Clostridium difficile infection (CDI). Almost 600,000 cases of CDI occur each year in the United States. Of these, an estimated 15,000 patients have a recurrence. The management of recurrent disease has been challenging for patients and clinicians. Increasingly, FMT has been recognized as an effective option for these patients. This article explores why FMT has reemerged as a practical therapeutic modality. In the process, the logistics by which the procedure is performed and the factors that may affect quality, safety, and patient outcomes will be described.

  12. Respiratory disease associated with bovine coronavirus infection in cattle herds in Southern Italy.

    Science.gov (United States)

    Decaro, Nicola; Campolo, Marco; Desario, Costantina; Cirone, Francesco; D'Abramo, Maria; Lorusso, Eleonora; Greco, Grazia; Mari, Viviana; Colaianni, Maria Loredana; Elia, Gabriella; Martella, Vito; Buonavoglia, Canio

    2008-01-01

    Four outbreaks of bovine respiratory disease (BRD) associated with bovine coronavirus (BCoV) infection in Italian cattle herds were reported. In 3 outbreaks, BRD was observed only in 2-3-month-old feedlot calves, whereas in the remaining outbreak, lactating cows, heifers, and calves were simultaneously affected. By using reverse transcription polymerase chain reaction (RT-PCR), BCoV RNA was detected in all outbreaks without evidence of concurrent viral pathogens (i.e., bovine respiratory syncytial virus, bovine herpesvirus type 1, bovine viral diarrhea virus, bovine parainfluenza virus). Common bacteria of cattle were recovered only from 2 outbreaks of BRD: Staphylococcus spp. and Proteus mirabilis (outbreak 1) and Mannheimia haemolytica (outbreak 4). A recently established real-time RT-PCR assay showed that viral RNA loads in nasal secretions ranged between 3.10 x 10(2) and 7.50 x 10(7) RNA copies/microl of template. Bovine coronavirus was isolated from respiratory specimens from all outbreaks except outbreak 1, in which real-time RT-PCR found very low viral titers in nasal swabs.

  13. A new bovine conjunctiva model shows that Listeria monocytogenes invasion is associated with lysozyme resistance.

    Science.gov (United States)

    Warren, Jessica; Owen, A Rhys; Glanvill, Amy; Francis, Asher; Maboni, Grazieli; Nova, Rodrigo J; Wapenaar, Wendela; Rees, Catherine; Tötemeyer, Sabine

    2015-08-31

    Listerial keratoconjunctivitis ('silage eye') is a wide spread problem in ruminants causing economic losses to farmers and impacts negatively on animal welfare. It results from direct entry of Listeria monocytogenes into the eye, often following consumption of contaminated silage. An isolation protocol for bovine conjunctival swabbing was developed and used to sample both infected and healthy eyes bovine eyes (n=46). L. monocytogenes was only isolated from one healthy eye sample, and suggests that this organism can be present without causing disease. To initiate a study of this disease, an infection model was developed using isolated conjunctiva explants obtained from cattle eyes post slaughter. Conjunctiva were cultured and infected for 20 h with a range of L. monocytogenes isolates (n=11), including the healthy bovine eye isolate and also strains isolated from other bovine sources, such as milk or clinical infections. Two L. monocytogenes isolates (one from a healthy eye and one from a cattle abortion) were markedly less able to invade conjunctiva explants, but one of those was able to efficiently infect Caco2 cells indicating that it was fully virulent. These two isolates were also significantly more sensitive to lysozyme compared to most other isolates tested, suggesting that lysozyme resistance is an important factor when infecting bovine conjunctiva. In conclusion, we present the first bovine conjunctiva explant model for infection studies and demonstrate that clinical L. monocytogenes isolates from cases of bovine keratoconjunctivitis are able to infect these tissues.

  14. 77 FR 20319 - Bovine Spongiform Encephalopathy; Importation of Bovines and Bovine Products

    Science.gov (United States)

    2012-04-04

    ...; ] DEPARTMENT OF AGRICULTURE Animal and Plant Health Inspection Service 9 CFR Part 93 RIN 0579-AC68 Bovine Spongiform Encephalopathy; Importation of Bovines and Bovine Products Correction In proposed rule...

  15. 78 FR 73993 - Bovine Spongiform Encephalopathy; Importation of Bovines and Bovine Products

    Science.gov (United States)

    2013-12-10

    ... Health Inspection Service 9 CFR Parts 92, 93, 94, 95, 96, and 98 RIN 0579-AC68 Bovine Spongiform Encephalopathy; Importation of Bovines and Bovine Products Corrections In rule document 2013-28228 appearing...

  16. Dynamic changes of the respiratory microbiota and its relationship to fecal and blood microbiota in healthy young cats

    Science.gov (United States)

    Rindt, Hansjorg; Grobman, Megan E.; Graham, Amber; Bishop, Kaitlin; Cohn, Leah A.; Reinero, Carol R.

    2017-01-01

    Advances in the field of metagenomics using culture-independent methods of microbial identification have allowed characterization of rich and diverse communities of bacteria in the lungs of healthy humans, mice, dogs, sheep and pigs. These data challenge the long held belief that the lungs are sterile and microbial colonization is synonymous with pathology. Studies in humans and animals demonstrate differences in the composition of airway microbiota in health versus disease suggesting respiratory dysbiosis occurs. Using 16S rRNA amplicon sequencing of DNA extracted from rectal and oropharyngeal (OP) swabs, bronchoalveolar lavage fluid (BALF), and blood, our objective was to characterize the fecal, OP, blood, and lower airway microbiota over time in healthy cats. This work in healthy cats, a species in which a respiratory microbiota has not yet been characterized, sets the stage for future studies in feline asthma in which cats serve as a comparative and translational model for humans. Fecal, OP and BALF samples were collected from six healthy research cats at day 0, week 2, and week 10; blood was collected at week 10. DNA was extracted, amplified via PCR, and sequenced using the Illumina MiSeq platform. Representative operational taxonomic units (OTUs) were identified and microbial richness and diversity were assessed. Principal component analysis (PCA) was used to visualize relatedness of samples and PERMANOVA was used to test for significant differences in microbial community composition. Fecal and OP swabs provided abundant DNA yielding a mean±SEM of 65,653±6,145 and 20,6323±4,360 sequences per sample, respectively while BALF and blood samples had lower coverage (1,489±430 and 269±18 sequences per sample, respectively). Oropharyngeal and fecal swabs were significantly richer than BALF (mean number OTUs 93, 88 and 36, respectively; p cats have a rich and distinct lower airway microbiome with dynamic bacterial populations. The microbiome is likely to be

  17. 21 CFR 866.5180 - Fecal calprotectin immunological test system.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Fecal calprotectin immunological test system. 866....5180 Fecal calprotectin immunological test system. (a) Identification. A fecal calprotectin... measure, by immunochemical techniques, fecal calprotectin in human stool specimens. The device is...

  18. Fecal Transplant Shows Early Promise Against Autism

    Science.gov (United States)

    ... 163263.html Fecal Transplant Shows Early Promise Against Autism Small study found giving healthy gut bacteria to ... study suggests a novel treatment for kids with autism: Give these young patients a fresh supply of ...

  19. Fecal Microbiota Transplantation: Just a Fancy Trend?

    Science.gov (United States)

    Vandenplas, Yvan; Pierard, Denis; De Greef, Elisabeth

    2015-07-01

    The risks and advantages of the administration of fecal material of healthy people to patients are heavily debated. In adults, recurrent Clostridium difficile has become an accepted indication. In addition to all of the possible indications, many other questions need to be answered before pediatric indications and recommendations can be established. Optimal donor selection, fresh versus frozen stools versus capsules containing only microbiota, volume, and route of administration are just a few examples of the areas with missing data to allow in formulating recommendations for fecal microbiota or fecal material administration in children. A careful but not-too-complex regulation is the first priority in order to minimize the risk of administration of fecal slurry from unselected donors at home without medical supervision.

  20. Fecal Microbiota Transplantation: Clinical and experimental studies

    NARCIS (Netherlands)

    van Nood, E.

    2015-01-01

    In this thesis, several aspects of donor feces infusion, also called Fecal Microbiota Transplantation (FMT), are investigated. Historically, FMTs are given mainly for antibiotic associated diarrhea, caused by the anaerobic bacteria Clostridium difficile. Clostridium difficile infections (CDI) are mo

  1. Torrefaction Processing of Human Fecal Waste Project

    Data.gov (United States)

    National Aeronautics and Space Administration — New technology is needed to collect, stabilize, safen, recover useful materials, and store human fecal waste for long duration missions. The current SBIR Phase I...

  2. Highly Efficient Fecal Waste Incinerator Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Volume reduction is a critical element of Solid Waste Management for manned spacecraft and planetary habitations. To this end, the proposed fecal waste incinerator...

  3. Molecular Comparison of Bacterial Communities on Peripheral Intravenous Catheters and Matched Skin Swabs.

    Directory of Open Access Journals (Sweden)

    Md Abu Choudhury

    Full Text Available Skin bacteria at peripheral intravenous catheter (PIVC insertion sites pose a serious risk of microbial migration and subsequent colonisation of PIVCs, and the development of catheter related bloodstream infections (CRBSIs. Common skin bacteria are often associated with CRBSIs, therefore the bacterial communities at PIVC skin sites are likely to have major implications for PIVC colonisation. This study aimed to determine the bacterial community structures on skin at PIVC insertion sites and to compare the diversity with associated PIVCs. A total of 10 PIVC skin site swabs and matching PIVC tips were collected by a research nurse from 10 hospitalised medical/surgical patients at catheter removal. All swabs and PIVCs underwent traditional culture and high-throughput sequencing. The bacterial communities on PIVC skin swabs and matching PIVCs were diverse and significantly associated (correlation coefficient = 0.7, p<0.001. Methylobacterium spp. was the dominant genus in all PIVC tip samples, but not so for skin swabs. Sixty-one percent of all reads from the PIVC tips and 36% of all reads from the skin swabs belonged to this genus. Staphylococcus spp., (26%, Pseudomonas spp., (10% and Acinetobacter spp. (10% were detected from skin swabs but not from PIVC tips. Most skin associated bacteria commonly associated with CRBSIs were observed on skin sites, but not on PIVCs. Diverse bacterial communities were observed at skin sites despite skin decolonization at PIVC insertion. The positive association of skin and PIVC tip communities provides further evidence that skin is a major source of PIVC colonisation via bacterial migration but microbes present may be different to those traditionally identified via culture methods. The results provide new insights into the colonisation of catheters and potential pathogenesis of bacteria associated with CRBSI, and may assist in developing new strategies designed to reduce the risk of CRBSI.

  4. Molecular Comparison of Bacterial Communities on Peripheral Intravenous Catheters and Matched Skin Swabs.

    Science.gov (United States)

    Choudhury, Md Abu; Marsh, Nicole; Banu, Shahera; Paterson, David L; Rickard, Claire M; McMillan, David J

    2016-01-01

    Skin bacteria at peripheral intravenous catheter (PIVC) insertion sites pose a serious risk of microbial migration and subsequent colonisation of PIVCs, and the development of catheter related bloodstream infections (CRBSIs). Common skin bacteria are often associated with CRBSIs, therefore the bacterial communities at PIVC skin sites are likely to have major implications for PIVC colonisation. This study aimed to determine the bacterial community structures on skin at PIVC insertion sites and to compare the diversity with associated PIVCs. A total of 10 PIVC skin site swabs and matching PIVC tips were collected by a research nurse from 10 hospitalised medical/surgical patients at catheter removal. All swabs and PIVCs underwent traditional culture and high-throughput sequencing. The bacterial communities on PIVC skin swabs and matching PIVCs were diverse and significantly associated (correlation coefficient = 0.7, pskin swabs. Sixty-one percent of all reads from the PIVC tips and 36% of all reads from the skin swabs belonged to this genus. Staphylococcus spp., (26%), Pseudomonas spp., (10%) and Acinetobacter spp. (10%) were detected from skin swabs but not from PIVC tips. Most skin associated bacteria commonly associated with CRBSIs were observed on skin sites, but not on PIVCs. Diverse bacterial communities were observed at skin sites despite skin decolonization at PIVC insertion. The positive association of skin and PIVC tip communities provides further evidence that skin is a major source of PIVC colonisation via bacterial migration but microbes present may be different to those traditionally identified via culture methods. The results provide new insights into the colonisation of catheters and potential pathogenesis of bacteria associated with CRBSI, and may assist in developing new strategies designed to reduce the risk of CRBSI.

  5. Ocular Decompression with Cotton Swabs Lowers Intraocular Pressure Elevation Following Intravitreal Injection

    Science.gov (United States)

    Gregori, Ninel Z.; Weiss, Matthew J.; Goldhardt, Raquel; Schiffman, Joyce C.; Vega, Edgardo; Mattis, Cherrie-Ann; Shi, Wei; Kelley, Linda; Hernandez, Vilma; Feuer, William J.

    2013-01-01

    Objective To determine the effect of pre-injection ocular decompression by cotton swabs on the immediate rise in intraocular pressure (IOP) after intravitreal injections. Methods Forty-eight patients receiving 0.05-ml ranibizumab injections in a retina clinic were randomized to two anesthetic methods in each eye on the same day (if bilateral disease) or on consecutive visits (if unilateral disease). One method utilized cotton swabs soaked in 4% lidocaine applied to the globe with moderate pressure and the other 3.5% lidocaine gel applied without pressure. IOPs were recorded at baseline (before injection) and at 0, 5, 10, and 15 minutes after the injection until the IOP was ≤30 mmHg. The IOP elevations from baseline were compared after the two anesthetic methods. Results The pre-injection mean IOP (SD, mmHg) was 15.5 (3.3) before the cotton swabs and 15.9 (3.0) before the gel (p=0.28). Mean IOP (SD, mmHg) change immediately after injection was 25.7 (9.2) after the cotton swabs and 30.9 (9.9) after the gel (P=0.001). Thirty-five percent of gel eyes had IOP ≥50 mmHg compared to only 10% of cotton swab eyes immediately after the injection (P<0.001). Conclusion Decompressing the eye with cotton swabs during anesthetic preparation prior to an intravitreal injection produces a significantly lower IOP spike after the injection. PMID:23632408

  6. Unlocking the bovine genome

    Directory of Open Access Journals (Sweden)

    Worley Kim C

    2009-04-01

    Full Text Available Abstract The draft genome sequence of cattle (Bos taurus has now been analyzed by the Bovine Genome Sequencing and Analysis Consortium and the Bovine HapMap Consortium, which together represent an extensive collaboration involving more than 300 scientists from 25 different countries.

  7. Evaluation of Liquid-Based Swab Transport Systems against the New Approved CLSI M40-A2 Standard.

    Science.gov (United States)

    Gizzie, Nina; Adukwu, Emmanuel

    2016-04-01

    Following revised information pertaining to newer swab types and testing protocols in the new CLSI M40-A2 standard, we evaluated three liquid swab transport systems for the recovery of aerobic, anaerobic, and fastidious organisms at room temperature and at 4°C. All tested liquid swab transport systems were fully compliant with the M40-A2 standard, with acceptable performance at both temperatures after the full specified holding period, using both qualitative (roll-plate) and quantitative (swab elution) methods.

  8. High-throughput sequencing of forensic genetic samples using punches of FTA cards with buccal swabs

    DEFF Research Database (Denmark)

    Kampmann, Marie-Louise; Buchard, Anders; Børsting, Claus;

    2016-01-01

    with buccal swabs and compared the results with those obtained with DNA extracted using the EZ1 DNA Investigator Kit. Concordant profiles were obtained for all samples. Our protocol includes simple punch, wash, and PCR steps, reducing cost and hands-on time in the laboratory. Furthermore, it facilitates......Here, we demonstrate that punches from buccal swab samples preserved on FTA cards can be used for high-throughput DNA sequencing, also known as massively parallel sequencing (MPS). We typed 44 reference samples with the HID-Ion AmpliSeq Identity Panel using washed 1.2 mm punches from FTA cards...

  9. Camel and bovine chymosin

    DEFF Research Database (Denmark)

    Langholm Jensen, Jesper; Mølgaard, Anne; Navarro Poulsen, Jens Christian;

    2013-01-01

    Bovine and camel chymosin are aspartic peptidases that are used industrially in cheese production. They cleave the Phe105-Met106 bond of the milk protein κ-casein, releasing its predominantly negatively charged C-terminus, which leads to the separation of the milk into curds and whey. Despite...... having 85% sequence identity, camel chymosin shows a 70% higher milk-clotting activity than bovine chymosin towards bovine milk. The activities, structures, thermal stabilities and glycosylation patterns of bovine and camel chymosin obtained by fermentation in Aspergillus niger have been examined...... interactions arising from variation in the surface charges and the greater malleability both in domain movements and substrate binding contribute to the better milk-clotting activity of camel chymosin towards bovine milk....

  10. Diagnosis of a mixed mycoplasma infection associated with a severe outbreak of bovine pinkeye in young calves.

    Science.gov (United States)

    Levisohn, Sharon; Garazi, Shlomo; Gerchman, Irinna; Brenner, Jacob

    2004-11-01

    Mycoplasma bovoculi and Mycoplasma bovis were both isolated from conjunctival swabs taken from young calves showing symptoms consistent with infectious bovine keratoconjunctivitis (pinkeye). No Moraxella spp. or other nonmycoplasma bacteria were isolated in association with this severe clinical outbreak. Based on laboratory tests and clinical observations, the first phase of the disease was likely pneumonic in nature, possibly caused by bovine respiratory syncytial virus and M. bovis. In the subsequent phase of the disease course, infection with both M. bovoculi and M. bovis resulted in ocular disease. A combination of microbiological, serological, and molecular diagnosticmethods was used to elucidate the etiology of the outbreak.

  11. Self-collected mid-turbinate swabs for the detection of respiratory viruses in adults with acute respiratory illnesses.

    Directory of Open Access Journals (Sweden)

    Oscar E Larios

    Full Text Available BACKGROUND: The gold standard for respiratory virus testing is a nasopharyngeal (NP swab, which is collected by a healthcare worker. Midturbinate (MT swabs are an alternative due to their ease of collection and possible self-collection by patients. The objective of this study was to compare the respiratory virus isolation of flocked MT swabs compared to flocked NP swabs. METHODS: Beginning in October 2008, healthy adults aged 18 to 69 years were recruited into a cohort and followed up for symptoms of influenza. They were asked to have NP and MT swabs taken as soon as possible after the onset of a fever or two or more respiratory symptoms with an acute onset. The swabs were tested for viral respiratory infections using Seeplex® RV12 multiplex PCR detection kit. Seventy six pairs of simultaneous NP and MT swabs were collected from 38 symptomatic subjects. Twenty nine (38% of these pairs were positive by either NP or MT swabs or both. Sixty nine (91% of the pair results were concordant. Two samples (3% for hCV OC43/HKU1 and 1 sample (1% for rhinovirus A/B were positive by NP but negative by MT. One sample each for hCV 229E/NL63, hCV OC43/HKU1, respiratory syncytial virus A, and influenza B were positive by MT but negative by NP. CONCLUSIONS: Flocked MT swabs are sensitive for the diagnosis of multiple respiratory viruses. Given the ease of MT collection and similar results between the two swabs, it is likely that MT swabs should be the preferred method of respiratory cell collection for outpatient studies. In light of this data, larger studies should be performed to ensure that this still holds true and data should also be collected on the patient preference of collection methods.

  12. Performance of self-collected penile-meatal swabs compared to clinician-collected urethral swabs for the detection of Chlamydia trachomatis, Neisseria gonorrhoeae, Trichomonas vaginalis, and Mycoplasma genitalium by nucleic acid amplification assays.

    Science.gov (United States)

    Dize, Laura; Barnes, Perry; Barnes, Mathilda; Hsieh, Yu-Hsiang; Marsiglia, Vincent; Duncan, Della; Hardick, Justin; Gaydos, Charlotte A

    2016-10-01

    Men were enrolled in a study to assess the performance and acceptability of self-collected penile meatal swabs as compared to clinician-collected urethral swabs for sexually transmitted infections (STIs). We expected penile-meatal swabs to perform favorably to urethral swabs for Chlamydia trachomatis (CT), Neisseria gonorrhoeae (NG), Trichomonas vaginalis (TV), and Mycoplasma genitalium (MG) detection by nucleic acid amplification assays (NAATs). Of 203 swab pairs tested; for CT, penile-meatal swab sensitivity was 96.8% and specificity was 98.8%. NG sensitivity and specificity were 100% and 98.9%, respectively. For TV, sensitivity was 85.0% and specificity was 96.7%. For MG sensitivity and specificity were 79.3% and 99.4%, respectively. No significant statistical differences between sample type accuracy (CT: P=0.625; NG: P=0.248; TV: P=0.344; and MG: P=0.070) existed. Most men, 90.1%, reported self-collection of penile-meatal swabs as "Very Easy" or "Easy". Self-collected penile-meatal swabs appeared acceptable for NAAT STI detection and an acceptable collection method by men.

  13. Fecal calprotectin in coeliac disease.

    Science.gov (United States)

    Capone, Pietro; Rispo, Antonio; Imperatore, Nicola; Caporaso, Nicola; Tortora, Raffaella

    2014-01-14

    We would like to share with the readers the results of our experience in 50 celiac disease (CD) patients, enrolled between September 2012 and April 2013, who were referred to our third-level CD Unit. The fecal calprotectin (FC) concentration of 50 adults with newly diagnosed CD was compared to that of a control group of 50 healthy subjects. FC level was determined by enzyme linked immunosorbent assay with diagnostic cut-off of 75 μg/g. In addition, we tried to correlate the FC level with symptoms, histological severity of CD (Marsh grade) and level of tissue transglutaminase antibodies (aTg) in CD patients. Finally, FC level was increased in five CD patients and in four controls (10% vs 8%, P = NS); mean FC concentration of patients and controls were 57.7 (SD ± 29.1) and 45.1 (SD ± 38.4) respectively. Furthermore, no significant correlation was seen between FC levels and symptoms/Marsh grade/aTg. The five CD patients did not show inflammatory lesions (e.g., ulcers, erosions) at upper endoscopy. The four healthy controls with positive FC were followed-up for further six months; in this observational period they did not show clinical signs of any underlying disease. On these bases, we think that FC is not able to investigate the subclinical inflammatory changes of active CD and FC should be considered a useless tool in the diagnostic work-up of uncomplicated CD but it should be accompanied by aTg when ruling out organic disease in patients with irritable bowel syndrome.

  14. Fecal calprotectin in coeliac disease

    Science.gov (United States)

    Capone, Pietro; Rispo, Antonio; Imperatore, Nicola; Caporaso, Nicola; Tortora, Raffaella

    2014-01-01

    We would like to share with the readers the results of our experience in 50 celiac disease (CD) patients, enrolled between September 2012 and April 2013, who were referred to our third-level CD Unit. The fecal calprotectin (FC) concentration of 50 adults with newly diagnosed CD was compared to that of a control group of 50 healthy subjects. FC level was determined by enzyme linked immunosorbent assay with diagnostic cut-off of 75 μg/g. In addition, we tried to correlate the FC level with symptoms, histological severity of CD (Marsh grade) and level of tissue transglutaminase antibodies (aTg) in CD patients. Finally, FC level was increased in five CD patients and in four controls (10% vs 8%, P = NS); mean FC concentration of patients and controls were 57.7 (SD ± 29.1) and 45.1 (SD ± 38.4) respectively. Furthermore, no significant correlation was seen between FC levels and symptoms/Marsh grade/aTg. The five CD patients did not show inflammatory lesions (e.g., ulcers, erosions) at upper endoscopy. The four healthy controls with positive FC were followed-up for further six months; in this observational period they did not show clinical signs of any underlying disease. On these bases, we think that FC is not able to investigate the subclinical inflammatory changes of active CD and FC should be considered a useless tool in the diagnostic work-up of uncomplicated CD but it should be accompanied by aTg when ruling out organic disease in patients with irritable bowel syndrome. PMID:24574734

  15. RNA-Based Methods Increase the Detection of Fecal Bacteria and Fecal Identifiers in Environmental Waters

    Science.gov (United States)

    We evaluated the use of qPCR RNA-based methods in the detection of fecal bacteria in environmental waters. We showed that RNA methods can increase the detection of fecal bacteria in multiple water matrices. The data suggest that this is a viable alternative for the detection of a...

  16. Sampling the Body Odor of Primates: Cotton Swabs Sample Semivolatiles Rather Than Volatiles.

    Science.gov (United States)

    Birkemeyer, Claudia S; Thomsen, Ruth; Jänig, Susann; Kücklich, Marlen; Slama, Anna; Weiß, Brigitte M; Widdig, Anja

    2016-07-01

    We assessed the suitability of a frequently used sampling method employing cotton swabs for collecting animal body odor for gas chromatography-mass spectrometry (GC-MS) analysis of volatile organic compounds (VOCs). Our method validation showed that both sampling material and sampling protocols affect the outcome of the analyses. Thus, among the tested protocols swabs of pure viscose baked before use and extracted with hexane had the least blank interferences in GC-MS analysis. Most critical for the recovery of VOCs was the handling time: the significant recovery losses of volatiles experienced with this sampling procedure suggest that a rapid processing of such samples is required. In a second part, we used swab sampling to sample the body odor of rhesus macaques (Macaca mulatta), which lack scent glands. First results after GC-MS analysis of the samples collected from these nonhuman primates emphasize that proper analytical performance is an indispensable prerequisite for successful automated data evaluation of the complex GC-MS profiles. Moreover, the retention times and the nature of the identified chemical compounds in our samples suggest that the use of swabs is generally more appropriate for collecting semivolatile rather than VOCs.

  17. How is the Xpert MRSA Gen 3 assay (Cepheid) performing on pooled eSwab medium?

    Science.gov (United States)

    Jonckheere, Stijn; Van Vaerenbergh, Kristien; Boel, An; Vankeerberghen, Anne; De Beenhouwer, Hans

    2015-11-01

    The performance of the Xpert MRSA Gen 3 was compared to the Xpert MRSA on pooled eSwab media from nose, throat, and perineum using broth enriched cultured as gold standard. A lower specificity was found for the Xpert MRSA Gen 3 compared to the Xpert MRSA (91.8% versus 97.9%; P<0.05).

  18. Identification of rhabdoviral sequences in oropharyngeal swabs from German and Danish bats

    DEFF Research Database (Denmark)

    Fischer, Melina; Freuling, Conrad M.; Müller, Thomas;

    2014-01-01

    Background: In the frame of active lyssavirus surveillance in bats, oropharyngeal swabs from German (N = 2297) and Danish (N = 134) insectivorous bats were investigated using a newly developed generic pan-lyssavirus real-time reverse transcriptase PCR (RT-qPCR).Findings: In total, 15 RT-qPCR posi...

  19. Detection of Streptococcus dysgalactiae subsp. equisimilis in equine nasopharyngeal swabs by PCR.

    Science.gov (United States)

    Preziuso, Silvia; Laus, Fulvio; Tejeda, Aurora Romero; Valente, Carlo; Cuteri, Vincenzo

    2010-03-01

    Streptococcus (S.) dysgalactiae subsp. equisimilis is responsible for severe diseases in humans, including primary bacteraemia, pneumonia, endocarditis, and toxic shock syndrome. Infection in some animal species can also occur, although a few studies have looked into cross-species infectivity. In horses, S. equisimilis is generally considered infrequent or opportunistic, but has recently been isolated from cases of strangles-like disease. Rapid and sensitive diagnostic techniques could enable epidemiological studies and effective investigation of outbreaks involving these bacteria. In this study, PCR protocols previously described in cattle and in humans to detect the species S. dysgalactiae and the subspecies equisimilis were evaluated to detect specific sequences in equine samples. For this purpose, 99 monolateral nasal swabs were collected from horses from stud farms with a history of S. equisimilis infection and were tested blindly by bacteriological isolation and by single and duplex PCR. DNA for PCR was extracted both from the colonies grown on agar media and from enrichment broth aliquots after incubation with nasal swab samples. S. equisimilis was identified by bacteriological isolation in 23 out of 99 swab samples, and PCR assays on these colonies were fully concordant with bacteriological identification (kappa statistic = 1.00). In addition, PCR of the enrichment broth aliquots confirmed the bacteriological results and detected S. equisimilis in 6 samples more than the bacteriological examination (kappa statistic = 0.84). The PCR protocols appeared to be reliable for the rapid identification of S. equisimilis in equine nasal swab samples, and could be useful for microbiological diagnosis.

  20. Bovine Herpesvirus 4 infections and bovine mastitis

    NARCIS (Netherlands)

    Wellenberg, Gerardus Johannus

    2002-01-01

    Mastitis is an often occurring disease in dairy cattle with an enormous economic impact for milk producers worldwide. Despite intensive research, which is historically based on the detection of bacterial udder pathogens, still around 20-35% of clinical cases of bovine mastitis have an unknown aetiol

  1. [Antibiotic sensitivity of beta-hemolytic streptococci isolated from throat swabs and purulent material].

    Science.gov (United States)

    Jachna-Sawicka, Katarzyna; Pietrzak, Anna; Bogiel, Tomasz; Gospodarek, Eugenia

    2010-01-01

    The aim of this study was to evaluate the prevalence and susceptibility of beta-hemolytic streptococci isolated from throat swabs (142--29.9%) and purulent material (333--70.1%) taken from patients treated at University Hospital dr. A. Jurasz in Bydgoszcz Collegium Medicum. L. Rydygier in Bydgoszcz, Nicolaus Copernicus University in Torun in 2005-2009. Of the 475 tested strains, 156 (32.8%) were identified as S. pyogenes. This species accounted for 38.8% of strains isolated from purulent material and 19.0% of swabs from the throat. Among the strains isolated from throat swabs of 62 (43.7%) were identified as Streptococcus group C. Only 5.1% strains were identified as Streptococcus group F. All strains of beta-hemolytic streptococci were susceptible to ampicillin or penicillin, fluoroquinolones, vancomycin and linezolid. Erythromycin-susceptible strains was 83.8%, and 89.1% for clindamycin. A total of 51.3% of erythromycin resistance strains had the cMLS(B) phenotype (63.3% for strains from throat swabs and 46.3% of the purulent materials). Sensitivity to tetracycline was characterized by 51.2% of strains of beta-hemolytic streptococci. The percentage of strains susceptible to this antibiotic among isolates from throat swabs was 63.1%, and purulent material--48.0%. The lowest percentage of strains susceptible to tetracycline (14.1%) were found among S. agalactiae and Streptococcus group G (33.6%) strains. During the study time, saw an increase in the percentage of strains susceptible to tetracycline and erythromycin.

  2. Fecal DNA Screening in Colorectal Cancer

    Directory of Open Access Journals (Sweden)

    Suzanne Richter

    2008-01-01

    Full Text Available Colorectal cancer (CRC is the third most common type of cancer diagnosed in Canada, and is the leading cause of cancer-related deaths in nonsmokers. Although CRC is considered to be 90% curable if detected early, the majority of patients present with advanced stage III or IV disease. An effective screening test may significantly decrease disease burden. The present paper examines the rationale and potential of fecal DNA testing as an alternative and adjunct to other CRC screening tests. The most efficacious fecal DNA test developed to date has a sensitivity and specificity of 87.5% and 82%, respectively. The approach has a higher positive predictive value than the currently used fecal occult blood test and offers a noninvasive option to patients. It is not reliant on the presence of bleeding, which may be intermittent or altogether absent. The test is now commercially available and is supported by a number of American insurers. Current challenges include cost reduction and demonstration of mortality benefit in a rigorous clinical trial. Despite current challenges, fecal DNA testing is worth pursuing. Both the American Gastroenterological Society and the American Cancer Society maintain that molecular testing is in its infancy but is promising. Fecal DNA testing has the potential to be an exciting addition to the current armament of CRC screening options.

  3. Evaluation of methods to improve the extraction and recovery of DNA from cotton swabs for forensic analysis.

    Science.gov (United States)

    Adamowicz, Michael S; Stasulli, Dominique M; Sobestanovich, Emily M; Bille, Todd W

    2014-01-01

    Samples for forensic DNA analysis are often collected from a wide variety of objects using cotton or nylon tipped swabs. Testing has shown that significant quantities of DNA are retained on the swab, however, and subsequently lost. When processing evidentiary samples, the recovery of the maximum amount of available DNA is critical, potentially dictating whether a usable profile can be derived from a piece of evidence or not. The QIAamp DNA Investigator extraction kit was used with its recommended protocol for swabs (one hour incubation at 56°C) as a baseline. Results indicate that over 50% of the recoverable DNA may be retained on the cotton swab tip, or otherwise lost, for both blood and buccal cell samples when using this protocol. The protocol's incubation time and temperature were altered, as was incubating while shaking or stationary to test for increases in recovery efficiency. An additional step was then tested that included periodic re-suspension of the swab tip in the extraction buffer during incubation. Aliquots of liquid blood or a buccal cell suspension were deposited and dried on cotton swabs and compared with swab-less controls. The concentration of DNA in each extract was quantified and STR analysis was performed to assess the quality of the extracted DNA. Stationary incubations and those performed at 65°C did not result in significant gains in DNA yield. Samples incubated for 24 hours yielded less DNA. Increased yields were observed with three and 18 hour incubation periods. Increases in DNA yields were also observed using a swab re-suspension method for both cell types. The swab re-suspension method yielded an average two-fold increase in recovered DNA yield with buccal cells and an average three-fold increase with blood cells. These findings demonstrate that more of the DNA collected on swabs can be recovered with specific protocol alterations.

  4. Evaluation of methods to improve the extraction and recovery of DNA from cotton swabs for forensic analysis.

    Directory of Open Access Journals (Sweden)

    Michael S Adamowicz

    Full Text Available Samples for forensic DNA analysis are often collected from a wide variety of objects using cotton or nylon tipped swabs. Testing has shown that significant quantities of DNA are retained on the swab, however, and subsequently lost. When processing evidentiary samples, the recovery of the maximum amount of available DNA is critical, potentially dictating whether a usable profile can be derived from a piece of evidence or not. The QIAamp DNA Investigator extraction kit was used with its recommended protocol for swabs (one hour incubation at 56°C as a baseline. Results indicate that over 50% of the recoverable DNA may be retained on the cotton swab tip, or otherwise lost, for both blood and buccal cell samples when using this protocol. The protocol's incubation time and temperature were altered, as was incubating while shaking or stationary to test for increases in recovery efficiency. An additional step was then tested that included periodic re-suspension of the swab tip in the extraction buffer during incubation. Aliquots of liquid blood or a buccal cell suspension were deposited and dried on cotton swabs and compared with swab-less controls. The concentration of DNA in each extract was quantified and STR analysis was performed to assess the quality of the extracted DNA. Stationary incubations and those performed at 65°C did not result in significant gains in DNA yield. Samples incubated for 24 hours yielded less DNA. Increased yields were observed with three and 18 hour incubation periods. Increases in DNA yields were also observed using a swab re-suspension method for both cell types. The swab re-suspension method yielded an average two-fold increase in recovered DNA yield with buccal cells and an average three-fold increase with blood cells. These findings demonstrate that more of the DNA collected on swabs can be recovered with specific protocol alterations.

  5. Clostridium difficile Infection and Fecal Microbiota Transplant.

    Science.gov (United States)

    Liubakka, Alyssa; Vaughn, Byron P

    2016-07-01

    Clostridium difficile infection (CDI) is a major source of morbidity and mortality for hospitalized patients. Although most patients have a clinical response to existing antimicrobial therapies, recurrent infection develops in up to 30% of patients. Fecal microbiota transplant is a novel approach to this complex problem, with an efficacy rate of nearly 90% in the setting of multiple recurrent CDI. This review covers the current epidemiology of CDI (including toxigenic and nontoxigenic strains, risk factors for infection, and recurrent infection), methods of diagnosis, existing first-line therapies in CDI, the role of fecal microbiota transplant for multiple recurrent CDIs, and the potential use of fecal microbial transplant for patients with severe or refractory infection.

  6. High prevalence of Schistosoma japonicum and Fasciola gigantica in bovines from Northern Samar, the Philippines.

    Directory of Open Access Journals (Sweden)

    Catherine A Gordon

    2015-02-01

    Full Text Available The cause of zoonotic schistosomiasis in the Philippines is Schistosoma japonicum, which infects up to 46 mammalian hosts, including humans and bovines. In China, water buffaloes have been identified as major reservoir hosts for schistosomiasis japonica, contributing up to 75% of human transmission. In the Philippines, water buffaloes (carabao; Bubalus bubalis carabanesis have, historically, been considered unimportant reservoirs. We therefore revisited the possible role of bovines in schistosome transmission in the Philippines, using the recently described formalin-ethyl acetate sedimentation (FEA-SD technique and a qPCR assay to examine fecal samples from 153 bovines (both carabao and cattle from six barangays in Northern Samar. A high prevalence of S. japonicum was found using qPCR and FEA-SD in both cattle (87.50% and 77.08%, respectively and carabao (80.00% and 55.24%, respectively. The average daily egg output for each bovine was calculated at 195,000. High prevalence and infection intensity of F. gigantica was also found in the bovines by qPCR and FEA-SD (95.33% and 96.00%, respectively. The identification of bovines as major reservoir hosts for S. japonicum transmission suggests that bovine treatment and/or vaccination, as one becomes available, should be included in any future control program that aims to reduce the disease burden due to schistosomiasis in the Philippines.

  7. Surge and swab pressures in wells with cross-section changes; Pressoes de surge and swab em pocos com variacao de secao

    Energy Technology Data Exchange (ETDEWEB)

    Fedevjcyk, Joao Victor; Junqueira, Silvio Luiz de Mello; Negrao, Cezar Otaviano Ribeiro [Universidade Tecnologica Federal do Parana (UTFPR). Laboratorio de Ciencias Termicas (Lacit) (Brazil)], e-mails: silvio@utfpr.edu.br, negrao@utfpr.edu.br

    2009-12-15

    Well drilling is performed by rotating and applying a weighted drill bit to the geological formation. Well diameter variations and the use of drill pipe accessories might cause changes to the annular cross section space between the drill pipe and the borehole. It should be noted cross section changes influence pressure losses within the well. This study proposes a mathematical/ numerical model to simulate the surge and swab problem in wells with variable cross section areas. The fluid flow yielded by the drill pipe motion is considered to be one-dimensional, isothermal, compressible and transient. The proposed model features the mass and momentum conservation equations, along with a state equation and a constitutive equation for Bingham or Power Law fluids. The governing equations were discretized by the Finite Volume Method. The well is assumed to be impermeable and the drill pipe end to be closed. The results were compared to measured data obtained at the Taquipe experimental well with good agreement. Predictions can now be made as to how changes in cross section areas may significantly affect the transient surge and swab pressures. (author)

  8. Prevalence of Bovine Herpesvirus-1 in cattle and buffaloes in Punjab

    Directory of Open Access Journals (Sweden)

    Gurpreet Kaur

    2013-12-01

    Full Text Available Aim: The aim of the present study was to identify the prevalence of Bovine Herpesvirus-1 (BHV-1 in cattle and buffaloes in the Punjab using PCR as diagnostic tool. Materials and Methods: A total of 63 samples (Semen- 57, placental cotyledons-1, vaginal secretions-1, foetal stomach contents-1 and tracheal swabs-3 from cattle and buffaloes were processed for identification of BHV-1 using PCR. Results: From January 2007 to December 2010 (Semen- 57, placental cotyledons-1, vaginal secretions-1, foetal stomach contents-1 and tracheal swabs-3 from cattle and buffaloes were collected. The DNA was extracted from a total of 63 samples and subjected to PCR revealed that none of the sample positive for the BHV-1 infection. Conclusion: From the study it was concluded that the farms screened were free from BHV-1 infection. [Vet World 2013; 6(6.000: 343-345

  9. Validation of Single and Pooled Manure Drag Swabs for the Detection of Salmonella Serovar Enteritidis in Commercial Poultry Houses.

    Science.gov (United States)

    Kinde, Hailu; Goodluck, Helen A; Pitesky, Maurice; Friend, Tom D; Campbell, James A; Hill, Ashley E

    2015-12-01

    Single swabs (cultured individually) are currently used in the Food and Drug Administration (FDA) official method for sampling the environment of commercial laying hens for the detection of Salmonella enterica ssp. serovar Enteritidis (Salmonella Enteritidis). The FDA has also granted provisional acceptance of the National Poultry Improvement Plan's (NPIP) Salmonella isolation and identification methodology for samples taken from table-egg layer flock environments. The NPIP method, as with the FDA method, requires single-swab culturing for the environmental sampling of laying houses for Salmonella Enteritidis. The FDA culture protocol requires a multistep culture enrichment broth, and it is more labor intensive than the NPIP culture protocol, which requires a single enrichment broth. The main objective of this study was to compare the FDA single-swab culturing protocol with that of the NPIP culturing protocol but using a four-swab pool scheme. Single and multi-laboratory testing of replicate manure drag swab sets (n  =  525 and 672, respectively) collected from a Salmonella Enteritidis-free commercial poultry flock was performed by artificially contaminating swabs with either Salmonella Enteritidis phage type 4, 8, or 13a at one of two inoculation levels: low, x¯  = 2.5 CFU (range 2.5-2.7), or medium, x¯  = 10.0 CFU (range 7.5-12). For each replicate, a single swab (inoculated), sets of two swabs (one inoculated and one uninoculated), and sets of four swabs (one inoculated and three uninoculated), testing was conducted using the FDA or NPIP culture method. For swabs inoculated with phage type 8, the NPIP method was more efficient (P 0.05) between the FDA method (single swabs) and the pooled NPIP method (four-pool swabs). The study concludes that the pooled NPIP method is not significantly different from the FDA method for the detection of Salmonella Enteritidis in drag swabs in commercial poultry laying houses. Consequently based on the FDA

  10. Fecal microbiota transplantation inducing remission in Crohn's colitis and the associated changes in fecal microbial profile.

    Science.gov (United States)

    Kao, Dina; Hotte, Naomi; Gillevet, Patrick; Madsen, Karen

    2014-08-01

    Inflammatory bowel disease (IBD) is a chronic relapsing disorder of the intestine of unclear etiology. Increasing evidence has pointed to intestinal dysbiosis as a potential factor in a genetically susceptible individual. Fecal microbiota transplantation (FMT) has been used to treat inflammatory bowel disease with variable degrees of success. Herein, we report a patient with Crohn's colitis, previously failing an immunosuppressant, who achieved clinical, endoscopic, and histologic remission after a single fecal microbiota transplantation infusion. We have further characterized the changes in the fecal microbiota associated with this observation.

  11. Neonatal diarrhea by bovine coronavirus (BCoV in beef cattle herds

    Directory of Open Access Journals (Sweden)

    Elis Lorenzetti

    2014-02-01

    Full Text Available Bovine coronavirus (BCoV is the second most important viral agent involved in neonatal diarrhea in calves worldwide. The reports on the frequency of BCoV infection in beef cattle herds under extensive management are uncommon in Brazil. The present study analyzed 93 diarrheic fecal samples of calves up to 60 days of age from 13 commercial beef cattle herds located in the states of Mato Grosso, Mato Grosso do Sul, Minas Gerais, Paraná, and Rondônia. The fecal samples were collected during 2009-2012 and were previously analyzed for the presence of bovine rotavirus group A (BoRVA, with negative results. The presence of BCoV in the fecal samples was evaluated by the partial amplification of the N gene by using the semi-nested PCR technique. The expected products of 251 bp length were amplified 33.3% (31/93 of the analyzed diarrheic fecal samples. The results revealed that coronaviruses has important participation in the neonatal diarrhea complex of beef cattle herds reared extensively from the different geographical regions of Brazil.

  12. Validation of a nylon-flocked-swab protocol for efficient recovery of bacterial spores from smooth and rough surfaces.

    Science.gov (United States)

    Probst, Alexander; Facius, Rainer; Wirth, Reinhard; Moissl-Eichinger, Christine

    2010-08-01

    In order to meet planetary-protection requirements, culturable bacterial spore loads are measured representatively for the total microbial contamination of spacecraft. However, the National Aeronautics and Space Administration's (NASA's) cotton swab protocols for spore load determination have not changed for decades. To determine whether a more efficient alternative was available, a novel swab was evaluated for recovery of different Bacillus atrophaeus spore concentrations on stainless steel and other surfaces. Two protocols for the nylon-flocked swab (NFS) were validated and compared to the present NASA standard protocol. The results indicate that the novel swab protocols recover 3- to 4-fold more (45.4% and 49.0% recovery efficiency) B. atrophaeus spores than the NASA standard method (13.2%). Moreover, the nylon-flocked-swab protocols were superior in recovery efficiency for spores of seven different Bacillus species, including Bacillus anthracis Sterne (recovery efficiency, 20%). The recovery efficiencies for B. atrophaeus spores from different surfaces showed a variation from 5.9 to 62.0%, depending on the roughness of the surface analyzed. Direct inoculation of the swab resulted in a recovery rate of about 80%, consistent with the results of scanning electron micrographs that allowed detailed comparisons of the two swab types. The results of this investigation will significantly contribute to the cleanliness control of future life detection missions and will provide significant improvement in detection of B. anthracis contamination for law enforcement and security efforts.

  13. Detection of Brucella spp. in bottlenose dolphins Tursiops truncatus by a real-time PCR using blowhole swabs.

    Science.gov (United States)

    Wu, Qingzhong; Conway, Jessica; Phillips, Kristen M; Stolen, Megan; Durden, Wendy N; Fauquier, Deborah; McFee, Wayne E; Schwacke, Lori

    2016-08-09

    Blowhole swabs are a simple and non-invasive method for collecting samples from cetaceans and can be used for screening large numbers of animals in the field. This study reports a real-time PCR assay for the detection of Brucella spp. using blowhole swab samples from bottlenose dolphins Tursiops truncatus stranded in the coastal region of Virginia, South Carolina and northern Florida, USA, between 2013 and 2015. We used real-time PCR results on lung samples from the same dolphins in order to estimate the relative sensitivity and specificity of real-time PCR of blowhole swabs. Brucella DNA was detected in lung tissue of 22% (18/81) and in blowhole swabs of 21% (17/81) of the sampled dolphins. The relative sensitivity and specificity of real-time PCR on blowhole swabs as compared to the real-time PCR on lung samples was 94% (17/18) and 100% (63/63), respectively. These results indicate that real-time PCR on blowhole swabs may be used as a non-invasive test for rapid detection of Brucella spp. in the respiratory tract of dolphins. To our knowledge, this is the first report on the use of blowhole swabs for detection of bacterial pathogens by real-time PCR in bottlenose dolphins.

  14. Use of polymerase chain reaction (PCR for detection of Chlamydia trachomatis infection in cervical swab samples

    Directory of Open Access Journals (Sweden)

    Mania-Pramanik Jayanti

    2001-09-01

    Full Text Available A polymerase chain reaction (PCR based method has been set up for detection of Chlamydia trachomatis (C. trachomatis infection in single cervical swab samples. A primer pair specific to the major outer membrane protein (MOMP gene common to all serotypes of C. trachomatis was used. This method was validated for its sensitivity as well as specificity. A minimum Ing of DNA could be used for detection of the infection. Specificity of the method was confirmed by carrying out a sample dilution curve. The cervical swab samples analysed in the present study were in coded form for validation of the PCR with an established commercial ELISA (Chlamydiazyme. Both the sensitivity and specificity of PCR was 100% when the ELISA results of these samples were decoded. Thus, this PCR technique could be used for better diagnosis of C. trachomatis infection in comparison to the commercially available ELISA technique.

  15. Enzymatic activity analysis of MMP-2 and 9 collected by swab from lower limb venous ulcers

    Directory of Open Access Journals (Sweden)

    Flávio Santos da Silva

    2014-09-01

    Full Text Available Metalloproteinases play a role in repair of venous ulcers of the lower limbs. The great majority of studies of metalloproteinase enzyme activity conducted to date have employed material from biopsies of ulcers. We evaluated the viability of using zymography to measure the enzyme activity of metalloproteinases 2 and 9 in samples of venous ulcer exudate collected on swabs. The method chosen for processing the samples proved viable in terms of its ability to provide adequate protein concentrations for analysis. Using zymography, we observed that the parameters that provided the best results for analysis of gelatinolytic activity were 0.125 to 0.5 μg of total protein content in the gels and enzymatic activation time of 19 hours (at 37 °C. Collection of venous ulcer fluid using swabs proved to be a simple, rapid and effective method for obtaining samples for measurement of gelatinolytic activity with a minimum degree of invasivity.

  16. Value of bacterial culture of vaginal swabs in diagnosis of vaginal infections

    Directory of Open Access Journals (Sweden)

    Nenadić Dane

    2015-01-01

    Full Text Available Bacground/Aim. Vaginal and cervical swab culture is still very common procedure in our country’s everyday practice whereas simple and rapid diagnostic methods have been very rarely used. The aim of this study was to show that the employment of simple and rapid diagnostic tools [vaginal fluid wet mount microscopy (VFWMM, vaginal pH and potassium hydroxide (KOH test] offers better assessment of vaginal environment than standard microbiologic culture commonly used in Serbia. Methods. This prospective study included 505 asymptomatic pregnant women undergoing VFWMM, test with 10% KOH, determination of vaginal pH and standard culture of cervicovaginal swabs. Combining findings from the procedures was used to make diagnoses of bacterial vaginosis (BV and vaginitis. In addition, the number of polymorphonuclear leukocytes (PMN was determined in each sample and analyzed along with other findings. Infections with Candida albicans and Trichomonas vaginalis were confirmed or excluded by microscopic examination. Results. In 36 (6% patients cervicovaginal swab cultures retrieved several aerobes and facultative anaerobes, whereas in 52 (11% women Candida albicans was isolated. Based on VFWMM findings and clinical criteria 96 (19% women had BV, 19 (4% vaginitis, and 72 (14% candidiasis. Of 115 women with BV and vaginitis, pH 4.5 was found in 5, and of 390 with normal findings 83 (21% had vaginal pH 4.5. Elevated numbers of PMN were found in 154 (30% women - in 83 (54% of them VFWMM was normal. Specificity and sensitivity of KOH test and vaginal pH determination in defining pathological vaginal flora were 95% and 81%, and 79% and 91%, respectively. Conclusion. Cervicovaginal swab culture is expensive but almost non-informative test in clinical practice. The use of simpler and rapid methods as vaginal fluid wet mount microscopy, KOH test and vaginal pH offers better results in diagnosis, and probably in the treatment and prevention of sequels of vaginal

  17. Detection and prediction of Streptococcus pneumoniae serotypes directly from nasopharyngeal swabs using PCR.

    Science.gov (United States)

    Lang, Amanda L S; McNeil, Shelly A; Hatchette, Todd F; Elsherif, May; Martin, Irene; LeBlanc, Jason J

    2015-08-01

    Monitoring Streptococcus pneumoniae serotype distribution is important to assess the impact and effectiveness of pneumococcal vaccine programs. With the challenges of Quellung serotyping, PCR-based serotype prediction is increasingly being used for large-scale epidemiological studies. This study used real-time (RT)-PCR targeting the genes encoding autolysin (lytA) and capsular biosynthesis gene A (cpsA) of S. pneumoniae in nucleic acids extracted directly from nasopharyngeal (NP) swabs submitted for viral studies. If the specimen was lytA or cpsA PCR-positive, then serotype prediction was performed on the same nucleic acid using eight conventional multiplex PCRs (cmPCRs) and seven real-time multiplex PCRs (rmPCRs). Of 1770 NP swabs, 132 (7.5  %) were lytA-positive and 122 (6.9  %) were positive for both targets (lytA and cpsA). Of the 122 lytA(+)cpsA(+) specimens, a serotype could be assigned in 52 (41.8  %) using cmPCR alone and the yield was increased to 70 (57.4  %) with the addition of rmPCR. Based on sensitivity, incremental yield and more efficient workflow, an algorithm was proposed where lytA and cpsA RT-PCR screening was followed by serotype deduction using rmPCR and a modified set of four instead of eight cmPCRs. This algorithm was validated for use on NP swabs, and the distribution of S. pneumoniae serotypes deduced from this approach showed good concordance with those obtained with cultured isolates serotyped by Quellung and PCR. Overall, molecular detection and serotyping of S. pneumoniae from NP swabs was found to be a valuable tool to assess S. pneumoniae colonization and monitor trends in serotype distribution.

  18. Detection of Streptococcus agalactiae colonization in pregnant women by using combined swab cultures: cross-sectional prevalence study

    Directory of Open Access Journals (Sweden)

    Camila Marconi

    Full Text Available CONTEXT AND OBJECTIVE: Maternal Streptococcus agalactiae colonization and early-onset neonatal sepsis have aroused interest in the worldwide literature. Streptococcal neonatal disease is associated with significant morbidity and mortality in the perinatal period, especially among premature neonates. The aim of this study was to assess the prevalence of maternal streptococcal colonization by using combined swab cultures, compared with swab collection from a single site. DESIGN AND SETTING: Cross-sectional study at Faculdade de Medicina de Botucatu, Universidade Estadual Paulista. METHODS: Samples were obtained from 405 patients at gestational ages of 35 to 37 weeks. Swabs from the perianal (rectal region, vaginal introitus and upper lateral vaginal vault were cultured in Todd-Hewitt selective broth. Colonies suggestive of Streptococcus agalactiae were subjected to the catalase and CAMP (Christie, Atkins, Munch-Petersen tests. To evaluate the positivity of combined swab cultures, Tukey's test was used for comparison of proportions. RESULTS: The prevalence of streptococcal colonization was 25.4%. Among the patients with positive cultures, 28.1% had this at only one collection site, 24.2% simultaneously at two sites and 47.5% at all three sites. Associating the swabs from two collection sites significantly increased streptococcal isolation, compared with a single swab (P < 0.05, except for perianal (rectal collection. Use of combined swabs from three collection sites showed statistically higher isolation rates. CONCLUSION: In combined swab cultures collected from three collection sites, the prevalence of maternal Streptococcus agalactiae colonization was higher than in swabs collected from a single site.

  19. Nasal, oral and ear swabs for canine visceral leishmaniasis diagnosis: new practical approaches for detection of Leishmania infantum DNA.

    Directory of Open Access Journals (Sweden)

    Sidney de Almeida Ferreira

    Full Text Available BACKGROUND: The aim of this study was to evaluate the potential use of nasal, oral, and ear swabs for molecular diagnosis of canine visceral leishmaniasis (CVL in an endemic urban area in Brazil. METHODOLOGY/PRINCIPAL FINDINGS: Sixty-two naturally infected and ten healthy dogs were enrolled in this study. Bone marrow aspirates, peripheral blood, skin biopsy, and conjunctival, nasal, oral, and ear swabs were collected. All samples, except blood, were submitted to conventional PCR (cPCR and quantitative real time PCR (qPCR to detect and quantify Leishmania infantum DNA, respectively. All dogs were submitted to thorough clinical analysis and were included based on a combination of serological (ELISA immunoassay and immunofluorescent antibody test and parasitological methods. The cPCR positivity obtained from nasal swab samples was 87% (54/62, equivalent to those from other samples (P>0.05. Positive results were obtained for 79% (22/28 in oral swabs and 43% (12/28 in ear swab samples. A significant difference was observed between these data (P=0.013, and the frequency of positive results from oral swab was equivalent to those from other samples (P>0.05. The use of ear swab samples for cPCR assays is promising because its result was equivalent to skin biopsy data (P>0.05. The qPCR data revealed that parasite loads in mucosal tissues were similar (P>0.05, but significantly lower than the parasite burden observed in bone marrow and skin samples (P<0.05. CONCLUSIONS: Nasal and oral swab samples showed a high potential for the qualitative molecular diagnosis of CVL because their results were equivalent to those observed in samples collected invasively. Considering that mucosae swab collections are painless, noninvasive, fast and practical, the combination of these samples would be useful in massive screening of dogs. This work highlights the potential of practical approaches for molecular diagnosis of CVL and human leishmaniasis infections.

  20. 78 FR 12763 - Fecal Microbiota for Transplantation; Public Workshop

    Science.gov (United States)

    2013-02-25

    ... HUMAN SERVICES Food and Drug Administration Fecal Microbiota for Transplantation; Public Workshop AGENCY... ``Fecal Microbiota for Transplantation.'' The purpose of the public workshop is to exchange information... fecal microbiota for transplantation (FMT). ] Date and Time: The public workshop will be held on May...

  1. Fecal Transplants: What Is Being Transferred?

    Directory of Open Access Journals (Sweden)

    Diana P Bojanova

    2016-07-01

    Full Text Available Fecal transplants are increasingly utilized for treatment of recurrent infections (i.e., Clostridium difficile in the human gut and as a general research tool for gain-of-function experiments (i.e., gavage of fecal pellets in animal models. Changes observed in the recipient's biology are routinely attributed to bacterial cells in the donor feces (~1011 per gram of human wet stool. Here, we examine the literature and summarize findings on the composition of fecal matter in order to raise cautiously the profile of its multipart nature. In addition to viable bacteria, which may make up a small fraction of total fecal matter, other components in unprocessed human feces include colonocytes (~107 per gram of wet stool, archaea (~108 per gram of wet stool, viruses (~108 per gram of wet stool, fungi (~106 per gram of wet stool, protists, and metabolites. Thus, while speculative at this point and contingent on the transplant procedure and study system, nonbacterial matter could contribute to changes in the recipient's biology. There is a cautious need for continued reductionism to separate out the effects and interactions of each component.

  2. Fecal microbiota transplantation and donor standardization.

    Science.gov (United States)

    Owens, Casey; Broussard, Elizabeth; Surawicz, Christina

    2013-09-01

    Clostridium difficile diarrhea is a common and severe infectious disease. Antibiotics, which are standard initial treatment, are less effective for treating refractory or recurrent infection. Fecal microbiota transplantation, where healthy donor stool is transplanted into a patient, is an alternative to antibiotic therapy that requires standardization for donors and patients.

  3. Therapeutic potential of fecal microbiota transplantation

    NARCIS (Netherlands)

    Smits, L.P.; Bouter, K.E.C.; Vos, de W.M.; Borody, T.J.; Nieuwdorp, M.

    2013-01-01

    There has been growing interest in the use of fecal microbiota for the treatment of patients with chronic gastrointestinal infections and inflammatory bowel diseases. Lately, there has also been interest in its therapeutic potential for cardiometabolic, autoimmune, and other extraintestinal conditio

  4. Inkjet-printed paper-based SERS dipsticks and swabs for trace chemical detection.

    Science.gov (United States)

    Yu, Wei W; White, Ian M

    2013-02-21

    We demonstrate a paper-based surface swab and lateral-flow dipstick that includes an inkjet-printed surface-enhanced Raman spectroscopy (SERS) substrate for analyte detection. Due to capillary-action wicking of cellulose, the paper dipstick enables extremely simple and pump-free loading of liquid samples into the detection device, and in addition provides inherent analyte concentration within the detection volume. Furthermore, the flexible nature of the paper-based SERS device also enables it to act as a swab to collect analyte molecules directly from a large-area surface; the collected analyte molecules can then be focused into a small-volume SERS-active region by lateral-flow concentration. These capabilities are unseen in today's SERS substrates and microfluidic SERS devices. Using these novel lateral-flow paper SERS devices, we achieved detection limits as low as 95 fg of Rhodamine 6G (R6G), 413 pg of the organophosphate malathion, 9 ng of heroin, and 15 ng of cocaine. Moreover, the measurements show that the technique is quantitative and is repeatable across multiple swabs and dipsticks. The results reported here may lead to ultra-low-cost portable applications in trace chemical detection.

  5. Evaluation of a PCR test for detection of treponema pallidum in swabs and blood.

    Science.gov (United States)

    Grange, P A; Gressier, L; Dion, P L; Farhi, D; Benhaddou, N; Gerhardt, P; Morini, J P; Deleuze, J; Pantoja, C; Bianchi, A; Lassau, F; Avril, M F; Janier, M; Dupin, N

    2012-03-01

    Syphilis diagnosis is based on clinical observation, serological analysis, and dark-field microscopy (DFM) detection of Treponema pallidum subsp. pallidum, the etiological agent of syphilis, in skin ulcers. We performed a nested PCR (nPCR) assay specifically amplifying the tpp47 gene of T. pallidum from swab and blood specimens. We studied a cohort of 294 patients with suspected syphilis and 35 healthy volunteers. Eighty-seven of the 294 patients had primary syphilis, 103 had secondary syphilis, 40 had latent syphilis, and 64 were found not to have syphilis. The T. pallidum nPCR results for swab specimens were highly concordant with syphilis diagnosis, with a sensitivity of 82% and a specificity of 95%. Reasonable agreement was observed between the results obtained with the nPCR and DFM methods (kappa = 0.53). No agreement was found between the nPCR detection of T. pallidum in blood and the diagnosis of syphilis, with sensitivities of 29, 18, 14.7, and 24% and specificities of 96, 92, 93, and 97% for peripheral blood mononuclear cell (PBMC), plasma, serum, and whole-blood fractions, respectively. HIV status did not affect the frequency of T. pallidum detection in any of the specimens tested. Swab specimens from mucosal or skin lesions seemed to be more useful than blood for the efficient detection of the T. pallidum genome and, thus, for the diagnosis of syphilis.

  6. Evaluation of two methods for monitoring surface cleanliness-ATP bioluminescence and traditional hygiene swabbing.

    Science.gov (United States)

    Davidson, C A; Griffith, C J; Peters, A C; Fielding, L M

    1999-01-01

    The minimum bacterial detection limits and operator reproducibility of the Biotrace Clean-Tracetrade mark Rapid Cleanliness Test and traditional hygiene swabbing were determined. Areas (100 cm2) of food grade stainless steel were separately inoculated with known levels of Staphylococcus aureus (NCTC 6571) and Escherichia coli (ATCC 25922). Surfaces were sampled either immediately after inoculation while still wet, or after 60 min when completely dry. For both organisms the minimum detection limit of the ATP Clean-Tracetrade mark Rapid Cleanliness Test was 10(4) cfu/100 cm2 (p 10(7) cfu/100 cm2. Hygiene swabbing percentage recovery rates for both organisms were less than 0.1% for dried surfaces but ranged from 0.33% to 8.8% for wet surfaces. When assessed by six technically qualified operators, the Biotrace Clean-Tracetrade mark Rapid Cleanliness Test gave superior reproducibility for both clean and inoculated surfaces, giving mean coefficients of variation of 24% and 32%, respectively. Hygiene swabbing of inoculated surfaces gave a mean CV of 130%. The results are discussed in the context of hygiene monitoring within the food industry.

  7. Utilization and Assessment of Throat Swab and Urine Specimens for Diagnosis of Chikungunya Virus Infection.

    Science.gov (United States)

    Raut, Chandrashekhar G; Hanumaiah, H; Raut, Wrunda C

    2016-01-01

    Chikungunya is a mosquito-borne infection with clinical presentation of fever, arthralgia, and rash. The etiological agent Chikungunya virus (CHIKV) is generally transmitted from primates to humans through the bites of infected Aedes aegypti and Aedes albopictus mosquitoes. Outbreaks of Chikungunya occur commonly with varied morbidity, mortality, and sequele according to the epidemiological, ecological, seasonal, and geographical impact. Investigations are required to be conducted as a part of the public health service to understand and report the suspected cases as confirmed by laboratory diagnosis. Holistic sampling at a time of different types would be useful for laboratory testing, result conclusion, and reporting in a valid way. The use of serum samples for virus detection, virus isolation, and serology is routinely practiced, but sometimes serum samples from pediatric and other cases may not be easily available. In such a situation, easily available throat swabs and urine samples could be useful. It is already well reported for measles, rubella, and mumps diseases to have the virus diagnosis from throat swabs and urine. Here, we present the protocols for diagnosis of CHIKV using throat swab and urine specimens.

  8. Swab culture monitoring of automated endoscope reprocessors after high-level disinfection

    Institute of Scientific and Technical Information of China (English)

    Lung-Sheng Lu; Keng-Liang Wu; Yi-Chun Chiu; Ming-Tzung Lin; Tsung-Hui Hu; King-Wah Chiu

    2012-01-01

    AIM:To conduct a bacterial culture study for monitoring decontamination of automated endoscope reprocessors (AERs) after high-level disinfection (HLD).METHODS:From February 2006 to January 2011,authors conducted randomized consecutive sampling each month for 7 AERs.Authors collected a total of 420 swab cultures,including 300 cultures from 5 gastroscope AERs,and 120 cultures from 2 colonoscope AERs.Swab cultures were obtained from the residual water from the AERs after a full reprocessing cycle.Samples were cultured to test for aerobic bacteria,anaerobic bacteria,and mycobacterium tuberculosis.RESULTS:The positive culture rate of the AERs was 2.0% (6/300) for gastroscope AERs and 0.8% (1/120)for colonoscope AERs.All the positive cultures,including 6 from gastroscope and 1 from colonoscope AERs,showed monofloral colonization.Of the gastroscope AER samples,50% (3/6) were colonized by aerobic bacterial and 50% (3/6) by fungal contaminations.CONCLUSION:A full reprocessing cycle of an AER with HLD is adequate for disinfection of the machine.Swab culture is a useful method for monitoring AER decontamination after each reprocessing cycle.Fungal contamination of AERs after reprocessing should also be kept in mind.

  9. Medical swab touch spray-mass spectrometry for newborn screening of nicotine and cotinine in meconium.

    Science.gov (United States)

    Yang, Bi-Cheng; Wang, Feng; Yang, Xiao; Zou, Wei; Wang, Jia-Chun; Zou, Yang; Liu, Fa-Ying; Liu, Huai; Huang, Ou-Ping

    2016-12-01

    Newborn screening is one of public health concerns designed to screen infants shortly after birth. Prenatal exposure to tobacco smoke such as nicotine has been reported to affect babies. Levels of nicotine and cotinine in meconium were widely used to evaluate the tobacco exposure of foetuses during pregnancy in a polluted environment. In this study, medical swabs were applied by using touch spray-mass spectrometry (TS-MS) to collect meconium from newborn infants for detection of nicotine and cotinine. Parameters such as choice of spray solvents, solvent volume and collision energy for screening of nicotine and cotinine were optimized. The limits of detection, reproducibility and matrix effect for analysis of meconium were also investigated. In this study, the levels of nicotine and cotinine in 54 puerpera volunteers were screened by TS-MS and were validated by using traditional liquid chromatography-mass spectrometry. These results showed that medical swab TS-MS would be useful for newborn screening of nicotine and cotinine in meconium with high reproducibility, speed, sensitivity and specificity. The use of disposable medical swabs involves no sample preparation and no chromatographic separation, significantly reducing the cost and time required for screening a large number of clinical sample. Copyright © 2016 John Wiley & Sons, Ltd.

  10. Sexing Bovine Embryos Using PCR Amplification of Bovine SRY Sequence

    Institute of Scientific and Technical Information of China (English)

    曾溢滔; 张美兰; 陈美珏; 周霞娣; 黄英; 任兆瑞; 黄淑帧; 胡明信; 吴学清; 高建明; 张斌; 徐慧如

    1994-01-01

    This study analyses the bovine SRY DNA sequence by direct sequencing procedure, followed by the designation of the PCR primers specific for bovine SRY. Using PCR amplification of bovine SRY gene, the embryo sex was determined. The results of the embryo sex identification were confirmed after the embryo transfer and pregnancies.

  11. Molecular detection of bovine coronavirus in a diarrhea outbreak in pasture-feeding Nellore steers in southern Brazil.

    Science.gov (United States)

    Ribeiro, Juliane; Lorenzetti, Elis; Alfieri, Alice Fernandes; Alfieri, Amauri Alcindo

    2016-03-01

    Worldwide diarrhea outbreaks in cattle herds are more frequently detected in calves being that diarrhea outbreaks in adult cattle are not common. Winter dysentery (WD) is a bovine coronavirus (BCoV) enteric infection that is more reported in Northern hemisphere. Seasonal outbreaks of WD in adult cattle occur mainly in dairy cows. WD has not been described in beef cattle herds of tropical countries. This study describes the molecular detection of BCoV in a diarrhea outbreak in beef cattle steers (Nellore) raised on pasture in Parana, southern Brazil. During the outbreak, the farm had about 600 fattening steers. Watery and bloody diarrhea unresponsive to systemic broad-spectrum antibiotic therapy reveals a morbidity rate of approximately 15 %. The BCoV N gene was identified in 42.9 % (6/14) of the diarrheic fecal samples evaluated by semi-nested polymerase chain reaction (SN-PCR) technique. Other enteric microorganisms occasionally identified in adult cattle and evaluated in this study such as bovine groups A, B, and C rotavirus, bovine viral diarrhea virus, bovine torovirus, aichivirus B, and Eimeria sp. were not identified in the fecal samples. To the best knowledge of the authors, this is the first description of the BCoV diagnosis in fecal samples collected in a diarrhea outbreak in adult beef cattle grazing in the grass in a tropical country.

  12. Enzootic bovine leukosis and Bovine leukemia virus

    OpenAIRE

    Amauri Alcindo Alfieri; Alice Fernandes Alfieri; Luis Álvaro Leuzzi Junior

    2004-01-01

    All over de World the Enzootic Bovine Leukosis is a important viral infection in cattle herds. This revision points out topics relative to the etiological agent, clinical signals, diagnosis methods, control and prophylaxis of the infection.A Leucose Enzoótica Bovina é uma infecção viral amplamente disseminada em rebanhos bovinos de todo o mundo. Esta revisão tem por objetivo apresentar tópicos relacionados ao agente etiológico, à doença clínica e aos métodos de diagnóstico, controle e profila...

  13. Glycoprotein C Gene Based Molecular Subtyping of a Bovine Herpesvirus -1 Isolate from Uttar Pradesh, India

    OpenAIRE

    2012-01-01

    Bovine herpesvirus -1 (BHV-1) is the etiological agent of many clinical syndromes in cattle which causes huge economic losses to the animal husbandry sector annually. Since the first report of its presence in India in 1976, the disease is considered to be endemic in the country. In the present study, a case of keratoconjunctivitis in a cow was investigated to find out the underlying cause of the condition. The clinical material (ocular swab) was tested by BHV-1 glycoprotein D gene specific PC...

  14. Culture-independent quantification of Salmonella enterica in carcass gauze swabs by flotation prior to real-time PCR

    DEFF Research Database (Denmark)

    Löfström, Charlotta; Schelin, Jenny; Norling, Börje

    2011-01-01

    To facilitate quantitative risk assessment in the meat production chain, there is a need for culture-independent quantification methods. The aim of this study was to evaluate the use of flotation, a non-destructive sample preparation method based on traditional buoyant density centrifugation......, for culture-independent quantification of intact Salmonella in pig carcass gauze swabs (100 cm2) prior to quantitative PCR (qPCR). A novel approach was investigated, excluding the homogenization step prior to flotation, to improve the detection limit and speed up the quantification procedure. The buoyant...... concentrations of ≥ 6.1 × 108 CFU/swab sample, but not by concentrations ≤ 6.1 × 106 CFU/swab sample. By using the gauze swabs directly in the flotation procedure, the homogenization step normally used for preparation of food-related samples could be excluded, which simplified the culture independent...

  15. [Optimisation of the antibiotic policy in the Netherlands. XII. The SWAB guideline for antimicrobial eradication of MRSA in carriers].

    NARCIS (Netherlands)

    Wertheim, H.F.; Ammerlaan, H.S.; Bonten, M.J.; Broek, P.J.J.A. van den; Troelstra, A.; Vandenbroucke-Grauls, C.M.; Vos, M.C.; Voss, A.; Nouwen, J.L.; Kluytmans, J.A.

    2008-01-01

    The 'Stichting Werkgroep Antibioticabeleid' (SWAB; Dutch Working Party on Antibiotics Policy) has developed evidence-based guidelines for the antimicrobial treatment of methicillin-resistant Staphylococcus aureus (MRSA) carriers for the eradication of MRSA. A distinction was made between uncomplicat

  16. Optimal swab processing recovery method for detection of bioterrorism-related Francisella tularensis by real-time PCR.

    Science.gov (United States)

    Walker, Roblena E; Petersen, Jeannine M; Stephens, Kenyatta W; Dauphin, Leslie A

    2010-10-01

    Francisella tularensis, the etiological agent of tularemia, is regarded as a potential bioterrorism agent. The advent of bioterrorism has heightened awareness of the need for validated methods for processing environmental samples. In this study we determined the optimal method for processing environmental swabs for the recovery and subsequent detection of F. tularensis by the use of real-time PCR assays. Four swab processing recovery methods were compared: heat, sonication, vortexing, and the Swab Extraction Tube System (SETS). These methods were evaluated using cotton, foam, polyester and rayon swabs spiked with six pathogenic strains of F. tularensis. Real-time PCR analysis using a multi-target 5'nuclease assay for F. tularensis showed that the use of the SETS method resulted in the best limit of detection when evaluated using multiple strains of F. tularensis. We demonstrated also that the efficiency of F. tularensis recovery from swab specimens was not equivalent for all swab processing methodologies and, thus, that this variable can affect real-time PCR assay sensitivity. The effectiveness of the SETS method was independent of the automated DNA extraction method and real-time PCR platforms used. In conclusion, diagnostic laboratories can now potentially incorporate the SETS method into specimen processing protocols for the rapid and efficient detection of F. tularensis by real-time PCR during laboratory bioterrorism-related investigations.

  17. Preliminary quality assessment of bovine colostrum

    Directory of Open Access Journals (Sweden)

    Alessandro Taranto

    2013-02-01

    Full Text Available Data on bovine colostrum quality are scarce or absent, although Commission Regulations No 1662/2006 and No 1663/2006 include colostrum in the context of chapters on milk. Thus the aim of the present work is to study some physical, chemical, hygiene and safety quality parameters of bovine colostrum samples collected from Sicily and Calabria dairy herds. Thirty individual samples were sampled after 2-3 days from partum. The laboratory tests included: pH, fat (FT, total nitrogen (TN, lactose (LTS and dry matter (NM percentage (Lactostar and somatic cell count (CCS (DeLaval cell counter DCC. Bacterial counts included: standard plate count (SPC, total psychrophilic aerobic count (PAC, total, fecal coliforms by MPN (Most Probable Number, sulphite-reducing bacteria (SR. Salmonella spp. was determined. Bacteriological examinations were performed according to the American Public Health Association (APHA methods, with some adjustements related to the requirements of the study. Statistical analysis of data was performed by Spearman’s rank correlation coefficient. The results showed a low variability of pH values and FT, TN and DM percentage between samples; whereas LTS trend was less noticeable. A significant negative correlation (P<0.01 was observed between pH, TN and LTS amount. The correlation between LTS and TN contents was highly significant (P<0.001. Highly significant and negative was the correlation (P<0.001 between DM, NT and LTS content. SPC mean values were 7.54 x106 CFU/mL; PAC mean values were also high (3.3x106 CFU/mL. Acceptable values of coagulase positive staphylococci were showed; 3 Staphylococcus aureus and 1 Staphylococcus epidermidis strains was isolated. Coagulase negative staphylococci counts were low. A high variability in the number of TC, as for FC was observed; bacterial loads were frequently fairly high. Salmonella spp. and SR bacteria were absent. It was assumed that bacteria from samples had a prevailing environmental origin

  18. Bovine milk glycome.

    Science.gov (United States)

    Tao, N; DePeters, E J; Freeman, S; German, J B; Grimm, R; Lebrilla, C B

    2008-10-01

    Bovine milk oligosaccharides have several potentially important biological activities including the prevention of pathogen binding to the intestinal epithelial and as nutrients for beneficial bacteria. It has been suggested that milk oligosaccharides are an important source of complex carbohydrates as supplements for the food and the pharmaceutical industries. However, only a small number of structures of bovine milk oligosaccharides (bMO) are known. There have been no systematic studies on bMO. High-performance mass spectrometry and separation methods are used to evaluate bMO, and nearly 40 oligosaccharides are present in bovine milk. Bovine milk oligosaccharides are composed of shorter oligomeric chains than are those in human milk. They are significantly more anionic with nearly 70%, measured abundances, being sialylated. Additionally, bMO are built not only on the lactose core (as are nearly all human milk oligosaccharides), but also on lactose amines. Sialic acid residues include both N-acetyl and N-glycolylneuraminic acid, although the former is significantly more abundant.

  19. Bovine milk exosome proteome

    Science.gov (United States)

    Exosomes are 40-100 nm membrane vesicles of endocytic origin and are found in blood, urine, amniotic fluid, bronchoalveolar lavage (BAL) fluid, as well as human and bovine milk. Exosomes are extracellular organelles important in intracellular communication/signaling, immune function, and biomarkers ...

  20. Intervet Symposium: bovine neosporosis

    NARCIS (Netherlands)

    Schetters, T.; Dubey, J.P.; Adrianarivo, A.; Frankena, K.; Romero, J.J.; Pérez, E.; Heuer, C.; Nicholson, C.; Russell, D.; Weston, J.

    2004-01-01

    This article summarises the most relevant data of presentations delivered at the 19th International Conference of the World Association for the Advancement of Veterinary Parasitology (WAAVP) held in New Orleans, LA, USA, from 10 to 14 August 2003) in a symposium session on bovine neosporosis. The sy

  1. Bovine Spongiform Encephalopathy

    Science.gov (United States)

    Bovine spongiform encephalopathy (BSE) is caused by a novel contagion, known to as a prion. Prions are proteins capable of converting a normal cellular protein into a prion, thereby propagating an infection. BSE is the first known prion zoonotic. As such it has attracted broad scientific and, to a r...

  2. [Research progress of fecal microbiota transplantation].

    Science.gov (United States)

    Dai, Ting; Tang, Tongyu

    2015-07-01

    Intestinal microbial ecosystem is the most complex and the largest micro-ecosystem of the mammals. The use of antibiotics can lead to a lot of major changes of the flora, making the intestinal flora damaged and impacted, even developing Clostridium difficile infection. Fecal microbiota transplantation (FMT) as a special organ transplant therapy, which can rebuild the intestinal flora, has raised the clinical concerns. It has been used in the refractory Clostridium difficile, inflammatory bowel disease, irritable bowel syndrome, chronic fatigue syndrome, and some non-intestinal diseases related to the metabolic disorders. But this method of treatment has not become a normal treatment, and many clinicians and patients can not accept it. This paper reviews relevant literature in terms of origin, indications, mechanism, production process, current situation and future research, and provide a reference for the clinical application of the treatment of fecal microbiota transplantation.

  3. Ethical aspects of Fecal Microbiota Transplantation (FMT).

    Science.gov (United States)

    Daloiso, V; Minacori, R; Refolo, P; Sacchini, D; Craxì, L; Gasbarrini, A; Spagnolo, A G

    2015-09-01

    The importance of human microbiota in preserving human organism healthy is nowadays well acknowledged. The alteration of the microbiota can be the consequence of a persistent use of antibiotics or immunosuppressive medications or abdominal irradiation or surgery, wrong diet, or can be caused by surgery or anatomical condition. These alterations can cause many infections and diseases that today can be treated with Fecal Microbiota Transplantation (FMT), also called Bacteriotherapy, that is the administration of a fecal solution from a donor into the intestinal tract of a recipient. Although to date, FMT appears to be safe and without serious adverse effects, there are some ethical issues that are worthy to be investigated. The aim of this article is to highlight these issues in order to give some notes for a better implementation of this particular clinical practice.

  4. The fecal microbiome in cats with diarrhea.

    Directory of Open Access Journals (Sweden)

    Jan S Suchodolski

    Full Text Available Recent studies have revealed that microbes play an important role in the pathogenesis of gastrointestinal (GI diseases in various animal species, but only limited data is available about the microbiome in cats with GI disease. The aim of this study was to evaluate the fecal microbiome in cats with diarrhea. Fecal samples were obtained from healthy cats (n = 21 and cats with acute (n = 19 or chronic diarrhea (n = 29 and analyzed by sequencing of 16S rRNA genes, and PICRUSt was used to predict the functional gene content of the microbiome. Linear discriminant analysis (LDA effect size (LEfSe revealed significant differences in bacterial groups between healthy cats and cats with diarrhea. The order Burkholderiales, the families Enterobacteriaceae, and the genera Streptococcus and Collinsella were significantly increased in diarrheic cats. In contrast the order Campylobacterales, the family Bacteroidaceae, and the genera Megamonas, Helicobacter, and Roseburia were significantly increased in healthy cats. Phylum Bacteroidetes was significantly decreased in cats with chronic diarrhea (>21 days duration, while the class Erysipelotrichi and the genus Lactobacillus were significantly decreased in cats with acute diarrhea. The observed changes in bacterial groups were accompanied by significant differences in functional gene contents: metabolism of fatty acids, biosynthesis of glycosphingolipids, metabolism of biotin, metabolism of tryptophan, and ascorbate and aldarate metabolism, were all significantly (p<0.001 altered in cats with diarrhea. In conclusion, significant differences in the fecal microbiomes between healthy cats and cats with diarrhea were identified. This dysbiosis was accompanied by changes in bacterial functional gene categories. Future studies are warranted to evaluate if these microbial changes correlate with changes in fecal concentrations of microbial metabolites in cats with diarrhea for the identification of potential diagnostic or

  5. Fecal microbiota transplantation for gastrointestinal diseases.

    Science.gov (United States)

    Matsuoka, Katsuyoshi; Mizuno, Shinta; Hayashi, Atsushi; Hisamatsu, Tadakazu; Naganuma, Makoto; Kanai, Takanori

    2014-01-01

    Fecal microbiota transplantation (FMT) is a treatment to restore the normal microbial composition of the gut by introducing fecal microbiota obtained from a healthy donor into a diseased individual. There has been a growing interest in the use of FMT as a treatment of various diseases including Clostridium difficile infection (CDI), inflammatory bowel disease, and irritable bowel syndrome. Despite the increasing application of FMT, there are no standard protocols. Many aspects of FMT procedures vary regarding donor selection, preparation of fecal materials, recipient preparation, and route of administration. FMT is most successful in treating recurrent CDI. A randomized controlled trial reported a success rate of approximaetly 90%. Ulcerative colitis (UC) is a potentially good indication for FMT, although limited evidence is available on the use of FMT for the treatment of UC. Only several small case series have been reported, and the results in terms of efficacy are inconsistent. FMT can also be used to treat diseases other than gastrointestinal disorders in which the gut microbiota is disturbed, e.g., cardiovascular diseases, autoimmune diseases, and metabolic disorders. There remain many unanswered questions with regard to FMT, and more research is required in this field.

  6. Therapeutic potential of fecal microbiota transplantation.

    Science.gov (United States)

    Smits, Loek P; Bouter, Kristien E C; de Vos, Willem M; Borody, Thomas J; Nieuwdorp, Max

    2013-11-01

    There has been growing interest in the use of fecal microbiota for the treatment of patients with chronic gastrointestinal infections and inflammatory bowel diseases. Lately, there has also been interest in its therapeutic potential for cardiometabolic, autoimmune, and other extraintestinal conditions that were not previously considered to be associated with the intestinal microbiota. Although it is not clear if changes in the microbiota cause these conditions, we review the most current and best methods for performing fecal microbiota transplantation and summarize clinical observations that have implicated the intestinal microbiota in various diseases. We also discuss case reports of fecal microbiota transplantations for different disorders, including Clostridium difficile infection, irritable bowel syndrome, inflammatory bowel diseases, insulin resistance, multiple sclerosis, and idiopathic thrombocytopenic purpura. There has been increasing focus on the interaction between the intestinal microbiome, obesity, and cardiometabolic diseases, and we explore these relationships and the potential roles of different microbial strains. We might someday be able to mine for intestinal bacterial strains that can be used in the diagnosis or treatment of these diseases.

  7. Fecal Molecular Markers for Colorectal Cancer Screening

    Directory of Open Access Journals (Sweden)

    Rani Kanthan

    2012-01-01

    Full Text Available Despite multiple screening techniques, including colonoscopy, flexible sigmoidoscopy, radiological imaging, and fecal occult blood testing, colorectal cancer remains a leading cause of death. As these techniques improve, their sensitivity to detect malignant lesions is increasing; however, detection of precursor lesions remains problematic and has generated a lack of general acceptance for their widespread usage. Early detection by an accurate, noninvasive, cost-effective, simple-to-use screening technique is central to decreasing the incidence and mortality of this disease. Recent advances in the development of molecular markers in faecal specimens are encouraging for its use as a screening tool. Genetic mutations and epigenetic alterations that result from the carcinogenetic process can be detected by coprocytobiology in the colonocytes exfoliated from the lesion into the fecal matter. These markers have shown promising sensitivity and specificity in the detection of both malignant and premalignant lesions and are gaining popularity as a noninvasive technique that is representative of the entire colon. In this paper, we summarize the genetic and epigenetic fecal molecular markers that have been identified as potential targets in the screening of colorectal cancer.

  8. Sample-based assessment of the microbial etiology of bovine necrotic vulvovaginitis.

    Science.gov (United States)

    Blum, S; Mazuz, M; Brenner, J; Friedgut, O; Stram, Y; Koren, O; Goshen, T; Elad, D

    2007-07-15

    A semiquantitative evaluation of potential bacterial pathogens was correlated to the severity of lesions during an outbreak of bovine necrotic vulvovaginitis (BNVV) on an Israeli dairy herd. Bacteriologic examination of 287 vaginal swabs from 104 post-calving heifers showed a highly significant correlation between Porphyromonas levii colony forming unit numbers and the clinical scores of the lesions, when assessed by an ordinal regression statistical model. No such correlation was found for the other bacteria included in the study. Nineteen samples taken for virological examinations resulted negative for bovine herpes viruses 1, 2, 4 and 5. Thus the results of this study substantiate the essential role of P. levii in the etiology of BNVV and indicate that BHV4 is not required as a predisposing factor to the syndrome.

  9. Rapid detection of Van genes in rectal swabs by real time PCR in Southern Brazil

    Directory of Open Access Journals (Sweden)

    Vlademir Cantarelli

    2011-10-01

    Full Text Available INTRODUCTION: Laboratory-based surveillance is an important component in the control of vancomycin resistant enterococci (VRE. METHODS: The study aimed to evaluate real-time polymerase chain reaction (RT-PCR (genes vanA-vanB for VRE detection on 115 swabs from patients included in a surveillance program. RESULTS: Sensitivity of RT-PCR was similar to primary culture (75% and 79.5%, respectively when compared to broth enriched culture, whereas specificity was 83.1%. CONCLUSIONS: RT-PCR provides same day results, however it showed low sensitivity for VRE detection.

  10. Alteration in Fecal Microbiota Associated with Grain-induced Subacute Ruminal Acidosis Challenge in Dairy Cows

    DEFF Research Database (Denmark)

    Danscher, Anne Mette; Derakshani, Hooman; Li, Shucong

    2014-01-01

    Introduction: High prevalence of subacute rumen acidosis (SARA) in dairy herds has been reported with large impact on production and welfare. The field diagnosis of SARA is currently unclear and primarily based on point measurements of rumen pH, which are inaccurate. Consequently, SARA cases in t...... of the disease. bovine, subacute ruminal acidosis, fecal microbiome, biological marker Host publication information...... in the field are often not detected. Thus, other and better markers of SARA are needed. The purpose of this research was to study the feces microbiome during SARA and assess the possibilities of using feces microbial markers as indicators of SARA. Methods: Six lactating, rumen cannulated, Danish Holstein cows...... value was estimated to R2: 87.0 and Q2: 73.2, respectively. Conclusion: Results confirm that intensive grain feeding changes the feces microbiome. The identification of specific taxa characteristic of SARA could provide new knowledge of the pathogenesis and might be useful as future biological markers...

  11. Isolation and identification of bovine Brucella isolates from Pakistan by biochemical tests and PCR.

    Science.gov (United States)

    Ali, Shahzad; Ali, Qurban; Melzer, Falk; Khan, Iahtasham; Akhter, Shamim; Neubauer, Heinrich; Jamal, Syed M

    2014-01-01

    Brucellosis is endemic in bovines in Pakistan. The Brucella species and biovars involved, however, are unknown. The objectives of the present study were to isolate and characterize brucellae from seropositive milk samples, aborted fetuses, and vaginal swabs of cattle and buffaloes which had recently aborted. The seropositive milk samples, aborted fetuses, and vaginal swabs of cattle and buffaloes were collected from the Potohar Plateau, Pakistan. Isolation of brucellae was done on modified Farrell's serum dextrose agar. Isolates were characterized by conventional biotyping methods, while molecular typing was done by genus (B4/B5) and species-specific (Brucella abortus, Brucella melitensis, Brucella ovis, and Brucella suis) polymerase chain reaction (PCR). A total of 30 isolates were recovered from milk (n = 5), aborted fetuses (n = 13), and vaginal swabs (n = 12). Most isolates were from cattle (56.7 %). All of them were identified as B. abortus biovar 1 based on conventional biotyping methods and genus and species-specific PCR. This preliminary study provides the first report on the prevalence of B. abortus biovar 1 in cattle and buffaloes in Pakistan.

  12. Evaluation of an autoclave resistant anatomic nose model for the testing of nasal swabs.

    Science.gov (United States)

    Bartolitius, Lennart; Frickmann, Hagen; Warnke, Philipp; Ottl, Peter; Podbielski, Andreas

    2014-09-01

    A nose model that allows for the comparison of different modes of sample acquisition as well as of nasal swab systems concerning their suitability to detect defined quantities of intranasal microorganisms, and further for training procedures of medical staff, was evaluated. Based on an imprint of a human nose, a model made of a silicone elastomer was formed. Autoclave stability was assessed. Using an inoculation suspension containing Staphylococcus aureus and Staphylococcus epidermidis, the model was compared with standardized glass plate inoculations. Effects of inoculation time, mode of sampling, and sample storage time were assessed. The model was stable to 20 autoclaving cycles. There were no differences regarding the optimum coverage from the nose and from glass plates. Optimum sampling time was 1 h after inoculation. Storage time after sampling was of minor relevance for the recovery. Rotating the swab around its own axis while circling the nasal cavity resulted in best sampling results. The suitability of the assessed nose model for the comparison of sampling strategies and systems was confirmed. Without disadvantages in comparison with sampling from standardized glass plates, the model allows for the assessment of a correct sampling technique due to its anatomically correct shape.

  13. Determination of Ampicillin Resistant Enterococci (ARE Isolated From Canine and Feline Rectal Swabs

    Directory of Open Access Journals (Sweden)

    Baran CELIK

    2017-01-01

    Full Text Available Enterococci species, which are normal inhabitants of the gut flora of healthy animals and human, began to be recognized as an important pathogen in both human and veterinary medicine due to the acquired resistance profiles. The aim of the study is to examine the diversity of ampicillin resistance enterococci (ARE species in cats and dogs, their antimicrobial susceptibility profiles and to determine some of the virulence related genes; ace, gelE, efaA, agg and esp. For this purpose, rectal swabs from companion animals were collected and processed for ampicillin resistant enterococci isolation. One hundred fifty seven swab samples (86 canine and 71 feline were examined. ARE were isolated from 18 canine and 18 feline samples. All isolates identified as E. faecium by PCR. Antimicrobial susceptibilities of the isolates were determined by disk diffusion method. The isolates were resistant to ampicillin, penicillin, tetracycline (100%, followed by rifampicin and erythromycin (97%, streptomycin (92%, gentamicin (81%, ciprofloxacin (61%, nitrofurantoin (19%. Only two of E. faecium isolates were resistant to vancomycin and one to chloramphenicol. Multidrug resistance (resistance ≥4 antimicrobials observed in all isolates. Virulence genes ace, agg and esp were not detected in any of the tested isolates. The efaA and gelE genes detection rates were, 13.8% and 11.1% respectively. The ARE isolation rate among pet animals was 22.9%. Screening of antimicrobial resistant enterococci among companion animals would be useful to detect any emerging antimicrobial resistance problem related with public health.

  14. Mycotic bovine nasal granuloma.

    Science.gov (United States)

    Conti Díaz, Ismael Alejandro; Vargas, Roberto; Apolo, Ada; Moraña, José Antonio; Pedrana, Graciela; Cardozo, Elena; Almeida, Edgardo

    2003-01-01

    A case of mycotic bovine nasal granuloma in a 10 year-old Jersey cow, produced by Drechslera halodes is presented. Histopathological sections showed abundant hyaline and pigmented extra and intracellular fungal structures together with a polymorphic cellular granuloma formed by neutrophils, lymphocytes, plasmocytes, histiocytes and giant cells of the Langhans type. It is the first case of mycotic bovine nasal granuloma recognized in Uruguay although this disease seems to be frequent according to the opinion of veterinarian specialists. Another similar clinical case also in a Jersey cow from the same dairy house with an intense cellular infiltrate rich in eosinophils without granulomatous image, together with extracellular hyaline and fuliginous fungal forms, is also referred for comparative purposes. Geotrichum sp. was isolated. The need of an early diagnosis and treatment of the disease is stressed.

  15. Complete Pelvic Floor Repair in Treating Fecal Incontinence

    OpenAIRE

    Lee, Patrick Y. H.; Steele, Scott R

    2005-01-01

    Fecal incontinence is associated with 20 to 40% of the patients with pelvic floor prolapse. Successful management of fecal incontinence requires not only an understanding of anorectal function but also a thorough understanding of pelvic floor anatomy and how pelvic floor prolapse affects fecal continence. Imaging techniques have been instrumental in visualizing pelvic floor prolapse and have helped correlate surgical findings. Stabilization of the perineal body appears to be a key component t...

  16. Profiling Living Bacteria Informs Preparation of Fecal Microbiota Transplantations

    OpenAIRE

    Chu, Nathaniel D.; Smith, Mark B.; Perrotta, Allison R.; Kassam, Zain; Alm, Eric J

    2017-01-01

    Fecal microbiota transplantation is a compelling treatment for recurrent Clostridium difficile infections, with potential applications against other diseases associated with changes in gut microbiota. But variability in fecal bacterial communities—believed to be the therapeutic agent—can complicate or undermine treatment efficacy. To understand the effects of transplant preparation methods on living fecal microbial communities, we applied a DNA-sequencing method (PMA-seq) that uses propidium ...

  17. Chapter A7. Section 7.2. Fecal Indicator Viruses

    Science.gov (United States)

    Bushon, Rebecca N.

    2003-01-01

    More than 100 types of human pathogenic viruses may be present in fecal-contaminated waters. Coliphages are used as indicators of virus-related fecal contamination and of the microbiological quality of waters. This report provides information on the equipment, sampling protocols, and laboratory methods that are in standard use by U.S. Geological Survey (USGS) personnel for the collection of data on fecal indicator viruses.

  18. Selenium in bovine spermatozoa.

    Science.gov (United States)

    Niemi, S M; Kuzan, F B; Senger, P L

    1981-05-01

    This study investigated the association of selenium with ejaculated bovine spermatozoa. Over 75% of the radioactive spermatozoa. Over 75% of the radioactive selenium-75 was released after 30 min of incubation in 2 X 10(-3) dithiothreitol. Of the selenium-75 released by dithiothreitol, 85% was associated with spermatozoal protein. Protein containing selenium-75 was found predominantly in a single band after polyacrylamide gel electrophoresis. Molecular weight was approximately 21,500 daltons.

  19. Infectious bovine keratoconjunctivitis (pinkeye)

    OpenAIRE

    Angelos, JA

    2015-01-01

    Copyright © 2015 Elsevier Inc. All rights reserved. As is the case for controlling other infectious livestock diseases, the most successful efforts to control infectious bovine keratoconjunctivitis (IBK) will include consideration of the host, the environment, herd management, and ongoing surveillance even after the immediate crisis has passed. Research over many years has led to the discovery of a variety of antibiotic treatments and antibiotic regimens that can be effective against IBK. The...

  20. Pilot study of participant-collected nasal swabs for acute respiratory infections in a low-income, urban population

    Directory of Open Access Journals (Sweden)

    Vargas CY

    2016-01-01

    Full Text Available Celibell Y Vargas,1 Liqun Wang,1 Yaritza Castellanos de Belliard,1 Maria Morban,1 Hilbania Diaz,1 Elaine L Larson,2,3 Philip LaRussa,1 Lisa Saiman,1,4 Melissa S Stockwell1,5,6 1Department of Pediatrics, 2School of Nursing, 3Department of Epidemiology, Mailman School of Public Health, Columbia University, 4Department of Infection Prevention and Control, NewYork-Presbyterian Hospital, 5Department of Population and Family Health, Mailman School of Public Health, Columbia University, 6NewYork-Presbyterian Hospital, New York, NY, USA Objective: To assess the feasibility and validity of unsupervised participant-collected nasal swabs to detect respiratory pathogens in a low-income, urban minority population. Methods: This project was conducted as part of an ongoing community-based surveillance study in New York City to identify viral etiologies of acute respiratory infection. In January 2014, following sample collection by trained research assistants, participants with acute respiratory infection from 30 households subsequently collected and returned a self-collected/parent-collected nasal swab via mail. Self/parental swabs corresponding with positive reverse transcription polymerase chain reaction primary research samples were analyzed. Results: Nearly all (96.8%, n=30/31 households agreed to participate; 100% reported returning the sample and 29 were received (median time: 8 days. Most (18; 62.1% of the primary research samples were positive. For eight influenza-positive research samples, seven (87.5% self-swabs were also positive. For ten other respiratory pathogen-positive research samples, eight (80.0% self-swabs were positive. Sensitivity of self-swabs for any respiratory pathogen was 83.3% and 87.5% for influenza, and specificity for both was 100%. There was no relationship between level of education and concordance of results between positive research samples and their matching participant swab. Conclusion: In this pilot study, self-swabbing

  1. Complete pelvic floor repair in treating fecal incontinence.

    Science.gov (United States)

    Lee, Patrick Y H; Steele, Scott R

    2005-02-01

    Fecal incontinence is associated with 20 to 40% of the patients with pelvic floor prolapse. Successful management of fecal incontinence requires not only an understanding of anorectal function but also a thorough understanding of pelvic floor anatomy and how pelvic floor prolapse affects fecal continence. Imaging techniques have been instrumental in visualizing pelvic floor prolapse and have helped correlate surgical findings. Stabilization of the perineal body appears to be a key component to the success of pelvic floor repair and fecal continence, but the optimal repair is far from being established.

  2. Evaluation of Three Swabbing Devices for Detection of Listeria monocytogenes on Different Types of Food Contact Surfaces

    Directory of Open Access Journals (Sweden)

    Evy Lahou

    2014-01-01

    Full Text Available Listeria monocytogenes can adhere to different types of food contact surfaces within a food processing environment. Therefore, environmental sampling devices should be capable of detecting unacceptable contamination. In this study, a sponge-stick, foam spatula and an environmental swab were evaluated on their ability to detect low concentrations of L. monocytogenes on different types of food contact surfaces. A cocktail of four L. monocytogenes serotypes was inoculated with a concentration of 100 CFU/250 cm2 onto stainless steel (SS, high density polyethylene (HDPE and rubber surfaces in a 250 cm2 area. Immediately after inoculation and after 1 h exposure, the surfaces were swabbed with the different swabbing devices. The results of the study show only minor differences in the ability of the swabbing devices to detect L. monocytogenes. All devices were capable to detect the contamination immediately after inoculation. However, when the surfaces were allowed to air-dry for 1 h, L. monocytogenes was undetected in 11.1% of the samples (n = 27 with the sponge stick, in 7.4% of the samples (n = 27 with the foam spatula and in 3.7% of the samples (n = 27 with the environmental swab, especially on SS surfaces. The detection ability of the different devices for L. monocytogenes can be concluded to be rather high on different types of food contact surfaces.

  3. Stability of bovine coronavirus on lettuce surfaces under household refrigeration conditions.

    Science.gov (United States)

    Mullis, Lisa; Saif, Linda J; Zhang, Yongbin; Zhang, Xuming; Azevedo, Marli S P

    2012-05-01

    Fecal suspensions with an aerosol route of transmission were responsible for a cluster of severe acute respiratory syndrome (SARS) cases in 2003 in Hong Kong. Based on that event, the World Health Organization recommended that research be implemented to define modes of transmission of SARS coronavirus through sewage, feces, food and water. Environmental studies have shown that animal coronaviruses remain infectious in water and sewage for up to a year depending on the temperature and humidity. In this study, we examined coronavirus stability on lettuce surfaces. A cell culture adapted bovine coronavirus, diluted in growth media or in bovine fecal suspensions to simulate fecal contamination was used to spike romaine lettuce. qRT-PCR detected viral RNA copy number ranging from 6.6 × 10⁴ to 1.7 × 10⁶ throughout the experimental period of 30 days. Whereas infectious viruses were detected for at least 14 days, the amount of infectious virus varied, depending upon the diluent used for spiking the lettuce. UV and confocal microscopic observation indicated attachment of residual labeled virions to the lettuce surface after the elution procedure, suggesting that rates of inactivation or detection of the virus may be underestimated. Thus, it is possible that contaminated vegetables may be potential vehicles for coronavirus zoonotic transmission to humans.

  4. Comparison of different diagnostic techniques for the detection of cryptosporidiosis in bovines

    Directory of Open Access Journals (Sweden)

    H. K. M. Rekha

    2016-02-01

    Full Text Available Aim: Aim of the present study was to compare different methods, viz., Sheather’s sugar flotation (SSF, Ziehl-Neelsen (ZN, Kinyoun’s acid-fast method (KAF, safranin-methylene blue staining (SMB, and negative staining techniques such as nigrosin staining, light green staining, and malachite green staining for the detection of Cryptosporidium spp. oocysts in bovines. Materials and Methods: A total of 455 fecal samples from bovines were collected from private, government farms and from the clinical cases presented to Department of Medicine, Veterinary College, Bengaluru. They were subjected for SSF, ZN, KAF, SMB and negative staining methods. Results: Out of 455 animal fecal samples screened 5.71% were found positive for Cryptosporidium spp. oocysts. The species were identified as Cryptosporidium parvum in calves and Cryptosporidium andersoni in adults based on the morphological characterization and micrometry of the oocysts. Conclusions: Of all the techniques, fecal flotation with sheather’s was found to be more specific and sensitive method for the detection of Cryptosporidium spp. oocysts. Among the conventional staining methods, the SMB gives better differentiation between oocysts and yeast. Among the three negative staining methods, malachite green was found sensitive over the other methods.

  5. Diagnostic imaging in bovine orthopedics.

    Science.gov (United States)

    Kofler, Johann; Geissbühler, Urs; Steiner, Adrian

    2014-03-01

    Although a radiographic unit is not standard equipment for bovine practitioners in hospital or field situations, ultrasound machines with 7.5-MHz linear transducers have been used in bovine reproduction for many years, and are eminently suitable for evaluation of orthopedic disorders. The goal of this article is to encourage veterinarians to use radiology and ultrasonography for the evaluation of bovine orthopedic disorders. These diagnostic imaging techniques improve the likelihood of a definitive diagnosis in every bovine patient but especially in highly valuable cattle, whose owners demand increasingly more diagnostic and surgical interventions that require high-level specialized techniques.

  6. Culture-independent qunatification of Salmonella enterica in carcass gauze swabs by flotation prior to real-time PCR

    DEFF Research Database (Denmark)

    Löfström, Charlotta; Schelin, Jenny; Norling, Börje;

    2010-01-01

    , for culture-independent quantification of intact Salmonella in pig carcass gauze swabs (100 cm2) prior to quantitative PCR (qPCR). A novel approach was investigated, excluding the homogenization step prior to flotation, to improve the detection limit and speed up the quantification procedure. The buoyant....... The method allowed accurate quantification from 4.4×102 to at least 2.2×107 CFU Salmonella per swab sample using qPCR (without preceding DNA extraction) or selective plating on xylose lysine deoxycholate agar. Samples with 50 CFU could be detected occasionally but fell outside the linear range...... of the standard curve. The swab samples showed a broad biological diversity; for seven samples not inoculated with Salmonella, the microbial background flora (BGF) was determined to 5.0 ± 2.2 log CFU/ml sample withdrawn after flotation. It was determined that the proceeding PCR step was inhibited by BGF...

  7. Characterizing relationships among fecal indicator bacteria ...

    Science.gov (United States)

    Bed sediments of streams and rivers may store high concentrations of fecal indicator bacteria (FIB) and pathogens. Due to resuspension events, these contaminants can be mobilized into the water column and affect overall water quality. Other bacterial indicators such as microbial source tracking (MST) markers, developed to determine potential sources of fecal contamination, can also be resuspended from bed sediments. The primary objective of this study was to predict occurrence of waterborne pathogens in water and streambed sediments using a simple statistical model that includes traditionally measured FIB, environmental parameters and source allocation, using MST markers as predictor variables. Synoptic sampling events were conducted during baseflow conditions downstream from agricultural (AG), forested (FORS), and wastewater pollution control plant (WPCP) land uses. Concentrations of FIB and MST markers were measured in water and sediments, along with occurrences of the enteric pathogens Campylobacter, Listeria and Salmonella, and the virulence gene that carries Shiga toxin, stx2. Pathogens were detected in water more often than in underlying sediments. Shiga toxin was significantly related to land use, with concentrations of the ruminant marker selected as an independent variable that could correctly classify 76% and 64% of observed Shiga toxin occurrences in water and sediment, respectively. FIB concentrations and water quality parameters were also selected a

  8. Protocol for Real-Time PCR Identification of Anthrax Spores from Nasal Swabs after Broth Enrichment

    Science.gov (United States)

    Oggioni, Marco R.; Meacci, Francesca; Carattoli, Alessandra; Ciervo, Alessandra; Orru, Germano; Cassone, Antonio; Pozzi, Gianni

    2002-01-01

    A mass-screening protocol for the diagnosis of anthrax from nasal swabs based on an enrichment step in liquid medium was devised. Incubation for growth was performed in autoclavable vials and racks which allow real-time PCR analysis of sterilized cultures. A dual-color PCR was set up with primers and probes for the chromosomal marker rpoB and the plasmid marker lef. Specific primer and probe sets were designed for the differentiation of Bacillus anthracis from B. cereus and for the differentiation of the Sterne vaccine strain from field isolates and the Ames strain, which was used in the recent anthrax bioterrorist attack. The present protocol thus combines the high specificity and sensitivity of real-time PCR with excellent biosafety and the low hands-on time necessary for the processing of large numbers of samples, which is extremely important during control programs involving the processing of large numbers of samples. PMID:12409358

  9. Molecular detection and genotyping of Acanthamoeba spp. among stray dogs using conjunctival swab sampling.

    Science.gov (United States)

    Karakuş, Mehmet; Aykur, Mehmet; Özbel, Yusuf; Töz, Seray; Dağcı, Hande

    2016-12-01

    Acanthamoeba is one of the most common free-living amoebas (FLA) that present in environment. In humans, Acanthamoeba can cause an infection of the eye termed Acanthamoeba keratitis, which mostly occurs in contact lens wearers. In the present study, we aimed to screen the presence of Acanthamoeba DNA in stray dogs using previously collected conjunctival swab samples in a hyper-endemic area for canine leishmaniasis. Totally, 184 dogs were included in the study and 27 of them (14.6%) were found positive for Acanthamoeba according to the 18s rRNA gene sequencing. Two different genotypes (T4 and T5) were identified and T5 was firstly reported in Turkey in the present study. Statistical analysis was performed and no correlation was found between Leishmania and Acanthamoeba positivity (PAcanthamoeba among stray dogs. Further studies are necessary to reveal the infection status and genotypes among dogs and its possible correlation with leishmaniasis.

  10. ISOLATION, IDENTIFICATION, PATHOTYPING AND ANTIBIOGRAM OF ESCHERICHIA COLI FROM RECTAL SWAB OF PET DOGS AND CATS

    Directory of Open Access Journals (Sweden)

    S. Das

    2012-07-01

    Full Text Available Two hundred seventy two rectal swabs were examined from diarrhoeic and nondiarrhoeic pet dogs and cats. Out of 240 samples from dogs, 131 (54.58% and out of 32 samples from cats, 15 (46.87% were positive for E. coli by cultural characteristic, gram staining, motility,biochemical reactions and sugar fermentation tests. Out of 146 total positive isolates, only 12 isolates were pathogenic. Out of 12 pathogenic isolates of E. coli 6 isolates were O group non- typable and rest 6 E. coli strains were O25, O86a, O44 and O1 from dogs and O36 and O8 from cats. Out of 12 isolates 9 were sensitive to ceftriaxone, 8 were sensitive to ciprofloxacin and gentamicin, 4 were sensitive to amikacin, neomycin and norfloxacin, 2 were to Co-trimoxazole and 1 was sensitive to lomefloxacin. None of the isolate was sensitive to amoxyclav & cephotaxime.

  11. Numerical model for surge and swab pressures on wells with cross-section variation

    Energy Technology Data Exchange (ETDEWEB)

    Fedevjcyk, Joao Victor; Junqueira, Silvio Luiz de Mello; Negrao, Cezar Otaviano Ribeiro [UTFPR - Federal University of Technology - Parana - Curitiba, PR (Brazil)], e-mails: silvio@utfpr.edu.br, negrao@utfpr.edu.br

    2010-07-01

    Drilling is one of the most complex steps in petroleum exploration. The process is accomplished by rotating a drill bit to compress the rock formation. During drilling, a fluid is pumped into the well to lubricate and cool down the drill bit, to clean up the well, to avoid the formation fluid influx to the well and also to stabilize the borehole walls. Fluid circulation, however, can be interrupted for maintenance reasons and the drill pipe can be moved to remove the drill bit. The downward or upward movement of the drill pipe displaces the fluid within the well causing either under pressure (swab) or over pressure (surge), respectively. If the pressure at the well bore overcomes the formation fracture pressure, a loss of circulation can take place. On the other way round, the upward movement may reduce the pressure below the pore pressure and an inflow of fluid to the well (kick) can occur. An uncontrolled kick may cause a blowout with serious damages. The transient flow induced by the axial movement of the drill pipe is responsible for the pressure changes at the well bore. Nevertheless, the well bore cross section variation may modify the pressure change within the pipe. In this paper, the effects of diameter variation of the drilling well on the surge and swab pressures are investigated. The equations that represent the phenomenon (mass and momentum conservation) are discretized by the finite volume method. Despite its non-Newtonian properties, the fluid is considered Newtonian in this first work. The drill pipe is considered closed and the flow is assumed as single-phased, one-dimensional, isothermal, laminar, compressible and transient. A sensitivity analysis of the flow parameters is carried out. The cross-section changes cause the reflection of the pressure wave, and consequently pressure oscillations. (author)

  12. Reduced fecal sterol excretion in subjects with familial hypoalphalipoproteinemia

    NARCIS (Netherlands)

    El Harchaoui, Karim; Franssen, Remco; Hovingh, G. Kees; Bisoendial, Radjesh J.; Stellaard, Frans; Kuipers, Folkert; Kastelein, John J. P.; Kuivenhoven, Jan Albert; Stroes, Erik S. G.; Groen, Albert K.

    2009-01-01

    BACKGROUND: Fecal bile acid and neutral sterol excretion are the obligate endpoints of the reverse cholesterol transport pathway (RCT). In studies in mice, no evidence was found for a relation between HDL-cholesterol (HDL-c) levels and fecal sterol excretion. In this study, we have evaluated this re

  13. Bovine coronavirus hemagglutinin protein.

    Science.gov (United States)

    King, B; Potts, B J; Brian, D A

    1985-02-01

    Treatment of purified bovine coronavirus (Mebus strain) with pronase destroyed the integrity of virion surface glycoproteins gp140, gp120, gp100, reduced the amount of gp26 and destroyed the hemagglutinating activity of the virus. Bromelain, on the other hand, destroyed the integrity of gp120, gp100 and gp26 but failed to remove gp140 and failed to destroy viral hemagglutinating activity. These experiments suggest that gp140 is the virion hemagglutinin. Immunoblotting studies using monospecific antiserum demonstrate that gp140 is a disulfide-linked dimeric structure reducible to monomers of 65 kDa.

  14. Infectious bovine keratoconjunctivitis (pinkeye).

    Science.gov (United States)

    Angelos, John A

    2015-03-01

    As is the case for controlling other infectious livestock diseases, the most successful efforts to control infectious bovine keratoconjunctivitis (IBK) will include consideration of the host, the environment, herd management, and ongoing surveillance even after the immediate crisis has passed. Research over many years has led to the discovery of a variety of antibiotic treatments and antibiotic regimens that can be effective against IBK. The discoveries of Mor bovoculi and reports of IBK associated with Mycoplasma spp without concurrent Mor bovis or Mor bovoculi have raised new questions into the roles that other organisms may play in IBK pathogenesis.

  15. Proteomic Analysis of Bovine Nucleolus

    Institute of Scientific and Technical Information of China (English)

    Amrutlal K.Patel; Doug Olson; Suresh K. Tikoo

    2010-01-01

    Nucleolus is the most prominent subnuclear structure, which performs a wide variety of functions in the eu-karyotic cellular processes. In order to understand the structural and functional role of the nucleoli in bovine cells,we analyzed the proteomie composition of the bovine nueleoli. The nucleoli were isolated from Madin Darby bo-vine kidney cells and subjected to proteomie analysis by LC-MS/MS after fractionation by SDS-PAGE and strongcation exchange chromatography. Analysis of the data using the Mascot database search and the GPM databasesearch identified 311 proteins in the bovine nucleoli, which contained 22 proteins previously not identified in theproteomic analysis of human nucleoli. Analysis of the identified proteins using the GoMiner software suggestedthat the bovine nueleoli contained proteins involved in ribosomal biogenesis, cell cycle control, transcriptional,translational and post-translational regulation, transport, and structural organization.

  16. Fecal microbial determinants of fecal and systemic estrogens and estrogen metabolites: a cross-sectional study

    Directory of Open Access Journals (Sweden)

    Flores Roberto

    2012-12-01

    Full Text Available Abstract Background High systemic estrogen levels contribute to breast cancer risk for postmenopausal women, whereas low levels contribute to osteoporosis risk. Except for obesity, determinants of non-ovarian systemic estrogen levels are undefined. We sought to identify members and functions of the intestinal microbial community associated with estrogen levels via enterohepatic recirculation. Methods Fifty-one epidemiologists at the National Institutes of Health, including 25 men, 7 postmenopausal women, and 19 premenopausal women, provided urine and aliquots of feces, using methods proven to yield accurate and reproducible results. Estradiol, estrone, 13 estrogen metabolites (EM, and their sum (total estrogens were quantified in urine and feces by liquid chromatography/tandem mass spectrometry. In feces, β-glucuronidase and β-glucosidase activities were determined by realtime kinetics, and microbiome diversity and taxonomy were estimated by pyrosequencing 16S rRNA amplicons. Pearson correlations were computed for each loge estrogen level, loge enzymatic activity level, and microbiome alpha diversity estimate. For the 55 taxa with mean relative abundance of at least 0.1%, ordinal levels were created [zero, low (below median of detected sequences, high] and compared to loge estrogens, β-glucuronidase and β-glucosidase enzymatic activity levels by linear regression. Significance was based on two-sided tests with α=0.05. Results In men and postmenopausal women, levels of total urinary estrogens (as well as most individual EM were very strongly and directly associated with all measures of fecal microbiome richness and alpha diversity (R≥0.50, P≤0.003. These non-ovarian systemic estrogens also were strongly and significantly associated with fecal Clostridia taxa, including non-Clostridiales and three genera in the Ruminococcaceae family (R=0.57−0.70, P=0.03−0.002. Estrone, but not other EM, in urine correlated significantly with

  17. Fecal pollution source tracking toolbox for identification, evaluation and characterization of fecal contamination in receiving urban surface waters and groundwater.

    Science.gov (United States)

    Tran, Ngoc Han; Gin, Karina Yew-Hoong; Ngo, Huu Hao

    2015-12-15

    The quality of surface waters/groundwater of a geographical region can be affected by anthropogenic activities, land use patterns and fecal pollution sources from humans and animals. Therefore, the development of an efficient fecal pollution source tracking toolbox for identifying the origin of the fecal pollution sources in surface waters/groundwater is especially helpful for improving management efforts and remediation actions of water resources in a more cost-effective and efficient manner. This review summarizes the updated knowledge on the use of fecal pollution source tracking markers for detecting, evaluating and characterizing fecal pollution sources in receiving surface waters and groundwater. The suitability of using chemical markers (i.e. fecal sterols, fluorescent whitening agents, pharmaceuticals and personal care products, and artificial sweeteners) and/or microbial markers (e.g. F+RNA coliphages, enteric viruses, and host-specific anaerobic bacterial 16S rDNA genetic markers) for tracking fecal pollution sources in receiving water bodies is discussed. In addition, this review also provides a comprehensive approach, which is based on the detection ratios (DR), detection frequencies (DF), and fate of potential microbial and chemical markers. DR and DF are considered as the key criteria for selecting appropriate markers for identifying and evaluating the impacts of fecal contamination in surface waters/groundwater.

  18. Can mailed swab samples be dry-shipped for the detection of Chlamydia trachomatis, Neisseria gonorrhoeae, and Trichomonas vaginalis by nucleic acid amplification tests?

    Science.gov (United States)

    Gaydos, Charlotte A.; Farshy, Carol; Barnes, Mathilda; Quinn, Nicole; Agreda, Patricia; Rivers, Charles A.; Schwebke, Jane; Papp, John

    2012-01-01

    Background Dry-shipped and mailed vaginal swabs collected at home have been used in research studies for the detection of C. trachomatis (CT), N. gonorrhoeae (GC), and Trichomonas vaginalis (TV) by nucleic acid amplification tests (NAATs) in screening programs. A verification study was performed to compare the limit of detection of CT, GC, and TV on swabs that were dry-shipped to paired swabs that were wet-shipped in transport media through the U.S. mail. Methods The Centers for Disease Control and Prevention prepared inocula in sterile water to mock simulated urogenital swabs with high to low concentrations of CT and GC. Replicate swabs were inoculated with 100µl of dilutions, were dry transported or placed into commercial transport media (“wet”) for mailing for NAAT testing. The University of Alabama prepared replicate concentrations of TV, which were similarly shipped and tested by NAAT. Results All paired dry and wet swabs were detectable for CT. For GC, all paired dry and wet swabs were detectable for GC at concentrations ≥103. At 102 and 10 CFU/ml, the 10 replicate GC results were variably positive. For TV, wet and dry shipped concentrations > 102 TV/ml tested positive, while results at 10 TV/ml were negative for dry swabs. Holding replicate dry swabs at 55°C 5 days before testing did not affect results. Conclusion NAATs were able to detect CT, GC, and TV on dry transported swabs. Using NAATs for testing home-collected, urogenital swabs mailed in a dry state to a laboratory may be useful for outreach screening programs. PMID:22578934

  19. Viral infections and bovine mastitis: a review

    NARCIS (Netherlands)

    Wellenberg, G.J.; Poel, van der W.H.M.; Oirschot, van J.T.

    2002-01-01

    This review deals with the role of viruses in the aetiology of bovine mastitis. Bovine herpesvirus 1, bovine herpesvirus 4, foot-and-mouth disease virus, and parainfluenza 3 virus have been isolated from milk from cows with clinical mastitis. Intramammary inoculations of bovine herpesvirus 1 or para

  20. [Potential Applicability of Fecal NIRs: A Review].

    Science.gov (United States)

    Yan, Xu; Du, Zhou-he; Bai, Shi-qie; Zuo, Yan-chun; Zhou, Xiao-kang; Kou, Jing; Yan, Jia-jun; Zhang, Jian-bo; Li, Ping; You, Ming-hong; Zhang, Yu; Li, Da-xu; Zhang, Chang-bing; Zhang, Jin

    2015-12-01

    Near-infrared reflectance spectroscopy (NIRS) is an inexpensive, rapid, environment-friendly and non-invasive analytical technique that has been extensively applied in the analysis of the dietary attributes and the animal products. Acquisition of dietary attributes is essential for nutritional diagnoses to provide animals with reasonable diet. Traditionally, the calibration equations for the prediction of dietary attributes (e. g. crude protein) are developed from feed NIR spectra and the results of conventional chemical analysis (i. e. reference data). It is difficult to obtain the NIR spectra of forages consumed by grazing animals, so the method of this calibration is inappropriate for free-grazing herbivores. Feces, as the animal's metabolites, contain the information about both the animal's diet and the animal itself. Recently, Fecal-NIRS (F. NIRS) has been directly used to monitor diet information (botanical composition, chemical composition and digestibility), based on correlation between reference data and fecal NIR profile. Subsequently, some additional application (such as sex and species discrimination, reproductive and parasite status) of F. NIRS also is outlined. In the last, application of NIRS in animal manure is summarized. NIRS was shown to be an alternative to conventional wet chemical methods for analyzing some nutrient concentrations in animal manure rapidly. Overall, this paper proves that F. NIRS is a rapid and valid tool for the determination of the dietary attributes and of the physiological status of animal, although more efforts need to be done to improve the accuracy of the F. NIRS technique. Several researchers in English have reviewed the applications of F. NIRS. In China, however, there is a paucity of research and application regarding F. NIRS. We expect that this paper in Chinese will be helpful to the development of F. NIRS in China. At the same time, we propose NIRS as a simple and rapid analytical method for predicting the main

  1. Genomic Load from Sputum Samples and Nasopharyngeal Swabs for Diagnosis of Pneumococcal Pneumonia in HIV-Infected Adults

    Science.gov (United States)

    Madhi, Shabir A.; Adrian, Peter V.; Telles, Jean-Noel; Paranhos-Baccalà, Glaucia; Klugman, Keith P.

    2014-01-01

    Quantitative lytA real-time PCR (rtPCR) results from nasopharyngeal (NP) swabs distinguish community-acquired pneumococcal pneumonia (CAP) from asymptomatic colonization. The use of an optimized cutoff value improved pneumococcal etiology determination compared to that of traditional diagnostic methods. Here, we compare the utility of lytA rtPCR from induced sputum and from NP swabs. Pneumococcus was considered the cause of CAP in HIV-infected South African adults if blood culture, induced-sputum culture or Gram stain, urine antigen test, or whole-blood lytA rtPCR revealed pneumococcus or if lytA rtPCR from NP swabs gave a result of >8,000 copies/ml. lytA rtPCR was also performed on induced sputum. Pneumococcus was detected by lytA rtPCR from sputum in 149 (67.1%) of 222 patients with available induced sputum, whereas the results of either Gram stain or culture of sputum were positive in 105 of 229 patients (45.9%; P < 0.001). The mean copy numbers from sputum were higher when the sputum cultures were positive than when the sputum cultures were negative (7.9 versus 5.6 log10 copies/ml; P < 0.001). Against the composite diagnostic standard, a cutoff value of 10,000 copies/ml for good-quality sputum lytA rtPCR had a sensitivity of 78.1% and a specificity of 80.0%. This cutoff value performed similarly to the previously identified cutoff value of 8,000 copies/ml for NP swab lytA rtPCR (area under the curve receiver operating characteristic [AUC-ROC], 80.4% for sputum of any quality versus 79.6% for NP swabs). The AUC-ROC for good-quality sputum was 83.2%. Overall, lytA rtPCR performs similarly well on induced sputum as on NP swabs for most patients but performs slightly better if good-quality sputum can be obtained. Due to the ease of specimen collection, NP swabs may be preferable for the diagnosis of pneumococcal pneumonia. PMID:25253798

  2. Estimation of nasal shedding and seroprevalence of organisms known to be associated with bovine respiratory disease in Australian live export cattle.

    Science.gov (United States)

    Moore, S Jo; O'Dea, Mark A; Perkins, Nigel; O'Hara, Amanda J

    2015-01-01

    The prevalence of organisms known to be associated with bovine respiratory disease (BRD) was investigated in cattle prior to export. A quantitative reverse transcription polymerase chain reaction assay was used to detect nucleic acids from the following viruses and bacteria in nasal swab samples: Bovine coronavirus (BoCV; Betacoronavirus 1), Bovine herpesvirus 1 (BoHV-1), Bovine viral diarrhea virus 1 (BVDV-1), Bovine respiratory syncytial virus (BRSV), Bovine parainfluenza virus 3 (BPIV-3), Histophilus somni, Mycoplasma bovis, Mannheimia haemolytica, and Pasteurella multocida. Between 2010 and 2012, nasal swabs were collected from 1,484 apparently healthy cattle destined for export to the Middle East and Russian Federation. In addition, whole blood samples from 334 animals were tested for antibodies to BoHV-1, BRSV, BVDV-1, and BPIV-3 using enzyme-linked immunosorbent assay. The nasal prevalence of BoCV at the individual animal level was 40.1%. The nasal and seroprevalence of BoHV-1, BRSV, BVDV-1, and BPIV-3 was 1.0% and 39%, 1.2% and 46%, 3.0% and 56%, and 1.4% and 87%, respectively. The nasal prevalence of H. somni, M. bovis, M. haemolytica, and P. multocida was 42%, 4.8%, 13.4%, and 26%, respectively. Significant differences in nasal and seroprevalence were detected between groups of animals from different geographical locations. The results of the current study provide baseline data on the prevalence of organisms associated with BRD in Australian live export cattle in the preassembly period. This data could be used to develop strategies for BRD prevention and control prior to loading.

  3. Consensus of microbiology reporting of ear swab results to primary care clinicians in patients with otitis externa.

    Science.gov (United States)

    Geyer, M; Howell-Jones, R; Cunningham, R; McNulty, C

    2011-01-01

    Otitis externa is a ubiquitous inflammatory disease; although it arises most commonly from an infection, there is no consensus in the UK for the reporting of ear swab culture results. This study aims to review current microbiology laboratory reporting of ear swab specimens to primary care and reach an evidence-based consensus for a reporting policy. Fifty consecutive ear swab reports were reviewed from each of 12 laboratories in the South West region to determine and discuss reporting practice. The Health Protection Agency (HPA) GP Microbiology Laboratory Use Group reviewed the underlying evidence and worked towards a consensus of expert microbiology opinion for laboratory reporting of ear swab results using a modified version of the Delphi technique. A total of 487 reports from primary care were reviewed (54% female; 46% male). Cultures most commonly yielded Pseudomonas species (36%), Staphylococcus species (21%), Streptococcus species (15%) and fungi (11%). Five reporting policies were agreed: Policy 1: Common pathogens such as group A beta-haemolytic streptococci, Streptococcus pneumoniae, Staphylococcus aureus - Always reported by name with antibiotic susceptibilities. Policy 2: Pseudomonas species - Always reported, but antibiotic susceptibilities only reported in severe disease. Policy 3: Aspergillus, Candida, coliforms and Proteus species, as well as non-group A streptococci and anaerobes - Only reported if moderate numbers of colonies and it is the predominant organism present; if appropriate report antibiotic susceptibilities. Policy 4: Coagulase-negative staphylococci, diphtheroids and enterococci - Not reported by name; generic terms used and antibiotic susceptibilities not reported. Policy 5: When antibiotic susceptibilities reported these must include susceptibility to a topical antibiotic. It is suggested that laboratories should consider adopting this evidence-based reporting consensus for ear swab culture results from primary care patients with

  4. Profiling Living Bacteria Informs Preparation of Fecal Microbiota Transplantations

    Science.gov (United States)

    Chu, Nathaniel D.; Smith, Mark B.; Perrotta, Allison R.; Kassam, Zain; Alm, Eric J.

    2017-01-01

    Fecal microbiota transplantation is a compelling treatment for recurrent Clostridium difficile infections, with potential applications against other diseases associated with changes in gut microbiota. But variability in fecal bacterial communities—believed to be the therapeutic agent—can complicate or undermine treatment efficacy. To understand the effects of transplant preparation methods on living fecal microbial communities, we applied a DNA-sequencing method (PMA-seq) that uses propidium monoazide (PMA) to differentiate between living and dead fecal microbes, and we created an analysis pipeline to identify individual bacteria that change in abundance between samples. We found that oxygen exposure degraded fecal bacterial communities, whereas freeze-thaw cycles and lag time between donor defecation and transplant preparation had much smaller effects. Notably, the abundance of Faecalibacterium prausnitzii—an anti-inflammatory commensal bacterium whose absence is linked to inflammatory bowel disease—decreased with oxygen exposure. Our results indicate that some current practices for preparing microbiota transplant material adversely affect living fecal microbial content and highlight PMA-seq as a valuable tool to inform best practices and evaluate the suitability of clinical fecal material. PMID:28125667

  5. Fecal corticoid monitoring in whooping cranes (Grus americana) undergoing reintroduction

    Science.gov (United States)

    Hartup, Barry K.; Olsen, Glenn H.; Czekala, Nancy M.

    2005-01-01

    We used radioimmunoassay to determine fecal corticoid concentrations and assess potential stress in 10 endangered whooping cranes (Grus americana) undergoing reintroduction to the wild. Fecal samples were collected shortly after hatching at a captive facility in Maryland, during field training in Wisconsin, and throughout a human-led migration to Florida. After a 14-day decline following hatching, fecal corticoid concentrations stabilized at baseline levels for the duration of the captive period, despite exposure to potentially stressful stimuli. Shipment of the cranes to the field training site was correlated with an eight- to 34-fold increase in fecal corticoid concentrations, which returned to baseline levels within 1 week. Increases were positively correlated with age but not body weight at the time of shipping. Fecal corticoid concentrations during the training period increased slightly and exhibited greater variation than levels observed at the captive facility, but were well within expected norms based on previous studies. Fecal corticoid concentrations increased twofold following premigration physical examinations and placement of radiotransmitters, and persisted for up to 4 days before they returned to baseline levels. Though fecal corticoid concentrations and variation during the migration period were similar to training levels, there was an overall decline in fecal corticoid concentrations during the artificial migration. Acute stressors, such as capture, restraint, and severe storms, were associated with stress responses by the cranes that varied in accordance with lasting physical or psychological stimuli. The overall reintroduction process of costume-rearing, ultralight aircraft habituation, training, and artificial migration was not associated with elevations in fecal corticoid concentrations suggestive of chronic stress.

  6. Study of criteria influencing the success rate of DNA swabs in operational conditions: A contribution to an evidence-based approach to crime scene investigation and triage.

    Science.gov (United States)

    Baechler, S

    2016-01-01

    DNA is nowadays swabbed routinely to investigate serious and volume crimes, but research remains scarce when it comes to determining the criteria that may impact the success rate of DNA swabs taken on different surfaces and situations. To investigate these criteria in fully operational conditions, DNA analysis results of 4772 swabs taken by the forensic unit of a police department in Western Switzerland over a 2.5-year period (2012-2014) in volume crime cases were considered. A representative and random sample of 1236 swab analyses was extensively examined and codified, describing several criteria such as whether the swabbing was performed at the scene or in the lab, the zone of the scene where it was performed, the kind of object or surface that was swabbed, whether the target specimen was a touch surface or a biological fluid, and whether the swab targeted a single surface or combined different surfaces. The impact of each criterion and of their combination was assessed in regard to the success rate of DNA analysis, measured through the quality of the resulting profile, and whether the profile resulted in a hit in the national database or not. Results show that some situations-such as swabs taken on door and window handles for instance-have a higher success rate than average swabs. Conversely, other situations lead to a marked decrease in the success rate, which should discourage further analyses of such swabs. Results also confirm that targeting a DNA swab on a single surface is preferable to swabbing different surfaces with the intent to aggregate cells deposited by the offender. Such results assist in predicting the chance that the analysis of a swab taken in a given situation will lead to a positive result. The study could therefore inform an evidence-based approach to decision-making at the crime scene (what to swab or not) and at the triage step (what to analyse or not), contributing thus to save resource and increase the efficiency of forensic science

  7. Bovine herpesvirus 1 infection and infectious bovine rhinotracheitis

    OpenAIRE

    2007-01-01

    International audience; Bovine herpesvirus 1 (BoHV-1), classified as an alphaherpesvirus, is a major pathogen of cattle. Primary infection is accompanied by various clinical manifestations such as infectious bovine rhinotracheitis, abortion, infectious pustular vulvovaginitis, and systemic infection in neonates. When animals survive, a life-long latent infection is established in nervous sensory ganglia. Several reactivation stimuli can lead to viral re-excretion, which is responsible for the...

  8. Intervet symposium: bovine neosporosis.

    Science.gov (United States)

    Schetters, T; Dubey, J P; Adrianarivo, A; Frankena, K; Romero, J J; Pérez, E; Heuer, C; Nicholson, C; Russell, D; Weston, J

    2004-10-28

    This article summarises the most relevant data of presentations delivered at the 19th International Conference of the World Association for the Advancement of Veterinary Parasitology (WAAVP)held in New Orleans, LA, USA, from 10 to 14 August 2003) in a symposium session on bovine neosporosis. The symposium was organised by Juan Muñoz-Bielsa,Wicher Holland, Enzo Foccoliand Theo Schetters (chairman). The focus was on the present state of knowledge of the biology, epidemiology(presented by J.P. Dubey) and immunology of Neospora infection (presented by A. Adrianarivo),with special emphasis on the prospects of vaccination of cattle against Neospora-induced abortion (presentations of K. Frankena (Costa Rican trial) and C. Heuer (New Zealand trial)).

  9. Self-collected genital swabs compared with cervicovaginal lavage for measuring HIV-1 and HSV-2 and the effect of acyclovir on viral shedding.

    Science.gov (United States)

    McNicholl, Janet M; Leelawiwat, Wanna; Whitehead, Sara; Hanson, Debra L; Evans-Strickfaden, Tammy; Cheng, Chen Y; Chonwattana, Wannee; Mueanpai, Famui; Kittinunvorakoon, Chonticha; Markowitz, Lauri; Dunne, Eileen F

    2017-03-01

    HIV-1 and HSV-2 are frequent genital co-infections in women. To determine how self-collected genital swabs compare to provider-collected cervicovaginal lavage, paired self-collected genital swabs and cervicovaginal lavage from women co-infected with HIV-1 and HSV-2 were evaluated. Women were in an acyclovir clinical trial and their samples were tested for HIV-1 RNA (361 samples) and HSV-2 DNA (378 samples). Virus shedding, quantity and acyclovir effect were compared. HIV-1 and HSV-2 were more frequently detected in self-collected genital swabs: 74.5% of self-collected genital swabs and 63.6% of cervicovaginal lavage had detectable HIV-1 (p ≤ 0.001, Fisher's exact test) and 29.7% of self-collected genital swabs and 19.3% of cervicovaginal lavage had detectable HSV-2 (p ≤ 0.001) in the placebo month. Cervicovaginal lavage and self-collected genital swabs virus levels were correlated (Spearman's rho, 0.68 for HIV; 0.61 for HSV-2) and self-collected genital swabs levels were generally higher. In multivariate modeling, self-collected genital swabs and cervicovaginal lavage could equally detect the virus-suppressive effect of acyclovir: for HIV-1, proportional odds ratios were 0.42 and 0.47 and for HSV-2, they were 0.10 and 0.03 for self-collected genital swabs and cervicovaginal lavage, respectively. Self-collected genital swabs should be considered for detection and measurement of HIV-1 and HSV-2 in clinical trials and other studies as they are a sensitive method to detect virus and can be collected in the home with frequent sampling.

  10. Occurrence of pathogenic Acanthamoeba genotypes in nasal swabs of cancer patients in Iran.

    Science.gov (United States)

    Memari, Fatemeh; Niyyati, Maryam; Haghighi, Ali; Seyyed Tabaei, Seyyed Javad; Lasjerdi, Z

    2015-05-01

    Incidences of Acanthamoeba granulomatous encephalitis (AGE) have been increased due to a rise in the number of high-risk people, such as immunodeficient patients. Indeed, immunosuppress situation can render the patient in acquiring opportunistic Acanthamoeba infections. In this study, analysis was carried out to verify the presence of free-living amoebae of Acanthamoeba genus in nasal swabs of cancer patients in hospitals of Tehran, Iran. Detection of isolates was based on morphotyping and PCR sequencing of the Diagnostic Fragment 3 (DF3) to identify strains at the genotype level. In addition, the pathogenic potential of the isolates was assayed using temperature and osmotolerance assays. The obtained results revealed that nine isolated strains belonging to T4 genotype-exhibited pathogenic potential. After sequencing, genotype T4 was found to be the most common one in the samples included in this study. Genotype T3 and T5 were also identified. To the best of our knowledge, this is the first study on the typing of Acanthamoeba strains at the genotype level in cancer patients in Iran and worldwide.

  11. Genotyping of potentially pathogenic Acanthamoeba strains isolated from nasal swabs of healthy individuals in Peru.

    Science.gov (United States)

    Cabello-Vílchez, Alfonso Martín; Martín-Navarro, Carmen María; López-Arencibia, Atteneri; Reyes-Batlle, María; González, Ana C; Guerra, Humberto; Gotuzzo, Eduardo; Valladares, Basilio; Piñero, José E; Lorenzo-Morales, Jacob

    2014-02-01

    Free Living Amoebae (FLA) of Acanthamoeba genus are widely distributed in the environment and can be found in the air, soil and water; and have also been isolated from air-conditioning units. In humans, they are causative agents of a sight-threating infection of the cornea, Acanthamoeba keratitis (AK) and a fatal infection of the central nervous system known as Granulomatous Amoebic Encephalitis (GAE). In this study, a survey was conducted in order to determine the presence and pathogenic potential of free-living amoebae of Acanthamoeba genus in nasal swabs from individuals in two regions of Peru. Identification of isolates was based on cyst morphology and PCR-sequencing of the Diagnostic Fragment 3 to identify strains at the genotype level. The pathogenic potential of the isolates was also assayed using temperature and osmotolerance assays and extracellular proteases zymograms. The obtained results revealed that all isolated strains exhibited pathogenic potential. After sequencing the highly variable DF3 (Diagnostic Fragment 3) region in the 18S rRNA gene as previously described, genotype T4 was found to be the most common one in the samples included in this study but also genotype T15 was identified. To the best of our knowledge, this is the first study on the characterization of Acanthamoeba strains at the genotype level and the first report of genotype T4 and T15 in Peru.

  12. Research of Optimization Method of Swabbing Parameters of All Rods Pumping Wells in the Entire Oilfield

    Directory of Open Access Journals (Sweden)

    Zhang Xishun

    2013-03-01

    Full Text Available Aiming at the drawbacks of the optimization and design methods and the practical production goal of least energy consumption, a new theory is raised that the gas of the layer released energy in the lifting process including two parts: dissolved-gas expansion energy and free-gas expansion energy. The motor’s input power of rod pumping system is divided into hydraulic horse power, gas expansion power, surface mechanical loss power, subsurface loss power. Using the theory of energy-conservation, the simulation model of free-gas expansion power has been established, the simulating models of the motor’s input power which are based on the energy method have been improved and the simulation precision of system efficiency has been enhanced. The entire optimization design models have been set up in which the single-well output is taken as the optimum design variable, the planed production of all oil wells in an overall oilfield as the restraint condition and the least input power of the overall oilfield as the object. Synthesizing the optimization design results of the single well and the entire oilfield, the optimal output and the optimal swabbing parameters of all wells can be got. The actual optimizing examples show that the total power consumption designed by the entire optimization method is less 12.95% than that by the single optimization method.

  13. IDENTIFICATION OF CHICKEN-SPECIFIC FECAL MICROBIAL SEQUENCES USING A METAGENOMIC APPROACH

    Science.gov (United States)

    In this study, we applied a genome fragment enrichment (GFE) method to select for genomic regions that differ between different fecal metagenomes. Competitive DNA hybridizations were performed between chicken fecal DNA and pig fecal DNA (C-P) and between chicken fecal DNA and an ...

  14. Changes of Cattle Fecal Microbiome Under Field Conditions

    Science.gov (United States)

    Next generation sequencing (NGS) has been applied to study the microbiome in wastewater, sewage sludge, and feces. Previous microbial survival studies have shown different fecal-associated microbes have different decay rates and regrowth behaviors.

  15. Fecal Indicator Bacteria and Environmental Observations: Validation of Virtual Beach

    Science.gov (United States)

    Contamination of recreational waters by fecal material is often assessed using indicator bacteria such as enterococci. Enumeration based on culturing methods can take up to 48 hours to complete, limiting the accuracy of water quality evaluations. Molecular microbial techniques em...

  16. Inspection of fecal contamination on strawberries using fluorescence imaging

    Science.gov (United States)

    Chuang, Yung-Kun; Yang, Chun-Chieh; Kim, Moon S.; Delwiche, Stephen R.; Lo, Y. Martin; Chen, Suming; Chan, Diane E.

    2013-05-01

    Fecal contamination of produce is a food safety issue associated with pathogens such as Escherichia coli that can easily pollute agricultural products via animal and human fecal matters. Outbreaks of foodborne illnesses associated with consuming raw fruits and vegetables have occurred more frequently in recent years in the United States. Among fruits, strawberry is one high-potential vector of fecal contamination and foodborne illnesses since the fruit is often consumed raw and with minimal processing. In the present study, line-scan LED-induced fluorescence imaging techniques were applied for inspection of fecal material on strawberries, and the spectral characteristics and specific wavebands of strawberries were determined by detection algorithms. The results would improve the safety and quality of produce consumed by the public.

  17. Saccharomyces cerevisiae colonization associated with fecal microbiota treatment failure

    Science.gov (United States)

    Background: Fecal microbiota therapy (FMT) has emerged as the gold standard for treatment of persistent, symptomatic Clostridium difficile infection (CDI) that does not respond to conventional antimicrobial treatment. Probiotics are commonly recommended in addition to antimicrobial treatment for CD...

  18. Study Questions 'Fecal Transplant' Treatment for Gut Infection

    Science.gov (United States)

    ... Fecal Transplant' Treatment for Gut Infection In direct comparison, researchers found no real difference compared to antibiotics To use the sharing features on this page, please enable JavaScript. (*this news item will not be available after ...

  19. Repeated fecal microbiota transplantation in a child with ulcerative colitis.

    Science.gov (United States)

    Shimizu, Hirotaka; Arai, Katsuhiro; Abe, Jun; Nakabayashi, Kazuhiko; Yoshioka, Takako; Hosoi, Kenji; Kuroda, Makoto

    2016-08-01

    We report the case of an 11-year-old girl with ulcerative colitis refractory to conventional therapy, who was subsequently treated successfully with repeated fecal microbiota transplantation (FMT). The patient was steroid dependent despite several infliximab treatments, and colectomy was proposed to improve quality of life. After repeated FMT, she was able to maintain remission with on minimal dose of steroid. Although her fecal microbiota was dysbiotic before FMT, it was restored to a similar pattern as the donor after repeated FMT.

  20. Colitis following fecal diversion: still a challenge

    Directory of Open Access Journals (Sweden)

    Castro Leonaldson dos Santos

    2000-01-01

    Full Text Available After fecal diversion, nonspecific colitis may be seen in the defunctionalized colon. The purpose of this prospective study is to identify specific findings that could help in the differential diagnosis between diversion colitis and other inflammatory bowel diseases in order to avoid inappropriate diagnosis and therapy. It was studied, prospectively, thirteen consecutive patients from two public hospitals of Rio de Janeiro who had undergone temporary colostomy for indications other than inflammatory bowel disease. They were submitted to endoscopy with biopsy of both proximal and distal colorectal segments, and prospectively evaluated before and after restoration of intestinal continuity. Endoscopy with biopsy of both proximal and distal excluded colorectal segments showed a nonspecific mucosal and submucosal inflammation, resembling ulcerative colitis ( p < 0.01. There was endoscopic resolution in all patients once restoration of intestinal continuity was established (p < 0.01 and also histologic improvement after the stoma closure. In conclusion there are no specific findings that make possible an unequivocal distinction between diversion colitis and other nonspecific inflammatory diseases. Diagnosis should be achieved if after stoma closure occur remission of endoscopic large bowel inflammatory signs with improvement in mucosal histologic appearance and prompt relief of clinical complaints.

  1. Fecal Microbiota Transplantation for Inflammatory Bowel Disease

    Science.gov (United States)

    Lopez, Joanna

    2016-01-01

    The gut bacterial microbiome, particularly its role in disease and inflammation, has gained international attention with the successful use of fecal microbiota transplantation (FMT) in the treatment of Clostridium difficile infection. This success has led to studies exploring the role of FMT in other conditions, including inflammatory bowel disease (IBD). Both Crohn’s disease and ulcerative colitis are chronic inflammatory conditions of the gastrointestinal system that have multifactorial etiologies. A shift in gut microbial composition in genetically susceptible individuals, an altered immune system, and environmental factors are all hypothesized to have a role in the pathogenesis of IBD. While numerous case reports and cohort studies have described the use of FMT in patients with IBD over the last 2 decades, the development of new sequencing techniques and results from 2 recent randomized, controlled trials have allowed for a better understanding of the relationship between the microbiome and the human host. However, despite these efforts, knowledge remains limited and the role of FMT in the management of IBD remains uncertain. Further investigation is necessary before FMT joins the current armamentarium of treatment options in clinical practice. PMID:27493597

  2. The role of fecal calprotectin in investigating inflammatory bowel diseases

    Directory of Open Access Journals (Sweden)

    Mustafa Erbayrak

    2009-05-01

    Full Text Available INTRODUCTION: Invasive and non-invasive tests can be used to evaluate the activity of inflammatory bowel diseases. OBJECTIVE: The aim of the present study was to investigate the role of fecal calprotectin in evaluating inflammatory bowel disease activity and the correlation of fecal calprotectin with the erythrocyte sedimentation rate and C reactive protein values in inflammatory bowel disease. METHOD: Sixty-five patients affected with inflammatory bowel disease were enrolled. Twenty outpatients diagnosed with inflammatory bowel disease comprised the control group. RESULTS: In the present study, all patients in the control group had an fecal calprotectin value lower than the cut-off point (50 mg/kg. CONCLUSION: In conclusion, fecal calprotectin was found to be strongly associated with colorectal inflammation indicating organic disease. Fecal calprotectin is a simple and non-invasive method for assessing excretion of macrophages into the gut lumen. Fecal calprotectin values can be used to evaluate the response to treatment, to screen asymptomatic patients, and to predict inflammatory bowel disease relapses.

  3. Validation of a same-day real-time PCR method for screening of meat and carcass swabs for Salmonella

    DEFF Research Database (Denmark)

    Löfström, Charlotta; Krause, Michael; Josefsen, Mathilde Hartmann

    2009-01-01

    of the published PCR methods for Salmonella have been validated in collaborative studies. This study describes a validation including comparative and collaborative trials, based on the recommendations from the Nordic organization for validation of alternative microbiological methods (NordVal) of a same-day, non......-commercial real-time PCR method for detection of Salmonella in meat and carcass swabs. Results: The comparative trial was performed against a reference method (NMKL-71:5, 1999) using artificially and naturally contaminated samples (60 minced veal and pork meat samples, 60 poultry neck-skins, and 120 pig carcass....... Partly based on results obtained in this study, the method has obtained NordVal approval for analysis of Salmonella in meat and carcass swabs. The PCR method was transferred to a production laboratory and the performance was compared with the BAX Salmonella test on 39 pork samples artificially...

  4. Most Probable Number Rapid Viability PCR Method to Detect Viable Spores of Bacillus anthracis in Swab Samples

    Energy Technology Data Exchange (ETDEWEB)

    Letant, S E; Kane, S R; Murphy, G A; Alfaro, T M; Hodges, L; Rose, L; Raber, E

    2008-05-30

    This note presents a comparison of Most-Probable-Number Rapid Viability (MPN-RV) PCR and traditional culture methods for the quantification of Bacillus anthracis Sterne spores in macrofoam swabs generated by the Centers for Disease Control and Prevention (CDC) for a multi-center validation study aimed at testing environmental swab processing methods for recovery, detection, and quantification of viable B. anthracis spores from surfaces. Results show that spore numbers provided by the MPN RV-PCR method were in statistical agreement with the CDC conventional culture method for all three levels of spores tested (10{sup 4}, 10{sup 2}, and 10 spores) even in the presence of dirt. In addition to detecting low levels of spores in environmental conditions, the MPN RV-PCR method is specific, and compatible with automated high-throughput sample processing and analysis protocols.

  5. A study of female genital swabs in a Nigerian Tertiary Hospital

    Institute of Scientific and Technical Information of China (English)

    Samuel Nwadioha; Julie O Egesie; Henry Emejuo; Elizabeth Iheanacho

    2010-01-01

    Objective:To detect some common microbial agents of vaginal discharge and improve the current syndromic management of abnormal vaginal discharge. Methods:A prospective study of female genital swabs collected from obstetrics and gynecology units of Aminu Kano Teaching Hospital, Kano, Nigeria and an analysed of microscopy, culture and sensitivity in the medical microbiology and parasitology laboratory of this hospital were conducted from December 2007 to December 2008. Data on epidemiologic indices were collected from the patients, using structured interviewer-administered questionnaires. Results:Eight hundred and forty Candida species were detected, constituting 60%(n=840) of 1 400 female genital discharge samples of microbial etiology in a total of 2 000 female genital samples received. The distribution of vaginal candidiasis was the highest in young adults aged 21 to 30 years with 43%(n=360) of the total 840 cases. Pregnant women that presented with vaginal candidiasis constituted 40%(n=360) of the total 840 cases. Other risk groups included the immuno-suppression with 24%(n=202), group on hormonal therapy with 15%(n=126) and broad spectrum antibiotics users with 16%(n=134). Conclusions:The results show that Candida is the most common cause of vaginitis and vulvo-vaginal candidiasis followed by C. albicans in the young adults aged 21 to 30 years, pregnant mothers, immuno-suppression, contraceptive and broad spectrum antibiotic users. Proper management of vaginal candidiasis and vulvo-vaginal candidiasis is recommended especially among the risk groups in order to avoid complications and reduce HIV transmission.

  6. Direct PCR amplification of the HVSI region in mitochondrial DNA from buccal cell swabs

    Directory of Open Access Journals (Sweden)

    Kovačević-Grujičić Nataša

    2012-01-01

    Full Text Available Amplification of human mitochondrial DNA (mtDNA has been widely used in population genetics, human evolutionary and molecular anthropology studies. mtDNA hypervariable segments I and II (HVSI and HVSII were shown to be a suitable tool in genetic analyses due to the unique properties of mtDNA, such as the lack of recombination, maternal mode of inheritance, rapid evolutionary rate and high population-specific polymorphisms. Here we present a rapid and low-cost method for direct PCR amplification of a 330 bp fragment of HVSI from buccal cell samples. Avoiding the DNA isolation step makes this method appropriate for the analysis of a large number of samples in a short period of time. Since the transportation of samples and fieldwork conditions can affect the quality of samples and subsequent DNA analysis, we tested the effects of long-term storage of buccal cell swabs on the suitability of such samples for direct PCR amplification. We efficiently amplified a 330 bp fragment of HVSI even after the long-term storage of buccal cells at room temperature, +4°C or at -20°C, for up to eight months. All examined PCR products were successfully sequenced, regardless of sample storage time and conditions. Our results suggest that the direct PCR amplification of the HVSI region from buccal cells is a method well suited for large-scale mtDNA population studies.[Acknowledgments. This work was supported by the Ministry of Education and Science of the Republic of Serbia (Grant no. III 47025.

  7. Clinical forensic sample collection techniques following consensual intercourse in volunteers - cervical canal brush compared to conventional swabs.

    Science.gov (United States)

    Joki-Erkkilä, Minna; Tuomisto, Sari; Seppänen, Mervi; Huhtala, Heini; Ahola, Arja; Rainio, Juha; Karhunen, Pekka J

    2014-10-01

    The purpose of the research was to evaluate gynecological evidence collection techniques; the benefit of cervical canal brush sample compared to vaginal fornix and cervical swab samples and the time frame for detecting Y-chromosomal material QiAmp DNA Mini Kit(®) and Quantifiler Y Human Male DNA Quantification Kit(®) in adult volunteers following consensual intercourse. Eighty-four adult female volunteers following consensual intercourse were recruited for the study. By combining all sample collecting techniques, 81.0% of the volunteers were Y-DNA positive. Up to 60 h the conventional swab sampling techniques detected more Y-DNA positive samples when compared to the brush technique. However, after 60 h, the cervical canal brush sample technique showed its benefit by detecting 27.3% (6/22) of Y-DNA positive samples, which were Y-DNA negative in both conventional swab sampling techniques. By combining swab and brush techniques, 75% of the volunteers were still Y-DNA positive in 72-144 post-coital hours. The rate of measurable Y-DNA decreased approximately 3% per hour. Despite reported consensual intercourse, 6.8% (3/44) of volunteers were Y-DNA negative within 48 h. Y-DNA was not detected after 144 post-coital hours (6 days). In conclusion, the brush as a forensic evidence collection method may provide additional biological trace evidence from the cervical canal, although the best biological trace evidence collection can be obtained by combining all three sampling techniques. The time frame for gynecological forensic evidence sample collection should be considered to be at least a week if sexual violence is suspected.

  8. Rapid diagnosis of diarrhea caused by Shigella sonnei using dipsticks; comparison of rectal swabs, direct stool and stool culture.

    Directory of Open Access Journals (Sweden)

    Claudia Duran

    Full Text Available BACKGROUND: We evaluated a dipstick test for rapid detection of Shigella sonnei on bacterial colonies, directly on stools and from rectal swabs because in actual field situations, most pathologic specimens for diagnosis correspond to stool samples or rectal swabs. METHODOLOGY/PRINCIPAL FINDINGS: The test is based on the detection of S. sonnei lipopolysaccharide (LPS O-side chains using phase I-specific monoclonal antibodies coupled to gold particles, and displayed on a one-step immunochromatographic dipstick. A concentration as low as 5 ng/ml of LPS was detected in distilled water and in reconstituted stools in 6 minutes. This is the optimal time for lecture to avoid errors of interpretation. In distilled water and in reconstituted stools, an unequivocal positive reaction was obtained with 4 x 10(6 CFU/ml of S. sonnei. The specificity was 100% when tested with a battery of Shigella and different unrelated strains. When tested on 342 rectal swabs in Chile, specificity (281/295 was 95.3% (95% CI: 92.9% - 97.7% and sensitivity (47/47 was 100%. Stool cultures and the immunochromatographic test showed concordant results in 95.5 % of cases (328/342 in comparative studies. Positive and negative predictive values were 77% (95% CI: 65% - 86.5% and 100% respectively. When tested on 219 stools in Chile, Vietnam, India and France, specificity (190/198 was 96% (95% CI 92%-98% and sensitivity (21/21 was 100%. Stool cultures and the immunochromatographic test showed concordant results in 96.3 % of cases (211/219 in comparative studies. Positive and negative predictive values were 72.4% (95% CI 56.1%-88.6% and 100 %, respectively. CONCLUSION: This one-step dipstick test performed well for diagnosis of S. sonnei both on stools and on rectal swabs. These data confirm a preliminary study done in Chile.

  9. A Novel Mycobacterium cosmeticum-Like Bacterium Isolated from the Ear Swab of a Patient with Otitis Externa

    Directory of Open Access Journals (Sweden)

    Jeanette W. P. Teo

    2015-01-01

    Full Text Available We describe the identification and characterization of a novel nontuberculous mycobacterium (NTM, isolated from an ear swab of an adult male patient with chronic otitis externa. Genetically, the bacterium is most closely related to Mycobacterium cosmeticum; however, growth and biochemical features indicate that it is distinctly different. Here, we highlight for the first time an unusual NTM that is a probable cause of ear infection.

  10. First approach to molecular epidemiology of bovine tuberculosis in Colombia

    Directory of Open Access Journals (Sweden)

    Jimena Jojoa-Jojoa

    2015-12-01

    Full Text Available Objective. To investigate the presence of Mycobacterium bovis and other Mycobacterium species in samples of cattle and buffalo in Colombia, to start the molecular characterization of M. bovis in the country. Material and methods. 492 samples were collected from herds identified with the presence of infected animals through the PPD, by the Group of Bovine Tuberculosis ICA Colombian Agricultural Institute in eight departments of Colombia. Lymph nodes of head, thorax and abdomen, gross lesions of tissues with tuberculosis, nasal swabs, milk, blood and fresh cheeses were included. Samples were subjected to detection of Mycobacterium bovis and other mycobacteria by conventional microbiological analysis and PCR-6110 and spoligotyping molecular assays. Results. In the samples analyzed especially in lymph nodes, Mycobacterium bovis was demonstrated with genotypes reported and not previously reported in the world, as well as M. tuberculosis in Antioquia, Cundinamarca, Boyacá and Magdalena departments. Conclusions. In Colombia there are at least 7 genotypes of M. bovis that are infected and sick cattle and buffalo from four different departments becoming serious threat to public health.

  11. Detection of Mycoplasma pneumoniae in simulated and true clinical throat swab specimens by nanorod array-surface-enhanced Raman spectroscopy.

    Directory of Open Access Journals (Sweden)

    Suzanne L Hennigan

    Full Text Available The prokaryote Mycoplasma pneumoniae is a major cause of respiratory disease in humans, accounting for 20% of all community-acquired pneumonia and the leading cause of pneumonia in older children and young adults. The limitations of existing options for mycoplasma diagnosis highlight a critical need for a new detection platform with high sensitivity, specificity, and expediency. Here we evaluated silver nanorod arrays (NA as a biosensing platform for detection and differentiation of M. pneumoniae in culture and in spiked and true clinical throat swab samples by surface-enhanced Raman spectroscopy (SERS. Three M. pneumoniae strains were reproducibly differentiated by NA-SERS with 95%-100% specificity and 94-100% sensitivity, and with a lower detection limit exceeding standard PCR. Analysis of throat swab samples spiked with M. pneumoniae yielded detection in a complex, clinically relevant background with >90% accuracy and high sensitivity. In addition, NA-SERS correctly classified with >97% accuracy, ten true clinical throat swab samples previously established by real-time PCR and culture to be positive or negative for M. pneumoniae. Our findings suggest that the unique biochemical specificity of Raman spectroscopy, combined with reproducible spectral enhancement by silver NA, holds great promise as a superior platform for rapid and sensitive detection and identification of M. pneumoniae, with potential for point-of-care application.

  12. Fast and discriminative CoSYPS detection system of viable Salmonella spp. and Listeria spp. in carcass swab samples.

    Science.gov (United States)

    Barbau-Piednoir, Elodie; Botteldoorn, Nadine; Mahillon, Jacques; Dierick, Katelijne; Roosens, Nancy H

    2015-01-02

    In this study, the complete CoSYPS Path Food workflow including all steps, namely swab sample enrichment, SYBR®Green qPCR detection of Salmonella spp. and Listeria spp., isolation and confirmation of the detected strain, was validated on beef carcass swabs. To perform the validation, the results of the complete workflow were compared, according to the ISO 16140:2003, with the ISO reference methods for detection, isolation and confirmation of Listeria monocytogenes and Salmonella spp. The results showed that the relative level of detection and the limit of detection of the complete workflow and ISO reference methods are in a range from 2 to 16 CFU/swab for both bacteria. The relative specificity, sensitivity and accuracy identified during this validation were all 100% since the results obtained with the complete CoSYPS Path Food workflow and the ISO reference methods were identical (Cohen's kappa index=1.00). In addition the complete CoSYPS Path Food workflow is able to provide detection results (negative or presumptive positive) in half the time needed as for the ISO reference methods. These results demonstrate that the performance of the complete CoSYPS Path Food workflow is not only comparable to the ISO reference methods but also provides a faster response for the verification of beef carcasses before commercial distribution.

  13. Loss of Vancomycin-Resistant Enterococcus Fecal Dominance in an Organ Transplant Patient With Clostridium difficile Colitis After Fecal Microbiota Transplant

    OpenAIRE

    Stripling, Joshua; Kumar, Ranjit; Baddley, John W.; Nellore, Anoma; DIXON, PAULA; Howard, Donna; Ptacek, Travis; Lefkowitz, Elliot J.; Tallaj, Jose A.; Benjamin, William H.; Morrow, Casey D.; Rodriguez, J Martin

    2015-01-01

    We report the use of fecal microbiota transplantation in a single heart-kidney transplant recipient with recurrent Clostridium difficile, vancomycin-resistant Enterococcus (VRE) fecal dominance, and recurrent VRE infections. Fecal microbiota transplantation resulted in the reconstruction of a diverse microbiota with (1) reduced relative abundance of C difficile and VRE and (2) positive clinical outcome.

  14. Bovine coronavirus detection in a collection of diarrheic stool samples positive for group a bovine rotavirus

    Directory of Open Access Journals (Sweden)

    Aline Fernandes Barry

    2009-11-01

    Full Text Available Neonatal diarrhea is an important cause of economic losses for cattle farmers. The main viral etiologies of enteric diseases are group A rotaviruses (GARV and the bovine coronavirus (BCoV. Although both viruses infect calves of the same age, the occurrence of mixed infections is still under studied. The present study describes the co-infection of BCoV and GARV in stool samples. Forty-four diarrheic fecal samples from calves up to 60 days old that had previously tested positive for GARV by SS-PAGE were analyzed using semi-nested PCR for BCoV. A product with 251 bp of the BCoV nucleoprotein gene was amplified in 15.9% (7/44 of the samples, demonstrating that co-infection is not an unusual event. These results reinforce the need for testing for both GARV and BCoV, even in fecal samples that previously tested positive for one virus.A diarreia neonatal é uma importante causa de perdas econômicas para a criação de bovinos. Os principais agentes etiológicos virais das doenças entéricas são o rotavírus bovino grupo A (GARV e o coronavírus bovino (BCoV. Embora ambos os vírus infectem bezerros na mesma faixa etária, infecções mistas ainda são pouco estudadas. O presente trabalho descreve a identificação do BCoV em amostras de fezes positivas para o GARV, caracterizando a ocorrência de infecções mistas. Quarenta e quatro amostras de fezes diarreicas de bezerros com até 60 dias de idade, previamente identificadas como positivas para o GARV bovino por meio da técnica de SS-PAGE, foram avaliadas quanto a presença do BCoV pela técnica de semi-nested PCR. Um produto com 251 pb do gene da nucleoproteína do BCoV foi amplificado em 15,9% (7/44 das amostras de fezes demonstrando que a co-infecção não é um evento raro. Esse resultado enfatizada a importância da realização simultânea do diagnóstico para esses dois importantes vírus entéricos de bezerros em surtos de diarreia neonatal tanto em rebanhos bovinos leiteiros quanto de

  15. Fecal Microbiota Transplant: Respice, Adspice, Prospice.

    Science.gov (United States)

    Brandt, Lawrence J

    2015-01-01

    Respice, Adspice, Prospice, look to the past, look to the present, look to the future, is one of life's valuable axioms; for it is only if one knows where one has been can one intelligently prepare for the future. I have used this approach here to review fecal microbiota transplant (FMT). First used in fourth-century China to treat an assortment of gastrointestinal (GI) symptoms, today FMT is primarily used for recurrent Clostridium difficile infection (RCDI). In the future, however, it is likely that microbiotic therapy will be extended beyond treatment of RCDI. Early on, fresh feces from patient-identified donors was used and administered by several routes. FMT cure rates for RCDI remain approximately 82% and 91% when fresh stool is given by the upper GI and lower GI routes, respectively, but now we are moving in the direction of using carefully vetted volunteers whose stool is processed into a variety of formulations including lyophilized material and even capsules. It is very likely that an array of products derived from feces or based on specific microbiotic profiles and commercially prepared in a controlled environment will be available to restore eubiosis to a dysbiotic intestinal microbial community, and thereby correct a variety of GI and non-GI disorders. We are witnessing a paradigm shift in therapeutics. Previously, bacteria were thought of only as potential pathogens, whereas now we appreciate that a diverse community of bacteria is crucial to the health of the host. We are now learning that to restore such diversity once it has been interrupted can result in miraculous cure. The future of microbiotic therapy is bright.

  16. Fecal Microbiota Transplantation in Inflammatory Bowel Disease.

    Science.gov (United States)

    Reinisch, Walter

    2017-01-01

    The etiology of inflammatory bowel disease (IBD) is unknown, but it is thought to arise from an aberrant immune response to a change in colonic environment in a genetically susceptible individual. The intestinal microbiota are located at the complex interface of the epithelial barrier and are sensitive to changes in environmental factors, such as diets, drugs or smoking and signals derived from the intestinal immune system and the gut-brain axis. In patients with IBD, an imbalance in the structural and/or functional configuration of the intestinal microbiota leading to the disruption of the host-microorganism homeostasis (dysbiosis) has been reproducibly reported. As animal models of IBD require gut bacteria to induce inflammation, it is hypothesized that the dysbiosis observed in patients is not only a surrogate of changes at the intestinal barrier but also a potential cause or at least enhancer of the mucosal inflammatory process. That burgeoning notion has stimulated thoughts to modify the intestinal microbiota and rekindled interest in previous work on the efficacy of antibiotics in patients with IBD. The feasibility and tremendous success of fecal microbiota transplantation (FMT) to treat antibiotic resistant Clostridium difficile has finally paved the way to embark into the unchartered territory of IBD using FMT. Different routes and number of administrations, choices of donors, disease status and permitted therapies might have contributed to mixed results, particularly from the so far published randomized controlled trials. However, microbiome analysis suggests that a durable transplantation of donor bacteria to the host appears feasible and might be associated with a higher likelihood of response. On the other hand, this raises the concern of transplanting not only anti-inflammatory active bacteria and their products, but also not-yet-known dispositions for other diseases including cancer. Attempts are being made to better characterize those components of

  17. Bovine respiratory disease model based on dual infections with infection with bovine viral diarrhea virus and bovine corona virus

    Science.gov (United States)

    Bovine respiratory disease complex (BRDC) is the leading cause of economic loss in the U.S. cattle industry. BRDC likely results from simultaneous or sequential infections with multiple pathogens including both viruses and bacteria. Bovine viral diarrhea virus (BVDV) and bovine corona virus (BoCV...

  18. Human-induced trophic cascades along the fecal detritus pathway.

    Directory of Open Access Journals (Sweden)

    Elizabeth Nichols

    Full Text Available Human presence and activity in tropical forest is thought to exert top-down regulation over the various 'green-world' pathways of plant-based foodwebs. However, these effects have never been explored for the 'brown-world' pathways of fecal-detritus webs. The strong effects of humans on tropical game mammals are likely to indirectly influence fecal detritivores (including Scarabaeine dung beetles, with subsequent indirect impacts on detrivore-mediated and plant-facilitating detrital processes. Across a 380-km gradient of human influence in the western Brazilian Amazon, we conducted the first landscape-level assessment of human-induced cascade effects on the fecal detritus pathway, by coupling data on human impact, game mammal and detritivore community structure, and rate measurements of a key detritus process (i.e. dung beetle-mediated secondary seed dispersal. We found evidence that human impact indirectly influences both the diversity and biomass of fecal detritivores, but not detritivore-mediated processes. Cascade strength varied across detritivore groups defined by species' traits. We found smaller-bodied dung beetles were at higher risk of local decline in areas of human presence, and that body size was a better predictor of cascade structure than fecal resource manipulation strategy. Cascade strength was also stronger in upland, unflooded forests, than in seasonally flooded forests. Our results suggest that the impact of human activity in tropical forest on fecal-detritus food web structure is mediated by both species' traits and habitat type. Further research will be required to determine the conditions under which these cascade effects influence fecal-detritus web function.

  19. Validation of a same-day real-time PCR method for screening of meat and carcass swabs for Salmonella

    Directory of Open Access Journals (Sweden)

    Hansen Flemming

    2009-05-01

    Full Text Available Abstract Background One of the major sources of human Salmonella infections is meat. Therefore, efficient and rapid monitoring of Salmonella in the meat production chain is necessary. Validation of alternative methods is needed to prove that the performance is equal to established methods. Very few of the published PCR methods for Salmonella have been validated in collaborative studies. This study describes a validation including comparative and collaborative trials, based on the recommendations from the Nordic organization for validation of alternative microbiological methods (NordVal of a same-day, non-commercial real-time PCR method for detection of Salmonella in meat and carcass swabs. Results The comparative trial was performed against a reference method (NMKL-71:5, 1999 using artificially and naturally contaminated samples (60 minced veal and pork meat samples, 60 poultry neck-skins, and 120 pig carcass swabs. The relative accuracy was 99%, relative detection level 100%, relative sensitivity 103% and relative specificity 100%. The collaborative trial included six laboratories testing minced meat, poultry neck-skins, and carcass swabs as un-inoculated samples and samples artificially contaminated with 1–10 CFU/25 g, and 10–100 CFU/25 g. Valid results were obtained from five of the laboratories and used for the statistical analysis. Apart from one of the non-inoculated samples being false positive with PCR for one of the laboratories, no false positive or false negative results were reported. Partly based on results obtained in this study, the method has obtained NordVal approval for analysis of Salmonella in meat and carcass swabs. The PCR method was transferred to a production laboratory and the performance was compared with the BAX Salmonella test on 39 pork samples artificially contaminated with Salmonella. There was no significant difference in the results obtained by the two methods. Conclusion The real-time PCR method for

  20. The use of PCR technique in the identification of Mycobacterium species responsible for bovine tuberculosis in cattle and buffaloes in Pakistan.

    Science.gov (United States)

    Akhtar, Farah; Javed, Muhammad Tariq; Aziz-ur-Rehman; Khan, Muhammad Nisar; Akhtar, Pervez; Hussain, Sayed Misdaq; Aslam, Muhammad Sohaib; Kausar, Razia; Qamar, Mehwish; Cagiola, Monica

    2015-08-01

    Bovine tuberculosis is one of the important diseases of dairy and wild animals. The disease is prevalent all over the world, though developed countries have tremendously reduced the prevalence through eradication campaigns. The prevalence of disease in Pakistan on the basis of tuberculin testing or culture isolation of the organism has been reported previously. It is, however, important to use the latest diagnostic tools, i.e. PCR to confirm the type of Mycobacterium infecting the animals in Pakistan. Therefore, the present study was carried out to assess the utility of direct PCR on milk samples and nasal swabs to confirm the type of Mycobacterium infecting the animals. This study was carried out on 215 cattle and buffaloes of more than 2 years of age present at two livestock farms. The tuberculin results showed 22.5% prevalence at one farm and 25.9% at the other with an overall prevalence of 24.7%. The 92.5% of milk samples and/or nasal swabs showed positive PCR for Mycobacterium genus, 86.8% for Mycobacterium tuberculosis complex and 77.4% for Mycobacterium bovis. The M. bovis by PCR was detected in 13.2% of milk samples, 24.5% of nasal swabs and 39.6% of both milk samples + nasal swabs. The results suggested that there are 60% higher chance for a nasal swab to yield a positive PCR for M. bovis than the milk sample. It can be concluded from the present study that tuberculin testing is a useful method in studying the prevalence of disease as the PCR for Mycobacterium genus was positive in 92.5%, M. tuberculosis complex in 86.8% and Mycobacterium bovis in 77.4% cases.

  1. Diversity, abundance, and possible sources of fecal bacteria in the Yangtze River.

    Science.gov (United States)

    Sun, Haohao; He, Xiwei; Ye, Lin; Zhang, Xu-Xiang; Wu, Bing; Ren, Hongqiang

    2017-03-01

    The fecal bacteria in natural waters may pose serious risks on human health. Although many source tracking methods have been developed and used to determine the possible sources of the fecal pollution, little is known about the overall diversity and abundance of fecal bacterial community in natural waters. In this study, a method based on fecal bacterial sequence library was introduced to evaluate the fecal bacterial profile in the Yangtze River (Nanjing section). Our results suggested that the Yangtze River water harbors diverse fecal bacteria. Fifty-eight fecal operational taxonomic units (97% identity level) were detected in the Yangtze River water samples and the relative abundance of fecal bacteria in these samples ranged from 0.1 to 8%. It was also found that the relative abundances of the fecal bacteria in locations near to the downstream of wastewater treatment plants were obviously higher than those in other locations. However, the high abundance of fecal bacteria could decrease to the normal level in 2~4 km in the river due to degradation or dilution, and the overall fecal bacteria level changed little when the Yangtze River flew through the Nanjing City. Moreover, the fecal bacteria in the Yangtze River water were found to be highly associated (Spearman rho = 0.804, P bacteria. Collectively, the findings in this study reveal the diversity, abundance, and possible sources of fecal bacteria in the Yangtze River and advance our understandings of the fecal bacteria community in the natural waters.

  2. Improved diagnosis of Trichomonas vaginalis infection by PCR using vaginal swabs and urine specimens compared to diagnosis by wet mount microscopy, culture, and fluorescent staining

    NARCIS (Netherlands)

    C. van der Schee (Cindy); A.F. van Belkum (Alex); L. Zwijgers (Lisette); E. van der Brugge; E.L. O'Neill; A. Luijendijk (Ad); T. van Rijsoort-Vos; W.I. van der Meijden (Willem); J.F. Sluiters (Hans); H.A. Verbrugh (Henri)

    1999-01-01

    textabstractFour vaginal cotton swab specimens were obtained from each of 804 women visiting the outpatient sexually transmitted disease clinic of the Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands, for validation of various forms of Trichomonas

  3. Deteksi Bovine Herpesvirus-1 Secara Immunohistokimia pada Membran Korioallantois Telur Ayam Berembrio (IMMUNOHISTOCHEMISTRY DETECTION OF BOVINE HERPESVIRUS-1 IN CORIOALLANTOIC MEMBRANE OF CHICKEN EMBRYONATED EGG

    Directory of Open Access Journals (Sweden)

    Yuli Purwandari Kristianingrum

    2016-01-01

    Full Text Available Infectious Bovine Rhinotracheitis (IBR is caused by Bovine Herpes virus-1 in the cattle. The clinicalsigns demonstrate depression, anorexia, swelling of the vulva, redness of the vestibule, pustule and ulceron the vaginal mucosal. Based on previous research, IBR virus from the nasal swab could be grown inchorio-allantoic membrane of embryonated chicken eggs. This study aim was to confirm whether IBR virusin cattle could be grown in embryonated chicken eggs as a substitute for cell culture. A total of five nasalswab samples from the cows that were positive for IBR infection (diagnosed by Polymerase Chain Reactionand cell culture were inoculated on the chorio-allantois membrane of embryonated chicken eggs.Observation of lesions performed at 3-5 days after inoculation. Re-inoculation (passage was done threetimes. Pock characteristic lesions were observed on the corioallantoic membrane with the size of 5-7 mm,rounded shape, opaque edge, with necrosis in the central area. Furthermore, pock lesions were processedfor hematoxylin and eosin staining and immuno-histochemistry. The result of hematoxylin and eosinstaining showed that the formation of intranuclear inclusion bodies and vacuolization of the epithelial cellof membrane was observed. Immuno-histochemistry staining showed positive reaction for antibodiesagainst BHV-1 in the epithelial cells membrane. In conclusion, embryonated chicken eggs could be usedas a medium for detection of IBR.

  4. Material Properties of Inorganic Bovine Cancellous Bovine: Nukbone

    Science.gov (United States)

    Piña, Cristina; Palma, Benito; Munguía, Nadia

    2006-09-01

    In this work, inorganic cancellous bovine bone implants prepared in the Instituto de Investigaciones en Materiales — UNAM were characterized. Elementary chemical analysis was made, toxic elements concentration were measured and the content of organic matter also. These implants fulfill all the requirements of the ASTM standards, and therefore it is possible their use in medical applications.

  5. CHROMagar mSuperCARBA performance in carbapenem-resistant Enterobacteriaceae isolates characterized at molecular level and routine surveillance rectal swab specimens.

    Science.gov (United States)

    García-Fernández, Sergio; Hernández-García, Marta; Valverde, Aránzazu; Ruiz-Garbajosa, Patricia; Morosini, María Isabel; Cantón, Rafael

    2017-03-01

    Performance of the CHROMagar mSuperCARBA media was assessed in both well-characterized carbapenem-resistant Enterobacteriaceae (n=52) and routine surveillance rectal swab specimens (n=211). Limit of detection ranged between 10(1) and 10(2)CFU/mL except for OXA-48 producers with low-carbapenem MICs (10(6)CFU/mL). High sensitivity (100%) and specificity (100%) were obtained with rectal swabs.

  6. Two, four, six, eight... stop and count before it is too late! An audit on swab, needle and instrument counts in theatre.

    LENUS (Irish Health Repository)

    Donnelly, T.

    2014-07-01

    A concurrent audit was conducted over a four week period to determine if the counting of swabs, needles and instruments for surgery adhered to local policy and recommended guidelines. Data were collected on 30 abdominal surgical procedures. This audit highlighted failings in the count process. It identified poor communication within the multidisciplinary team. There needs to be an increased awareness about local policy, national and international guidelines regarding the counting of swabs, needles and instruments for all surgical procedures.

  7. Chinese physicians’ perceptions of fecal microbiota transplantation

    Science.gov (United States)

    Ren, Rong-Rong; Sun, Gang; Yang, Yun-Sheng; Peng, Li-Hua; Wang, Shu-Fang; Shi, Xiao-Hong; Zhao, Jing-Quan; Ban, Yong-Ling; Pan, Fei; Wang, Xue-Hong; Lu, Wei; Ren, Jian-Lin; Song, Ying; Wang, Jiang-Bin; Lu, Qi-Ming; Bai, Wen-Yuan; Wu, Xiao-Ping; Wang, Zi-Kai; Zhang, Xiao-Mei; Chen, Ye

    2016-01-01

    AIM: To explore Chinese physicians’ perceptions towards fecal microbiota transplantation (FMT) and to provide information and an assessment of FMT development in China. METHODS: A self-administered questionnaire was developed according to the FMT practice guidelines and was distributed to physicians in hospitals via Internet Research Electronic Data Capture (REDcap) software and electronic mails to assess their attitudes toward and knowledge of FMT. The questionnaire included a brief introduction of FMT that was followed by 20 questions. The participants were required to respond voluntarily, under the condition of anonymity and without compensation. Except for the fill-in-the-blank questions, all of the other questions were required in the REDcap data collection systems, and the emailed questionnaires were completed based on eligibility. RESULTS: Up to December 9, 2014, 844 eligible questionnaires were received out of the 980 distributed questionnaires, with a response rate of 86.1%. Among the participants, 87.3% were from tertiary hospitals, and there were 647 (76.7%) gastroenterologists and 197 (23.3%) physicians in other departments (non-gastroenterologists). Gastroenterologists’ awareness of FMT prior to the survey was much higher than non-gastroenterologists’ (54.3 vs 16.5%, P FMT was not statistically different (92.4 vs 87.1%, P = 0.1603). Major concerns of FMT included the following: acceptability to patients (79.2%), absence of guidelines (56.9%), and administration and ethics (46.5%). On the basis of understanding, the FMT indications preferred by physicians were recurrent Clostridium difficile infection (86.7%), inflammatory bowel disease combined with Clostridium difficile infection (78.6%), refractory ulcerative colitis (70.9%), ulcerative colitis (65.4%), Crohn’s disease (59.4%), chronic constipation (43.7%), irritable bowel syndrome (39.1%), obesity (28.1%) and type 2 diabetes (23.9%). For donor selection, the majority of physicians preferred

  8. Dietary marker effects on fecal microbial ecology, fecal VFA, nutrient digestibility coefficients, and growth performance in finishing pigs.

    Science.gov (United States)

    Kerr, B J; Weber, T E; Ziemer, C J

    2015-05-01

    Use of indigestible markers such as Cr2O3, Fe2O3, and TiO2 are commonly used in animal studies to evaluate digesta rate of passage and nutrient digestibility. Yet, the potential impact of indigestible markers on fecal microbial ecology and subsequent VFA generation is not known. Two experiments utilizing a total of 72 individually fed finishing pigs were conducted to describe the impact of dietary markers on fecal microbial ecology, fecal ammonia and VFA concentrations, nutrient digestibility, and pig performance. All pigs were fed a common diet with no marker or with 0.5% Cr2O3, Fe2O3, or TiO2. In Exp. 1, after 33 d of feeding, fresh fecal samples were collected for evaluation of microbial ecology, fecal ammonia and VFA concentrations, and nutrient digestibility, along with measures of animal performance. No differences were noted in total microbes or bacterial counts in pig feces obtained from pigs fed the different dietary markers while Archaea counts were decreased (P = 0.07) in feces obtained from pigs fed the diet containing Fe2O 3compared to pigs fed the control diet. Feeding Cr2O3, Fe2O3, or TiO2 increased fecal bacterial richness (P = 0.03, 0.01, and 0.10; respectively) when compared to pigs fed diets containing no marker, but no dietary marker effects were noted on fecal microbial evenness or the Shannon-Wiener index. Analysis of denaturing gradient gel electrophoresis gels did not reveal band pattern alterations due to inclusion of dietary markers in pig diets. There was no effect of dietary marker on fecal DM, ammonia, or VFA concentrations. Pigs fed diets containing Cr2O3 had greater Ca, Cu, Fe, and P (P ≤ 0.02), but lower Ti ( P= 0.08) digestibility compared to pigs fed the control diet. Pigs fed diets containing Fe2O3 had greater Ca (P = 0.08) but lower Ti (P = 0.01) digestibility compared to pigs fed the control diet. Pigs fed diets containing TiO2 had greater Fe and Zn (P ≤ 0.09), but lower Ti ( P= 0.01) digestibility compared to pigs fed the

  9. Comparative functional genomics and the bovine macrophage response to strains of the Mycobacterium genus

    Directory of Open Access Journals (Sweden)

    Kévin eRue-Albrecht

    2014-11-01

    Full Text Available Mycobacterial infections are major causes of morbidity and mortality in cattle and are also potential zoonotic agents with implications for human health. Despite the implementation of comprehensive animal surveillance programs, many mycobacterial diseases have remained recalcitrant to eradication in several industrialized countries. Two major mycobacterial pathogens of cattle are Mycobacterium bovis and M. avium subspecies paratuberculosis (MAP, the causative agents of bovine tuberculosis and Johne’s disease, respectively. Bovine tuberculosis is a chronic, granulomatous disease of the respiratory tract that is spread via aerosol transmission, while Johne’s disease is a chronic granulomatous disease of the intestines that is transmitted via the fecal-oral route. Although these diseases exhibit differential tissue tropism and distinct complex etiologies, both M. bovis and MAP infect, reside and replicate in host macrophages—the key host innate immune cell that encounters mycobacterial pathogens after initial exposure and mediates the subsequent immune response. The persistence of M. bovis and MAP in macrophages relies on a diverse series of immunomodulatory mechanisms, including the inhibition of phagosome maturation and apoptosis, generation of cytokine-induced necrosis enabling dissemination of infection through the host, local pathology, and ultimately shedding of the pathogen. Here, we review the bovine macrophage response to infection with M. bovis and MAP. In particular, we describe how recent advances in functional genomics are shedding light on the host macrophage-pathogen interactions that underlie different mycobacterial diseases. To illustrate this, we present new analyses of previously published bovine macrophage transcriptomics data following in vitro infection with virulent M. bovis, the attenuated vaccine strain M. bovis BCG, and MAP, and discuss our findings with respect to the differing etiologies of bovine tuberculosis and

  10. Fecal microbiota transplantation via colonoscopy for recurrent C. difficile Infection.

    Science.gov (United States)

    Allegretti, Jessica R; Korzenik, Joshua R; Hamilton, Matthew J

    2014-12-08

    Fecal Microbiota Transplantation (FMT) is a safe and highly effective treatment for recurrent and refractory C. difficile infection (CDI). Various methods of FMT administration have been reported in the literature including nasogastric tube, upper endoscopy, enema and colonoscopy. FMT via colonoscopy yields excellent cure rates and is also well tolerated. We have found that patients find this an acceptable and tolerable mode of delivery. At our Center, we have initiated a fecal transplant program for patients with recurrent or refractory CDI. We have developed a protocol using an iterative process of revision and have performed 24 fecal transplants on 22 patients with success rates comparable to the current published literature. A systematic approach to patient and donor screening, preparation of stool, and delivery of the stool maximizes therapeutic success. Here we detail each step of the FMT protocol that can be carried out at any endoscopy center with a high degree of safety and success.

  11. [The usefulness of fecal tests in colorectal cancer screening].

    Science.gov (United States)

    Castells, Antoni

    2014-09-01

    Colorectal cancer is a paradigm of neoplasms that are amenable to preventative measures, especially screening. Currently, to carry this out, there are various strategies that have proven effective and efficient. In countries that have organized population-level screening programs, the most common strategy is fecal occult blood testing. In recent years, new methods have appeared that could constitute viable alternatives in the near future, among which the detection of changes in fecal DNA is emphasized. In this article, we review the most relevant papers on colorectal cancer screening presented at the annual meeting of the American Gastroenterological Association held in Chicago in May 2014, with special emphasis on the medium and long-term performance of strategies to detect occult blood in feces and the first results obtained with fecal DNA testing.

  12. Fecal coliform analyses. Method evaluation for stressed organisms

    Energy Technology Data Exchange (ETDEWEB)

    Smith, L B; Winston, H G

    1986-01-01

    No significant difference was found between two tests for fecal coliform densities using water samples from the treated sanitary waste outfalls at the Savannah River Plant, a nuclear materials production site located near Aiken, SC. These two methods of concern were the most probable number index (MPN) and the membrane filtration procedure (MF). The MPN method is the accepted method for determining fecal coliform densities in chlorinated effluents, but requires more than the MF procedure. Per Microbiological Methods for Monitoring the Environment (1978) by EPA, any decision to use the MF test for stressed organisms requires parallel testing with the MPN test. The MPN index is the number of fecal coliform bacteria that, more probably than any other number, would give the results shown by laboratory examination. It is not an actual count of coliform bacteria. The MF procedure is a direct plating method and the colonies are directly counted.

  13. Media Discourse on the Social Acceptability of Fecal Transplants.

    Science.gov (United States)

    Chuong, Kim H; O'Doherty, Kieran C; Secko, David M

    2015-10-01

    Advances in human microbiome research have generated considerable interest in elucidating the role of bacteria in health and the application of microbial ecosystem therapies and probiotics. Fecal transplants involve the introduction of gut microbes from a healthy donor's stool to the patient and have been documented as effective for treating Clostridium difficile infections (CDIs) and some other gastrointestinal disorders. However, the treatment has encountered regulatory hurdles preventing widespread uptake. We examined dominant representations of fecal transplants in Canadian media and found that fecal transplants are often represented as being inherently disgusting or distasteful (the "ick factor"). This "ick factor" is used to construct different messages about the treatment's social acceptability and legitimacy. We conclude that an over-emphasis on the "ick factor" constrains public discourse from a more nuanced discussion of the social challenges, scientific concerns, and regulatory issues surrounding the treatment.

  14. Low dietary copper increases fecal free radical production, fecal water alkaline phosphatase activity and cytotoxicity in healthy men.

    Science.gov (United States)

    Davis, Cindy D

    2003-02-01

    One possible dietary factor that may increase susceptibility to colon cancer is inadequate copper intake. The objective of this study was to investigate the effects of low and adequate copper intakes on copper nutriture and putative risk factors for colon cancer susceptibility in healthy men. Seventeen healthy free-living nonsmoking men aged 21-52 y completed a 13-wk controlled feeding study in a randomized crossover design. The basal diet contained 0.59 mg Cu/13.65 MJ. After a 1-wk equilibration period in which the men consumed the basal diet supplemented with 1.0 mg Cu/d, they were randomly assigned to receive either the basal diet or the basal diet supplemented with 2 mg Cu/d for 6 wk. After the first dietary period, the men immediately began to consume the other level of Cu for the last 6 wk. They collected their feces during the equilibration period and during the last 2 wk of the two dietary periods for free radical and fecal water analysis. Low dietary copper significantly (P copper significantly (P copper concentrations but did not affect fecal water volume, pH, iron or zinc concentrations. In contrast to the fecal analysis, hematological indicators of copper status were not significantly affected by the dietary treatments. These results suggest that low dietary copper adversely affects fecal free radical production and fecal water alkaline phosphatase activity, which are putative risk factors for colon cancer.

  15. Bovine spongiform encephalopathy in sheep?

    NARCIS (Netherlands)

    Schreuder, B.E.C.; Somerville, R.A.

    2003-01-01

    Bovine spongiform encephalopathy (BSE) in sheep has not been identified under natural conditions at the time of writing and remains a hypothetical issue. However, rumours about the possible finding of a BSE-like isolate in sheep have led to great unrest within the sheep industry, among the general p

  16. A Content Incontinent: Report of Liposomal Bupivacaine Induced Fecal Incontinence

    Directory of Open Access Journals (Sweden)

    Emanuel A. Shapera

    2016-01-01

    Full Text Available Proper surgical management of anal fistula demands sound clinical judgment and extraordinary care to prevent incontinence and adequate postoperative pain control and provide satisfactory resolution to optimize quality of life. Fecal incontinence can be a devastating complication of procedures performed for fistula in ano. We report a unique case in which temporary incontinence (for less than 4 days followed injection of liposomal bupivacaine for postoperative pain control after draining seton placement for fistula in ano. Patients and physicians should be aware as it may be mistaken for a more serious anatomical and permanent cause of fecal incontinence.

  17. Fecal pellets: role in sedimentation of pelagic diatoms.

    Science.gov (United States)

    Schrader, H J

    1971-10-01

    Membrane-enclosed fecal pellets of planktonic herbivores were sampled at several depths in the Baltic Sea (459 meters deep) and off Portugal (4000 meters deep) by means of a Simonsen multinet. Pellets contained mainly empty shells of planktonic diatoms and silicoflagellates. Two kinds of fecal pellets were found, those with the remains of one species (for example, Thalassiosira baltica) and those with the remains of several species (for example, Chaetoceros, Achnanthes, and Thalassiosira). Siliceous skeletons were protected from dissolution during settling by a membrane around the pellet.

  18. Fecal specimens preparation methods for PCR diagnosis of human taeniosis

    Directory of Open Access Journals (Sweden)

    Nunes Cáris Maroni

    2006-01-01

    Full Text Available Sample preparation and DNA extraction protocols for DNA amplification by PCR, which can be applied in human fecal samples for taeniasis diagnosis, are described. DNA extracted from fecal specimens with phenol/chloroform/isoamilic alcohol and DNAzol® reagent had to be first purified to generate fragments of 170 pb and 600 pb by HDP2-PCR. This purification step was not necessary with the use of QIAmp DNA stool mini kit®. Best DNA extraction results were achieved after eggs disruption with glass beads, either with phenol/chloroform/isoamilic alcohol, DNAzol® reagent or QIAmp DNA stool mini kit®.

  19. Current Microbial Isolates from Wound Swab and Their Susceptibility Pattern in a Private Medical College Hospital in Dhaka city

    Directory of Open Access Journals (Sweden)

    Shahin Sultana

    2015-03-01

    Full Text Available Background: Wound infection is one of the major health problems that are caused and aggravated by the invasion of pathogenic organisms where empiric treatment is routine. Objective: To isolate and identify the bacteria causing wound infection and to determine the antimicrobial susceptibility pattern. Materials and method: A total of 263 wound swab and pus samples were collected during the period of January to December 2012 from Delta Medical College and Hospital, Dhaka, Bangladesh. Swabs from the wound were inoculated on appropriate media and cultured and the isolates were identified by standard procedures as needed. Antimicrobial susceptibility testing was performed by disk diffusion method according to ‘The Clinical Laboratory Standard Institute’ guidelines. Results: In this study 220 bacterial isolates were recovered from 263 samples showing an isolation rate of 83.65%. The predominant bacteria isolated from infected wounds were Staphylococcus aureus 89 (40.45% followed by Escherichia coli 62 (28.18%, Pseudomonas aeruginosa 34 (15.45%, Enterococci 18 (8.18%, Acinetobacter 5 (2.27%, Klebsiella 9 (4.09% and Proteus 3 (3.36%. Staphylococcus aureus was sensitive to linezolid (94.38%, fusidic acid (91.01%, vancomycin (87.64%, amikacin (74.15% and gentamicin (73.03%. Among the Gram negative isolates Escherichia coli was predominant and showed sensitivity to imipenem (93.54% amikacin (83.87% colistin (53.22% and piperacillin and tazobactum (53.22% and pseudomonas showed sensitivity to amikacin (73.52%, imipenem (70.58% and colistin (70.58%. Conclusion: Staphylococcus aureus was the most frequently isolated pathogen from wound swab and the antibiotic sensitivity pattern of various isolates help to assist the clinician in appropriate selection of empirical antibiotics against wound infection.

  20. [Investigation of Chlamydia trachomatis with Cell Culture, DFA and PCR Methods in the Genital Swab Samples of Symptomatic Patients].

    Science.gov (United States)

    Ozüberk, Osman Özüberk; Gökahmetoğlu, Selma; Ozçelik, Bülent; Ekmekçioğlu, Oğuz

    2013-01-01

    Chlamydia trachomatis infection is considered the most prevalent bacterial sexually transmitted disease worldwide. C.trachomatis causes eye infections such as trachoma and newborn inclusion conjunctivitis, newborn pneumonia, genitourinary system infections and suppurative inguinal lymphadenitis namely lymphogranuloma venerum. The aim of this study was to investigate C.trachomatis by direct fluorescent antibody (DFA), polymerase chain reaction (PCR) and cell culture methods in the clinical samples sent to the microbiology laboratory with the prediagnosis of genital infections. A total of 50 swab samples obtained from adult patients (49 female, 1 male) who were admitted to Erciyes University Hospital, Kayseri, Turkey between February-March 2010, were included in the study. C.trachomatis antigens were investigated by a commercial DFA (PathoDx, Remel, USA) method. McCoy cell cultures prepared in microplate wells were used for the isolation of C.trachomatis. The growth of C.trachomatis in cell cultures was confirmed by DFA and iodine staining methods. C.trachomatis DNA was investigated by commercially available PCR (Chlamydia trachomatis 330/740 IC; Sacace, Italy) method. In our study, 4 (8%) of the 50 swab samples were found positive with DFA, 1 (2%) was positive with cell culture, and 1 (2%) was positive with PCR. The only sample that gave positive results with all of the three methods was an urethral swab. Three cervical swab samples that were found positive only with DFA method was evaluated as false positivity. When cell culture was considered as the reference method, the sensitivity and specificity of DFA method were estimated as 100% and 94%, respectively, while those rates for PCR were 100% and 100%, respectively. In conclusion, although cell culture is still the gold standard in the diagnosis of C.trachomatis. infections, since it is time consuming and difficult to apply, more rapid and reliable PCR methods may be applied in diagnosis. DFA method which is

  1. Helminth Parasites of Conventionally Maintained Laboratory Mice: II- Inbred Strains with an Adaptation of the Anal Swab Technique

    Directory of Open Access Journals (Sweden)

    Lucineide Gonçalves

    1998-01-01

    Full Text Available Worm burdens recovered from inbred mice strains, namely C57Bl/6, C57Bl/10, CBA, BALB/c, DBA/2 and C3H/He, conventionally maintained in two institutional animal houses in the State of Rio de Janeiro, RJ, Brazil, were analyzed and compared, regarding their prevalences and mean intensities.Three parasite species were observed: the nematodes Aspiculuris tetraptera, Syphacia obvelata and the cestode Vampirolepis nana. A modification of the anal swab technique is also proposed for the first time as an auxiliary tool for the detection of oxyurid eggs in mice

  2. Enterococcus and Escherichia coli fecal source apportionment with microbial source tracking genetic markers - is it feasible?

    Science.gov (United States)

    Fecal pollution is measured in surface waters using culture-based measurements of enterococci and Escherichia coli bacteria. Source apportionment of these two fecal indicator bacteria is an urgent need for prioritizing remediation efforts and quantifying health risks associated...

  3. Differential decay of Enterococci and Escherichia coli originating from two fecal pollution sources

    Science.gov (United States)

    Using in situ subtropical aquatic mesocosms, fecal source (cattle manure versus sewage) was shown to be the most important contributor to differential loss in viability of fecal indicator bacteria (FIB), specifically enterococci in freshwater and Escherichia coli in marine habita...

  4. HUMAN FECAL SOURCE IDENTIFICATION: REAL-TIME QUANTITATIVE PCR METHOD STANDARDIZATION - abstract

    Science.gov (United States)

    Method standardization or the formal development of a protocol that establishes uniform performance benchmarks and practices is necessary for widespread adoption of a fecal source identification approach. Standardization of a human-associated fecal identification method has been...

  5. Human Fecal Source Identification: Real-Time Quantitative PCR Method Standardization

    Science.gov (United States)

    Method standardization or the formal development of a protocol that establishes uniform performance benchmarks and practices is necessary for widespread adoption of a fecal source identification approach. Standardization of a human-associated fecal identification method has been...

  6. 77 FR 15847 - Bovine Spongiform Encephalopathy; Importation of Bovines and Bovine Products

    Science.gov (United States)

    2012-03-16

    ... been fed ruminant protein, other than milk protein, during their lifetime; The bovines from which the... from animals that are not known to have been fed ruminant protein, other than milk protein, during... community is that the agent is an abnormal form of a normal protein known as cellular prion protein. The...

  7. Advances in Fecal Occult Blood Tests: The FIT Revolution

    NARCIS (Netherlands)

    G.P. Young; E.L. Symonds (Erin L.); J.E. Allison (James E.); S.R. Cole (Stephen R.); C.G. Fraser (Callum G.); S. Halloran (S.); E.J. Kuipers (Ernst); H.E. Seaman (Helen E.)

    2015-01-01

    textabstractThere is a wide choice of fecal occult blood tests (FOBTs) for colorectal cancer screening. Goal: To highlight the issues applicable when choosing a FOBT, in particular which FOBT is best suited to the range of screening scenarios. Four scenarios characterize the constraints and expectat

  8. Fecal Microbiota Transplantation for Clostridium difficile-Associated Diarrhea.

    Science.gov (United States)

    Cohen, Nathaniel A; Ben Ami, Ronen; Guzner-Gur, Hanan; Santo, Moshe E; Halpern, Zamir; Maharshak, Nitsan

    2015-08-01

    Clostridium difficile-associated diarrhea is a problem most hospital-based physicians will face in their career. This review aims to refresh current knowledge with regard to Clostridium difficile infection and bring physicians up to date with the latest developments in the growing field of fecal microbiota transplantation, the benefits it offers, and the promise this and other developments hold for the future.

  9. Fecal Microbiota Transplant Protocol for Clostridium Difficile Infection

    OpenAIRE

    Tauxe, William M.; Dhere, Tanvi; Ward, Angela; Racsa, Lori D.; Varkey, Jay B.; Kraft, Colleen S.

    2015-01-01

    Fecal microbiota transplant has become more acceptable as a therapeutic for recurrent Clostridium difficile infection. The FDA has an enforcement discretion policy for practitioner's performing this therapy, which includes informed consent for this experimental treatment. This manuscript describes a typical procedure that can be followed that includes the important aspects of this preparation and treatment.

  10. What do fecal coliforms indicate in tropical waters

    Energy Technology Data Exchange (ETDEWEB)

    Hazen, T.C.

    1988-01-01

    High densities of total and fecal coliform bacteria have been detected in pristine streams and in ground water samples collected from many tropical parts of the world, even in epiphytic vegetation 10 m above ground in the rain forest of Puerto Rico. Nucleic acid (DNA) analyses of Escherichia coli from pristine tropical environs has indicated that they are identical to clinical isolates of E. coli. Many tropical source waters have been shown to have enteric pathogens in the complete absence of coliforms. Diffusion chamber studies with E. coli at several tropical sites reveal that this bacterium can survive indefinitely in most freshwaters in Puerto Rico. An evaluation of methods for the enumeration of fecal coliforms showed that currently used media have poor reliability as a result of large numbers of false positive and false negative results when applied to tropical water samples. Total and fecal coliform bacteria are not reliable indicators of recent biological contamination of waters in tropical areas. Fecal streptococci and coliphages in tropical waters, violate the same under lying assumptions of indicator assays as the coliforms. Anaerobic bacteria like Bifidobacterium spp. and Clostridium perfringens show some promise in terms of survival but not in ease of enumeration and media specificity. The best course at present lies in using current techniques for direct enumeration of pathogens by fluorescent staining and nucleic acid analysis and developing tropical maximum containmant levels for certain resistant pathogens in tropical waters. 66 refs.

  11. Avian influenza infection alters fecal odor in mallards.

    Directory of Open Access Journals (Sweden)

    Bruce A Kimball

    Full Text Available Changes in body odor are known to be a consequence of many diseases. Much of the published work on disease-related and body odor changes has involved parasites and certain cancers. Much less studied have been viral diseases, possibly due to an absence of good animal model systems. Here we studied possible alteration of fecal odors in animals infected with avian influenza viruses (AIV. In a behavioral study, inbred C57BL/6 mice were trained in a standard Y-maze to discriminate odors emanating from feces collected from mallard ducks (Anas platyrhynchos infected with low-pathogenic avian influenza virus compared to fecal odors from non-infected controls. Mice could discriminate odors from non-infected compared to infected individual ducks on the basis of fecal odors when feces from post-infection periods were paired with feces from pre-infection periods. Prompted by this indication of odor change, fecal samples were subjected to dynamic headspace and solvent extraction analyses employing gas chromatography/mass spectrometry to identify chemical markers indicative of AIV infection. Chemical analyses indicated that AIV infection was associated with a marked increase of acetoin (3-hydroxy-2-butanone in feces. These experiments demonstrate that information regarding viral infection exists via volatile metabolites present in feces. Further, they suggest that odor changes following virus infection could play a role in regulating behavior of conspecifics exposed to infected individuals.

  12. Chocolate consumption, fecal water antioxidant activity, and hydroxyl radical production.

    Science.gov (United States)

    Record, Ian R; McInerney, Jennifer K; Noakes, Manny; Bird, Anthony R

    2003-01-01

    As part of a larger study into the effects of polyphenols derived from chocolate on bowel health we have compared the effects of consumption of chocolate containing either 200 mg of flavanols and related procyanidins or a similar chocolate containing less than 10 mg of polyphenols on fecal free radical production and antioxidant activity in 18 volunteers. In a double-blind crossover trail volunteers consumed chocolate for two 4-wk periods separated by a 4-wk washout period. During the time the volunteers consumed the chocolate they also consumed a low-polyphenol diet. Free radical production in the fecal water was lowered from 122 +/- 10 micromol/l/h to 94 +/- 9 micromol/l/h (P = 0.009) when the high procyanidin chocolate diet was consumed and from 117 +/- 14 micromol/l/h to 86 +/- 12 micromol/l/h when the low procyanidin chocolate was consumed (P = 0.014). Fecal water antioxidant capacity measured by either the Trolox equivalent antioxidant capacity or ferric reducing ability of plasma procedure was not significantly affected. Consumption of either chocolate reduced the production of free radicals in fecal water. This suggests that some component of the chocolate other than the flavanols and related procyanidins may have been effective.

  13. Requirement of the laying hen for apparent fecal digestible lysine

    NARCIS (Netherlands)

    Schutte, J.B.; Smink, W.

    1998-01-01

    A study was conducted to determine the requirement for lysine of a White Leghorn strain of hens with a body weight of approximately 1,600 g. Before starting the experiment, apparent fecal digestibility of amino acids of the basal diet was determined in an in vivo digestibility trial with six individ

  14. Prevalence of equine herpesvirus type 2 (EHV-2) DNA in ocular swabs and its cell tropism in equine conjunctiva.

    Science.gov (United States)

    Borchers, K; Ebert, M; Fetsch, A; Hammond, T; Sterner-Kock, A

    2006-12-20

    Equine herpes virus 2 (EHV-2), a gamma(2)-herpesvirus, is common in horses of all ages. Its role as a primary pathogen is unclear but there is an association between EHV-2, respiratory disease and keratoconjunctivitis. The purpose of this study was to gain more information on the prevalence of EHV-2 DNA in conjunctival swabs from horses with and without ocular disease and to define the anatomical site and cell type harbouring viral genome or antigen. By polymerase chain reaction (PCR) 22 out of 77 (28.6%) ocular swabs of clinically healthy and only 4 out of 48 (8.3%) samples from diseased horses were positive. To define the main virus reservoir ocular tissue from 13 randomly selected horses without pathological evidence of ocular disease were analysed by nested PCR. In two horses optic nerve, lacrimal gland and conjunctiva, in further two cases lacrimal gland and conjunctiva and in four horses the conjunctiva only were EHV-2 PCR positive. For specifying the target cell we focused on conjunctivae and selected 3 out of 15 clinically healthy slaughterhouse horses positive for EHV-2 by PCR. In situ hybridisation on sections of these paraffin embedded conjunctivae localized viral genome in histiocyte-like cells of the submucosa. Immunohistochemical staining with an EHV-2 or S100 specific polyclonal antiserum demonstrated that Langerhans cells were co-localized in the same region of the sample section where virus positive cells were detected. Furthermore, we concluded that detection of viral antigen revealed a productive virus infection.

  15. Evaluation of 292 ocular swabs, vitreous and aqueous cultures in pathologies with severe prognosis during a 24-month observation period

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    Franco Giardini

    2010-12-01

    Full Text Available Introduction. Different part of the eye can be infected by bacteria, fungi, parasites and viruses (5. The aim of this study was to assess the importance of ocular swabs culture in pathologies with severe prognosis. Methods.We examined 292 patients with a severe diseases: 98% of those used topical and/or systemic antibiotic therapy.All sample were cultured both into a chocolate agar medium and into an Haemophilus selective agar and, at the same time, inoculated onto a modified blood cuture. Results. 75 out of 292 (25.7% patients tested negative.The most representative microorganisms were: Coagulase-negative staphylococci (CNS (20%, Staphylococcus aureus (12%, member of the Pseudomonadaceae family (10.9%, Streptococcus pneumoniae (9%, alpha haemolytic streptococci (8.2%, Fungus and Yeast (5.4%. Considering the type of cultures: 54.5% of the vitreous cultures were positive and 45.5% were negative; 38.2% of the positive cultures were referred to endophthalmitis, with prevalence of CNS (32.5% and S. aureus (22.9%, while 27.6% were due to an abscesces, with prevalence of members of the Pseudomonadaceae family (53.3%, CNS (23.3% and S. pneumoniae (16.7%. Conclusions. This data suggest the importance of the ocular swabs, vitreous and aqueous cultures in the therapeutic approach of the diseases with a severe prognosis and emphasize the good performance of the modified Bactec Plus system.

  16. "DETECTION OF BACTERIAL, METHICILLIN RESISTANCE, AND β-LACTAMASE GENES FOUND IN WOUND SWABS BY MULTIPLEX POLYMERASE CHAIN REACTION"

    Directory of Open Access Journals (Sweden)

    S. Sadeghian

    2004-05-01

    Full Text Available Coagulase-positive and coagulase negative, methicillin-resistant staphylococci are major causes of serious nosocomial infections and it is very important to have a reliable test to detect these bacteria. A multiplex polymerase chain reaction (mPCR was used on 100 clinical samples for simultaneous amplification of the universal bacterial, mec-A encoding the penicillin binding protein 2a, which is associated with staphylococcal methicillin resistance and TEM-1 encoding the β-lactamase, which accounts for the majority of all cases of the plasmid β-lactamase resistance worldwide. Out of 100 wound swabs tested, 99% with universal primers, 26% with TEM-1 primers and 6% with mec-A primers were positive. Dot blot Digoxigenin hybridization on the 30 samples was carried out to confirm identified bacteria with specific bacterial probes. Out of 100 wound swabs, 38% were positive with Staphylococcus aureus probe, 23% were positive with enteric bacteria probe, 7% were positive with Streptococcus agalactia probe and 1% were positive with Haemophilus influenza probe. The mPCR method used in this study, was designed to be incorporated into the workflow of the clinical microbiology laboratory and allows for the identification of intrinsic resistance in a timely and reliable manner.

  17. Evaluation of the SimPlate method for enumeration of Escherichia coli in swab samples from beef and lamb carcasses.

    Science.gov (United States)

    Hauge, Sigrun J; Nesbakken, Truls; Skjerve, Eystein; Dommarsnes, Kari; Østensvik, Øyvin

    2010-08-15

    Abattoirs have to enumerate Escherichia coli on carcass surfaces as part of compulsory HACCP monitoring and they therefore need rapid and reliable methods. The objective of this study was to compare a conventional plating method with a faster, simpler method for detection and enumeration of E. coli in samples from naturally contaminated carcasses. The two methods were the conventional pour plate method of the Nordic Committee on Food Analysis; NMKL Method No. 125, and the enzymatic method of SimPlate Coliforms &E. coli. Materials were 588 cotton-cloth samples used for swabbing 100 cm(2) areas on four sites on cattle and lamb carcasses in three commercial abattoirs in Norway. E. coli was detected by at least one of the methods in 270 (46%) of the samples. Forty-five samples (8%) were positive only by SimPlate while 28 samples (5%) were positive only by NMKL125. Cohen's kappa value was 0.74 for detection/non-detection results, which showed a high level of agreement between the two methods. E. coli counts determined by the conventional NMKL125 method showed a high concordance correlation (ccc 0.80, slope 0.99) with most probable number (MPN) values obtained with SimPlate. SimPlate is a rapid and reliable method for detection and enumeration of E. coli and a suitable alternative method for use with swab samples from cattle and lamb carcasses.

  18. Isolation and characterization of bovine parainfluenza virus type 3 from water buffaloes (Bubalus bubalis in Argentina

    Directory of Open Access Journals (Sweden)

    Maidana Silvina S

    2012-06-01

    Full Text Available Abstract Background Parainfluenza virus type 3 (PIV3 was isolated from dairy buffaloes (Bubalus bubalis naturally affected with respiratory and reproductive clinical conditions. Results Examination of nasal and vaginal swabs collected from 12 diseased buffaloes led to the isolation of three paramyxovirus isolates from two animals. Antigenic, morphological and biological characteristics of these three isolates were essentially similar to those of members of the Paramyxoviridae family. Antigenic analysis by direct immunofluorescence and cross neutralization test placed these isolates together with bovine parainfluenza virus type 3 (BPIV3. Nucleotide and amino acid phylogenetic analysis of partial matrix gene sequences of the buffalo isolates and six field BPIV3 isolates from bovines in Argentina were studied. Buffalo isolates were similar to genotype B (BPIV3b while the six BPIV3 isolates were similar to genotypes A (BPIV3a and C (BPIV3c. Conclusions This is the first characterization of BPIV3 in water buffalo. According to the samples analyzed, in Argentina, the genotype B was found in buffalo and the genotypes A and C were found in cattle.

  19. Bovine cysticercosis situation in Brazil

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    Gabriel Augusto Marques Rossi

    2014-02-01

    Full Text Available The taeniasis-cysticercosis complex is a long known zoonotic parasitosis characteristic of underdeveloped countries. In addition to its public health significance, this parasitosis is cause of economic losses to the beef production chain, and synonymous of technical inadequacy in relation to the adoption of Good Agricultural Practices. The occurrences of both human teniasis and bovine cysticercosis could and should be controlled with basic sanitary measures. However, there is much variation in the occurrence of the disease in cattle, characterizing a low rate of technical development as well as problems related to the adoption of basic sanitation measures. This review describes, in details, the causative agent and its epidemiological chain, besides raising current information about the occurrence of bovine cysticercosis in different regions of Brazil, aiming at the adoption of prophylactic measures by different segments responsible.

  20. Antibiotic resistance analysis of fecal coliforms to determine fecal pollution sources in a mixed-use watershed.

    Science.gov (United States)

    Burnes, Brian S

    2003-06-01

    Antibiotic resistance analysis was performed on fecal coliform (FC) bacteria from a mixed-use watershed to determine the source, human or nonhuman, of fecal coliform contamination. The study consisted of discriminant analysis of antibiotic resistance patterns generated by exposure to four concentrations of six antibiotics (ampicillin, gentamicin sulfate, kanamycin, spectinomycin dihydrochloride, streptomycin sulfate, and tetracycline hydrochloride). A reference database was constructed from 1125 fecal coliform isolates from the following sources: humans, domestic animals (cats and dogs), agricultural animals (chickens, cattle, and horses), and wild animals. Based on similar antibiotic resistance patterns, cat and dog isolates were grouped as domestic animals and horse and cattle isolates were grouped as livestock. The resulting average rate of correct classification (ARCC) for human and nonhuman isolates was 94%. A total of 800 FC isolates taken from the watershed during either a dry event or a wet event were classified according to source. Human sources contribute a majority (> 50%) of the baseflow FC isolates found in the watershed in urbanized areas. Chicken and livestock sources are responsible for the majority of the baseflow FC isolates found in the rural reaches of the watershed. Stormwater introduces FC isolates from domestic (approximately 16%) and wild (approximately 21%) sources throughout the watershed and varying amounts (up to 60%) from chicken and livestock sources. These results suggest that antibiotic resistance patterns of FC may be used to determine sources of fecal contamination and aid in the direction of water quality improvement.

  1. Infectious bovine keratoconjunctivitis: a review.

    Science.gov (United States)

    Brown, M H; Brightman, A H; Fenwick, B W; Rider, M A

    1998-01-01

    The economic impact of infectious bovine keratoconjunctivitis (IBK) warrants continued investigation of the mechanisms by which Moraxella bovis survives on and colonizes the corneal surface. Virulent strains of M bovis produce hemolysin and exhibit different plasmid profiles than nonvirulent strains. Interactions among host, environment, vector, season, and concurrent infection influence the prevalence of IBK. Mycoplasma sp. or infectious bovine rhinotracheitis virus may enhance or hasten the disease process. The manifestations of IBK may range from mild conjunctivitis to severe ulceration, corneal perforation, and blindness. Treatment of IBK is dictated by economic considerations, intended animal use, and feasibility of administration. Antibiotic therapy is aimed at achieving drug concentrations in tears to meet or exceed the minimum inhibitory concentration for prolonged periods. At present, IBK is not a preventable disease. Affected animals must be separated from the herd and vector control vigorously instituted. Carrier animals must be identified and removed from the herd. Vaccination trials have been unsuccessful because of pili antigen cross-reactivity, variable strains, and uncontrolled environmental factors. Recent investigations have determined that M bovis may utilize host iron sources via iron-repressible outer membrane proteins and siderophores for growth. Elucidation of normal defense mechanisms of the bovine eye may lead to new strategies to enhance the immune response against M bovis.

  2. A predictive model combining fecal calgranulin B and fecal occult blood tests can improve the diagnosis of colorectal cancer.

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    Byung Chang Kim

    Full Text Available AIM: Current fecal screening tools for colorectal cancer (CRC, such as fecal occult blood tests (FOBT, are limited by their low sensitivity. Calgranulin B (CALB was previously reported as a candidate fecal marker for CRC. This study investigated whether a combination of the FOBT and fecal CALB has increased sensitivity and specificity for a diagnosis of CRC. MATERIALS AND METHODS: Patients with CRC (n = 175, and healthy individuals (controls; n = 151 were enrolled into the development (81 cases and 51 controls and validation (94 cases and 100 controls sets. Stool samples were collected before bowel preparation. CALB levels were determined by western blotting. FOBT and fecal CALB results were used to develop a predictive model based on logistic regression analysis. The benefit of adding CALB to a model with only FOBT was evaluated as an increased area under the receiver operating curve (AUC, partial AUC, and reclassification improvement (RI in cases and controls, and net reclassification improvement (NRI. RESULTS: Mean CALB level was significantly higher in CRC patients than in controls (P<0.001. CALB was not associated with tumor stage or cancer site, but positivity on the FOBT was significantly higher in advanced than in earlier tumor stages. At a specificity of 90%, the cross-validated AUC and sensitivity were 89.81% and 82.72%, respectively, in the development set, and 92.74% and 79.79%, respectively, in the validation set. The incremental benefit of adding CALB to the model, as shown by the increase in AUC, had a p-value of 0.0499. RI in cases and controls and NRI all revealed that adding CALB significantly improved the prediction model. CONCLUSION: A predictive model using a combination of FOBT and CALB may have greater sensitivity and specificity and AUC for predicting CRC than models using a single marker.

  3. Correcting for Microbial Blooms in Fecal Samples during Room-Temperature Shipping

    Science.gov (United States)

    Amir, Amnon; McDonald, Daniel; Navas-Molina, Jose A.; Debelius, Justine; Morton, James T.; Hyde, Embriette; Robbins-Pianka, Adam

    2017-01-01

    ABSTRACT The use of sterile swabs is a convenient and common way to collect microbiome samples, and many studies have shown that the effects of room-temperature storage are smaller than physiologically relevant differences between subjects. However, several bacterial taxa, notably members of the class Gammaproteobacteria, grow at room temperature, sometimes confusing microbiome results, particularly when stability is assumed. Although comparative benchmarking has shown that several preservation methods, including the use of 95% ethanol, fecal occult blood test (FOBT) and FTA cards, and Omnigene-GUT kits, reduce changes in taxon abundance during room-temperature storage, these techniques all have drawbacks and cannot be applied retrospectively to samples that have already been collected. Here we performed a meta-analysis using several different microbiome sample storage condition studies, showing consistent trends in which specific bacteria grew (i.e., “bloomed”) at room temperature, and introduce a procedure for removing the sequences that most distort analyses. In contrast to similarity-based clustering using operational taxonomic units (OTUs), we use a new technique called “Deblur” to identify the exact sequences corresponding to blooming taxa, greatly reducing false positives and also dramatically decreasing runtime. We show that applying this technique to samples collected for the American Gut Project (AGP), for which participants simply mail samples back without the use of ice packs or other preservatives, yields results consistent with published microbiome studies performed with frozen or otherwise preserved samples. IMPORTANCE In many microbiome studies, the necessity to store samples at room temperature (i.e., remote fieldwork) and the ability to ship samples without hazardous materials that require special handling training, such as ethanol (i.e., citizen science efforts), is paramount. However, although room-temperature storage for a few days has

  4. Bovine Chymosin: A Computational Study of Recognition and Binding of Bovine κ-Casein

    DEFF Research Database (Denmark)

    Palmer, David S.; Christensen, Anders Uhrenholt; Sørensen, Jesper

    2010-01-01

    Bovine chymosin is an aspartic protease that selectively cleaves the milk protein κ-casein. The enzyme is widely used to promote milk clotting in cheese manufacturing. We have developed models of residues 97-112 of bovine κ-casein complexed with bovine chymosin, using ligand docking, conformational...

  5. Stability of Bovine viral diarrhea virus 1 nucleic acid in fetal bovine samples stored under different conditions.

    Science.gov (United States)

    Ridpath, Julia F; Neill, John D; Chiang, Yu-Wei; Waldbillig, Jill

    2014-01-01

    Infection of pregnant cattle with both species of Bovine viral diarrhea virus (BVDV) can result in reproductive disease that includes fetal reabsorption, mummification, abortion, stillbirths, congenital defects affecting structural, neural, reproductive, and immune systems, and the birth of calves persistently infected with BVDV. Accurate diagnosis of BVDV-associated reproductive disease is important to control BVDV at the production unit level and assessment of the cost of BVDV infections in support of BVDV control programs. The purpose of the current study was to examine the stability of viral nucleic acid in fetal tissues exposed to different conditions, as measured by detection by polymerase chain reaction. Five different types of fetal tissue, including brain, skin and muscle, ear, and 2 different pooled organ samples, were subjected to conditions that mimicked those that might exist for samples collected after abortions in production settings or possible storage conditions after collection and prior to testing. In addition, tissues were archived for 36 months at -20°C and then retested, to mimic conditions that might occur in the case of retrospective surveillance studies. Brain tissue showed the highest stability under the conditions tested. The impact of fecal contamination was increased following archiving in all tissue types suggesting that, for long-term storage, effort should be made to reduce environmental contaminants before archiving.

  6. Comparing urine samples and cervical swabs for Chlamydia testing in a female population by means of Strand Displacement Assay (SDA

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    Wentzel-Larsen Tore

    2010-03-01

    Full Text Available Abstract Background There has been an increasing number of diagnosed cases of Chlamydia trachomatis in many countries, in particular among young people. The present study was based on a growing request to examine urine as a supplementary or primary specimen in screening for Chlamydia trachomatis in women, with the Becton Dickinson ProbeTec (BDPT Strand Displacement Assay (SDA. Urine samples may be particularly important in screening young people who are asymptomatic. Methods A total of 603 women aged 15 and older were enrolled from the Sexually Transmitted Infection (STI clinic at Haukeland University Hospital, Norway, in 2007. Only 31 women were older than 35 years. Cervical swabs and urine samples were tested with BDPT for all participants. In cases of discrepant test results from a given patient, both samples were retested by Cobas TaqManCT and a Polymerase Chain Reaction (PCR-method (in-house. Prevalence of C. trachomatis, sensitivity, and specificity were estimated by latent class analysis using all test results available. Bootstrap BC confidence intervals (10 000 computations were estimated for sensitivity and specificity, and their differences in cervix vs. urine tests. Results A total of 1809 specimens were collected from 603 patients. 80 women (13.4% were positive for C. trachomatis. Among these, BDPT identified 72 and 73 as positive in cervix and urine samples, respectively. Of the 523 C. trachomatis negative women, BDPT identified 519 as negative based on cervical swabs, and 514 based on urine samples. Sensitivity for cervical swabs and urine samples with the BDPT were 89.0% (95% CI 78.8, 98.6 and 90.2% (95% CI 78.1, 95.5, respectively. The corresponding values for specificity were 99.2% (95% CI 98.3, 100 and 98.3% (95% CI 96.4, 100. Conclusions This study indicates that urine specimens are adequate for screening high-risk groups for C. trachomatis by the SDA method (BDPT. Such an approach may facilitate early detection and treatment

  7. Three-dimensional modeling of fecal coliform in the Tidal Basin and Washington Channel, Washington, DC.

    Science.gov (United States)

    Bai, Sen; Lung, Wu-Seng

    2006-01-01

    Fecal coliform are widely used as bacterial indicator in the United States and around the world. Fecal coliform impaired water is highly possible to be polluted by pathogenic bacteria. The Tidal Basin and Washington Channel in Washington, DC are on the Total Maximum Daily Load (TMDL) list due to the high fecal coliform level. To support TMDL development, a three-dimensional numerical model of fecal coliform was developed using the EFDC framework. The model calculates the transport of fecal coliform under the influences of flap gate operations and tidal elevation. The original EFDC code was modified to calculate the die-off of fecal coliform under the impact of temperature and solar radiation intensity. The watershed contribution is expressed as storm water inflow and the load carried by the runoff. Model results show that fecal coliform vary strongly in space in both the Tidal Basin and Washington Channel. The storm water only impacts a small area around the storm water outfall in the Tidal Basin and the impacts are negligible in the Washington Channel due to dilution. The water from the Potomac River may affect the fecal coliform level in the area close to the flap gate in the Tidal Basin. The fecal coliform level in the Washington Channel is mainly controlled by the fecal coliform level in the Anacostia River, which is located at the open boundary of the Washington Channel. The potential sediment layer storage of fecal coliform was analyzed and it was found that the sediment layer fecal coliform level could be much higher than the water column fecal coliform level and becomes a secondary source under high bottom shear stress condition. The developed model built solid connection of fecal coliform source and concentration in the water column and has been used to develop TMDL.

  8. Bovine viral diarrhoea, bovine herpesvirus and parainfluenza-3 virus infection in three cattle herds in Egypt in 2000.

    Science.gov (United States)

    Aly, N M; Shehab, G G; Abd el-Rahim, I H A

    2003-12-01

    This study reported field outbreaks of bovine viral diarrhoea virus (BVDV) infection, either alone or mixed with bovine herpesvirus-1 (BHV-1) and/or parainfluenza-3 virus (PI-3V) in Egypt during 2000. In Lower Egypt, young calves in three cattle herds in El-Minufiya Province, El-Fayoum Province and in governmental quarantine in El-Behira Province, showed symptoms of enteritis, either alone or accompanied by respiratory manifestations. The affected herds were visited and the diseased animals were clinically examined. Many epidemiological aspects, such as morbidities, mortalities and case fatalities, as well as the abortive rate, were calculated. Ethylenediamine tetra-acetic acid-blood samples, sterile nasal swabs and serum samples were obtained for virological and serological diagnosis. The laboratory investigations revealed that the main cause of calf mortalities in the three herds was infection with BVDV, either alone, as on the El-Minufiya farm, or mixed with PI-3V, as on the El-Fayoum farm, or mixed with both BHV-1 and PI-3V, as in the herd in governmental quarantine in El-Behira Province. A total of nine dead calves from the three herds were submitted for thorough post-mortem examination. Tissue samples from recently dead calves were obtained for immunohistochemical and histopathological studies. The most prominent histopathological findings were massive degeneration, necrosis and erosions of the lining epithelium of the alimentary tract. Most of the lymphoreticular organs were depleted of lymphocytes. In pneumonic cases, bronchopneumonia and atypical interstitial pneumonia were evident. The present study suggested that the immunosuppressive effect of BVDV had predisposed the animals to secondary infection with BHV-1 and PI-3V. This study concluded that concurrent infection with BVDV, BHV-1 and PI-3V should be considered as one of the infectious causes of pneumoenteritis and, subsequently, the high morbidities and mortalities among young calves in Egypt

  9. Detection of Trichomonas vaginalis DNA by use of self-obtained vaginal swabs with the BD ProbeTec Qx assay on the BD Viper system.

    Science.gov (United States)

    Van Der Pol, Barbara; Williams, James A; Taylor, Stephanie N; Cammarata, Catherine L; Rivers, Charles A; Body, Barbara A; Nye, Melinda; Fuller, Deanna; Schwebke, Jane R; Barnes, Mathilda; Gaydos, Charlotte A

    2014-03-01

    Trichomonas vaginalis is the most prevalent nonviral sexually transmitted infection worldwide, and improved diagnostic methods are critical for controlling this pathogen. Diagnostic assays that can be used in conjunction with routine chlamydia/gonorrhea nucleic acid-based screening are likely to have the most impact on disease control. Here we describe the performance of the new BD T. vaginalis Qx (TVQ) amplified DNA assay, which can be performed on the automated BD Viper system. We focus on data from vaginal swab samples, since this is the specimen type routinely used for traditional trichomonas testing and the recommended specimen type for chlamydia/gonorrhea screening. Vaginal swabs were obtained from women attending sexually transmitted disease or family planning clinics at 7 sites. Patient-collected vaginal swabs were tested by the TVQ assay, and the Aptima T. vaginalis (ATV) assay was performed using clinician-collected vaginal swabs. Additional clinician-collected vaginal swabs were used for the wet mount and culture methods. Analyses included comparisons versus the patient infection status (PIS) defined by positive results with the wet mount method or culture, direct comparisons assessed with κ scores, and latent class analysis (LCA) as an unbiased estimator of test accuracy. Data from 838 women, 116 of whom were infected with T. vaginalis, were analyzed. The TVQ assay sensitivity and specificity estimates based on the PIS were 98.3% and 99.0%, respectively. The TVQ assay was similar to the ATV assay (κ=0.938) in direct analysis. LCA estimated the TVQ sensitivity and specificity as 98.3 and 99.6%, respectively. The TVQ assay performed well using self-collected vaginal swabs, the optimal sample type, as recommended by the CDC for chlamydia/gonorrhea screening among women.

  10. Distribution of bovine fasciolosis and associated factors in south Espírito Santo, Brazil: an update

    Directory of Open Access Journals (Sweden)

    Isabella Vilhena Freire Martins

    Full Text Available The geographical distribution and factors associated with bovine fasciolosis in the south of Espírito Santo were updated and the prevalences of this disease and of snails of the genus Lymnaea in the municipality of Jerônimo Monteiro were calculated. In the first stage, fecal samples were collected from 10% of the herds of 115 farms in 23 municipalities and interviews were conducted with owners. Generalized linear mixed models were used. In the second stage, in Jerônimo Monteiro municipality, feces and mollusks were collected from all farms registered in the milk cooperatives in the region. The mollusks were identified and examined for infection by Fasciola hepatica. Fasciolosis was diagnosed in 18 (78% of the 23 municipalities. Of the 1157 fecal samples examined, 19.01% were positive for eggs of F. hepatica. The final model shows statistical evidence of associations between positive farms and previous cases of fasciolosis and concomitant grazing of cattle with other definitive hosts. In the evaluated farms from the studied municipality the prevalence of fasciolosis and Lymnaea was of 66.7% and 23.8%, respectively. Mollusks were found in flooded areas and the animals' drinking water troughs. The wide geographical distribution of bovine fasciolosis in the south of Espírito Santo requires control measures to prevent its expansion towards the north of this state and other places characterized as F. hepatica free-infection.

  11. The utility of polyester and cotton as swabbing substrates for the removal of cellular material from surfaces.

    Science.gov (United States)

    Mulligan, Christina M; Kaufman, Stacie R; Quarino, Lawrence

    2011-03-01

    Various types of cotton and polyester fabrics were tested to ascertain the optimal physical and chemical characteristics of fabrics needed for the removal of cellular material from surfaces. DNA quantitation values obtained on dried saliva stains showed no difference between cotton and polyester across all constructions and solvent conditions. Fabrics used dry and with water yielded higher quantitation values than those used with isopropanol. Quantitation values were also higher for wovens and nonwovens than knits across all solvent conditions. Low thread count fabrics used with water yielded higher quantitation values, but no correlation between thread count and quantitation values was observed with dry fabrics. A low thread count woven fabric, however, outperformed other tested fabrics when swabbing object surfaces in a highly used room. Full DNA profiles from fingerprints on glass surfaces were obtained with low thread count woven and nonwoven fabrics but not with the knit fabric tested.

  12. The role of a commercial enzyme immuno assay antigen detection system for diagnosis of C. trachomatis in genital swab samples

    Directory of Open Access Journals (Sweden)

    A Mukherjee

    2011-01-01

    Full Text Available In the present pilot study, endocervical and urethral swabs collected from 100 patients attending sexually transmitted disease (STD clinics and regional centre for STD in two referral hospitals in New Delhi were analyzed by enzyme immune assay (EIA, polymerase chain reaction (PCR and direct fluorescent antibody (DFA for detection of C. trachomatis. It was found that EIA could detect a very low number of cases (3/100 as against DFA (11/100 and PCR (9/100. Thus, in spite of the widespread availability, lower cost and ease of performance of the enzyme-linked-immunosorbent serologic assay, the present study highlights the need to employ sophisticated diagnostic tools like DFA and PCR for detection of Chlamydia trachomatis in STD patients.

  13. APTIMA assay on SurePath liquid-based cervical samples compared to endocervical swab samples facilitated by a real time database

    Directory of Open Access Journals (Sweden)

    Khader Samer

    2010-01-01

    Full Text Available Background: Liquid-based cytology (LBC cervical samples are increasingly being used to test for pathogens, including: HPV, Chlamydia trachomatis (CT and Neisseria gonorrhoeae (GC using nucleic acid amplification tests. Several reports have shown the accuracy of such testing on ThinPrep (TP LBC samples. Fewer studies have evaluated SurePath (SP LBC samples, which utilize a different specimen preservative. This study was undertaken to assess the performance of the Aptima Combo 2 Assay (AC2 for CT and GC on SP versus endocervical swab samples in our laboratory. Materials and Methods: The live pathology database of Montefiore Medical Center was searched for patients with AC2 endocervical swab specimens and SP Paps taken the same day. SP samples from CT- and/or GC-positive endocervical swab patients and randomly selected negative patients were studied. In each case, 1.5 ml of the residual SP vial sample, which was in SP preservative and stored at room temperature, was transferred within seven days of collection to APTIMA specimen transfer tubes without any sample or patient identifiers. Blind testing with the AC2 assay was performed on the Tigris DTS System (Gen-probe, San Diego, CA. Finalized SP results were compared with the previously reported endocervical swab results for the entire group and separately for patients 25 years and younger and patients over 25 years. Results: SP specimens from 300 patients were tested. This included 181 swab CT-positive, 12 swab GC-positive, 7 CT and GC positive and 100 randomly selected swab CT and GC negative patients. Using the endocervical swab results as the patient′s infection status, AC2 assay of the SP samples showed: CT sensitivity 89.3%, CT specificity 100.0%; GC sensitivity and specificity 100.0%. CT sensitivity for patients 25 years or younger was 93.1%, versus 80.7% for patients over 25 years, a statistically significant difference (P = 0.02. Conclusions: Our results show that AC2 assay of 1.5 ml SP

  14. [Fecal microbiota transplantation: first case report in Chile and review].

    Science.gov (United States)

    Espinoza, Ricardo; Quera, Rodrigo; Meyer, Lital; Rivera, Daniela

    2014-08-01

    Clostridium difficile (CD) infection is increasing in frequency and severity in in-hospital and outpatient clinical settings, with a recurrence that can reach 30% after first episode. The recurrences are usually treated with longer courses of metronidazole or vancomycin. Other treatments have been used, such as probiotics, fidaxomicin, rifaximin, immunoglobulins and monoclonal antibodies against toxins A and B. Fecal microbiota transplantation (FMT) has emerged as a promising strategy in this group of patients, with effectiveness greater than 90%. We present the first case reported in Chile of this therapeutic strategy in a patient with Crohn's disease and recurrent CD infection who presented after the fecal transplantation an Escherichia coli bacteremia, suggesting the need for caution in the use of this strategy. 10 months after the FMT the patient presented a new episode of E. coli bacteremia and two episodes of diarrhea due to CD infection, treated both of them with vancomycin with good clinical response.

  15. Fecal microbiota transplantation: current clinical efficacy and future prospects

    Directory of Open Access Journals (Sweden)

    Bowman KA

    2015-10-01

    Full Text Available Kathryn A Bowman,1 Elizabeth K Broussard,2 Christina M Surawicz2 1Department of Medicine, 2Division of Gastroenterology, University of Washington School of Medicine, Seattle, WA, USA Abstract: Fecal microbiota transplantation (FMT has gained mainstream attention with its remarkable efficacy in treating recurrent Clostridium difficile infection (RCDI when there are no other effective therapies. Methods of selecting donors and routes of administration vary among studies, but there are now randomized controlled trials showing efficacy of FMT in treating RCDI. Ongoing trials of FMT for other disease such as inflammatory bowel disease are underway; this therapy should not be used for these conditions unless there is strong evidence for efficacy. Long-term safety data are sorely needed, as well as clarification of regulatory concerns. Keywords: fecal microbiota transplant, recurrent Clostridium difficile infection, Clostridium difficile infection, microbiome, inflammatory bowel disease

  16. Fecal microbiota transplantation in treating Clostridium difficile infection.

    Science.gov (United States)

    Brown, William R

    2014-08-01

    Clostridium difficile infection (CDI) is an increasingly common and severe international health problem. Customary treatment of this infection, usually with antibiotics, is often ineffective and its recurrence is common. In recent years the treatment of recurrent or refractory CDI by the transfer of stool from an uninfected person, so called fecal "microbiota transplantation" has become recognized as effective and generally safe. The effectiveness of this novel treatment is incompletely defined but is likely to be due to its correction of the intestinal dysbiosis that characterizes the disease. Practical methods for the administration of the transplantation have been described. This review summarizes the current reported experiences with fecal microbiota transplantation in the treatment for CDI.

  17. How to Manipulate the Microbiota: Fecal Microbiota Transplantation.

    Science.gov (United States)

    Fuentes, Susana; de Vos, Willem M

    2016-01-01

    Fecal microbiota transplantation (FMT) is a rather straightforward therapy that manipulates the human gastrointestinal (GI) microbiota, by which a healthy donor microbiota is transferred into an existing but disturbed microbial ecosystem. This is a natural process that occurs already at birth; infants are rapidly colonized by a specific microbial community, the composition of which strongly depends on the mode of delivery and which therefore most likely originates from the mother (Palmer et al. 2007; Tannock et al. 1990). Since this early life microbial community already contains most, if not all, of the predominantly anaerobic microbes that are only found in the GI tract, it is reasonable to assume that early life colonization is the ultimate natural fecal transplantation.

  18. Fecal Microbiota Transplantation: Current Applications, Effectiveness, and Future Perspectives.

    Science.gov (United States)

    Choi, Hyun Ho; Cho, Young-Seok

    2016-05-01

    Fecal microbiota transplantation (FMT) is the infusion of liquid filtrate feces from a healthy donor into the gut of a recipient to cure a specific disease. A fecal suspension can be administered by nasogastric or nasoduodenal tube, colonoscope, enema, or capsule. The high success rate and safety in the short term reported for recurrent Clostridium difficile infection has elevated FMT as an emerging treatment for a wide range of disorders, including Parkinson's disease, fibromyalgia, chronic fatigue syndrome, myoclonus dystopia, multiple sclerosis, obesity, insulin resistance, metabolic syndrome, and autism. There are many unanswered questions regarding FMT, including donor selection and screening, standardized protocols, long-term safety, and regulatory issues. This article reviews the efficacy and safety of FMT used in treating a variety of diseases, methodology, criteria for donor selection and screening, and various concerns regarding FMT.

  19. Treating Obesity and Metabolic Syndrome with Fecal Microbiota Transplantation

    Science.gov (United States)

    Marotz, Clarisse A.; Zarrinpar, Amir

    2016-01-01

    The worldwide prevalence of metabolic syndrome, which includes obesity and its associated diseases, is rising rapidly. The human gut microbiome is recognized as an independent environmental modulator of host metabolic health and disease. Research in animal models has demonstrated that the gut microbiome has the functional capacity to induce or relieve metabolic syndrome. One way to modify the human gut microbiome is by transplanting fecal matter, which contains an abundance of live microorganisms, from a healthy individual to a diseased one in the hopes of alleviating illness. Here we review recent evidence suggesting efficacy of fecal microbiota transplant (FMT) in animal models and humans for the treatment of obesity and its associated metabolic disorders. PMID:27698622

  20. Fecal Microbiota Transplantation: Current Applications, Effectiveness, and Future Perspectives

    Science.gov (United States)

    Choi, Hyun Ho; Cho, Young-Seok

    2016-01-01

    Fecal microbiota transplantation (FMT) is the infusion of liquid filtrate feces from a healthy donor into the gut of a recipient to cure a specific disease. A fecal suspension can be administered by nasogastric or nasoduodenal tube, colonoscope, enema, or capsule. The high success rate and safety in the short term reported for recurrent Clostridium difficile infection has elevated FMT as an emerging treatment for a wide range of disorders, including Parkinson’s disease, fibromyalgia, chronic fatigue syndrome, myoclonus dystopia, multiple sclerosis, obesity, insulin resistance, metabolic syndrome, and autism. There are many unanswered questions regarding FMT, including donor selection and screening, standardized protocols, long-term safety, and regulatory issues. This article reviews the efficacy and safety of FMT used in treating a variety of diseases, methodology, criteria for donor selection and screening, and various concerns regarding FMT. PMID:26956193

  1. Treatment strategies in obstructed defecation and fecal incontinence

    Institute of Scientific and Technical Information of China (English)

    Marat Khaikin; Steven D Wexner

    2006-01-01

    Obstructed defecation (OD) and fecal incontinence(FI) are challenging clinical problems, which are commonly encountered in the practice of colorectal surgeons and gastroenterologists. These disorders socially and psychologically distress patients and greatly impair their quality of life. The underlying anatomical and pathophysiological changes are complex, often incompletely understood and cannot always be determined. As a consequence, many medical, surgical,and behavioral approaches have been described, with no panacea. Over the past decade, advances in an understanding of these disorders together with rational and similar methods of evaluation in anorectal physiology laboratories (ARP), radiology studies, and new surgical techniques have led to promising results. In this brief review, we discuss treatment strategies and recent updates on clinical and therapeutic aspects of obstructed defecation and fecal incontinence.

  2. Fecal microbiota imbalance in Mexican children with type 1 diabetes.

    Science.gov (United States)

    Mejía-León, María Esther; Petrosino, Joseph F; Ajami, Nadim Jose; Domínguez-Bello, María Gloria; de la Barca, Ana María Calderón

    2014-01-22

    Dysbiosis of the intestinal microbiota affecting the gut barrier could be triggering Type 1 Diabetes (T1D), the second most frequent autoimmune disease in childhood. This study compared the structure of the fecal microbiota in 29 mestizo children aged 7-18 years, including 8 T1D at onset, 13 T1D after 2 years treatment, and 8 healthy controls. Clinical information was collected, predisposing haplotypes were determined; the fecal DNA was extracted, the V4 region of the 16S rRNA gene amplified and 454-pyrosequenced. The newly diagnosed T1D cases had high levels of the genus Bacteroides (p microbiota dominated by Prevotella. Children with T1D treated for ≥2 years had levels of Bacteroides and Prevotella compared to those of the control group. The gut microbiota of newly diagnosed T1D cases is altered, but whether it is involved in disease causation or is a consequence of host selection remains unclear.

  3. Single-port laparoscopic fecal diversion: more than cosmetic benefits?

    Science.gov (United States)

    Aytac, Erman; Stocchi, Luca; Williams, Ryan; Remzi, Feza H; Costedio, Meagan M

    2014-08-01

    Single-port laparoscopic surgery is usually performed on patients with minor comorbidities. The aim of the study was to evaluate feasibility and efficacy of single-port fecal diversion in patients who had previous abdominal operations or comorbidities. Between October 2010 and March 2012, 14 patients with a median age of 57 years were diverted. The reasons for diversion were perianal infection/abscess (n=5), anal incontinence (n=3), radiation proctitis (n=2), colovesical fistula causing sepsis (n=1), outlet obstruction of ileal S pouch (n=1), perforation during pouchoscopy (n=1), and peritoneal carcinomatosis with enterocutaneus fistula (n=1). Median estimated blood loss was 20 mL, operative time was 52 minutes, and length of hospital stay was 4 days. Two patients had ileus postoperatively. One patient had a parastomal hernia 4 months after diversion. Single-port laparoscopic fecal diversion is a safe and feasible operation for patients with significant comorbidities and a history of multiple abdominal operations.

  4. [Effects of nifuroxazide on fecal flora in healthy subjects].

    Science.gov (United States)

    Buisson, Y; Larribaud, J

    1989-01-01

    Effect of nifuroxazide on fecal flora was studied in 12 healthy volunteers receiving, in hazardous order and double-blind procedure, three six-days courses of treatment separated by eight-days spaces of time: the conventional dosage of 400 mg twice a day, a dosage of 1200 mg once a day, and placebo. Among six settled bacteriological index (wealth of the fecal flora, percentage of gram-negative bacteria, numbers of E. coli, Enterococcus, Clostridium and Bacteroides), no significant variation was found by means of statistical study between D0, D2 and D7, nor between the three courses of treatment. Therefore nifuroxazide, even in high dosage, does not injure integrity of microbial intestinal ecosystem under so defined experimental conditions, similar with clinical conditions.

  5. Assessment of Salmonella spp. in feces, cloacal swabs, and eggs (eggshell and content separately) from a laying hen farm.

    Science.gov (United States)

    García, C; Soriano, J M; Benítez, V; Catalá-Gregori, P

    2011-07-01

    Microbial pathogens of the genus Salmonella are among the leading causes of foodborne illness in the world. The present study was done on a laying hen farm with a Salmonella enterica serovar Enteritidis-positive result according to the testing specified by European regulation 2160/2003. The aim of this study was to compare the Salmonella contamination on a laying hen farm with the Salmonella presence in the hen eggs. The strains were isolated by ISO method 6579:2002 (standard method for the detection of Salmonella spp. in the European regulation for food and animal feeding stuffs, animal feces, and environmental samples from the primary production stage, including poultry farms) and were confirmed as Salmonella Enteritidis by the Kauffmann-White method. In addition, strains were compared with genomic macrorestriction followed by pulsed-field gel electrophoresis. Four types of samples, namely, feces (n = 50), cloacal swabs (n = 150), eggshells (n = 50), and egg contents (n = 50), were taken from each of 50 randomly selected battery cages. Results demonstrated that feces (92%) were the most positive sample, followed by eggshells (34%) and cloacal swabs (4%). No Salmonella spp. were detected in the egg contents. Our results show that a Salmonella Enteritidis-positive result on a laying hen farm, according to the testing specified by European regulation 2160/2003, did not imply the presence of the pathogen in the egg contents. Additionally, XbaI-digested genomic DNA of Salmonella Enteritidis strains isolated from several samples resulted in the same pattern, so were probably of the same origin.

  6. Comparison of culture and PCR to detect Mycoplasma agalactiae and Mycoplasma mycoides subsp. capri in ear swabs taken from goats.

    Science.gov (United States)

    Amores, Joaquín; Corrales, Juan C; Martín, Angel Gómez; Sánchez, Antonio; Contreras, Antonio; de la Fe, Christian

    2010-01-06

    This study was designed to evaluate the validity of PCR for the direct detection of Mycoplasma (M.) agalactiae and Mycoplasma mycoides subsp. capri (Mmc), as the two species most frequently causing contagious agalactia (CA) in goats. The PCR method was compared with the traditional culture technique to determine which method was most efficient at identifying all auricular carriers present in herds. The samples analyzed were 307 ear swabs taken from goats reared in a CA endemic area. We assessed the validity of each technique to detect each species and agreement between both methods. For each species, the result was taken as true-positive when at least one of the two tests was positive. Of the swabs tested, 246 were scored positive by PCR (235 and 11 for Mmc and M. agalactiae, respectively) and 117 showed a positive culture result (113 for Mmc and 4 for M. agalactiae). 133 of the PCR-positive samples (124 and 9 for Mmc and M. agalactiae, respectively) yielded negative culture results and 4 culture-positive samples tested negative using PCR (2 for each species). Sensitivity and negative predictive values for PCR were 84.62 and 99.32 (for M. agalactiae) and 99.16 and 97.22% (for Mmc) respectively, and for culture were 30.77 and 97.03 (for M. agalactiae) and 47.08 and 36.08% (for Mmc), respectively. PCR proved to be a rapid and sensitive method for the detection of mycoplasmas in the external ear of asymptomatic carriers. Tools such as this are needed to adopt efficient control measures against CA.

  7. Survival of Fecal Coliforms in Dry-Composting Toilets

    OpenAIRE

    Redlinger, Thomas; Graham, Jay; Corella-Barud, Verónica; Avitia, Raquel

    2001-01-01

    The dry-composting toilet, which uses neither water nor sewage infrastructure, is a practical solution in areas with inadequate sewage disposal and where water is limited. These systems are becoming increasingly popular and are promoted to sanitize human excreta and to recycle them into fertilizer for nonedible plants, yet there are few data on the safety of this technology. This study analyzed fecal coliform reduction in approximately 90 prefabricated, dry-composting toilets (Sistema Integra...

  8. Survival of fecal coliforms in dry-composting toilets.

    Science.gov (United States)

    Redlinger, T; Graham, J; Corella-Barud, V; Avitia, R

    2001-09-01

    The dry-composting toilet, which uses neither water nor sewage infrastructure, is a practical solution in areas with inadequate sewage disposal and where water is limited. These systems are becoming increasingly popular and are promoted to sanitize human excreta and to recycle them into fertilizer for nonedible plants, yet there are few data on the safety of this technology. This study analyzed fecal coliform reduction in approximately 90 prefabricated, dry-composting toilets (Sistema Integral de Reciclamiento de Desechos Orgánicos [SIRDOs]) that were installed on the U.S.-Mexico border in Ciudad Juárez, Chihuahua, Mexico. The purpose of this study was to determine fecal coliform reduction over time and the most probable method of this reduction. Biosolid waste samples were collected and analyzed at approximately 3 and 6 months and were classified based on U.S. Environmental Protection Agency standards. Results showed that class A compost (high grade) was present in only 35.8% of SIRDOs after 6 months. The primary mechanism for fecal coliform reduction was found to be desiccation rather than biodegradation. There was a significant correlation (P = 0.008) between classification rating and percent moisture categories of the biosolid samples: drier samples had a greater proportion of class A samples. Solar exposure was critical for maximal class A biosolid end products (P = 0.001). This study only addressed fecal coliforms as an indicator organism, and further research is necessary to determine the safety of composting toilets with respect to other pathogenic microorganisms, some of which are more resistant to desiccation.

  9. Fecal microbiota transplantation: current clinical efficacy and future prospects

    OpenAIRE

    Bowman KA; Broussard EK; Surawicz CM

    2015-01-01

    Kathryn A Bowman,1 Elizabeth K Broussard,2 Christina M Surawicz2 1Department of Medicine, 2Division of Gastroenterology, University of Washington School of Medicine, Seattle, WA, USA Abstract: Fecal microbiota transplantation (FMT) has gained mainstream attention with its remarkable efficacy in treating recurrent Clostridium difficile infection (RCDI) when there are no other effective therapies. Methods of selecting donors and routes of administration vary among studies, but there are now ra...

  10. Fecal microbiota transplantation for the management of Clostridium difficile infection.

    Science.gov (United States)

    Rao, Krishna; Young, Vincent B

    2015-03-01

    This article discusses the use of fecal microbiota transplantation (FMT) for the treatment of recurrent Clostridium difficile infection (CDI). The disruption of the normal gut microbiota is central to the pathogenesis of CDI, and disruption persists in recurrent disease. The use of FMT for recurrent CDI is characterized by a high response rate and short term safety is excellent, although the long-term effects of FMT are as yet unknown.

  11. Can chronic gastritis cause an increase in fecal calprotectin concentrations?

    Institute of Scientific and Technical Information of China (English)

    Massimo; Montalto; Antonella; Gallo; Gianluca; Ianiro; Luca; Santoro; Ferruccio; D; Onofrio; Riccardo; Ricci; Giovanni; Cammarota; Marcello; Covino; Monica; Vastola; Antonio; Gasbarrini; Giovanni; Gasbarrini

    2010-01-01

    AIM:To evaluate fecal calprotectin concentrations(FCCs) in subjects with chronic gastritis and the correlation between FCCs and gastritis activity score.METHODS:FCCs were measured in 61 patients with histological diagnosis of gastritis and in 74 healthy volunteers.Histological grading of gastritis was performed according to the updated Sydney gastritis classification.Patients were subdivided into 2 groups according to the presence/absence of an active gastritis.Patients with chronic active gastritis were di...

  12. Production of a fecal mutagen by Bacteroides spp.

    OpenAIRE

    Van Tassel, R L; MacDonald, D K; Wilkins, T D

    1982-01-01

    Forty species of anaerobes were screened for the ability to produce an ether-extractable mutagen which is present in the feces of 15 to 20% of individuals in populations at high risk for colon cancer. This mutagen can be produced in vitro by incubating the feces of these individuals anaerobically or by supplementing anaerobic broths with methanol extracts of the feces and incubating them with a dilute fecal inoculum. Of the anaerobes screened, strains of five species of Bacteroides (B. thetai...

  13. Dietary Fiber Supplementation for Fecal Incontinence: A Randomized Clinical Trial

    OpenAIRE

    2014-01-01

    Dietary fiber supplements are used to manage fecal incontinence (FI), but little is known about the fiber type to recommend or the level of effectiveness of such supplements, which appear related to the fermentability of the fiber. The aim of this single-blind, randomized controlled trial was to compare the effects of three dietary fiber supplements (carboxymethylcellulose [CMC], gum arabic [GA], or psyllium) with differing levels of fermentability to a placebo in community-living individuals...

  14. Detection of bovine herpesvirus 1 sequences in yaks (Bos grunniens) with keratoconjunctivitis, using a highly sensitive nested polymerase chain reaction.

    Science.gov (United States)

    Bandyopadhyay, S; Das, S; Baruah, K K; Chakravarty, P; Chakrabarty, D; Sarkar, T; Pal, B; De, S; Pan, D; Bera, A K; Bandyopadhyay, S; Bhattacharya, D

    2010-12-01

    Thirty-seven yaks (Bos grunniens) with keratoconjunctivitis and 22 healthy yaks were used to investigate the role of bovine herpesvirus 1 (BoHV-1) in keratoconjunctivitis in yaks. Nucleic acid sequences of BoHV-1 glycoproteins B and E were detected in conjunctival swabs from all yaks with keratoconjunctivitis using a nested polymerase chain reaction (PCR). In 21 yaks, BoHV-1 sequences were detected along with Moraxella bovis (M. bovis) and Neisseria spp. The amplified BoHV-1 sequences were identical, and no nucleotide variation was observed when compared with a BoHV-1 reference strain using single-strand conformation polymorphism analysis of the amplified DNA sequences. Interestingly, BoHV-1 sequences could not be detected in samples from healthy yaks. However, conjunctival swabs from two healthy yaks (9.09%) yielded M. bovis and Neisseria spp. Samples from 35 yaks with keratoconjunctivitis showed positive reactions in an avidin biotin enzyme-linked immunosorbent assay for BoHV-1 antibodies; all the healthy yaks were seronegative. This is the first report of a possible association of BoHV-1 with keratoconjunctivitis in yaks.

  15. Fecal microbiota transplantation in the treatment of Clostridium difficile infections.

    Science.gov (United States)

    Austin, Matthew; Mellow, Mark; Tierney, William M

    2014-06-01

    In recent years, Clostridium difficile infections have become more frequent, more severe, more refractory to standard treatment, and more likely to recur. Current antibiotic treatment regimens for Clostridium difficile infection alter the normal gut flora, which provide colonization resistance against Clostridium difficile. Over the past few years, there has been a marked increase in the knowledge of the gut microbiota and its role in health maintenance and disease causation. This has, fortuitously, coincided with the use of a unique microbial replacement therapy, fecal microbiota transplantation, in the treatment of patients with multiple recurrent Clostridium difficile infections. We briefly review current knowledge of the gut microbiota's functions. We then review the indications for use of fecal microbiota transplantation in Clostridium difficile infection, the techniques employed, and results of treatment. Fecal microbiota transplantation has been shown to be efficacious for patients with multiply recurrent Clostridium difficile infections (reported cure rates of 90%), with an excellent short-term safety profile, and has been included in the American College of Gastroenterology treatment guidelines for this troublesome disease.

  16. Fecal microbiota transplantation for management of Clostridium difficile infection.

    Science.gov (United States)

    Vaishnavi, Chetana

    2014-07-01

    The widespread use of antibiotics has led Clostridium difficile infection (CDI) to become a common problem with pronounced medical and economic effects. The recurrence of CDI after treatment with standard antibiotics is becoming more common with the emergence of more resistant strains of C. difficile. As CDI is an antibiotic-associated disease, further treatment with antibiotic is best avoided. As the gut flora is severely disturbed in CDI, approaches that restore the gut microbiota may become good alternative modes of CDI therapies. Fecal microbiota transplantation (FMT) is the procedure of transplantation of fecal bacteria from a healthy donor individual into a patient for restoration of the normal colonic flora. Thus, FMT helps in the eradication of C. difficile and resolution of clinical symptoms such as diarrhea, cramping, and urgency. Though this approach to treatment is not new, presently, it has become an alternative and promising way of combating infections. The procedure is not in regular use because of the time required to identify a suitable donor, the risk of introducing opportunistic pathogens, and a general patient aversion to the transplant. However, FMT is gaining popularity because of its success rate as a panacea for recurrent attacks of CDI and is being increasingly used in clinical practice. This review describes the rationale, the indications, the results, the techniques, the potential donors, the benefits as well as the complications of fecal microbiota instillation to CDI patients in order to restore the normal gut flora.

  17. Fecal microbiome analysis as a diagnostic test for diverticulitis.

    Science.gov (United States)

    Daniels, L; Budding, A E; de Korte, N; Eck, A; Bogaards, J A; Stockmann, H B; Consten, E C; Savelkoul, P H; Boermeester, M A

    2014-11-01

    Disease-specific variations in intestinal microbiome composition have been found for a number of intestinal disorders, but little is known about diverticulitis. The purpose of this study was to compare the fecal microbiota of diverticulitis patients with control subjects from a general gastroenterological practice and to investigate the feasibility of predictive diagnostics based on complex microbiota data. Thirty-one patients with computed tomography (CT)-proven left-sided uncomplicated acute diverticulitis were included and compared with 25 control subjects evaluated for a range of gastrointestinal indications. A high-throughput polymerase chain reaction (PCR)-based profiling technique (IS-pro) was performed on DNA isolates from baseline fecal samples. Differences in bacterial phylum abundance and diversity (Shannon index) of the resulting profiles were assessed by conventional statistics. Dissimilarity in microbiome composition was analyzed with principal coordinate analysis (PCoA) based on cosine distance measures. To develop a prediction model for the diagnosis of diverticulitis, we used cross-validated partial least squares discriminant analysis (PLS-DA). Firmicutes/Bacteroidetes ratios and Proteobacteria load were comparable among patients and controls (p = 0.20). The Shannon index indicated a higher diversity in diverticulitis for Proteobacteria (p Diverticulitis patients have a higher diversity of fecal microbiota than controls from a mixed population, with the phylum Proteobacteria defining the difference. The analysis of intestinal microbiota offers a novel way to diagnose diverticulitis.

  18. Altered fecal microbiota composition in patients with major depressive disorder.

    Science.gov (United States)

    Jiang, Haiyin; Ling, Zongxin; Zhang, Yonghua; Mao, Hongjin; Ma, Zhanping; Yin, Yan; Wang, Weihong; Tang, Wenxin; Tan, Zhonglin; Shi, Jianfei; Li, Lanjuan; Ruan, Bing

    2015-08-01

    Studies using animal models have shown that depression affects the stability of the microbiota, but the actual structure and composition in patients with major depressive disorder (MDD) are not well understood. Here, we analyzed fecal samples from 46 patients with depression (29 active-MDD and 17 responded-MDD) and 30 healthy controls (HCs). High-throughput pyrosequencing showed that, according to the Shannon index, increased fecal bacterial α-diversity was found in the active-MDD (A-MDD) vs. the HC group but not in the responded-MDD (R-MDD) vs. the HC group. Bacteroidetes, Proteobacteria, and Actinobacteria strongly increased in level, whereas that of Firmicutes was significantly reduced in the A-MDD and R-MDD groups compared with the HC group. Despite profound interindividual variability, levels of several predominant genera were significantly different between the MDD and HC groups. Most notably, the MDD groups had increased levels of Enterobacteriaceae and Alistipes but reduced levels of Faecalibacterium. A negative correlation was observed between Faecalibacterium and the severity of depressive symptoms. These findings enable a better understanding of changes in the fecal microbiota composition in such patients, showing either a predominance of some potentially harmful bacterial groups or a reduction in beneficial bacterial genera. Further studies are warranted to elucidate the temporal and causal relationships between gut microbiota and depression and to evaluate the suitability of the microbiome as a biomarker.

  19. Fecal source tracking in water using a mitochondrial DNA microarray.

    Science.gov (United States)

    Vuong, Nguyet-Minh; Villemur, Richard; Payment, Pierre; Brousseau, Roland; Topp, Edward; Masson, Luke

    2013-01-01

    A mitochondrial-based microarray (mitoArray) was developed for rapid identification of the presence of 28 animals and one family (cervidae) potentially implicated in fecal pollution in mixed activity watersheds. Oligonucleotide probes for genus or subfamily-level identification were targeted within the 12S rRNA - Val tRNA - 16S rRNA region in the mitochondrial genome. This region, called MI-50, was selected based on three criteria: 1) the ability to be amplified by universal primers 2) these universal primer sequences are present in most commercial and domestic animals of interest in source tracking, and 3) that sufficient sequence variation exists within this region to meet the minimal requirements for microarray probe discrimination. To quantify the overall level of mitochondrial DNA (mtDNA) in samples, a quantitative-PCR (Q-PCR) universal primer pair was also developed. Probe validation was performed using DNA extracted from animal tissues and, for many cases, animal-specific fecal samples. To reduce the amplification of potentially interfering fish mtDNA sequences during the MI-50 enrichment step, a clamping PCR method was designed using a fish-specific peptide nucleic acid. DNA extracted from 19 water samples were subjected to both array and independent PCR analyses. Our results confirm that the mitochondrial microarray approach method could accurately detect the dominant animals present in water samples emphasizing the potential for this methodology in the parallel scanning of a large variety of animals normally monitored in fecal source tracking.

  20. In vitro production of bovine embryos

    DEFF Research Database (Denmark)

    Stroebech, L.; Mazzoni, Gianluca; Pedersen, Hanne Skovsgaard;

    2015-01-01

    In vitro production (IVP) of bovine embryos has become a widespread technology implemented in cattle breeding and production. The implementation of genomic selection and systems biology adds great dimensions to the impact of bovine IVP. The physical procedures included in the IVP process can still...

  1. One year duration of immunity of the modified live bovine viral diarrhea virus type 1 and type 2 and bovine herpesvirus-1 fractions of Vista® Once SQ vaccine.

    Science.gov (United States)

    Purtle, Lisa; Mattick, Debra; Schneider, Corey; Smith, Linda; Xue, Wenzhi; Trigo, Emilio

    2016-03-18

    Three studies were performed to determine the duration of immunity of the bovine viral diarrhea virus type 1 and type 2 (BVDV-1 and BVDV-2) and bovine herpesvirus-1 (BHV-1) fractions of a commercially prepared modified-live vaccine. Vista® Once SQ (Vista®) vaccine contains five modified-live viruses, BVDV-1, BVDV-2, BHV-1, bovine respiratory syncytial virus, and bovine parainfluenza 3 virus, and two modified-live bacteria, Pasteurella multocida and Mannheimia haemolytica. For all three studies, calves were administered a single dose of vaccine or placebo vaccine subcutaneously, and were challenged with one of the three virulent viruses at least one year following vaccination. Calves were evaluated daily following challenge for clinical signs of disease associated with viral infection, nasal swab samples were evaluated for virus shedding, and serum was tested for neutralizing antibodies. Following the BVDV-1 and BVDV-2 challenges, whole blood was evaluated for white blood cell counts, and for the BVDV-2 study, whole blood was also evaluated for platelet counts. Calves vaccinated with BVDV type 1a, were protected from challenge with BVDV type 1b, and had significant reductions in clinical disease, fever, leukopenia, and virus shedding compared to control calves. Vaccinated calves in the BVDV-2 study were protected from clinical disease, mortality, fever, leukopenia, thrombocytopenia, and virus shedding compared to controls. Vaccinated calves in the BHV-1 study were protected from clinical disease and fever, and had significantly reduced duration of nasal virus shedding. These three studies demonstrated that a single administration of the Vista® vaccine to healthy calves induces protective immunity against BVDV-1, BVDV-2 and BHV-1 that lasts at least one year following vaccination.

  2. Behavior of Salmonella heidelberg and Salmonella enteritidis strains following broiler chick inoculation: evaluation of cecal morphometry, liver and cecum bacterial counts and fecal excretion patterns

    Directory of Open Access Journals (Sweden)

    Anderlise Borsoi

    2011-03-01

    Full Text Available Over the years, Salmonella Heidelberg (SH has gained prominence in North America poultry production and in the poultry production of other countries. Salmonella Heidelberg has been isolated and reported from poultry and poultry products in Brazil since 1962, whereas Salmonella Enteritidis (SE has only emerged as a serious problem in poultry and public health since 1993. These strains of Salmonella can cause intestinal problems in newly hatched chicks, and infection may persist until adulthood. Upon slaughter of chickens, Salmonella can contaminate carcasses, a condition that poses a threat to human health. The aim of this study was to compare the fecal excretion of Salmonella Enteritidis and Salmonella Heidelberg in newly hatched chicks (orally inoculated with 10(5ufc/mL each until 20 days of age. In addition, the ratio of cecal villus height:crypt depth (morphometry and liver and cecum cell counts was analyzed in chicks ranging from 0 to 3 days of age and infected with these two Salmonella strains. One hundred seventeen chicks were separated into one of three experimental groups: a control group, an SE-infected group and an SH-infected group. Eight chicks per group were euthanized at 6, 12 and 72 hours post-inoculation (pi to allow for Salmonella isolation from the liver and cecum and for the collection of the cecum for villi and crypt analysis. Other birds were allowed to mature to 20 days of age and cloacal swabs were taken at 2, 6, 13 and 20 days pi to compare the fecal excretion of inoculated strains. The Salmonella Enteritidis group had a higher number of cells excreted during the trial. Both strains were isolated from the liver and cecum by 6h pi. At 12h pi the Salmonella Heidelberg group had high cell counts in the cecum. No difference was found in liver cell counts. Both strains showed lower villus height:crypt depth ratio than the control group post-infection.

  3. Behavior of salmonella heidelberg and salmonella enteritidis strains following broiler chick inoculation: evaluation of cecal morphometry, liver and cecum bacterial counts and fecal excretion patterns.

    Science.gov (United States)

    Borsoi, Anderlise; Ruschel do Santos, Luciana; Beatriz Rodrigues, Laura; Luiz de Souza Moraes, Hamilton; Tadeu Pippi Salle, Carlos; Pinheiro do Nascimento, Vladimir

    2011-01-01

    Over the years, Salmonella Heidelberg (SH) has gained prominence in North America poultry production and in the poultry production of other countries. Salmonella Heidelberg has been isolated and reported from poultry and poultry products in Brazil since 1962, whereas Salmonella Enteritidis (SE) has only emerged as a serious problem in poultry and public health since 1993. These strains of Salmonella can cause intestinal problems in newly hatched chicks, and infection may persist until adulthood. Upon slaughter of chickens, Salmonella can contaminate carcasses, a condition that poses a threat to human health. The aim of this study was to compare the fecal excretion of Salmonella Enteritidis and Salmonella Heidelberg in newly hatched chicks (orally inoculated with 10(5)ufc/mL each) until 20 days of age. In addition, the ratio of cecal villus height:crypt depth (morphometry) and liver and cecum cell counts was analyzed in chicks ranging from 0 to 3 days of age and infected with these two Salmonella strains. One hundred seventeen chicks were separated into one of three experimental groups: a control group, an SE-infected group and an SH-infected group. Eight chicks per group were euthanized at 6, 12 and 72 hours post-inoculation (pi) to allow for Salmonella isolation from the liver and cecum and for the collection of the cecum for villi and crypt analysis. Other birds were allowed to mature to 20 days of age and cloacal swabs were taken at 2, 6, 13 and 20 days pi to compare the fecal excretion of inoculated strains. The Salmonella Enteritidis group had a higher number of cells excreted during the trial. Both strains were isolated from the liver and cecum by 6h pi. At 12h pi the Salmonella Heidelberg group had high cell counts in the cecum. No difference was found in liver cell counts. Both strains showed lower villus height:crypt depth ratio than the control group post-infection.

  4. Clostridium Difficile and Fecal Microbial Transplant in Critically Ill Patients

    Directory of Open Access Journals (Sweden)

    Sarvin Sanaie

    2014-07-01

    Full Text Available Critically-ill patients constitute majority of the patients hospitalized in ICU wards (1, 2. This group of patients demands special considerations and measures of care (3-6. Clostridium difficile infection causes dangerous, painful and persistent diarrhea in critically ill patients. Its treatment consists of enteral metronidazol or vancomycin in combination with IV antibiotics cessation. Recently, probiotics have been considered as an alternative treatment for pseudomembranous colitis. In 1958, fecal microbial transplant was first described from healthy individuals to sick patients to displace pathogenic microbes from the intestine by re-establishing a healthy microbial community. Since then, it has gained value as “express stool treatment” or currently known as “fecal transplant”. Last year, FDA classified stool as drug, which typically requires an Investigational New Drug application (IND. However, in July 2013, the FDA issued guidance stating that it would exercise enforcement discretion for physicians administering FMT to treat patients with recurrent Clostridium difficile infection. Accordingly, considering stool as a tissue product or giving it its own classification, as FDA approved for blood, would keep patients safe, ensure broad access and facilitate research (7. It should be taken into consideration that some complications might accompany fecal microbial transplant such as making patients susceptible for conditions like obesity or autoimmune disorders. Safety and quality assurance starts from pre-enrollment donor screening, donor testing (17 serological and stool-based assays, donor monitoring and process control. The composition of the bacterial community has been shown to change when stored at -80oC compared to the samples stored at -20oC and it has been recommended to store the samples of intestinal content at -20oC before use for bacterial community analysis, instead of the current practice at -80oC (7, 8. However, if

  5. The impact of long-term dietary pattern of fecal donor on in vitro fecal fermentation properties of inulin.

    Science.gov (United States)

    Yang, Junyi; Rose, Devin J

    2016-04-01

    Although the composition of the gut microbiota is of interest, the functionality, or metabolic activity, of the gut microbiota is of equal importance: the gut microbiota can produce either harmful metabolites associated with human disease or beneficial metabolites that protect against disease. The purposes of this study were to determine the associations between dietary intake variables and fecal short and branched chain fatty acid (S/BCFA) concentrations; to determine the associations between dietary intake variables and inulin degradation, short and branched chain fatty acid (S/BCFA) production, and ammonia production during in vitro fecal fermentation of a highly fermentable substrate (inulin); and finally to compare results from the fermentation of inulin with those obtained in a previous report using a poorly fermentable substrate (whole wheat; Yang and Rose, Nutr. Res., 2014, 34, 749-759). Stool samples from eighteen individuals that had completed one-year dietary records were used in an in vitro fecal fermentation system with long-chain inulin as substrate. Few dietary intake variables were correlated with fecal S/BCFA concentrations; however, intakes of several plant-based foods, especially whole grain, dry beans, and certain vegetables that provided dietary fiber, plant protein, and B vitamins, were associated with acetate, propionate, butyrate, and total SCFA production during inulin fermentation. In contrast, intake of dairy and processed meats that provided cholesterol and little fiber, were associated with ammonia and BCFA production. Comparing results between inulin and whole wheat fermentations, significant correlations were only found for butyrate and BCFA, suggesting that regardless of the type of carbohydrate provided to the microbiota, long-term diet may have a pronounced effect on the propensity of the gut microbiota toward either beneficial metabolism (butyrate production) or detrimental metabolism (BCFA production). These results may help in

  6. Bovine milk antibodies for health.

    Science.gov (United States)

    Korhonen, H; Marnila, P; Gill, H S

    2000-11-01

    The immunoglobulins of bovine colostrum provide the major antimicrobial protection against microbial infections and confer a passive immunity to the newborn calf until its own immune system matures. The concentration in colostrum of specific antibodies against pathogens can be raised by immunising cows with these pathogens or their antigens. Immune milk products are preparations made of such hyperimmune colostrum or antibodies enriched from it. These preparations can be used to give effective specific protection against different enteric diseases in calves and suckling pigs. Colostral immunoglobulin supplements designed for farm animals are commercially available in many countries. Also, some immune milk products containing specific antibodies against certain pathogens have been launched on the market. A number of clinical studies are currently in progress to evaluate the efficacy of immune milks in the prevention and treatment of various human infections, including those caused by antibiotic resistant bacteria. Bovine colostrum-based immune milk products have proven effective in prophylaxis against various infectious diseases in humans. Good results have been obtained with products targeted against rotavirus, Shigella flexneri, Escherichia coli, Clostridium difficile, Streptococcus mutans, Cryptosporidium parvum and Helicobacter pylori. Some successful attempts have been made to use immune milk in balancing gastrointestinal microbial flora. Immune milk products are promising examples of health-promoting functional foods, or nutraceuticals. This review summarises the recent progress in the development of these products and evaluates their potential as dietary supplements and in clinical nutrition.

  7. [Toxinology of bovine paraplegic syndrome].

    Science.gov (United States)

    Sevcik, C; Brito, J C; D'Suze, G; Mijares, A J; Domínguez, M G

    1993-01-01

    A clinical entity named "Bovine Paraplegic Syndrome" ("Síndrome Parapléjico de los Bovinos") has spread alarmingly, in the cattle growing areas of the central and eastern plains of Venezuela. Approximately four million cattle are bread in the area were the disease occurs. The mortality index due to the disease ranges 5 to 25% of the animals at risk, mostly cows, pregnant or lactating. The principal characteristic of the bovine paraplegic syndrome is decubitus, ventral or sternal, in animals that make vane efforts to stand when stimulated. The diagnosis is established ruling out, clinically and with laboratory findings, that the animals are suffering known diseases with similar symptoms such as paralytic rabies, botulism and blood parasites such Trypanosoma sp., Babesia sp., and Anaplasma sp.. Death occurs always, usually after few days, and to this date there is no known treatment able to save the sick cows. In this work, we describe results that suggest the presence of a toxin in the cattle suffering and prone to suffer the syndrome; it is a natural toxin produced by ruminal bacteria. In squid giant axons under voltage clamp conditions, this toxin is very specific to block sodium current during nerve electrical activity.

  8. Bovine somatic cell nuclear transfer.

    Science.gov (United States)

    Ross, Pablo J; Cibelli, Jose B

    2010-01-01

    Somatic cell nuclear transfer (SCNT) is a technique by which the nucleus of a differentiated cell is introduced into an oocyte from which its genetic material has been removed by a process called enucleation. In mammals, the reconstructed embryo is artificially induced to initiate embryonic development (activation). The oocyte turns the somatic cell nucleus into an embryonic nucleus. This process is called nuclear reprogramming and involves an important change of cell fate, by which the somatic cell nucleus becomes capable of generating all the cell types required for the formation of a new individual, including extraembryonic tissues. Therefore, after transfer of a cloned embryo to a surrogate mother, an offspring genetically identical to the animal from which the somatic cells where isolated, is born. Cloning by nuclear transfer has potential applications in agriculture and biomedicine, but is limited by low efficiency. Cattle were the second mammalian species to be cloned after Dolly the sheep, and it is probably the most widely used species for SCNT experiments. This is, in part due to the high availability of bovine oocytes and the relatively higher efficiency levels usually obtained in cattle. Given the wide utilization of this species for cloning, several alternatives to this basic protocol can be found in the literature. Here we describe a basic protocol for bovine SCNT currently being used in our laboratory, which is amenable for the use of the nuclear transplantation technique for research or commercial purposes.

  9. Evaluation of Presto(plus) assay and LightMix kit Trichomonas vaginalis assay for detection of Trichomonas vaginalis in dry vaginal swabs.

    Science.gov (United States)

    de Waaij, Dewi J; Ouburg, Sander; Dubbink, Jan Henk; Peters, Remco P H; Morré, Servaas A

    2016-08-01

    This is an evaluation study of the Presto(plus) Assay for T. vaginalis by comparing to the TIB MOLBIOL LightMix Kit Trichomonas vaginalis Assay using 615 dry collected vaginal and rectal swabs. Discordant samples were analyzed by the Qiagen® Microbial DNA qPCR for TV Assay. Both assays showed comparable performances (McNemar p>0.05).

  10. Use of kidney inhibition swab test to evaluate antimicrobial residues in pork kidney from a market survey in Fargo, North Dakota

    Science.gov (United States)

    Introduction: The USDA-Food Safety and Inspection Service (FSIS) recently changed the on-site antimicrobial screening method to the Kidney Inhibition Swab (KIS™) test to be used at all livestock slaughter establishments. Although the newly adapted screening method can detect different classes of an...

  11. Pooling Ocular Swab Specimens from Tanzania for testing by Roche Amplicor and Aptima Combo 2 Assays for the detection of Chlamydia trachomatis: Accuracy and Cost Savings

    Science.gov (United States)

    Dize, Laura; West, Sheila; Quinn, Thomas C.; Gaydos, Charlotte A.

    2014-01-01

    Ocular swabs collected in Tanzania were evaluated by Amplicor CT and Aptima Combo2 assays for the detection of Chlamydia trachomatis (CT) to determine if pooling could be used to reduce the cost of detection. Pooling would be an accurate method and so far resulted in a cost-savings of 62.2%. PMID:24079951

  12. Development of a real time PCR for the detection of Taylorella equigenitalis directly from genital swabs and discrimination from Taylorella asinigenitalis

    NARCIS (Netherlands)

    Wakeley, P.R.; Errington, J.; Hannon, S.; Roest, H.I.J.; Carson, T.; Hunt, B.; Sawyer, J.; Heath, P.

    2006-01-01

    discriminatory real time PCR for the detection of Taylorella equigenitalis, the causative agent of contagious equine metritis (CEM), and the related species T. asinigenitalis was developed for the direct examination of genital swabs. The 112 bp amplicons produced from the two species were discrimina

  13. SWAB/NVALT (Dutch Working Party on Antibiotic Policy and Dutch Association of Chest Physicians) Guidelines on the Management of Community-Acquired Pneumonia in Adults

    NARCIS (Netherlands)

    Wiersinga, W. J.; Bonten, M. J.; Boersma, W. G.; Jonkers, R. E.; Aleva, R. M.; Kullberg, B. J.; Schouten, J. A.; Degener, J. E.; Janknegt, R.; Verheij, T. J.; Sachs, A. P. E.; Prins, J. M.

    2012-01-01

    The Dutch Working Party on Antibiotic Policy (SWAB) and the Dutch Association of Chest Physicians (NVALT) convened a joint committee to develop evidence-based guidelines on the diagnosis and treatment of community-acquired pneumonia (CAP). The guidelines are intended for adult patients with CAP who

  14. 21 CFR 184.1034 - Catalase (bovine liver).

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 3 2010-04-01 2009-04-01 true Catalase (bovine liver). 184.1034 Section 184.1034... Listing of Specific Substances Affirmed as GRAS § 184.1034 Catalase (bovine liver). (a) Catalase (bovine liver) (CAS Reg. No. 81457-95-6) is an enzyme preparation obtained from extracts of bovine liver. It...

  15. Development and application of a fecal antigen diagnostic sandwich ELISA for estimating prevalence of Fasciola gigantica in cattle in central Java, Indonesia.

    Science.gov (United States)

    Estuningsih, Endah; Spithill, Terry; Raadsma, Herman; Law, Ruby; Adiwinata, G; Meeusen, Els; Piedrafita, David

    2009-04-01

    The purpose of this study was to compare the sensitivity and specificity of an ELISA test to detect Fasciola gigantica antigens (coproantigens) in bovine feces, with fecal egg counting and an ELISA for detecting anti-F. gigantica antibodies in serum. Monoclonal antibodies to cathepsin L were generated and used to capture this antigen in feces of infected cattle. Blood, feces, and livers were collected from 150 cattle at an abattoir in Jakarta, Indonesia, for anti-Fasciola antibodies, coproantigen detection, and F. gigantica egg and worm counts. Fluke recovery varied from 1 to 426 per host, with a mean of 32 flukes. The results showed that the sensitivity and specificity of coproantigen detecting ELISA (95 and 91%, respectively) was better than the anti-F. gigantica antibody ELISA (91 and 88%, respectively) and to fecal egg counting (87 and 100%, respectively). The coproantigen ELISA was able to detect 100% of the cattle with >15 flukes. A survey of 305 cattle in central Java over a 10-mo period validated this test in the field, demonstrating a high prevalence of fascioliasis and establishing the test as a useful diagnostic method to determine patent F. gigantica infections in cattle.

  16. Stimulation of fecal bacteria in ambient waters by experimental inputs of organic and inorganic phosphorus.

    Science.gov (United States)

    Chudoba, Elizabeth A; Mallin, Michael A; Cahoon, Lawrence B; Skrabal, Stephen A

    2013-06-15

    Fecal microbial pollution of recreational and shellfishing waters is a major human health and economic issue. Microbial pollution sourced from stormwater runoff is especially widespread, and strongly associated with urbanization. However, non-point source nutrient pollution is also problematic, and may come from sources different from fecal-derived pollution (i.e. fertilization of farm fields, lawns and gardens, and ornamental urban areas). Fecal bacteria require nutrients; thus the impact of such nutrient loading on survival and abundance of fecal coliform bacteria in ambient waters was experimentally investigated in a constructed wetland in coastal North Carolina, USA. A series of nutrient-addition bioassays testing impacts of inorganic and organic nitrogen and phosphorus demonstrated that additions of neither organic nor inorganic nitrogen stimulated fecal coliform bacteria. However, phosphorus additions provided significant stimulation of fecal coliform growth at times; on other occasions such additions did not. Dilution bioassays combined with nutrient additions were subsequently devised to assess potential impacts of microzooplankton grazing on the target fecal bacteria populations. Results demonstrated grazing to be a significant bacterial reduction factor in 63% of tests, potentially obscuring nutrient effects. Thus, combining dilution experiments with nutrient addition bioassays yielded simultaneous information on microzooplankton grazing rates on fecal bacteria, fecal bacterial growth rates, and nutrient limitation. Overall, when tested against a non-amended control, additions of either organic or inorganic phosphorus significantly stimulated fecal coliform bacterial growth on 50% of occasions tested, with organic phosphorus generally providing greater stimulation. The finding of significant phosphorus stimulation of fecal bacteria indicates that extraneous nutrient loading can, at times, augment the impacts of fecal microbial pollution of shellfishing

  17. Assessment of Fecal Contamination in Oklahoma Water Systems through the Use of Sterol Fingerprints

    OpenAIRE

    Yueming Lu; R. Paul Philp; Coralie Biache

    2016-01-01

    Fecal contamination is a major concern for water quality management, since the fecal materials are associated with pathogens that can cause illness wherever water is used for recreational, drinking and aquaculture purposes. In order to monitor source(s) of fecal contamination in Oklahoma water systems, sterol profiles were previously examined in rural and urban samples collected from the Illinois River Basin and the Norman Wastewater Treatment Plant (WWTP), respectively. Two distinctive, qual...

  18. Comparison of nasopharyngeal and oropharyngeal swabs for the diagnosis of eight respiratory viruses by real-time reverse transcription-PCR assays.

    Directory of Open Access Journals (Sweden)

    Curi Kim

    Full Text Available BACKGROUND: Many acute respiratory illness surveillance systems collect and test nasopharyngeal (NP and/or oropharyngeal (OP swab specimens, yet there are few studies assessing the relative measures of performance for NP versus OP specimens. METHODS: We collected paired NP and OP swabs separately from pediatric and adult patients with influenza-like illness or severe acute respiratory illness at two respiratory surveillance sites in Kenya. The specimens were tested for eight respiratory viruses by real-time reverse transcription-polymerase chain reaction (qRT-PCR. Positivity for a specific virus was defined as detection of viral nucleic acid in either swab. RESULTS: Of 2,331 paired NP/OP specimens, 1,402 (60.1% were positive for at least one virus, and 393 (16.9% were positive for more than one virus. Overall, OP swabs were significantly more sensitive than NP swabs for adenovirus (72.4% vs. 57.6%, p<0.01 and 2009 pandemic influenza A (H1N1 virus (91.2% vs. 70.4%, p<0.01. NP specimens were more sensitive for influenza B virus (83.3% vs. 61.5%, p = 0.02, parainfluenza virus 2 (85.7%, vs. 39.3%, p<0.01, and parainfluenza virus 3 (83.9% vs. 67.4%, p<0.01. The two methods did not differ significantly for human metapneumovirus, influenza A (H3N2 virus, parainfluenza virus 1, or respiratory syncytial virus. CONCLUSIONS: The sensitivities were variable among the eight viruses tested; neither specimen was consistently more effective than the other. For respiratory disease surveillance programs using qRT-PCR that aim to maximize sensitivity for a large number of viruses, collecting combined NP and OP specimens would be the most effective approach.

  19. Evaluation of pooled ocular and vaginal swabs by the Cepheid GeneXpert CT/NG assay for the detection of Chlamydia trachomatis and Neisseria gonorrhoeae compared to the GenProbe Aptima Combo 2 Assay

    Science.gov (United States)

    Dize, L.; West, S.K.; Mkocha, H.; Quinn, T.C.; Gaydos, C.A.

    2015-01-01

    Ocular swabs from Tanzania were tested for Chlamydia trachomatis (CT), and self-collected vaginal swabs collected through a home collection program, iwantthekit.org, were tested for Neisseria gonorrhoeae and CT to evaluate Cepheid GeneXpert for the use of pooling multiple specimens before testing. GeneXpert shows to be a promising test for pooling. PMID:25497459

  20. Simulation of surge and swab pressures in well drilling operations; Simulacao do problema de 'surge' e 'swab' em atividades de perfuracao de pocos de petroleo

    Energy Technology Data Exchange (ETDEWEB)

    Almeida, Fernando T.G.M.C. de; Kimura, Hudson Faglioni; Ramalho, Vanessa; Negrao, Cezar O. Ribeiro; Junqueira, Silvio L.M. [Universidade Tecnologica Federal do Parana (UTFPR), Curitiba, PR (Brazil); Martins, Andre Leibsohn [PETROBRAS, Rio de Janeiro, RJ (Brazil)

    2008-07-01

    The movements of the well drilling pipe, known as trips, cause variations in the well inner pressure. When the pipe is moving downwards, in an operation called 'running', the pressure increases and is known as surge pressure and, when it is moving upwards, in an operation called 'pulling', the pressure decreases and it is so called a swab pressure. The study of this phenomenon is of great importance not only due to financial reasons but also for the determination of speeds and accelerations which should be used in running and pulling operations. Among the researchers have studied this problem, Fontenot and Clark are two of the most important. They formulated the problem solution through considerations about the friction factor. The present work's target is to develop a computational program which allows the calculus of those pressures, according to previous investigations and models found in the literature and for different types of fluids as well, such as Bingham fluid and Power Law fluid. (author)

  1. Inflixmab in pediatric inflammatory bowel disease rapidly decreases fecal calprotectin levels

    Institute of Scientific and Technical Information of China (English)

    Anssi H(a)m(a)l(a)inen; Taina Sipponen; Kaija-Leena Kolho

    2011-01-01

    AIM: To study the response to infliximab in pediatric inflammatory bowel disease (IBD), as reflected in fecal calprotectin levels.METHODS: Thirty-six pediatric patients with IBD [23 Crohn’s disease (CD), 13 ulcerative colitis (UC); median age 14 years] were treated with infliximab. Fecal calprotectin was measured at baseline, and 2 and 6 wk after therapy, and compared to blood inflammatory markers. Maintenance medication was unaltered until the third infusion but glucocorticoids were tapered off if the patient was doing well.RESULTS: At introduction of infliximab, median fecal calprotectin level was 1150 μg/g (range 54-6032 μg/g). By week 2, the fecal calprotectin level had declined to a median 261 μg/g (P < 0.001). In 37% of the patients, fecal calprotectin was normal (< 100 μg/g) at 2 wk. By week 6, there was no additional improvement in the fecal calprotectin level (median 345 μg/g). In 22% of the patients, fecal calprotectin levels increased by week 6 to pretreatment levels or above, suggesting no response (or a loss of early response). Thus, in CD, the proportion of non-responsive patients by week 6 seemed lower, because only 9% showed no improvement in their fecal calprotectin level when compared to the respective figure of 46% of the UC patients (P < 0.05).CONCLUSION: When treated with infliximab, fecal calprotectin levels reflecting intestinal inflammation normalized rapidly in one third of pediatric patients suggesting complete mucosal healing.

  2. Fecal lactoferrin, a marker of intestinal inflammation in children with inflammatory bowel disease.

    Science.gov (United States)

    Borkowska, Anna; Liberek, Anna; Łuczak, Grażyna; Jankowska, Agnieszka; Plata-Nazar, Katarzyna; Korzon, Maria; Kamińska, Barbara

    2015-01-01

    The aim of this study was to analyze the usefulness of fecal lactoferrin in the diagnosis and monitoring of inflammatory bowel disease (IBD) in children. The study included 52 children with IBD (24 with Crohn's disease and 28 with ulcerative colitis) aged between 0.92 and 18 years, and 41 IBD-free controls of similar age. Fecal concentration of lactoferrin was determined with a quantitative immunoenzymatic test. Fecal concentration of lactoferrin in children with IBD was significantly higher than in the controls. The cut-off value of fecal lactoferrin concentration optimally distinguishing between the children with IBD and the controls was identified as 13 μg/g. The sensitivity and specificity of this cut-off value equaled 80.7% and 92.7%, respectively, and its positive and negative prognostic values were 96.8% and 63.3%, respectively. Patients diagnosed with moderate Crohn's disease had significantly higher fecal concentrations of lactoferrin than children with the mild or inactive disease. Similarly, children with moderate ulcerative colitis showed significantly higher fecal concentrations of lactoferrin than individuals with the mild condition. No significant relationship was found between the fecal concentration of lactoferrin and the severity of endoscopic lesions. Patients with IBD and a positive result of fecal occult blood test were characterized by significantly higher concentrations of lactoferrin than the individuals with IBD and a negative result of this test. In conclusion, fecal concentration of lactoferrin seems to be a useful parameter for diagnosis and monitoring of IBD in children.

  3. Assessment of the climate change impacts on fecal coliform contamination in a tidal estuarine system.

    Science.gov (United States)

    Liu, Wen-Cheng; Chan, Wen-Ting

    2015-12-01

    Climate change is one of the key factors affecting the future microbiological water quality in rivers and tidal estuaries. A coupled 3D hydrodynamic and fecal coliform transport model was developed and applied to the Danshuei River estuarine system for predicting the influences of climate change on microbiological water quality. The hydrodynamic and fecal coliform model was validated using observational salinity and fecal coliform distributions. According to the analyses of the statistical error, predictions of the salinity and the fecal coliform concentration from the model simulation quantitatively agreed with the observed data. The validated model was then applied to predict the fecal coliform contamination as a result of climate change, including the change of freshwater discharge and the sea level rise. We found that the reduction of freshwater discharge under climate change scenarios resulted in an increase in the fecal coliform concentration. The sea level rise would decrease fecal coliform distributions because both the water level and the water volume increased. A reduction in freshwater discharge has a negative impact on the fecal coliform concentration, whereas a rising sea level has a positive influence on the fecal coliform contamination. An appropriate strategy for the effective microbiological management in tidal estuaries is required to reveal the persistent trends of climate in the future.

  4. Use of Direct LAMP Screening of Broiler Fecal Samples for Campylobacter jejuni and Campylobacter coli in the Positive Flock Identification Strategy.

    Science.gov (United States)

    Sabike, Islam I; Uemura, Ryoko; Kirino, Yumi; Mekata, Hirohisa; Sekiguchi, Satoshi; Okabayashi, Tamaki; Goto, Yoshitaka; Yamazaki, Wataru

    2016-01-01

    Rapid identification of Campylobacter-positive flocks before slaughter, following freezing and heat treatment for the Campylobacter-positive carcasses at the slaughterhouses is an effective control strategy against foodborne campylobacteriosis. We evaluated a loop-mediated isothermal amplification (LAMP) assay for the direct screening of naturally contaminated chicken cloacal swabs for C. jejuni/C. coli to compare this assay with conventional quantitative culture methods. In a comparison study of 165 broilers, the LAMP assay showed 82.8% (48/58 by conventional culture) sensitivity, 100% (107/107) specificity, 100% (48/48) positive predictive value (PPV), and 91.5% (107/117) negative predictive value (NPV). In a comparison of 55 flocks, LAMP showed 90.5% (19/21) sensitivity, 100% (34/34) specificity, 100% (19/19) PPV, and 94.4% (34/36) NPV. In the cumulative total of 28 farm-level comparisons, LAMP showed 100% (12/12) sensitivity, 100% (16/16) specificity, 100% (12/12) PPV, and 100% (16/16) NPV. The LAMP assay required less than 90 min from the arrival of the fecal samples to final results in the laboratory. This suggests that the LAMP assay will facilitate the identification of C. jejuni/C. coli-positive broiler flocks at the farm level or in slaughterhouses before slaughtering, which would make it an effective tool in preventing the spread of Campylobacter contamination.

  5. Clinical applications of bovine colostrum therapy

    DEFF Research Database (Denmark)

    Rathe, Mathias; Müller, Klaus; Sangild, Per Torp

    2014-01-01

    to populations, outcomes, and methodological quality, as judged by the Jadad assessment tool. Many studies used surrogate markers to study the effects of bovine colostrum. Studies suggesting clinical benefits of colostrum supplementation were generally of poor methodological quality, and results could...... not be confirmed by other investigators. Bovine colostrum may provide gastrointestinal and immunological benefits, but further studies are required before recommendations can be made for clinical application. Animal models may help researchers to better understand the mechanisms of bovine colostrum supplementation......, the dosage regimens required to obtain clinical benefits, and the optimal methods for testing these effects in humans....

  6. Virulence profiles of Shiga toxin-producing Escherichia coli and other potentially diarrheagenic E.coli of bovine origin, in Mendoza, Argentina

    Directory of Open Access Journals (Sweden)

    M.A. Pizarro

    2013-12-01

    Full Text Available This study described a group of strains obtained from a slaughter house in Mendoza, in terms of their pathogenic factors, serotype, antibiotype and molecular profile. Ninety one rectal swabs and one hundred eight plating samples taken from carcasses of healthy cattle intended for meat consumption were analyzed. Both the swab and the plate samples were processed to analyze the samples for the presence of virulence genes by PCR: stx1, stx2, eae and astA. The Stx positive strains were confirmed by citotoxicity assay in Vero cells. The isolates were subsequently investigated for their O:H serotype, antimicrobial susceptibility and molecular profile by Random Amplification of Polymorphic DNA (RAPD. Twelve E.coli strains were identified by their pathogenicity. Nine were from fecal origin and three from carcasses. Three strains carried the stx1 gene, three the stx2 gene, two carried eae and four the astA gene. The detected serotypes were: O172:H-; O150:H8; O91:H21; O178:H19 and O2:H5. The strains showed a similarity around 70% by RAPD. Some of the E.coli strains belonged to serogroups known for certain life-threatening diseases in humans. Their presence in carcasses indicates the high probability of bacterial spread during slaughter and processing.

  7. Immunoprophylaxis of bovine respiratory syndrome

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    Rogan Dragan

    2010-01-01

    Full Text Available Bovine Respiratory Syndrome (BRS is a multifactorial disease caused by the interaction of infective agents, the environment and the individual immunological response of animals in the herd. Despite five decades of research on BRS, no clear understanding of how environmental factors influence pathogenic outcomes of the disease has been defined. As such, the development of immunoprophylaxis and vaccine programmes to prevent outbreaks of BRS in cattle has not been successful. The current paper discusses vaccination programmes for all categories of cattle and presents a review of existing vaccines being used for immunoprophylaxis of respiratory syndrome in cattle and discusses the advantages and disadvantages of the currently used vaccines and vaccination programmes. Lastly, a discussion detailing the design of future perfect vaccines is presented.

  8. Fecal microbiota transplantation: current clinical efficacy and future prospects.

    Science.gov (United States)

    Bowman, Kathryn A; Broussard, Elizabeth K; Surawicz, Christina M

    2015-01-01

    Fecal microbiota transplantation (FMT) has gained mainstream attention with its remarkable efficacy in treating recurrent Clostridium difficile infection (RCDI) when there are no other effective therapies. Methods of selecting donors and routes of administration vary among studies, but there are now randomized controlled trials showing efficacy of FMT in treating RCDI. Ongoing trials of FMT for other disease such as inflammatory bowel disease are underway; this therapy should not be used for these conditions unless there is strong evidence for efficacy. Long-term safety data are sorely needed, as well as clarification of regulatory concerns.

  9. Daily variability of strongyle fecal egg counts in horses

    DEFF Research Database (Denmark)

    Carstensen, Helena; Larsen, Lene; Ritz, Christian

    2013-01-01

    Strongyle parasites are ubiquitous in grazing horses and constitute a potential threat to equine health. Feces were collected from six horses four times daily over a period of 5 days. Fecal egg counts (FECs) were performed to identify any diurnal rhythms in strongyle egg shedding and to quantify...... variability at the different levels: individual horses, repeated counts, repeated subsamples, different time points, and different days. No significant differences in FECs were found between the different time points (P = .11). The variables-horse, day, subsample, and egg count-accounted for a variance of 104...

  10. Isolation, identification, and complete genome sequence of a bovine adenovirus type 3 from cattle in China

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    Zhu Yuan-Mao

    2011-12-01

    Full Text Available Abstract Background Bovine adenovirus type 3 (BAV-3 belongs to the Mastadenovirus genus of the family Adenoviridae and is involved in respiratory and enteric infections of calves. The isolation of BAV-3 has not been reported prior to this study in China. In 2009, there were many cases in cattle showing similar clinical signs to BAV-3 infection and a virus strain, showing cytopathic effect in Madin-Darby bovine kidney cells, was isolated from a bovine nasal swab collected from feedlot cattle in Heilongjiang Province, China. The isolate was confirmed as a bovine adenovirus type 3 by PCR and immunofluorescence assay, and named as HLJ0955. So far only the complete genome sequence of prototype of BAV-3 WBR-1 strain has been reported. In order to further characterize the Chinese isolate HLJ0955, the complete genome sequence of HLJ0955 was determined. Results The size of the genome of the Chinese isolate HLJ0955 is 34,132 nucleotides in length with a G+C content of 53.6%. The coding sequences for gene regions of HLJ0955 isolate were similar to the prototype of BAV-3 WBR-1 strain, with 80.0-98.6% nucleotide and 87.5-98.8% amino acid identities. The genome of HLJ0955 strain contains 16 regions and four deletions in inverted terminal repeats, E1B region and E4 region, respectively. The complete genome and DNA binding protein gene based phylogenetic analysis with other adenoviruses were performed and the results showed that HLJ0955 isolate belonged to BAV-3 and clustered within the Mastadenovirus genus of the family Adenoviridae. Conclusions This is the first study to report the isolation and molecular characterization of BAV-3 from cattle in China. The phylogenetic analysis performed in this study supported the use of the DNA binding protein gene of adenovirus as an appropriate subgenomic target for the classification of different genuses of the family Adenoviridae on the molecular basis. Meanwhile, a large-scale pathogen and serological epidemiological

  11. Bovine Mastitis: Frontiers in Immunogenetics

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    Kathleen eThompson-Crispi

    2014-10-01

    Full Text Available Mastitis is one of the most prevalent and costly diseases in the dairy industry with losses attributable to reduced milk production, discarded milk, early culling, veterinary services, and labor costs. Typically, mastitis is an inflammation of the mammary gland most often, but not limited to, bacterial infection, and is characterized by the movement of leukocytes and serum proteins from the blood to the site of infection. It contributes to compromised milk quality and the potential spread of antimicrobial resistance if antibiotic treatment is not astutely applied. Despite the implementation of management practises and genetic selection approaches, bovine mastitis control continues to be inadequate. However, some novel genetic strategies have recently been demonstrated to reduce mastitis incidence by taking advantage of a cow’s natural ability to make appropriate immune responses against invading pathogens. Specifically, dairy cattle with enhanced and balanced immune responses have a lower occurrence of disease, including mastitis, and they can be identified and selected for using the High Immune Response (HIR technology. Enhanced immune responsiveness is also associated with improved response to vaccination, increased milk and colostrum quality. Since immunity is an important fitness trait, beneficial associations with longevity and reproduction are also often noted. This review highlights the genetic regulation of the bovine immune system and its vital contributions to disease resistance. Genetic selection approaches currently used in the dairy industry to reduce the incidence of disease are reviewed, including the HIR technology, genomics to improve disease resistance or immune response, as well as the Immunity+TM sire line. Improving the overall immune responsiveness of cattle is expected to provide superior disease resistance, increasing animal welfare and food quality while maintaining favourable production levels to feed a growing

  12. Comparison of eight methods for the extraction of Bacillus atrophaeus spore DNA from eleven common interferents and a common swab.

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    Helen L Rose

    Full Text Available Eight DNA extraction products or methods (Applied Biosystems PrepFiler Forensic DNA Extraction Kit; Bio-Rad Instagene Only, Bio-Rad Instagene & Spin Column Purification; EpiCentre MasterPure DNA & RNA Kit; FujiFilm QuickGene Mini80; Idaho Technologies 1-2-3 Q-Flow Kit; MoBio UltraClean Microbial DNA Isolation Kit; Sigma Extract-N-Amp Plant and Seed Kit were adapted to facilitate extraction of DNA under BSL3 containment conditions. DNA was extracted from 12 common interferents or sample types, spiked with spores of Bacillus atropheaus. Resulting extracts were tested by real-time PCR. No one method was the best, in terms of DNA extraction, across all sample types. Statistical analysis indicated that the PrepFiler method was the best method from six dry powders (baking, biological washing, milk, plain flour, filler and talcum and one solid (Underarm deodorant, the UltraClean method was the best from four liquids (aftershave, cola, nutrient broth, vinegar, and the MasterPure method was the best from the swab sample type. The best overall method, in terms of DNA extraction, across all sample types evaluated was the UltraClean method.

  13. Bordetella holmesii DNA is not detected in nasopharyngeal swabs from Finnish and Dutch patients with suspected pertussis.

    Science.gov (United States)

    Antila, Mia; He, Qiushui; de Jong, Caroline; Aarts, Ingrid; Verbakel, Harold; Bruisten, Sylvia; Keller, Suzanne; Haanperä, Marjo; Mäkinen, Johanna; Eerola, Erkki; Viljanen, Matti K; Mertsola, Jussi; van der Zee, Anneke

    2006-08-01

    Bordetella holmesii is a Gram-negative bacterium first identified in 1995. It can cause pertussis-like symptoms in humans. B. holmesii contains insertion sequences IS481 and IS1001, two frequently used targets in the PCR diagnosis of Bordetella pertussis and Bordetella parapertussis infections. To investigate the prevalence of B. holmesii in Finnish and Dutch patients with pertussis-like symptoms and whether B. holmesii has caused any false-positive results in diagnostic PCRs, B. holmesii-specific real-time PCRs were developed. The Finnish methods were conventional IS481 PCR and B. holmesii-specific real-time PCR (LightCycler, Roche) targeting the B. holmesii recA gene. The Dutch methods were IS481 and IS1001 PCRs with conventional or real-time formats and B. holmesii-specific real-time PCR targeting the homologue of IS1001. Of 11,319 nasopharyngeal swabs, 2804 were collected from Finnish patients from 2000 to 2003, and 8515 from Dutch patients from 1992 to 2003. B. holmesii DNA was not found in the samples analysed. The results suggest that B. holmesii is not among the causative agents of pertussis-like symptoms in Finnish and Dutch patients and thus does not in practice confound IS481 and IS1001 PCRs.

  14. Healthy Farms in Slovakia: Antibiotic Sensitivity of Escherichia coli Isolated from Rectal Swabs of Chicken and Ram

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    Jaroslav Pochop

    2012-10-01

    Full Text Available The aim of this experiment was determine of antibiotic resistance profile of Escherichia coli isolated from rectal swabs of chicken and ram from two different conventional breeding from Slovakia. For the antibiotic susceptibility testing disk diffusion method was used. A tested bacterium, Escherichia coli was exposed against four antibiotics: amikacin, gentamycin, tetracycline and chloramphenicol. For the identification of this strain, we used Chromogenic coliform agar, Triple sugar iron agar and biochemical test (ENTEROtest 24. For genetic identification of Escherichia coli Step One Real Time PCR with using special primer was used. Was determined that antibiotic resistance in Escherichia coli was not found. Was found susceptibility in all cases of Escherichia coli isolates. Antibiotic resistance is a biological danger. Bacteria, which we study, are considered to reservoirs of resistant genes and they are facultative and obligate pathogens. If these pathogen bacteria cause diseases those these diseases are difficult to treat. In this study, we determined that we have healthy farms in Slovakia too. In this farm antibiotic was not use and we do not determined any resistance to antibiotics, which we used in experiment.

  15. Comparative functional genomics and the bovine macrophage response to strains of the mycobacterium genus.

    Science.gov (United States)

    Rue-Albrecht, Kévin; Magee, David A; Killick, Kate E; Nalpas, Nicolas C; Gordon, Stephen V; MacHugh, David E

    2014-01-01

    Mycobacterial infections are major causes of morbidity and mortality in cattle and are also potential zoonotic agents with implications for human health. Despite the implementation of comprehensive animal surveillance programs, many mycobacterial diseases have remained recalcitrant to eradication in several industrialized countries. Two major mycobacterial pathogens of cattle are Mycobacterium bovis and Mycobacterium avium subspecies paratuberculosis (MAP), the causative agents of bovine tuberculosis (BTB) and Johne's disease (JD), respectively. BTB is a chronic, granulomatous disease of the respiratory tract that is spread via aerosol transmission, while JD is a chronic granulomatous disease of the intestines that is transmitted via the fecal-oral route. Although these diseases exhibit differential tissue tropism and distinct complex etiologies, both M. bovis and MAP infect, reside, and replicate in host macrophages - the key host innate immune cell that encounters mycobacterial pathogens after initial exposure and mediates the subsequent immune response. The persistence of M. bovis and MAP in macrophages relies on a diverse series of immunomodulatory mechanisms, including the inhibition of phagosome maturation and apoptosis, generation of cytokine-induced necrosis enabling dissemination of infection through the host, local pathology, and ultimately shedding of the pathogen. Here, we review the bovine macrophage response to infection with M. bovis and MAP. In particular, we describe how recent advances in functional genomics are shedding light on the host macrophage-pathogen interactions that underlie different mycobacterial diseases. To illustrate this, we present new analyses of previously published bovine macrophage transcriptomics data following in vitro infection with virulent M. bovis, the attenuated vaccine strain M. bovis BCG, and MAP, and discuss our findings with respect to the differing etiologies of BTB and JD.

  16. Parasitological diagnosis of schistosomiasis mansoni: fecal examination and rectal biopsy

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    Ana Lúcia Teles Rabello

    1992-01-01

    Full Text Available Even with all progress in the search of sensitive and methods for the immunological diagnosis of schistosomiasis, the microscopic detection of eggs of the parasite in the stool still remains the most widely used tool for the actual diagnosis of active infection. Among the coproscopic methods, Kato's technic modified by Katz et al (Kato/Katz has the advantages of higher sensitivity, the possibility of egg quantification, its low operational cost and its feasibility in areas with minimal infra-structure. The oorgram of the rectal mucosa is valuable in initial clinical trials of schistosomicides, when it is needed to observe egg morphology in tissue. It could be an alternative method for individual diagnosis, being more sensitive than a single stool exam in low intensity infection. However, the increased sensitivity of a higher number of fecal exams makes that invasiveprocedure unnecessary. In the assessment of cure of schistosomiasis, Kato/Katz method (three fecal samples in one, three and six months after treatment and the rectal biopsy four months after treatment, are equally reliable.

  17. Gut microbiota modulation: probiotics, antibiotics or fecal microbiota transplantation?

    Science.gov (United States)

    Cammarota, Giovanni; Ianiro, Gianluca; Bibbò, Stefano; Gasbarrini, Antonio

    2014-06-01

    Gut microbiota is known to have a relevant role in our health, and is also related to both gastrointestinal and extradigestive diseases. Therefore, restoring the alteration of gut microbiota represents an outstanding clinical target for the treatment of gut microbiota-related diseases. The modulation of gut microbiota is perhaps an ancestral, innate concept for human beings. At this time, the restoration of gut microbiota impairment is a well-established concept in mainstream medicine, and several therapeutic approaches have been developed in this regard. Antibiotics, prebiotics and probiotics are the best known and commercially available options to overcome gastrointestinal dysbiosis. Fecal microbiota transplantation is an old procedure that has recently become popular again. It has shown a clear effectiveness in the treatment of C. difficile infection, and now represents a cutting-edge option for the restoration of gut microbiota. Nevertheless, such weapons should be used with caution. Antibiotics can indeed harm and alter gut microbiota composition. Probiotics, instead, are not at all the same thing, and thinking in terms of different strains is probably the only way to improve clinical outcomes. Moreover, fecal microbiota transplantation has shown promising results, but stronger proofs are needed. Considerable efforts are needed to increase our knowledge in the field of gut microbiota, especially with regard to the future use in its modulation for therapeutic purposes.

  18. Alcohol induced alterations to the human fecal VOC metabolome.

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    Robin D Couch

    Full Text Available Studies have shown that excessive alcohol consumption impacts the intestinal microbiota composition, causing disruption of homeostasis (dysbiosis. However, this observed change is not indicative of the dysbiotic intestinal microbiota function that could result in the production of injurious and toxic products. Thus, knowledge of the effects of alcohol on the intestinal microbiota function and their metabolites is warranted, in order to better understand the role of the intestinal microbiota in alcohol associated organ failure. Here, we report the results of a differential metabolomic analysis comparing volatile organic compounds (VOC detected in the stool of alcoholics and non-alcoholic healthy controls. We performed the analysis with fecal samples collected after passage as well as with samples collected directly from the sigmoid lumen. Regardless of the approach to fecal collection, we found a stool VOC metabolomic signature in alcoholics that is different from healthy controls. The most notable metabolite alterations in the alcoholic samples include: (1 an elevation in the oxidative stress biomarker tetradecane; (2 a decrease in five fatty alcohols with anti-oxidant property; (3 a decrease in the short chain fatty acids propionate and isobutyrate, important in maintaining intestinal epithelial cell health and barrier integrity; (4 a decrease in alcohol consumption natural suppressant caryophyllene; (5 a decrease in natural product and hepatic steatosis attenuator camphene; and (6 decreased dimethyl disulfide and dimethyl trisulfide, microbial products of decomposition. Our results showed that intestinal microbiota function is altered in alcoholics which might promote alcohol associated pathologies.

  19. Solid-phase microextraction and the human fecal VOC metabolome.

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    Emma Dixon

    Full Text Available The diagnostic potential and health implications of volatile organic compounds (VOCs present in human feces has begun to receive considerable attention. Headspace solid-phase microextraction (SPME has greatly facilitated the isolation and analysis of VOCs from human feces. Pioneering human fecal VOC metabolomic investigations have utilized a single SPME fiber type for analyte extraction and analysis. However, we hypothesized that the multifarious nature of metabolites present in human feces dictates the use of several diverse SPME fiber coatings for more comprehensive metabolomic coverage. We report here an evaluation of eight different commercially available SPME fibers, in combination with both GC-MS and GC-FID, and identify the 50/30 µm CAR-DVB-PDMS, 85 µm CAR-PDMS, 65 µm DVB-PDMS, 7 µm PDMS, and 60 µm PEG SPME fibers as a minimal set of fibers appropriate for human fecal VOC metabolomics, collectively isolating approximately 90% of the total metabolites obtained when using all eight fibers. We also evaluate the effect of extraction duration on metabolite isolation and illustrate that ex vivo enteric microbial fermentation has no effect on metabolite composition during prolonged extractions if the SPME is performed as described herein.

  20. Control of the gut microbiome by fecal microRNA

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    Shirong Liu

    2016-03-01

    Full Text Available Since their discovery in the early 90s, microRNAs (miRNAs, small non-coding RNAs, have mainly been associated with posttranscriptional regulation of gene expression on a cell-autonomous level. Recent evidence has extended this role by adding inter-species communication to the manifold functional range. In our latest study [Liu S, et al., 2016, Cell Host & Microbe], we identified miRNAs in gut lumen and feces of both mice and humans. We found that intestinal epithelial cells (IEC and Hopx+ cells were the two main sources of fecal miRNA. Deficiency of IEC-miRNA resulted in gut dysbiosis and WT fecal miRNA transplantation restored the gut microbiota. We investigated potential mechanisms for this effect and found that miRNAs were able to regulate the gut microbiome. By culturing bacteria with miRNAs, we found that host miRNAs were able to enter bacteria, specifically regulate bacterial gene transcripts and affect bacterial growth. Oral administration of synthetic miRNA mimics affected specific bacteria in the gut. Our findings describe a previously unknown pathway by which the gut microbiome is regulated by the host and raises the possibility that miRNAs may be used therapeutically to manipulate the microbiome for the treatment of disease.

  1. An occurrence of sepsis during inpatient fecal disimpaction.

    Science.gov (United States)

    Darrow, Cory J; Devito, Justin F

    2014-01-01

    Functional constipation is a common pediatric problem that is often treated through well-established algorithms. Fecal disimpaction is the initial therapeutic step, and severe cases require hospitalization for intensive therapies. We describe a significant unexpected complication of this common clinical situation. An 8-year-old boy with suspected chronic functional constipation was hospitalized for disimpaction by continuous nasogastric administration of polyethylene glycol electrolyte (PEG-E) solution. On the sixth day of disimpaction, the patient abruptly developed fever, tachycardia, and tachypnea. Evaluation included blood culture, which grew Escherichia coli, and treatment with a course of appropriate antibiotics was provided. The safety of PEG-E solutions has been shown in studies of children with constipation, which made this patient's illness surprising. Several potential etiologies of his infection were considered, including bacterial translocation (BT). BT is defined as the passage of live microbes and microbial products from the gastrointestinal tract to extraintestinal sites, such as the bloodstream. It has been shown to occur in a variety of clinical conditions but is of unclear clinical significance. In this case, physical damage to the intestinal mucosa was thought to contribute to the potential occurrence of BT, and prolonged disimpaction was considered as a risk factor. E coli sepsis in a child undergoing inpatient nasogastric fecal disimpaction with PEG-E represents a clinical problem never before reported in the literature and should increase clinicians' indices of suspicion for uncommon complications of common procedures.

  2. Unsealed Tubewells Lead to Increased Fecal Contamination of Drinking Water

    Science.gov (United States)

    Knappett, Peter S. K.; McKay, Larry D.; Layton, Alice; Williams, Daniel E.; Alam, Md. J.; Mailloux, Brian J.; Ferguson, Andrew S.; Culligan, Patricia J.; Serre, Marc L.; Emch, Michael; Ahmed, Kazi M.; Sayler, Gary S.; van Geen, Alexander

    2013-01-01

    Bangladesh is underlain by shallow aquifers in which millions of drinking water wells are emplaced without annular seals. Fecal contamination has been widely detected in private tubewells. To evaluate the impact of well construction on microbial water quality 35 private tubewells (11 with intact cement platforms, 19 without) and 17 monitoring wells (11 with the annulus sealed with cement, 6 unsealed) were monitored for cultured E. coli over 18 months. Additionally, two “snap shot” sampling events were performed on a subset of wells during late-dry and early-wet seasons, wherein the fecal indicator bacteria (FIB) E. coli, Bacteroidales and the pathogenicity genes eltA (ETEC E. coli), ipaH (Shigella) and 40/41 hexon (adenovirus) were detected using qPCR. No difference in E. coli detection frequency was found between tubewells with and without platforms. Unsealed private wells, however, contained cultured E. coli more frequently and higher concentrations of FIB than sealed monitoring wells (p<0.05), suggestive of rapid downward flow along unsealed annuli. As a group the pathogens ETEC, Shigella and adenovirus were detected more frequently (10/22) during the wet season than the dry season (2/20). This suggests proper sealing of private tubewell annuli may lead to substantial improvements in microbial drinking water quality. PMID:23165714

  3. Fecal Microbiota and Diet of Children with Chronic Constipation

    Directory of Open Access Journals (Sweden)

    Joyce Gomes de Moraes

    2016-01-01

    Full Text Available Many factors explain dysbiosis in chronic constipation (CC, such as a low-fiber diet. The objective of this study was to compare the fecal microbiota of constipated and nonconstipated children and their intake frequencies of food. Methods. This observational study included 79 children (M/F 43/36 aged six to 36 months divided into two groups: cases (39 constipated children and controls (40 nonconstipated children. We used a structured form to collect demographic variables, conducted anthropometric assessment, and collected food intake frequency data. The fecal microbiota of the stool samples was analyzed by real-time polymerase chain reaction (PCR using the fluorophore SYBR® Green. Results. Constipated children had a smaller concentration of Lactobacillus per milligram of stool (p=0.015 than nonconstipated children, but the concentration of Bifidobacterium per milligram of stool (p=0.323 and the intake of fruits, vegetables (p=0.563, and junk food (p=0.093 of the two groups did not differ. Constipated children consumed more dairy products (0.45±0.8; p>0.001, were more frequently delivered via caesarean section (69.2%, were weaned earlier (median: 120; 60Q1–240Q3, and had a family history of constipation (71.8%. Conclusions. Children with CC have a smaller concentration of Lactobacillus in their stools and consume more dairy products.

  4. Fecal Microbiota and Diet of Children with Chronic Constipation.

    Science.gov (United States)

    de Moraes, Joyce Gomes; Motta, Maria Eugênia Farias de Almeida; Beltrão, Monique Ferraz de Sá; Salviano, Taciana Lima; da Silva, Giselia Alves Pontes

    2016-01-01

    Many factors explain dysbiosis in chronic constipation (CC), such as a low-fiber diet. The objective of this study was to compare the fecal microbiota of constipated and nonconstipated children and their intake frequencies of food. Methods. This observational study included 79 children (M/F 43/36) aged six to 36 months divided into two groups: cases (39 constipated children) and controls (40 nonconstipated children). We used a structured form to collect demographic variables, conducted anthropometric assessment, and collected food intake frequency data. The fecal microbiota of the stool samples was analyzed by real-time polymerase chain reaction (PCR) using the fluorophore SYBR® Green. Results. Constipated children had a smaller concentration of Lactobacillus per milligram of stool (p = 0.015) than nonconstipated children, but the concentration of Bifidobacterium per milligram of stool (p = 0.323) and the intake of fruits, vegetables (p = 0.563), and junk food (p = 0.093) of the two groups did not differ. Constipated children consumed more dairy products (0.45 ± 0.8; p > 0.001), were more frequently delivered via caesarean section (69.2%), were weaned earlier (median: 120; 60Q1-240Q3), and had a family history of constipation (71.8%). Conclusions. Children with CC have a smaller concentration of Lactobacillus in their stools and consume more dairy products.

  5. Ureaplasma diversum as a cause of pustular vulvovaginitis in bovine females in Vale Guapore, Mato Grosso State, Brazil.

    Science.gov (United States)

    Gaeti, João Guilherme L N; Lana, Marconni V C; Silva, Gustavo S; Lerner, Letycia; de Campos, Camila G; Haruni, Fernanda; Colodel, Edson M; Costa, Eduardo F; Corbellini, Luis G; Nakazato, Luciano; Pescador, Caroline A

    2014-08-01

    Ureaplasma diversum has been associated with various reproductive problems in cattle that include granular vulvovaginitis, weak calves, and abortion. This study was conducted in a beef herd situated in the Middle-West region of Brazil, and the objectives were to verify the presence of U. diversum and to elucidate its possible relationships with independent variables in this bovine herd population. A total of 134 vaginal mucous swabs were taken for polymerase chain reaction (PCR). Of these, 51 (38 %) were PCR positive for U. diversum. Of the 58 heifers with vulvovaginal lesions characterized by hyperemia, granulated lesions, and edema distributed throughout the vulvar mucosa, 37 (64 %) were U. diversum positive; of the 76 heifers without reproductive lesions, 14 (18 %) were U. diversum positive. All tested samples were negative for bovine herpesvirus 1 (BoHV-1). Multivariate logistic regression revealed that the following two variables were significantly associated with the presence of U. diversum: the presence of vulvar lesions (p = 0.001) and the presence of a progesterone (P4) device (p = 0.001). These findings indicate that U. diversum should be considered a pathogen that is associated with pustular vulvovaginitis in heifers from the Mato Grosso state and that additional studies of the risk factors associated with intravaginal P4 device transmission should be performed.

  6. Characterization of Mannheimia haemolytica isolated from feedlot cattle that were healthy or treated for bovine respiratory disease.

    Science.gov (United States)

    Klima, Cassidy L; Alexander, Trevor W; Hendrick, Steve; McAllister, Tim A

    2014-01-01

    Mannheimia haemolytica is the principal bacterial pathogen associated with bovine respiratory disease (BRD). As an opportunistic pathogen, M. haemolytica is also frequently isolated from the respiratory tract of healthy cattle. This study examined the characteristics of M. haemolytica collected using deep nasal swabs from healthy cattle (n = 49) and cattle diagnosed with BRD (n = 41). Isolates were analyzed by pulsed-field gel electrophoresis (PFGE), serotyped, and tested for antimicrobial susceptibility. Polymerase chain reaction (PCR) was used to screen isolates for virulence [leukotoxin C (lktC), putative adhesin (ahs), outer-membrane lipoprotein (gs60), O-sialoglycoprotease (gcp), transferring-binding protein B (tbpB) and UDP-N-acetyl-D-glucosamine-2-epimerase (nmaA)] and antimicrobial resistance [tet(H), bla ROB-1, erm(X), erm(42), msr(E)-mph(E) and aphA-1] genes. Isolates were genetically diverse but in three instances, M. haemolytica with the same pulsotype, resistance phenotype, and genotype were collected from cattle with BRD. This occurred once between cattle located in two different feedlots, once between cattle in the same feedlot, but in different pens, and once among cattle from the same feedlot in the same pen. Isolates from healthy cattle were primarily serotype 2 (75.5%) while those from individuals with BRD were serotype 1 (70.7%) or 6 (19.5%). Resistance to at least one antibiotic occurred more frequently (P bovine respiratory disease in western Canadian feedlots.

  7. Development of Cross-Assembly Phage PCR-Based Methods for Human Fecal Source Identification

    Science.gov (United States)

    Technologies that can characterize human fecal pollution in environmental waters offer many advantages over traditional general indicator approaches. However, many human-associated methods cross-react with non-human animal sources and lack suitable sensitivity for fecal source id...

  8. Fecal microbial composition of ulcerative colitis and Crohn's disease patients in remission and subsequent exacerbation

    NARCIS (Netherlands)

    Wills, E.S.; Jonkers, D.M.; Savelkoul, P.H.; Masclee, A.A.M.; Pierik, M.J.; Penders, J.

    2014-01-01

    BACKGROUND: Limited studies have examined the intestinal microbiota composition in relation to changes in disease course of IBD over time. We aimed to study prospectively the fecal microbiota in IBD patients developing an exacerbation during follow-up. DESIGN: Fecal samples from 10 Crohn's disease (

  9. Fecal progestagens to detect and monitor pregnancy in captive female cheetahs (Acinonyx jubatus).

    Science.gov (United States)

    Adachi, Itsuki; Kusuda, Satoshi; Kawai, Hitomi; Ohazama, Megumi; Taniguchi, Atsushi; Kondo, Natsuko; Yoshihara, Masato; Okuda, Ryuta; Ishikawa, Tatsuya; Kanda, Iwai; Doi, Osamu

    2011-04-01

    The purposes of the present study were to establish a noninvasive monitoring assay of fecal progestagen measurement to detect pregnancy and to identify the components of fecal progestagens in early, middle and late pregnancy in cheetahs. Feces were collected from 7 female cheetahs and analyzed from 30 days before the last copulation to parturition in 9 pregnancies. Blood was collected from one cheetah. Fecal progestagen and serum progesterone concentrations were determined by enzyme immunoassay (EIA). The profiles of the fecal progestagen concentrations were similar to the serum progesterone profile. Fecal progestagen and serum progesterone concentrations remained at the baseline until copulation. In the mean fecal progestagen profile during pregnancy (92.8 ± 0.4 days; from the last copulation to parturition), the concentrations increased 3-4 days after the last copulation and remained high until parturition. To investigate changes in the components of progestagen metabolites in the tripartite periods of gestation, fecal progestagens were analyzed by HPLC-EIA. Marked immunoreactive peaks consistent with 5α-pregnan-3α/β-ol-20-one and 5α-pregnan-3,20-dione and small peaks consistent with 5β-pregnan-3α/β-ol-20-one were detected. There were no distinct difference in the components of progestagens among the first, second and third trimesters of pregnancy. The hormone assay, as an indicator of fecal 5α-reduced pregnanes, is useful for detecting pregnancy and monitoring pregnant luteal activity in cheetahs.

  10. Waveband selection and algorithm development to distinguish fecal contamination using multispectral imaging with solar light

    Science.gov (United States)

    Fecal contamination in fresh produce fields caused by animals or livestock entering the fields can lead to outbreaks of foodbourne illnesses. E.coli O157:H7 originating in the intestines of animals can transfer onto leafy greens via fecal matter. Leafy greens are often eaten fresh without thermal tr...

  11. Can the outcome of pelvic-floor rehabilitation in patients with fecal incontinence be predicted?

    NARCIS (Netherlands)

    M.P. Terra; M. Deutekom (Marije); A.C. Dobben (Annette); C.G.M.I. Baeten; L.W.M. Janssen (Lucas); G.E. Boeckxstaens (Guy); A.F. Engel (Alexander); R.J.F. Felt-Bersma; J.F.W. Slors; M.F. Gerhards (Michael); A.B. Bijnen (Bart); E. Everhardt; W.R. Schouten (Ruud); B. Berghmans; P.M.M. Bossuyt (Patrick); J. Stoker (Jacob)

    2008-01-01

    textabstractPurpose: Pelvic-floor rehabilitation does not provide the same degree of relief in all fecal incontinent patients. We aimed at studying prospectively the ability of tests to predict the outcome of pelvic-floor rehabilitation in patients with fecal incontinence. Materials and methods: Two

  12. Metabonomics of human fecal extracts characterize ulcerative colitis, Crohn's disease and healthy individuals

    DEFF Research Database (Denmark)

    Bjerrum, Jacob Tveiten; Wang, Yulan; Hao, Fuhua

    2015-01-01

    This study employs spectroscopy-based metabolic profiling of fecal extracts from healthy subjects and patients with active or inactive ulcerative colitis (UC) and Crohn's disease (CD) to substantiate the potential use of spectroscopy as a non-invasive diagnostic tool and to characterize the fecal...

  13. Pathogenesis of a Chinese strain of bovine adenovirus type 3 infection in albino guinea pigs.

    Science.gov (United States)

    Shi, Hong-Fei; Zhu, Yuan-Mao; Yan, Hao; Ma, Lei; Wang, Xue-Zhi; Xue, Fei

    2014-12-01

    Bovine adenovirus type 3 (BAV-3) is considered one of the most important respiratory tract agents of cattle and is widespread among cattle around the world. A BAV-3 strain was isolated from a bovine nasal swab for the first time in China in 2009 and named HLJ0955. Subsequently, BAV-3 has frequently been isolated from calves with respiratory diseases in China. To date, only limited study on the pathogenesis of BAV-3 infection in cotton rats has been conducted, and the pathogenesis of BAV-3 infection in guinea pigs has not been reported. Therefore, sixteen albino guinea pigs were inoculated intranasally with HLJ0955. All of the infected guinea pigs had apparently elevated rectal temperatures (39.2 °C-39.9 °C) at 2-7 days post-inoculation (PI). Consolidation and petechial hemorrhage were also observed in guinea pigs experimentally infected with HLJ0955. Viral replication was detectable by virus isolation and titration and by immunohistochemistry in the lungs of guinea pigs as early as 24 h PI. Viral DNA was detectable in the lungs of infected guinea pigs during 11 days of observation by real-time PCR. Virus-neutralizing antibodies against BAV-3 were detectable from 11 days PI and reached a peak titer at 15 days PI. Histopathological changes mainly occurred in the lungs of infected guinea pigs and were characterized by thickening of alveolar septa, mononuclear cell infiltration, hemorrhage and alveolar epithelial necrosis. These results indicate that HLJ0955 can replicate in the lungs of guinea pigs and cause fever and gross and histological lesions. The guinea pig infection model of BAV-3 would serve as a useful system for monitoring the infection process and pathogenesis of the Chinese BAV-3 strain HLJ0955, as well as immune responses to BAV-3 vaccines.

  14. Application of leftover sample material from waterborne protozoa monitoring for the molecular detection of Bacteroidales and fecal source tracking markers

    Science.gov (United States)

    In this study, we examined the potential for detecting fecal bacteria and microbial source tracking markers in samples discarded during the concentration of Cryptosporidium and Giardia using USEPA Method 1623. Recovery rates for different fecal bacteria were determined using sp...

  15. Sediment and Fecal Indicator Bacteria Loading in a Mixed Land Use Watershed: Contributions from Suspended and Bed Load Transport

    Science.gov (United States)

    Water quality studies that quantify sediment and fecal bacteria loading commonly focus on suspended contaminants transported during high flows. Fecal contaminants in bed sediments are typically ignored and need to be considered because of their potential to increase pathogen load...

  16. Long-term dietary pattern of fecal donor correlates with butyrate production and markers of protein fermentation during in vitro fecal fermentation.

    Science.gov (United States)

    Yang, Junyi; Rose, Devin J

    2014-09-01

    Diet influences gut microbiota composition. Therefore, we hypothesized that diet would impact the extent of dietary fiber utilization and the types of metabolic end-products produced by the microbiota during in vitro fecal fermentation. By obtaining long-term dietary records from fecal donors, we aimed to determine the correlations between dietary intake variables and dietary fiber degradation and short-/branched-chain fatty acid (BCFA) and ammonia production during in vitro fecal fermentation. Eighteen subjects completed 1-year diet history questionnaires and provided fecal samples that were used for in vitro fermentation of a whole wheat substrate. The percentage of dietary fiber fermented was not correlated with nutrient intakes; however, butyrate production was correlated with fecal donor intake of many nutrients of which principal component analysis revealed were mostly contributed by grain-, nut-, and vegetable-based foods. Negative correlations were found for propionate with intake of total carbohydrate, added sugar, and sucrose and for ammonia and BCFA production with intake of unsaturated fats. Thus, our analysis did not support our first hypothesis: the percentage of dietary fiber fermented during in vitro fermentation was not correlated with dietary records. However, production of butyrate; BCFA; ammonia; and, to a lesser extent, propionate was correlated with the diet records of fecal donors, thus supporting our second hypothesis. These results suggest that diets high in plant-based foods and high in unsaturated fats are associated with microbial metabolism that is consistent with host health.

  17. Experimental Design for a Macrofoam Swab Study Relating the Recovery Efficiency and False Negative Rate to Low Concentrations of Two Bacillus anthracis Surrogates on Four Surface Materials

    Energy Technology Data Exchange (ETDEWEB)

    Piepel, Gregory F.; Hutchison, Janine R.

    2014-04-16

    This report describes the experimental design for a laboratory study to quantify the recovery efficiencies and false negative rates of a validated, macrofoam swab sampling method for low concentrations of Bacillus anthracis Sterne (BAS) and Bacillus atrophaeus (BG) spores on four surface materials (stainless steel, glass, vinyl tile, plastic light cover panel). Two analytical methods (plating/counting and polymerase chain reaction) will be used. Only one previous study has investigated false negative as a function of affecting test factors. The surrogates BAS and BG have not been tested together in the same study previously. Hence, this study will provide for completing gaps in the available information on the performance of macrofoam swab sampling at low concentrations.

  18. Experimental Design for a Macrofoam-Swab Study Relating the Recovery Efficiency and False Negative Rate to Low Concentrations of Two Bacillus anthracis Surrogates on Four Surface Materials

    Energy Technology Data Exchange (ETDEWEB)

    Piepel, Gregory F. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Hutchison, Janine R. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2014-12-05

    This report describes the experimental design for a laboratory study to quantify the recovery efficiencies and false negative rates of a validated, macrofoam-swab sampling method for low concentrations of Bacillus anthracis Sterne (BAS) and Bacillus atrophaeus (BG) spores on four surface materials (stainless steel, glass, vinyl tile, plastic light cover panel). Two analytical methods (culture and polymerase chain reaction) will be used. Only one previous study has investigated how the false negative rate depends on test factors. The surrogates BAS and BG have not been tested together in the same study previously. Hence, this study will provide for completing gaps in the available information on the performance of macrofoam-swab sampling at low concentrations.

  19. Relative quantification and detection of different types of infectious bursal disease virus in bursa of Fabricius and cloacal swabs using real time RT-PCR SYBR green technology

    DEFF Research Database (Denmark)

    Li, Yiping; Handberg, K.J.; Kabell, Susanne;

    2007-01-01

    or F52/70 inoculation were detected as virus positive at day I post inoculation (p.i.). The D78 viral load peaked at day 4 and day 8 p.i., while the DK01 and F52/70 viral load showed relatively high levels at day 2 p.i. In cloacal swabs, viruses detectable were at day 2 p.i. for DK01 and F52/70, day 8......In present study, different types of infectious bursal disease virus (IBDV), virulent strain DK01, classic strain F52/70 and vaccine strain D78 were quantified and detected in infected bursa of Fabricius (BF) and cloacal swabs using quantitative real time RT-PCR with SYBR green dye. For selection...

  20. Efficacy of combined jejunal and colonic fecal microbiota transplantation for recurrent Clostridium difficile Infection.

    Science.gov (United States)

    Dutta, Sudhir K; Girotra, Mohit; Garg, Shashank; Dutta, Anand; von Rosenvinge, Erik C; Maddox, Cynthia; Song, Yang; Bartlett, John G; Vinayek, Rakesh; Fricke, W Florian

    2014-09-01

    The prevalence of recurrent Clostridium difficile infection (RCDI) is increasing; fecal microbiota transplantation (FMT) is an effective therapy. However, there have been no studies of the efficacy of a single session of combined enteral and colonic FMT or characterizations of changes in the microbiota between donors and recipients. We performed a study of 27 patients with RCDI who were given a fixed volume of processed fecal filtrate via enteroscopy and colonoscopy in a single session. Patients were closely monitored, and fecal samples were collected from 2 patient-donor pairs for 16S rRNA analysis. All patients had reduced stool frequency, abdominal pain, white blood cell counts, and elimination of fecal C difficile toxin (P fecal microbiota in 2 patients with RCDI.

  1. Feeding on copepod fecal pellets: a new trophic role of dinoflagellates as detritivores

    DEFF Research Database (Denmark)

    Poulsen, Louise K.; Moldrup, M.; Berge, T.;

    2011-01-01

    Recent field studies indicate that dinoflagellates are key degraders of copepod fecal pellets. This study is the first to publish direct evidence of pellet grazing by dinoflagellates. Feeding and growth on copepod fecal pellets were studied for both heterotrophic (4 species) and mixotrophic...... dinoflagellates (3 species) using a combination of classic incubation experiments and video recordings of feeding behavior. Fecal pellets were produced by adult Acartia tonsa feeding on Rhodomonas salina. Two mixotrophic species (Karlodinium armiger, a gymnodinoid dinoflagellate, Gy1) and all heterotrophic...... dinoflagellates (Gyrodinium dominans, Gyrodinium spirale, Diplopsalis lenticula, Protoperidinium depressum) studied fed on fecal pellets. Using natural concentrations of dinoflagellates and copepod fecal pellets, average ingestion rates of 0.2 and 0.1 pellets cell−1 d−1 and clearance rates of between 0.2 and 0...

  2. Value of the oral swab for the molecular diagnosis of dogs in different stages of infection with Leishmania infantum.

    Science.gov (United States)

    Aschar, Mariana; de Oliveira, Eveline Tozzi Braga; Laurenti, Marcia Dalastra; Marcondes, Mary; Tolezano, Jose Eduardo; Hiramoto, Roberto Mitsuyoshi; Corbett, Carlos Eduardo P; da Matta, Vania Lucia Ribeiro

    2016-07-30

    This study was based on the need to employ a sensitive and specific method with samples that could be easily collected for diagnosing dogs infected with Leishmania infantum. To this end, we used real time-PCR (qPCR) to assess the value of the oral swab (OS) in detecting infected sick dogs (SD; n=62), including, for the first time, the analysis of apparently healthy infected dogs (AD; n=30), both from endemic areas for visceral leishmaniasis (VL). For comparison, we also evaluated the performance of the conjunctival swab (CS), blood (BL), lymph node (LN) and serology. We detected the presence of Leishmania DNA in the oral cavity in 62 out of the 92 dogs studied. The OS positivity (67.4%) was equivalent to the CS (68.5%) (p>0.05), higher than BL (52.2%) (p≤0.05), and lower than LN (84.8%) (p≤0.05). OS and CS performed well in SD dogs (82.3% and 83.9%, respectively) but not in AD dogs (36.7% for both samples). BL showed the lowest positivity (52.2%) and provided equivalent results between AD (60.0%) and SD (48.4%) dogs (p>0.05). LN yielded the highest positivity (84.8%), and it was also higher in the SD population (93.5%) compared to the AD population (66.7%) (p≤0.05). Parasite load was high in LN, moderate in OS and CS, and low in BL, showing the relationship between the levels of parasitism and the positivity rates found in these samples. Serology was positive in 82.2% of the SD group and in 70% of the AD dogs (p>0.05). Among the 20 seronegative dogs, seven (35%) were positive in either OS or CS, and 12 (60%) were positive when both noninvasive samples were jointly considered. The OS/CS combination resulted in a significant increase of positivity (p≤0.05) for the AD dogs (from 36.7% to 63.4%), as well as OS/serology (80%) and OS/CS/serology (83.4%). For the SD population, positivity reached up to 95.2% with the same combinations, showing that combination of samples and/or tests is required for the identification of dogs infected with L. infantum and that the

  3. Identification of Candida spp. isolated from vaginal swab by phenotypic methods and multiplex PCR in Duhok, Iraq

    Directory of Open Access Journals (Sweden)

    Ahmed Basheer Mohammed

    2015-11-01

    Full Text Available Background: Candida species are the second most common cause of vulvovaginitis worldwide. The purpose of this study was to identify the species of vaginal Candida isolates by using phenotypic and Multiplex PCR techniques. Methods: 91 isolates from patients admitted to Azadi hospital and Maternity hospital in Duhok city were collected. The vaginal swab specimens were inoculated on Sabouraud dextrose agar. Colonies were then sub cultured on Chromogenic Candida agar. Genomic DNA extraction was performed using a Genomic DNA Extraction kit. For rapid identification of Candida spp., specific primers based on the genomic sequence of DNA topoisomerase 11 of C. albicans, C. parapsilosis I, C. parapsilosis II, C. guilliermondi, C. dubliniensis, C. krusei, C. kefyr and C. glabrata, C. tropicalis I, C. tropicalis II, C. lusitaniae were used. The multiplex PCR products were separated by electrophoresis in 1.5% agarose gel, visualized by staining with ethidium bromide, and photographed. Results: 4 Candida species, namely C. albicans, C. glabrata, C. krusei and C. tropicalis were distinguished by Chromogenic Candida agar on the basis of colony colour and morphology. PCR with the primer mixes yielded 7 different sized of PCR products corresponding to C. albicans, C. guilliermondii, C. dubliniensis, C. glabrata, C. kefyr, C. krusei and C. tropicalis II. The analysis revealed C. glabrata and C. albicans were the most common species isolated with the percentage 40% and 30% respectively. Conclusions: This study concluded that phenotypic characteristics on selective agar medium such as chromogenic candida agar are useful for presumptive identification of Candiada spp. with the support of molecular method such as multiplex PCR. [Int J Res Med Sci 2015; 3(11.000: 3211-3216

  4. Variation in MRSA identification results from different generations of Xpert MRSA real-time PCR testing kits from nasal swabs.

    Science.gov (United States)

    Rabaan, Ali A; Bazzi, Ali M

    2017-02-06

    GeneXpert MRSA kits (Cepheid) are based on a multiplex, real-time PCR method for methicillin-resistant Staphylococcus aureus (MRSA) detection, with primers to detect each SCCmec type and the chromosomal orfX-SCCmec junction. Modifications in recent kit versions were proposed to help overcome false-positive issues in earlier kit versions. The main objective of this study was to determine whether use of any version of the GeneXpert MRSA multiplex, real-time PCR kits yielded higher than expected MRSA+ results. We also estimated the level of MRSA in our healthcare facility as a proportion of total S. aureus between 2010 and 2015. We examined results from five generations of the kits used between 2008 and 2015. Results were from nasal swab samples from 16,431 patients in the Johns Hopkins Aramco Healthcare facility in Saudi Arabia. The percentage of isolates scored as MRSA+ for the original Xpert MRSA kit was 18.57%, compared to 6.93±1.12% (mean±SD) for the other four kits. The Xpert MRSA-SA Nasal kit yielded 6.48% Invalid results, compared to 0.73±0.28% for the other four kits. The succeeding Xpert MRSA-SA Nasal G3 and Xpert MRSA-SA Nasal Complete G3 kits yielded Invalid results rates of 0.29% and 1.04% respectively. Levels of MRSA-positive isolates as a percentage of total S. aureus-containing samples ranged between 19.81% and 26.74%. In conclusion, the original Xpert MRSA kit yielded higher than expected rates of MRSA+. Issues with over-estimation of MRSA+ and/or numerous Invalid results have been overcome in the most recent modified kits.

  5. The Use of Multiplex PCR to Determine the Prevalence of Enterotoxigenic Staphylococcus aureus Isolated from Raw Milk, Feta Cheese, and Hand Swabs.

    Science.gov (United States)

    Zeinhom, Mohamed M A; Abdel-Latef, Gihan K; Jordan, Kieran

    2015-12-01

    Staphylococcus aureus (S. aureus) can cause mastitis in cattle and, therefore, can be present in milk. This study was undertaken to determine the prevalence of coagulase positive S. aureus and its enterotoxin genes sea, seb, and sec in isolates recovered from raw milk, feta cheese, and human hand swabs of milk and cheese handlers in Beni-Suef province, Egypt. A total of 100 samples of raw milk and 50 samples of pasteurized-milk feta cheese were collected. In addition, 50 hand swabs from milk handlers and 25 hand swabs from cheese handlers were examined for the presence of coagulase positive S. aureus. The isolates were characterized by multiplex PCR for detection of sea, seb, and sec genes, and for resistance to 5 classes of commonly used antibiotics. Twelve (12/100), 12 (6/50), and 17% (13/75) of milk, cheese, and hand swab samples, respectively, were positive for coagulase positive S. aureus. One isolate was obtained from each positive sample (31 isolates), and none contained genes for SEA or SEC production. Twenty-five percent, 33%, and 31%, respectively, of the isolates contained the genes for SEB, resulting in 3%, 4%, and 5% of samples being positive for toxin producing coagulase positive S. aureus, respectively. At least one isolate was resistant to each of the antibiotics tested. Despite the low potential for SEB production shown, preventative measures, such as maintenance of the cold-chain and good hygienic practices should be implemented to further reduce the potential risk to public health from SEB, and to reduce the spread of antimicrobial resistance.

  6. Neisseria gonorrhoeae False-Positive Result Obtained from a Pharyngeal Swab by Using the Roche cobas 4800 CT/NG Assay in New Zealand in 2012

    OpenAIRE

    Upton, Arlo; Bromhead, Collette; Whiley, David M

    2013-01-01

    The Roche cobas 4800 CT/NG assay is a commonly used commercial system for screening for Neisseria gonorrhoeae infection, and previous studies have shown the method to be highly sensitive and specific for urogenital samples. We present the first confirmed clinical N. gonorrhoeae false-positive result using the cobas 4800 NG assay, obtained from testing a pharyngeal swab sample and caused by cross-reaction with a commensal Neisseria strain.

  7. Use of eschar swabbing for the molecular diagnosis and genotyping of Orientia tsutsugamushi causing scrub typhus in Quang Nam province, Vietnam

    Science.gov (United States)

    Le Viet, Nhiem; Laroche, Maureen; Thi Pham, Hoa L.; Viet, Nho L.; Mediannikov, Oleg; Raoult, Didier; Parola, Philippe

    2017-01-01

    Background Scrub typhus is a rickettsiosis which is caused by Orientia tsutsugamushi and occurs throughout the Asia-Pacific region. Molecular diagnosis of rickettsioses using eschar swabs has recently emerged, and may be very useful for the diagnosis of these diseases in tropical settings. Methodology/Principal findings Quantitative polymerase chain reaction (qPCR) was used to detect O. tsutsugamushi DNA in whole blood and eschar swab specimens of 67 patients who were clinically suspected of scrub typhus in Quang Nam province, Vietnam. Among the 20 patients for whom both eschar and whole blood were obtained, 17 (85%) of the eschar specimens and 5 (25%) of the whole blood specimens tested positive for O. tsutsugamushi. Genetic analysis of the 56-kDa TSA gene sequences demonstrated that the 14 sequences obtained in this study, including 12 eschar swabs and 2 whole blood specimens, were related to 4 groups: Karp, Kawasaki, Gilliam (JG-v and TG-v) and TA716. The majority (9/14; 64.4%) of contemporary O. tsutsugamushi genotypes in Quang Nam province were related to the Karp group. Conclusions These results suggest that polyclonal antigen pools used for serological testing in the future should contain at least Karp, Kawasaki, Gilliam and TA716 antigens for Vietnamese patients, as well as patients who have traveled to Vietnam. qPCR after eschar swabbing should be considered for molecular diagnosis of scrub typhus in endemic patients as well as in travelers, since it is easy to perform and appears very useful for the rapid detection of Orientia tsutsugamushi in the early phase of infection. PMID:28241043

  8. High-throughput DNA sequence analysis reveals stable engraftment of gut microbiota following transplantation of previously frozen fecal bacteria

    OpenAIRE

    Hamilton, Matthew J.; Weingarden, Alexa R.; Unno, Tatsuya; Khoruts, Alexander; Michael J Sadowsky

    2013-01-01

    Fecal microbiota transplantation (FMT) is becoming a more widely used technology for treatment of recurrent Clostridum difficile infection (CDI). While previous treatments used fresh fecal slurries as a source of microbiota for FMT, we recently reported the successful use of standardized, partially purified and frozen fecal microbiota to treat CDI. Here we report that high-throughput 16S rRNA gene sequencing showed stable engraftment of gut microbiota following FMT using frozen fecal bacteria...

  9. Impact of Population and Latrines on Fecal Contamination of Ponds in Rural Bangladesh

    Science.gov (United States)

    Knappett, Peter S. K.; Escamilla, Veronica; Layton, Alice; McKay, Larry D.; Emch, Michael; Williams, Daniel E.; Huq, Md. R.; Alam, Md. J.; Farhana, Labony; Mailloux, Brian J.; Ferguson, Andy; Sayler, Gary S.; Ahmed, Kazi M.; van Geen, Alexander

    2011-01-01

    A majority of households in Bangladesh rely on pond water for hygiene. Exposure to pond water fecal contamination could therefore still contribute to diarrheal disease despite the installation of numerous tubewells for drinking. The objectives of this study are to determine the predominant sources (human or livestock) of fecal pollution in ponds and examine the association between local population, latrine density, latrine quality and concentrations of fecal bacteria and pathogens in pond water. Forty-three ponds were analyzed for E. coli using culture-based methods and E. coli, Bacteroidales and adenovirus using quantitative PCR. Population and sanitation spatial data were collected and measured against pond fecal contamination. Humans were the dominant source of fecal contamination in 79% of the ponds according to Bacteroidales measurements. Ponds directly receiving latrine effluent had the highest concentrations of fecal indicator bacteria (up to 106 Most Probable Number (MPN) of culturable E. coli per 100 mL). Concentrations of fecal indicator bacteria correlated with population surveyed within a distance of 30-70 m (p<0.05) and total latrines surveyed within 50-70 m (p<0.05). Unsanitary latrines (visible effluent or open pits) within the pond drainage basin were also significantly correlated to fecal indicator concentrations (p<0.05). Water in the vast majority of the surveyed ponds contained unsafe levels of fecal contamination attributable primarily to unsanitary latrines, and to lesser extent to sanitary latrines and cattle. Since the majority of fecal pollution is derived from human waste, continued use of pond water could help explain the persistence of diarrheal disease in rural South Asia. PMID:21632095

  10. Descriptive study of California egg layer premises and analysis of risk factors for Salmonella enterica serotype enteritidis as characterized by manure drag swabs.

    Science.gov (United States)

    Castellan, David M; Kinde, Hailu; Kass, Philip H; Cutler, Gregg; Breitmeyer, Richard E; Bell, Donald D; Ernst, Ralph A; Kerr, David C; Little, Herbert E; Willoughby, David; Riemann, Hans P; Ardans, Alex; Snowdon, Jill A; Kuney, Douglas R

    2004-09-01

    This cross-sectional, double-blind study reports the prevalence of Salmonella enterica serotype enteritidis (SE) on California egg layer premises using single vs. pooled manure drag swabs and presents a description of egg production and management systems in the state and an initial analysis of risk factors for SE. The study included 91% of all known eligible egg premises in California, representing the majority of eggs produced in the state. The overall prevalence of SE on California egg layer premises was 10.5%, while 1.1% of all rows sampled were positive for SE. The percentage of positive rows for SE on any premises never exceeded 25% of the 16 swabs collected per premises. A description of egg production and management on California egg layer premises is presented. Statistically significant associations for SE were not evident and were limited because of sample size and the low prevalence of SE on California egg layer premises. Several biological and management factors, such as flock health, stage of production, manure management, ventilation, and watering systems, show trend associations with premises positive for SE and require further investigation. Manure drag swabs serve as a useful tool to validate the core components of an egg quality assurance program for SE based on process control principles.

  11. Multiplex detection of bacteria associated with normal microbiota and with bacterial vaginosis in vaginal swabs by use of oligonucleotide-coupled fluorescent microspheres.

    Science.gov (United States)

    Dumonceaux, Tim J; Schellenberg, John; Goleski, Vanessa; Hill, Janet E; Jaoko, Walter; Kimani, Joshua; Money, Deborah; Ball, T Blake; Plummer, Francis A; Severini, Alberto

    2009-12-01

    Bacterial vaginosis (BV) is a recurrent condition that is associated with a range of negative outcomes, including the acquisition of human immunodeficiency virus and other sexually transmitted diseases, preterm births, and pelvic inflammatory disease. In contrast to the Lactobacillus-dominated normal vaginal microbiota, BV is characterized by a lack of lactobacilli and an abundance of anaerobic and gram-negative organisms, including Gardnerella vaginalis and Atopobium vaginae. To date, the laboratory diagnosis of BV has relied upon the fulfillment of criteria determined by microscopic observation of Gram-stained vaginal swabs. We describe a molecular-based method for the easy determination of the species profile within the vaginal microbiota based on the amplification of the chaperonin-60 genes of all bacteria present in the swab and hybridization of the amplicon to species-specific oligonucleotide-coupled fluorescent beads that are identified by flow cytometry with a Luminex instrument. We designed a nineplex Luminex array for characterization of the vaginal microbiota and applied it to the analysis of vaginal swabs from individuals from Africa and North America. Using the presence of A. vaginae or G. vaginalis, or both, as the defining criterion for BV, we found that the method was highly specific and sensitive for the diagnosis of BV using microscopy as a gold standard.

  12. Cleaning validation for residual estimation of olmesartan medoxomil on stainless steel surface of pharmaceutical manufacturing equipments using swab sampling and HPLC-DAD method

    Directory of Open Access Journals (Sweden)

    Nitin Dubey

    2013-06-01

    Full Text Available Prevention of cross contamination with active pharmaceutical ingredient is crucial and requires special attention in pharmaceutical industry. Current method validation describes residual determination of olmesartan medoxomil (OLME on stainless steel surface using swab sampling with a sensitive HPLC-DAD analysis. The acceptance limit was decided as 2 μg swab pro 100 cm2. Cotton swabs impregnated with extraction solution were used to determine residual drug content. Recoveries were 95.81%, 93.06%, and 96%. 24% with RSD below 1.5% at three concentration levels. Residual concentration was found to be linear in the range of 0.557–5.62 μg/mL, when estimated using Phenomenex Luna C18 (25 cm × 5 μm × 4.6 mm i.d. column at 1.0 mL/min flow rate at 258 nm. The mobile phase consisted of a mixture of acetonitrile: methanol: phosphate buffer pH 3.5: tetrahydrofuran (28:13:58:1 v/v/v/v. The LOD and LOQ for OLME were found to be 0.07 and 0.22 μg/mL, respectively. The validated method was found to be simple, selective and sensitive for demonstration of cleaning validation of OLME residues on the stainless steel surface.

  13. Evaluation of the HB&L carbapenemase and extended spectrum beta lactamase-AmpC automated screening kits for the rapid detection of resistant Enterobacteriaceae in rectal swabs

    Directory of Open Access Journals (Sweden)

    Sara Marani

    2017-03-01

    Full Text Available Background. In the past two decades, a rapid increase of infections due to multidrug-resistant Enterobacteriaceae was reported worldwide, including in Italy. These bacteria express genes encoding for extended-spectrum β-lactamases (ESBL or bear a plasmid-mediated AmpC that induce phenotypically a resistance to the last-generation cephalosporins; even more worrying is the rapid increase of Enterobacteriaceae carrying genes conferring resistance to carbapenems (CPE. Materials and methods. The gut may serve as reservoir for these antibiotic drug-resistant bacteria: as a consequence, the rapid detection of drug resistant Enterobacteriaceae from rectal swabs is an important tool to identify rectal carriage of resistant bacteria. This procedure is the basic tool to successfully implement the infection control measures in the hospital wards. The study evaluated the capability of the HB&L ESBL/AmpC and CARBAPENEMASE screening kit (Alifax, Padua, Italy to rapidly identify the drug resistant enterobacteriaceae from rectal swabs: the performance was compared with the conventional method. Results and conclusions. The overall agreement was very good (91% for the detection of ESBL-AmpC, and 96.2% for the identification of CPE; this method is thus an efficient tool to quickly report positive multidrug resistant bacteria in rectal swabs.

  14. Comparison of illumigene Group A Streptococcus Assay with Culture of Throat Swabs from Children with Sore Throats in the New Zealand School-Based Rheumatic Fever Prevention Program.

    Science.gov (United States)

    Upton, Arlo; Bissessor, Liselle; Farrell, Elizabeth; Shulman, Stanford T; Zheng, Xiaotian; Lennon, Diana

    2016-01-01

    Group A streptococcal (GAS) pharyngitis is a particularly important condition in areas of New Zealand where the incidence of acute rheumatic fever remains unacceptably high. Prompt diagnosis and treatment of GAS pharyngitis are cornerstones of the Rheumatic Fever Prevention Programme, but these are hindered by the turnaround time of culture. Tests with excellent performance and rapid turnaround times are needed. For this study, throat swabs (Copan ESwabs) were collected from schoolchildren self-identifying with a sore throat. Samples were tested by routine culture and the illumigene GAS assay using loop-mediated isothermal amplification. Discrepant results were resolved by retesting of the same specimen by an alternative molecular assay. Seven hundred fifty-seven throat swab specimens were tested by both methods. The performance characteristics of the illumigene assay using culture on blood agar as the "gold standard" and following discrepancy analysis were as follows: sensitivity, 82% and 87%, respectively; specificity, 93% and 98%, respectively; positive predictive value, 61% and 88%, respectively; and negative predictive value, 97% and 97%, respectively. In our unique setting of a school-based throat swabbing program, the illumigene assay did not perform quite as well as described in previous reports. Despite this, its improved sensitivity and rapid turnaround time compared with those of culture are appealing.

  15. Genetic Characterization of Fungi Isolated from the Environmental Swabs collected from a Compounding Center Known to Cause Multistate Meningitis Outbreak in United States Using ITS Sequencing

    Directory of Open Access Journals (Sweden)

    Irshad M. Sulaiman

    2014-08-01

    Full Text Available A multistate fungal meningitis outbreak started in September of 2012 which spread in 20 states of the United States. The outbreak has been fatal so far, and has affected 751 individuals with 64 deaths among those who received contaminated spinal injections manufactured by a Compounding Center located in Massachusetts. In a preliminary study, Food and Drug Administration (FDA investigated the outbreak in collaboration with Centers for Disease Control and Prevention (CDC, state and local health departments, and identified four fungal and several bacterial contaminations in the recalled unopened injection vials. This follow-up study was carried out to assess DNA sequencing of the ITS1 region of rRNA gene for rapid identification of fungal pathogens during public health outbreak investigations. A total of 26 environmental swabs were collected from several locations at the manufacturing premises of the Compounding Center known to have caused the outbreak. The swab samples were initially examined by conventional microbiologic protocols and a wide range of fungal species were recovered. Species-identification of these microorganisms was accomplished by nucleotide sequencing of ITS1 region of rRNA gene. Analysis of data confirmed 14 additional fungal species in the swabs analyzed.

  16. Vaccination with attenuated Salmonella enterica Dublin expressing E coli O157:H7 outer membrane protein Intimin induces transient reduction of fecal shedding of E coli O157:H7 in cattle

    Directory of Open Access Journals (Sweden)

    Fang Ferric C

    2010-07-01

    Full Text Available Abstract Background Escherichia coli serogroup O157:H7 has emerged as an important zoonotic bacterial pathogen, causing a range of symptoms from self-limiting bloody diarrhea to severe hemorrhagic colitis and hemolytic-uremic syndrome in humans. Beef and dairy cattle are considered the most important animal reservoirs for this pathogen. One of the important virulence characteristics of E. coli O157:H7 is the eaeA gene encoding the 97 kDa surface protein intimin. Intimin is required for attachment and effacement during the interaction of enterohemorrhagic E. coli with human and bovine neonatal enterocytes. The present study was undertaken to test the hypothesis that an adaptive mucosal immune response directed against intimin will reduce or prevent enteric colonization and fecal shedding of E. coli O157:H7 in cattle. Results Cattle were orally inoculated with either milk (control, milk with live attenuated Salmonella enterica serovar Dublin (vector, or milk with live attenuated recombinant S. Dublin expressing intimin (vaccinated on days 0, 14 and 28. On day 98, all calves were challenged orally with E. coli O157:H7 to evaluate whether vaccination with the recombinant S. Dublin expressing intimin would reduce the level of E. coli O157:H7 fecal shedding. During the first 28 days, vaccinated calves shed both the vector strain and the intimin-expressing S. Dublin strain at a similar level. The vector strain was shed for a significantly longer period as compared to the level of recombinant vaccine strain. Calves that received the intimin-expressed vaccine ceased shedding S. Dublin from day 28 to day 63. All calves were challenged with E. coli O157:H7 on day 98 to determine the effect on fecal shedding of E. coli O157:H7. The amount of E. coli O157:H7 in feces was measured for 30 days post-challenge. We observed a transient clearance of E. coli O157:H7 from the feces in the vaccinated calves. The magnitude of fecal E. coli O157:H7 shedding did not

  17. Bovine colostrum: an emerging nutraceutical.

    Science.gov (United States)

    Bagwe, Siddhi; Tharappel, Leo J P; Kaur, Ginpreet; Buttar, Harpal S

    2015-09-01

    Nutraceutical, a term combining the words "nutrition" and "pharmaceuticals", is a food or food product that provides health benefits as an adjuvant or alternative therapy, including the treatment and prevention of infectious diseases in children and adults. There is emerging evidence that bovine colostrum (BC) may be one of the promising nutraceuticals which can prevent or mitigate various diseases in newborns and adults. Immunity-related disorders are one of the leading causes of mortality in the world. BC is rich in immunity, growth and antimicrobial factors, which promote tissue growth and the maturation of digestive tract and immune function in neonatal animals and humans. The immunoglobulins and lactoferrin present in colostrum are known to build natural immunity in newborns which helps to reduce the mortality rate in this population. Also, the side-effect profile of colostrum proteins and possible lactose intolerance is relatively less in comparison with milk. In general, BC is considered safe and well tolerated. Since colostrum has several important nutritional constituents, well-designed, double-blind, placebo-controlled studies with colostrum products should be conducted to widen its therapeutic use. The objectives of this review are to create awareness about the nutraceutical properties of colostrum and to discuss the various ongoing alternative treatments of colostrum and its active ingredients as well as to address colostrum's future nutraceutical and therapeutic implications in humans.

  18. Pooling of porcine fecal samples for quantification of Lawsonia intracellularis by real-time polymerase chain reaction

    DEFF Research Database (Denmark)

    Pedersen, Ken Steen; Johansen, Markku; Jorsal, Sven Erik Lind;

    2014-01-01

    obtained by averaging test results from individual fecal samples in relation to a quantitative polymerase chain reaction (qPCR) test for Lawsonia intracellularis. Ten diarrheic and 10 normal fecal samples were submitted from each of 43 Danish swine herds (n = 860 fecal samples). Pools (n = 43), each...

  19. ASSESSMENT OF FECAL POLLUTION SOURCES IN PLUM CREEK WATERSHED USING PCR AND PHYLOGENETIC ANALYSES OF BACTEROIDETES 16S RDNA

    Science.gov (United States)

    Traditional methods for assessing fecal pollution in environmental systems, such as monitoring for fecal coliforms are not capable of discriminating between different sources fecal pollution. Recently, 16S rDNA Bacteroidetes-targeted PCR assays were developed to discriminate betw...

  20. Contamination of bovine, sheep and goat meat with Brucella spp.

    OpenAIRE

    Francesco Casalinuovo; Lucia Ciambrone; Antonio Cacia; Paola Rippa

    2016-01-01

    A study was conducted in order to evaluate the contamination by Brucella spp. of meat from animals slaughtered because they had resulted positive for brucellosis at some time during their life. After slaughter and before delivery to market outlets, swab samples were taken from 307 carcasses of infected animals: 40 cattle, 60 sheep and 207 goats. The swabs were subsequently analysed by means of polymerase chain reaction (PCR) tests. In addition, bacteriological tests were carried out on the ly...

  1. Glycoprotein C gene based molecular subtyping of a bovine herpesvirus -1 isolate from uttar pradesh, India.

    Science.gov (United States)

    Ravishankar, Chintu; Nandi, S; Chander, V; Mohapatra, T K

    2012-12-01

    Bovine herpesvirus -1 (BHV-1) is the etiological agent of many clinical syndromes in cattle which causes huge economic losses to the animal husbandry sector annually. Since the first report of its presence in India in 1976, the disease is considered to be endemic in the country. In the present study, a case of keratoconjunctivitis in a cow was investigated to find out the underlying cause of the condition. The clinical material (ocular swab) was tested by BHV-1 glycoprotein D gene specific PCR using in house designed primers and found to be positive by the presence of a 212 bp DNA product in agarose gel electrophoresis. The virus was isolated in MDBK cell line in the third passage and the serum from the animal, was positive for antibodies against BHV-1 by ELISA. A 575 bp segment of the glycoprotein C gene of the isolate was amplified by PCR, cloned and sequenced. On phylogenetic analysis, it was seen that the sequence matched with published BHV-1.1 sequences from USA and Uruguay whereas it was divergent from Brazilian BHV-1.1 isolates. This study highlights the isolation, rapid and sensitive detection of BHV-1 virus from clinical cases and its subtyping by nucleotide sequencing and subsequent phylogenetic analysis which gives invaluable information about the molecular epidemiology of BHV-1 subtypes prevalent in the country.

  2. Detection of an untyped strain of bovine respiratory syncytial virus in a dairy herd

    Directory of Open Access Journals (Sweden)

    Ingrid Bortolin Affonso

    2014-10-01

    Full Text Available Bovine respiratory syncytial virus (BRSV causes important lower respiratory tract illness in calves. According to F and G proteins genetic sequences, three BRSV subgroups have been reported and characterized in several countries, showing differences in its distribution. In Brazil, the virus is widely disseminated throughout the herds and the few characterized isolates revealed the solely occurrence of the subgroup B. This study describes the detection and characterization of an untyped BRSV strain from a twenty-days-old calf from a herd without clinical respiratory disease. Nasal swabs were analyzed by RT-nested PCR for the F and G proteins genes. One sample has amplified the F protein gene. Sequencing and subsequent phylogenetic reconstruction were accomplished, revealing that the strain could not be grouped with any other BRSV subgroups reported. This result may suggest that the BRSV is in constantly evolution, even in Brazil, where the vaccination is not a common practice. More detailed studies about BRSV characterization are necessary to know the virus subgroups distribution among the Brazilian herds to recommend appropriated immunoprophylaxis.

  3. Microbial diversity in fecal samples depends on DNA extraction method

    DEFF Research Database (Denmark)

    Mirsepasi, Hengameh; Persson, Søren; Struve, Carsten

    2014-01-01

    BACKGROUND: There are challenges, when extracting bacterial DNA from specimens for molecular diagnostics, since fecal samples also contain DNA from human cells and many different substances derived from food, cell residues and medication that can inhibit downstream PCR. The purpose of the study...... was to evaluate two different DNA extraction methods in order to choose the most efficient method for studying intestinal bacterial diversity using Denaturing Gradient Gel Electrophoresis (DGGE). FINDINGS: In this study, a semi-automatic DNA extraction system (easyMag®, BioMérieux, Marcy I'Etoile, France......) and a manual one (QIAamp DNA Stool Mini Kit, Qiagen, Hilden, Germany) were tested on stool samples collected from 3 patients with Inflammatory Bowel disease (IBD) and 5 healthy individuals. DNA extracts obtained by the QIAamp DNA Stool Mini Kit yield a higher amount of DNA compared to DNA extracts obtained...

  4. Fecal microbiota transplantation: A 'How-To' guide for nurses.

    Science.gov (United States)

    Leis, Sharyn; Borody, Thomas Julius; Jiang, Chongnan; Campbell, Jordana

    2015-01-01

    Fecal microbiota transplantation is emerging as one of the most exciting treatments of this century. Rarely has one treatment provided the opportunity to treat a myriad of diseases, not only within the gastrointestinal tract but also in extra-intestinal organs; such is the power of the gastrointestinal microbiota to modulate the immune system and eradicate infections, even where antibiotics have previously failed. The demand for this therapy, both among patients and physicians, is increasing, and a search of the literature reveals numerous reviews, case reports and discussion on the topic. However, to date, much of the literature addresses the procedure from a physician's point of view, and can therefore be lacking in practical detail. As nurses are often the 'unsung heroes' of the procedure, it is timely to address the subject from a nursing perspective.

  5. Transient bladder and fecal incontinence following epidural blood patch

    Science.gov (United States)

    Palomero-Rodríguez, Miguel Angel; Palacio-Abinzada, Francisco J.; Campollo, Sara Chacón; Laporta-Báez, Yolanda; Mendez Cendón, Jose Carlos; López-García, Andres

    2015-01-01

    Epidural blood patch (EBP) is the currently accepted treatment of choice for postdural puncture headache because of its high initial success rates and infrequent complications. Many authors recommended a small volume (10-20 mL) of blood to be delivered for an effective EBP. Here, we report an obstetric patient who developed a transient bladder and fecal incontinence after 19 mL of blood EBP at L1 -L2 level. Since the magnetic resonance image did not demonstrate any definitive spinal cord lesion, the exact mechanism remains unclear. We suggest that accumulation of blood performed at L1 to L2 level in a closed relationship with the sacral cord, may have trigger a significant pressure elevation of the epidural space at this level, resulting in a temporal spinal cord-related injury in the sacral cord. PMID:26543470

  6. MR Colonography with fecal tagging: Barium vs. barium ferumoxsil

    DEFF Research Database (Denmark)

    Achiam, M.P.; Chabanova, E.; Logager, V.B.;

    2008-01-01

    and Methods. Twenty patients referred to CC underwent dark lumen MRC prior to the colonoscopy. Two groups of patients received two different oral contrast agents (barium sulfate and barium sulfate/ferumoxsil) as a laxative-free fecal tagging prior to the MRC. After MRC, the contrast agent was rated...... qualitatively (with the standard method using contrast-to-wall ratio) and subjectively (using a visual analog scale [VAS]) by three different blinded observers. Results. Evaluated both qualitatively and subjectively, the tagging efficiency of barium sulfate/ferumoxsil was significantly better (P ... barium sulfate alone. The VAS method for evaluating the tagging efficiency of contrast agents showed a high correlation (observer 11, r = 0.91) to the standard method using contrast-to-wall ratio and also a high interclass correlation (observer 11 and III = 0.89/0.85). MRC found I of 22 (5%) polyps

  7. Fecal microbiota transplantation: indications, methods, evidence, and future directions.

    Science.gov (United States)

    Borody, Thomas J; Paramsothy, Sudarshan; Agrawal, Gaurav

    2013-08-01

    Fecal microbiota transplantation (FMT) has attracted great interest in recent years, largely due to the global Clostridium difficile infection (CDI) epidemic and major advances in metagenomic sequencing of the gastrointestinal (GI) microbiota, with growing understanding of its structure and function. FMT is now recommended as the most effective therapy for relapsing CDI and, with further refinement, may even be used in "first-time" CDI. There is interest also in other conditions related to GI dysbiosis--for example, inflammatory bowel disease, irritable bowel syndrome, obesity, and diabetes mellitus--although quality evidence is at present lacking. A few trials are now underway in FMT for ulcerative colitis. Many unanswered questions remain, including FMT methodology--for example, optimal route of administration, what makes a "good donor," safety issues, and long-term effects of FMT.

  8. Hypogonadism alters cecal and fecal microbiota in male mice.

    Science.gov (United States)

    Harada, Naoki; Hanaoka, Ryo; Hanada, Kazuki; Izawa, Takeshi; Inui, Hiroshi; Yamaji, Ryoichi

    2016-11-01

    Low testosterone levels increase the risk for cardiovascular disease in men and lead to shorter life spans. Our recent study showed that androgen deprivation via castration altered fecal microbiota and exacerbated risk factors for cardiovascular disease, including obesity, impaired fasting glucose, excess hepatic triglyceride accumulation, and thigh muscle weight loss only in high-fat diet (HFD)-fed male mice. However, when mice were administered antibiotics that disrupted the gut microbiota, castration did not increase cardiovascular risks or decrease the ratio of dried feces to food intake. Here, we show that changes in cecal microbiota (e.g., an increased Firmicutes/Bacteroidetes ratio and number of Lactobacillus species) were consistent with changes in feces and that there was a decreased cecal content secondary to castration in HFD mice. Castration increased rectal body temperature and plasma adiponectin, irrespective of diet. Changes in the gut microbiome may provide novel insight into hypogonadism-induced cardiovascular diseases.

  9. Increased fecal viral content associated with obesity in mice

    Institute of Scientific and Technical Information of China (English)

    Hariom; Yadav; Shalini; Jain; Ravinder; Nagpal; Francesco; Marotta

    2016-01-01

    AIM: To investigate the presence of total gut viral content in obese mice, and establish correlation with obesity associated metabolic measures and gut microbiome.METHODS: Fresh fecal samples were collected from normal and obese(Leptin deficient Lepob/ob) mice. Total viral DNA and RNA was isolated and quantified for establishing the correlation with metabolic measures and composition of gut bacterial communities.RESULTS: In this report, we found that obese mice feces have higher viral contents in terms of total viral DNA and RNA(P 0.6), whilst negatively correlated with bacteroidetes and bifidobacteria. CONCLUSION: This study suggests the strong correlation of increased viral population into the gut of obese mice and opens new avenues to explore the role of gut virome in pathophysiology of obesity.

  10. Abordaje quirúrgico de la incontinencia fecal

    Directory of Open Access Journals (Sweden)

    Norma Ceciliano-Romero

    2013-09-01

    Full Text Available Antecedentes: los pacientes con incontinencia fecal enfrentan graves problemas sociales y psicológicos, por lo que el propósito fue analizar la evolución de 27 pacientes operados con la técnica de Malone, de Neo-apéndice y botón de Chait, para hacerles enemas anterógrados, así como evaluar la repercusión en su calidad de vida. Metodología: la investigación es descriptiva-retrospectiva. Los datos se obtuvieron de los expedientes clínicos del periodo 2000-2010. Para la definición de caso fue necesario que tuvieran incontinencia fecal y que se les hubiera hecho una operación de Malone, Neo-apéndice y colocación de botón de Chait durante ese periodo. Resultados: de los 27 pacientes analizados, 21 tenían como causa de la incontinencia una malformación anorrectal, 3 mielomeningocele, 1 enfermedad de Hirschsprung, 1 rabdomiosarcoma y 1 constipación. En 17 se realizó la técnica de Malone, en 6 un Neo-apéndice, y en 4 se colocó un botón de Chait. Las complicaciones observadas fueron: fuga del neo-apéndice con peritonitis y reintervención en 1 caso, estenosis de la boca en 9 casos, granulomas en 4 casos y prolapso en 1. En 24 casos los pacientes se mantienen limpios de heces y tanto ellos como sus familiares están satisfechos. En 10 casos ellos son independientes y se realizan sus propios enemas. Conclusiones: los resultados obtenidos permiten considerar que las intervenciones quirúrgicas efectuadas para hacer los enemas anterógrados, son una buena opción para mejorar la calidad de su vida.

  11. Recent Progress in Cryopreservation of Bovine Oocytes

    Directory of Open Access Journals (Sweden)

    In-Sul Hwang

    2014-01-01

    Full Text Available Principle of oocyte cryoinjury is first overviewed and then research history of cryopreservation using bovine oocytes is summarized for the last two decades with a few special references to recent progresses. Various types of cryodevices have been developed to accelerate the cooling rate and applied to the oocytes from large domestic species enriched with cytoplasmic lipid droplets. Two recent approaches include the qualitative improvement of IVM oocytes prior to the vitrification and the short-term recovery culture of vitrified-warmed oocytes prior to the subsequent IVF. Supplementation of L-carnitine to IVM medium of bovine oocytes has been reported to reduce the amount of cytoplasmic lipid droplets and improve the cryotolerance of the oocytes, but it is still controversial whether the positive effect of L-carnitine is reproducible. Incidence of multiple aster formation, a possible cause for low developmental potential of vitrified-warmed bovine oocytes, was inhibited by a short-term culture of the postwarm oocytes in the presence of Rho-associated coiled-coil kinase (ROCK inhibitor. Use of an antioxidant α-tocopherol, instead of the ROCK inhibitor, also supported the revivability of the postwarm bovine oocytes. Further improvements of the vitrification procedure, combined with pre- and postvitrification chemical treatment, would overcome the high sensitivity of bovine oocytes to cryopreservation.

  12. Use of Sacral Nerve Stimulation for the Treatment of Overlapping Constipation and Fecal Incontinence

    Science.gov (United States)

    Sreepati, Gouri; James-Stevenson, Toyia

    2017-01-01

    Patient: Female, 51 Final Diagnosis: Fecal incontinence Symptoms: Constipation • fecal incontinence Medication: — Clinical Procedure: Sacral nerve stimulator Specialty: Gastroenterology and Hepatology Objective: Rare co-existance of disease or pathology Background: Fecal incontinence and constipation are common gastrointestinal complaints, but rarely occur concurrently. Management of these seemingly paradoxical processes is challenging, as treatment of one symptom may exacerbate the other. Case Report: A 51-year-old female with lifelong neurogenic bladder secondary to spina bifida occulta presented with progressive symptoms of daily urge fecal incontinence as well as hard bowel movements associated with straining and a sensation of incomplete evacuation requiring manual disimpaction. Pelvic floor testing showed poor ability to squeeze the anal sphincter, which indicated sphincter weakness as a major contributor to her fecal incontinence symptoms. Additionally, on defecography she was unable to widen her posterior anorectal angle or relax the anal sphincter during defecation consistent with dyssynergic defecation. A sacral nerve stimulator was placed for management of her fecal incontinence. Interestingly, her constipation also dramatically improved with sacral neuromodulation. Conclusions: This unique case highlights the emerging role of sacral nerve stimulation in the treatment of complex pelvic floor dysfunction with improvement in symptoms beyond fecal incontinence in a patient with dyssynergic-type constipation. PMID:28265107

  13. Reproductive effects on fecal nitrogen as an index of diet quality: an experimental assessment

    Science.gov (United States)

    Monteith, Kyle B.; Monteith, Kevin L.; Bowyer, R. Terry; Leslie,, David M.; Jenks, Jonathan A.

    2014-01-01

    Concentration of fecal nitrogen has been used widely as an indicator of dietary quality for free-ranging ruminants. Differences in digestive function between species of dimorphic ungulates render interspecific comparisons of fecal nitrogen unreliable; however, whether intraspecific sexual differences in digestive function also bias this nutritional index is unknown. Our objective was to compare sex-specific variation in concentration of fecal nitrogen using male, nonlactating female, and lactating female white-tailed deer (Odocoileus virginianus) on high- and low-quality diets. During weekly trials over spring and summer (2008-2009), we monitored intake rates, collected feces twice daily, and used micro-Kjeldahl procedures to determine percent fecal nitrogen. We also determined nitrogen content of feces following a neutral detergent fiber (NDF) rinse during pre-, peak, and postlactation. Fecal nitrogen reflected general differences in dietary quality between diets; however, fecal nitrogen of lactating females in both dietary groups was lower than for males or nonlactating females throughout lactation. Nitrogen concentration following an NDF rinse also was lower for lactating females during peak lactation. We hypothesize that the remodeling of the digestive tract and increased rumination by lactating females may enhance their ability to extract nitrogen from their forage. These adjustments may expand the foraging options of lactating females by increasing their ability to process low-quality foods, but also affects the interpretation of fecal nitrogen during the season of lactation.

  14. Update on clinical and research application of fecal biomarkers for gastrointestinal diseases

    Science.gov (United States)

    Siddiqui, Imran; Majid, Hafsa; Abid, Shahab

    2017-01-01

    Gastrointestinal (GI) diseases comprise a large spectrum of clinical conditions ranging from indigestion to inflammatory bowel diseases (IBDs) and carcinomas. Endoscopy is the usual method employed to diagnose these condition. Another noninvasive way to assess and diagnose GI conditions are fecal biomarkers. Fecal biomarkers provide information regarding a specific disease process and are perhaps more acceptable to clinicians and patients alike because of their non-invasivity compared to endoscopy. Aim of this review was to evaluate the current status of the fecal biomarkers in clinical and research for in GI diseases. Multiple types of fecal biomarkers are discussed in this review including; markers to assess IBD, which are released as a results of an inflammatory insults to intestinal epithelia such as antimicrobial peptides (lactoferrin) or inflammation related proteins (calprotectin). While markers related to function of digestion are primarily related to partially digested food or mucosal proteins such as abnormal amount of fecal fat α1-antitrypsin, elastase and secretary IgA. The upcoming fecal biomarker like M2 pyruvate kinase and neutrophil gelatinase associated lipocalin are discussed as well. Apart from above mention, the fecal biomarkers under exploration for possible clinical use in future are also discussed. These include cathelicidins, osteoprotegerin, β-glucuronidase, Eosinophil proteins, etc. PMID:28217373

  15. Anal plugs and retrograde colonic irrigation are helpful in fecal incontinence or constipation

    Institute of Scientific and Technical Information of China (English)

    Marcel Cazemier; Richelle JF Felt-Bersma; Chris JJ Mulder

    2007-01-01

    AIM: To evaluate the feasibility, clinical effect and predicting factors for favorable outcome of treatment with anal plugs in fecal incontinence and retrograde colonic irrigation (RCI) in patients with fecal incontinence or constipation.METHODS: Patients who received treatment with an anal plug or RCI between 1980 and 2005 were investigated with a questionnaire.RESULTS: Of the 201 patients (93 adults, 108 children), 101 (50%) responded. Adults: anal plugs (8), five stopped immediately, one stopped after 20 mo and two used it for 12-15 mo. RCI (40, 28 fecal incontinence, 12 constipation), 63% are still using it (mean 8.5 years), 88% was satisfied. Younger adults (< 40 years) were more satisfied with RCI (94 % vs 65%, P = 0.05). Children: anal plugs (7), 5 used it on demand for an average of 2.5 years with satisfactory results, one stopped immediately and one after 5 years. RCI (26 fecal incontinence, 22 constipation), 90% are still using it (mean time 6.8 years) and felt satisfied. Children tend to be more satisfied (P = 0.001). Besides age, no predictive factors for success were found. There was no difference in the outcome between patients with fecal incontinence or constipation.CONCLUSION: RCI is more often applied than anal plugs and is helpful in patients with fecal incontinence or constipation, especially for younger patients. Anal plugs can be used incidentally for fecal incontinence, especially in children.

  16. The evolution of bovine viral diarrhea: a review

    OpenAIRE

    Goens, Denise

    2002-01-01

    The economic importance of bovine viral diarrhea is increasing with the emergence of seemingly more virulent viruses, as evidenced by outbreaks of hemorrhagic syndrome and severe acute bovine viral diarrhea beginning in the 1980s and 1990s. It appears that evolutionary changes in bovine viral diarrhea virus were responsible for these outbreaks. The genetic properties of the classical bovine viral diarrhea virus that contribute to the basis of current diagnostic tests, vaccines, and our unders...

  17. Neurological disorder in cattle associated with bovine herpesvirus 4

    OpenAIRE

    2011-01-01

    A nested PCR assay was used to diagnose bovine encephalitis through herpesviruses including bovine herpesvirus 5 (BHV-5), bovine herpesvirus 1 (BHV-1), Aujeszky's disease virus (SHV-1), and ovine herpesvirus 2 (OHV-2) in 14 fragments of central nervous system (CNS) from cattle that died with neurological signs. In addition, as some samples of bovine herpesvirus type 4 (BHV-4) have been isolated from neural tissue, it was also tested by nested PCR. The cases of encephalitis occurred in isolati...

  18. Sacral nerve stimulation for fecal incontinence Neuromodulación de raíces sacras en incontinencia fecal

    Directory of Open Access Journals (Sweden)

    Isabel Pascual

    2011-07-01

    Full Text Available Objective: to analyze short-term outcomes and complications for our first fifty patients with fecal incontinence undergoing sacral root stimulation. Patients: fifty patients with fecal incontinence receiving sacral neuromodulation in 4 hospitals are reviewed. Discussed variables include: age, sex, incontinence duration, incontinence cause, prior surgery for incontinence, Wexner scale score, anorectal manometry parameters, and endoanal ultrasonographic findings. Following the procedure Wexner scale score, anorectal manometry parameters, and associated complications are reviewed. Results: mean age of patients is 59.9 years, with females predominating. Most common causes of incontinence include obstetric procedures, idiopathic origin, and prior anal surgery. Mean follow-up is 17.02 months. Follow-up revealed a statistically significant reduction in Wexner scale score and increase in voluntary anal pressure. Technique-derived minor complications included: 2 surgical wound infections that led to stimulator withdrawal; 2 patients with pain who were managed conservatively; 1 case of externalization in a gluteal stimulator; and 1 broken tetrapolar electrode. Conclusions: sacral nerve stimulation is a simple technique that improves Wexner scores in a statistically significant manner with a low complications rate.Objetivo: analizar los resultados y complicaciones a corto plazo de nuestros primeros cincuenta pacientes con incontinencia fecal tratados mediante estimulación de raíces sacras. Pacientes: se revisan cincuenta pacientes con incontinencia fecal tratados mediante neuromodulación de raíces sacras en 4 centros hospitalarios. Las variables analizadas son: edad, sexo, tiempo de evolución de la incontinencia, causa de la incontinencia, cirugías previas para tratar la incontinencia, puntuación en la escala de Wexner, parámetros de la manometría anorrectal y los hallazgos en la ecografía endoanal. Tras la intervención se revisa la puntuaci

  19. Arachidonate metabolism in bovine gallbladder muscle

    Energy Technology Data Exchange (ETDEWEB)

    Nakano, M.; Hidaka, T.; Ueta, T.; Ogura, R.

    1983-04-01

    Incubation of (1-/sup 14/C)arachidonic acid (AA) with homogenates of bovine gallbladder muscle generated a large amount of radioactive material having the chromatographic mobility of 6-keto-PGF1 alpha (stable product of PGI2) and smaller amounts of products that comigrated with PGF2 alpha PGE2. Formation of these products was inhibited by the cyclooxygenase inhibitor indomethacin. The major radioactive product identified by thin-layer chromatographic mobility and by gas chromatography - mass spectrometric analysis was found to be 6-keto-PGF1 alpha. The quantitative metabolic pattern of (1-/sup 14/C)PGH2 was virtually identical to that of (1-/sup 14/C)AA. Incubation of arachidonic acid with slices of bovine gallbladder muscle released labile anti-aggregatory material in the medium, which was inhibited by aspirin or 15-hydroperoxy-AA. These results indicate that bovine gallbladder muscle has a considerable enzymatic capacity to produce PGI2 from arachidonic acid.

  20. 76 FR 26239 - Bovine Tuberculosis and Brucellosis; Public Meetings

    Science.gov (United States)

    2011-05-06

    ...; ] DEPARTMENT OF AGRICULTURE Animal and Plant Health Inspection Service Bovine Tuberculosis and Brucellosis... framework being developed for the bovine tuberculosis and brucellosis programs in the United States. The... tuberculosis (TB) and bovine brucellosis in the United States. In keeping with its commitment to...

  1. 76 FR 38602 - Bovine Tuberculosis and Brucellosis; Program Framework

    Science.gov (United States)

    2011-07-01

    ... Animal and Plant Health Inspection Service Bovine Tuberculosis and Brucellosis; Program Framework AGENCY... extending the comment period on a new framework being developed for the bovine tuberculosis and brucellosis... bovine brucellosis in the United States. The notice stated that USDA would hold four public...

  2. 9 CFR 113.310 - Bovine Rhinotracheitis Vaccine.

    Science.gov (United States)

    2010-01-01

    ... 9 Animals and Animal Products 1 2010-01-01 2010-01-01 false Bovine Rhinotracheitis Vaccine. 113... REQUIREMENTS Live Virus Vaccines § 113.310 Bovine Rhinotracheitis Vaccine. Bovine Rhinotracheitis Vaccine shall... as pure, safe, and immunogenic shall be used for preparing the production seed virus for...

  3. 9 CFR 113.309 - Bovine Parainfluenza3 Vaccine.

    Science.gov (United States)

    2010-01-01

    ... 9 Animals and Animal Products 1 2010-01-01 2010-01-01 false Bovine Parainfluenza3 Vaccine. 113.309... Virus Vaccines § 113.309 Bovine Parainfluenza3 Vaccine. Bovine Parainfluenza3 Vaccine shall be produced..., and immunogenic shall be used for preparing the production seed virus for vaccine production....

  4. 9 CFR 113.311 - Bovine Virus Diarrhea Vaccine.

    Science.gov (United States)

    2010-01-01

    ... 9 Animals and Animal Products 1 2010-01-01 2010-01-01 false Bovine Virus Diarrhea Vaccine. 113.311... Virus Vaccines § 113.311 Bovine Virus Diarrhea Vaccine. Bovine Virus Diarrhea Vaccine shall be prepared..., and immunogenic shall be used for preparing the production seed virus for vaccine production....

  5. Cloning and sequencing of the bovine gastrin gene

    DEFF Research Database (Denmark)

    Lund, T; Rehfeld, J F; Olsen, Jørgen

    1989-01-01

    In order to deduce the primary structure of bovine preprogastrin we therefore sequenced a gastrin DNA clone isolated from a bovine liver cosmid library. Bovine preprogastrin comprises 104 amino acids and consists of a signal peptide, a 37 amino acid spacer-sequence, the gastrin-34 sequence followed...

  6. 21 CFR 522.1125 - Hemoglobin glutamer-200 (bovine).

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 6 2010-04-01 2010-04-01 false Hemoglobin glutamer-200 (bovine). 522.1125 Section... § 522.1125 Hemoglobin glutamer-200 (bovine). (a) Specifications. Each 125 milliliter bag contains 13 grams per deciliter of polymerized hemoglobin of bovine origin in modified Lactated Ringer's...

  7. Fecal microbiota transplantation for fulminant Clostridium difficile infection in an allogeneic stem cell transplant patient.

    Science.gov (United States)

    Neemann, K; Eichele, D D; Smith, P W; Bociek, R; Akhtari, M; Freifeld, A

    2012-12-01

    We present a case of severe Clostridium difficile infection (CDI) in a non-neutropenic allogeneic hematopoietic stem cell transplant recipient who was treated successfully with fecal microbiota therapy after standard pharmacologic therapy had failed. Following naso-jejunal instillation of donor stool, the patient's symptoms resolved within 48 h. Bowel resection was averted. This is the first case in the literature, to our knowledge, to describe fecal microbiota therapy in a profoundly immunocompromised host with severe CDI. We propose that fecal microbiota therapy be considered as a therapeutic option in immunosuppressed patients with refractory severe CDI.

  8. Concentrations of fecal coliform bacteria in creeks, Anchorage, Alaska, August and September 1998

    Science.gov (United States)

    Dorava, Joseph M.; Love, Andra

    1999-01-01

    Water samples were collected from five creeks in undeveloped, semi-developed, and developed areas of Anchorage, Alaska, during August and September 1998 to determine concentrations of fecal coliform bacteria. In undeveloped areas of Ship, Chester, and Campbell Creeks, and the semi-developed area of Rabbit Creek, concentrations of fecal coliform bacteria ranged from less than 1 to 16 colonies per 100 milliliters of water. In the semi-developed area of Little Rabbit Creek, concentrations ranged from 30 to 860 colonies per 100 milliliters of water. In developed areas of the creeks, concentrations of fecal coliform bacteria ranged from 6 to 80 colonies per 100 milliliters of water.

  9. Phenotype definition is a main point in genome-wide association studies for bovine Mycobacterium avium ssp. paratuberculosis infection status.

    Science.gov (United States)

    Küpper, J; Brandt, H; Donat, K; Erhardt, G

    2014-10-01

    Paratuberculosis caused by Mycobacterium avium ssp. paratuberculosis (MAP) causes economic losses and is present in dairy herds worldwide. Different studies used different diagnostic tests to detect infection status and are the basis of genome-wide association (GWA) studies with inconsistent results. Therefore, the aim of this study was to identify and compare genomic regions associated with MAP susceptibility in the same cohort of cattle using different diagnostic tests. The GWA study was performed in German Holsteins within a case-control assay using 305 cows tested for MAP by fecal culture and additional with four different commercial ELISA-tests. Genotyping was performed with the Illumina Bovine SNP50 BeadChip. The results using fecal culture or ELISA test led to the identification of different genetic loci. Two single-nucleotide polymorphisms showed significant association with the ELISA-status. However, no significant association for MAP infection could be confirmed. Our results show that the definition of the MAP-phenotype has an important impact on the outcome of GWA studies for paratuberculosis.

  10. A microbial signature approach to identify fecal pollution in the waters off an urbanized coast of Lake Michigan.

    Science.gov (United States)

    Newton, Ryan J; Bootsma, Melinda J; Morrison, Hilary G; Sogin, Mitchell L; McLellan, Sandra L

    2013-05-01

    Urban coasts receive watershed drainage from ecosystems that include highly developed lands with sewer and stormwater infrastructure. In these complex ecosystems, coastal waters are often contaminated with fecal pollution, where multiple delivery mechanisms that often contain multiple fecal sources make it difficult to mitigate the pollution. Here, we exploit bacterial community sequencing of the V6 and V6V4 hypervariable regions of the bacterial 16S rRNA gene to identify bacterial distributions that signal the presence of sewer, fecal, and human fecal pollution. The sequences classified to three sewer infrastructure-associated bacterial genera, Acinetobacter, Arcobacter, and Trichococcus, and five fecal-associated bacterial families, Bacteroidaceae, Porphyromonadaceae, Clostridiaceae, Lachnospiraceae, and Ruminococcaceae, served as signatures of sewer and fecal contamination, respectively. The human fecal signature was determined with the Bayesian source estimation program SourceTracker, which we applied to a set of 40 sewage influent samples collected in Milwaukee, WI, USA to identify operational taxonomic units (≥ 97 % identity) that were most likely of human fecal origin. During periods of dry weather, the magnitudes of all three signatures were relatively low in Milwaukee's urban rivers and harbor and nearly zero in Lake Michigan. However, the relative contribution of the sewer and fecal signature frequently increased to > 2 % of the measured surface water communities following sewer overflows. Also during combined sewer overflows, the ratio of the human fecal pollution signature to the fecal pollution signature in surface waters was generally close to that of sewage, but this ratio decreased dramatically during dry weather and rain events, suggesting that nonhuman fecal pollution was the dominant source during these weather-driven scenarios. The qPCR detection of two human fecal indicators, human Bacteroides and Lachno2, confirmed the urban fecal footprint

  11. Altered microbiomes in bovine digital dermatitis lesions, and the gut as a pathogen reservoir.

    Directory of Open Access Journals (Sweden)

    Martin Zinicola

    Full Text Available Bovine digital dermatitis (DD is the most important infectious disease associated with lameness in cattle worldwide. Since the disease was first described in 1974, a series of Treponema species concurrent with other microbes have been identified in DD lesions, suggesting a polymicrobial etiology. However, the pathogenesis of DD and the source of the causative microbes remain unclear. Here we characterized the microbiomes of healthy skin and skin lesions in dairy cows affected with different stages of DD and investigated the gut microbiome as a potential reservoir for microbes associated with this disease. Discriminant analysis revealed that the microbiomes of healthy skin, active DD lesions (ulcerative and chronic ulcerative and inactive DD lesions (healing and chronic proliferative are completely distinct. Treponema denticola, Treponema maltophilum, Treponema medium, Treponema putidum, Treponema phagedenis and Treponema paraluiscuniculi were all found to be present in greater relative abundance in active DD lesions when compared with healthy skin and inactive DD lesions, and these same Treponema species were nearly ubiquitously present in rumen and fecal microbiomes. The relative abundance of Candidatus Amoebophilus asiaticus, a bacterium not previously reported in DD lesions, was increased in both active and inactive lesions when compared with healthy skin. In conclusion, our data support the concept that DD is a polymicrobial disease, with active DD lesions having a markedly distinct microbiome dominated by T. denticola, T. maltophilum, T. medium, T. putidum, T. phagedenis and T. paraluiscuniculi. Furthermore, these Treponema species are nearly ubiquitously found in rumen and fecal microbiomes, suggesting that the gut is an important reservoir of microbes involved in DD pathogenesis. Additionally, the bacterium Candidatus Amoebophilus asiaticus was highly abundant in active and inactive DD lesions.

  12. Scientific Opinion on bovine lactoferrin

    Directory of Open Access Journals (Sweden)

    EFSA Panel on Dietetic Products, Nutrition and Allergies

    2012-07-01

    Full Text Available

    Following a request from the European Commission, the EFSA Panel on Dietetic Products, Nutrition and Allergies (NDA was asked to carry out the additional assessment for ‘lactoferrin’ as a food ingredient in the context of Regulation (EC No 258/97 taking into account the comments and objections of a scientific nature raised by Member States. Bovine lactoferrin (bLF is a protein that occurs naturally in cow’s milk. The applicant intends to market bLF that is isolated from cheese whey and skimmed milk, and purified. The applicant intends to add bLF to foods for particular nutritional uses, i.e. infant and follow-on formulae, dietary food for special medical purposes, dairy products, yoghurts and yoghurt drinks, and chewing gums. According to the applicant, the high intake estimate for infants would be 1.1 g bLF per day. For adults, the applicant’s calculation estimates a mean and 97.5th percentile intake of 0.6 and 2.1 mg/kg bodyweight per day, respectively, and a mean and 97.5th percentile daily intake of about 45 mg and 150 mg, respectively. The Panel notes that the safety of bLF as a novel food ingredient has already been assessed with a favourable outcome. That evaluation was to a significant extent based on safety data on bLF produced by Morinaga. The Panel also notes that the applicant intends maximum use levels of bLF in foods which are equivalent or lower than those intended by the applicant of the previous Opinion, and that the range of foods to which it is intended to add bLF is smaller. Consequently, the estimated intake levels described for the present application are comparable for infants and lower for all other population groups. The Panel concludes that the novel food ingredient, bLF, is safe under the proposed uses and use levels.

  13. Molecular differentiation of bovine sarcocysts.

    Science.gov (United States)

    Akhlaghi, Majedeh; Razavi, Mostafa; Hosseini, Arsalan

    2016-07-01

    Cattle are common intermediate hosts of Sarcocystis, and the prevalence in adult bovine muscle is close to 100 % in most regions of the world. Three Sarcocystis spp. are known to infect cattle as intermediate hosts, namely, S. cruzi, S. hirsuta, and S. hominis. The aim of the present study was the molecular identification and differentiation of these three species, Neospora caninum and Besnoitia by PCR and RFLP methods. Tissue samples were obtained from diaphragmatic muscle of 101 cattle slaughtered in Shiraz, Fars Province, Iran, for both smear preparation and DNA extraction. The samples were digested by Pepsin, washed three times with PBS solution before taking smears, fixed in absolute methanol and stained with 10 % Giemsa. The slides were examined microscopically for Sarcocystis bradyzoites and DNA was extracted from 100 mg of Sarcocystis-infected meat samples. Since the primers also bind to 18S rRNA gene of some tissue cyst-forming coccidian protozoa, DNA was also extracted from 100 μl of tachyzoite-containing suspension of N. caninum and Besnoitia isolated from goat to compare RFLP pattern. Polymerase chain reaction (PCR) was performed on DNA of samples which were microscopically positive for Sarcocystis. Five restriction enzymes Dra1, EcoRV, RsaI, AvaI, and SspI were used for RFLP and DNA of one sample from protozoa was sequenced. Based on the RFLP results, 87 (98.9 %) DNA samples were cut with DraI, indicating infection by S. cruzi. One sample (1.1 %) of PCR products of infected samples was cut only with EcoRV which showed S. hominis infection. Forty-eight samples (53.3 %) of PCR products were cut with both DraI, EcoRV, or with DraI, EcoRV, and RsaI while none of them was cut with SspI, which shows the mixed infection of both S. cruzi and S. hominis and no infection with S. hirsuta. It seems by utilizing these restriction enzymes, RLFP could be a suitable method not only for identification of Sarcocystis species but also for differentiating them

  14. Evaluation of dietary fructan supplementation on growth performance, nutrient digestibility, meat quality, fecal microbial flora, and fecal noxious gas emission in finishing pigs.

    Science.gov (United States)

    Zhao, P Y; Wang, J P; Kim, I H

    2013-11-01

    This study was conducted to determine the effect of dietary fructan supplementation on growth performance, nutrient digestibility, meat quality, fecal microbial flora, and fecal noxious gas emission in finishing pigs. A total of 96 finishing pigs [(Yorkshire×Landrace)×Duroc] with an average BW of 73.1±2.5 kg were used in a 6-wk study. Pigs were randomly allotted to 1 of 3 dietary treatments: 1) CON, basal diet, 2) CON+1% fructan (FC1), and 3) CON+2% fructan (FC2) with 8 replicate pens per treatment and 2 barrows and 2 gilts per pen. During the overall study, pigs fed the fructan supplementation diets had a greater (Ppigs fed the CON diet. The levels of fructan supplementation did not affect growth performance and ATTD of DM, N, and GE. Fecal E. coli concentrations in the fructan treatments were lower (Ppigs.

  15. Effect of diet on fecal and urinary estrogenic activity.

    Science.gov (United States)

    Tucker, H A; Knowlton, K F; Meyer, M T; Khunjar, W O; Love, N G

    2010-05-01

    The United States Environmental Protection Agency has identified estrogens from animal feeding operations as a major environmental concern, but few data are available to quantify the excretion of estrogenic compounds by dairy cattle. The objectives of this study were to quantify variation in estrogenic activity in feces and urine due to increased dietary inclusion of phytoestrogens. Ten Holstein heifers were assigned to 2 groups balanced for age and days pregnant; groups were randomly assigned to treatment sequence in a 2-period crossover design. Dietary treatments consisted of grass hay or red clover hay, and necessary supplements. Total collection allowed for sampling of feed refusals, feces, and urine during the last 4 d of each period. Feces and urine samples were pooled by heifer and period, and base extracts were analyzed for estrogenic activity (estrogen equivalents) using the yeast estrogen screen bioassay. Feces and urine samples collected from 5 heifers were extracted and analyzed using liquid chromatography-tandem mass spectrometry (LC-MS/MS) to quantify excretion of 7 phytoestrogenic compounds. Excretion of 17-beta estradiol equivalents in urine was higher and tended to be higher in feces for heifers fed red clover hay (84.4 and 120.2 mg/d for feces and urine, respectively) compared with those fed grass hay (57.4 and 35.6 mg/d). Analysis by LC-MS/MS indicated greater fecal excretion of equol, genistein, daidzein, coumestrol, and formononetin by heifers fed red clover hay (1634, 29.9, 96.3, 27.8, and 163 mg/d, respectively) than heifers fed grass hay (340, 3.0, 46.2, 8.8, and 18.3 mg/d, respectively). Diet had no effect on fecal biochanin A or 2-carbethoxy-5, 7-dihydroxy-4'-methoxyisoflavone. Four phytoestrogens were detected in urine (2-carbethoxy-5, 7-dihydroxy-4'-methoxyisoflavone, daidzein, equol, and formononetin) and their excretion was not affected by diet. Identifying sources of variation in estrogenic activity of manure will aid in the

  16. Treatment of relapsing Clostridium difficile infection using fecal microbiota transplantation

    Directory of Open Access Journals (Sweden)

    Pathak R

    2013-12-01

    Full Text Available Rahul Pathak,1 Hill Ambrose Enuh,1 Anish Patel,1 Prasanna Wickremesinghe21Department of Internal Medicine, New York Medical College, Internal Medicine Program at Richmond University Medical Center, Staten Island, NY, USA; 2Department of Gastrointestinal Medicine, New York Medical College, Internal Medicine Program at Richmond University Medical Center, Staten Island, NY, USABackground: Clostridium difficile infection (CDI has become a global concern over the last decade. In the United States, CDI escalated in incidence from 1996 to 2005 from 31 to 64/100,000. In 2010, there were 500,000 cases of CDI with an estimated mortality up to 20,000 cases a year. The significance of this problem is evident from the hospital costs of over 3 billion dollars annually. Fecal microbiota transplant (FMT was first described in 1958 and since then about 500 cases have been published in literature in various small series and case reports. This procedure has been reported mainly from centers outside of the United States and acceptance of the practice has been difficult. Recently the US Food and Drug Administration (FDA labeled FMT as a biological drug; as a result, guidelines will soon be required to help establish it as a mainstream treatment. More US experience needs to be reported to popularize this procedure here and form guidelines.Method: We did a retrospective review of our series of patients with relapsing CDI who were treated with FMT over a 3-year period. We present our experience with FMT at a community hospital as a retrospective review and describe our procedure.Results: There were a total of 12 patients who underwent FMT for relapsing C. difficile. Only one patient failed to respond and required a second FMT. There were no complications associated with the transplant and all patients had resolution of symptoms within 48 hours of FMT.Conclusion: FMT is a cheap, easily available, effective therapy for recurrent CDI; it can be safely performed in a

  17. Fecal Calprotectin in Healthy Children Aged 1-4 Years.

    Directory of Open Access Journals (Sweden)

    Qingling Zhu

    Full Text Available Calprotectin has been well emulated recently in adults as well as in children. The aim of this study was to assess fecal calprotectin concentrations in healthy children aged from 1 to 4 years.Volunteers were enlisted from 3 nurseries. A brief questionnaire was used to ensure these children meet the inclusion criteria, and some clinical and sociodemographic factors were collected. Anthro software (version 3.1 was used to calculated Length-for-age Z-scores (LAZ, weight-for-age Z-scores (WAZ, and weight-for-length Z-scores (WLZ respectively. Fecal calprotectin was detected by a commercially available ELISA.In total 274 children were recruited, with age ranging from 1 to 4 years old. The median FC concentration was 83.19 μg/g [range 4.58 to 702.50 μg/g, interquartile range (IQR 14.69-419.45 μg/g] or 1.92 log10 μg/g (range 0.66 log10 to 2.85 log10 μg/g, IQR 1.17 log10-2.62 log10 μg/g. All of the children were divided into three groups, 1-2 years (12-24 months, 2-3 years (24-36 months, 3-4 years (36-48 months, with median FC concentrations 96.14 μg/g (1.98 log10 μg/g, 81.48 μg/g (1.91 log10 μg/g, 65.36 μg/g (1.82 log10 μg/g, respectively. There was similar FC level between boys and girls. FC concentrations showed a downward trend by the growing age groups. A statistic difference was found in FC concentrations among groups 1-2 years, 2-3 years and 3-4 years (P = 0.016. In inter-groups comparison, a significant difference was found between children aged 1-2 years and children aged 3-4 years (P = 0.007. A negative correlation trend was found between age and FC concentration (Spearman's rho = -0.167, P = 0.005 in all the participants. A simple correlation was performed among WLZ, WAZ, birth weight, or birth length with FC, and there was no correlation being observed.Children aged from 1 to 4 years old have lower FC concentrations compared with healthy infants (<1years, and higher FC concentrations when comparing with children older than 4

  18. Colite de derivação fecal Diversion colitis

    Directory of Open Access Journals (Sweden)

    Francisco Edilson Leite Pinto Júnior

    1999-06-01

    Full Text Available A colite de derivação fecal (CD é um processo inflamatório que ocorre no segmento colorretal desfuncionalizado, após uma cirurgia de desvio do trânsito intestinal. As principais características dessa entidade clínica são: apresenta-se na desfuncionalização do cólon ou reto; não há doença inflamatória intestinal preexistente; nunca acomete o sítio proximal à colostomia e ocorre resolução do processo após a restauração do trânsito intestinal. Diversas são as hipóteses postuladas para explicar o seu aparecimento; todavia, a deficiência nutricional do epitélio colônico, pela ausência dos ácidos graxos de cadeia curta (AGCC, no segmento desfuncionalizado, é a mais aceita na atualidade. Os autores fazem uma revisão da literatura enfocando os aspectos clínicos, histopatológicos e terapêuticos desta doença.The authors present a revision of diversion colitis. It is an inflammatory disorder that occurs in the colorectum segment after a diverting colostomy. The main features of this disease are: colon or rectum disfunction; no previous intestinal inflammatory disorder; it never attacks the colon upper colostomy; after intestinal transit restoration, the inflammatory process is solved. Many hypothesis are postulated to explain its occurrance. They include: fecal stasis; changes in the bacterial population of colon; nutritional deficiency of colonic epithelium due to the absence of short chain fatty acids in the defunctionalized segment is the most accepted nowadays. The absence of fatty acids produces energetic defficiency in colon mucosa, reduced electrolite absorption and secretion, and reduced mucus production. The patients have abdominal pain, mucus diarrhoea and bleeding. Histopathological features include chronical inflamation of colon wall, vascular congestion and changes in mucosa cripts. Lynphoid hiperplasy of mucosa and submucosa are common. The diagnosis is done by endoscopy, radiology, pathology and

  19. Pediatric fecal microbiota harbor diverse and novel antibiotic resistance genes.

    Directory of Open Access Journals (Sweden)

    Aimée M Moore

    Full Text Available Emerging antibiotic resistance threatens human health. Gut microbes are an epidemiologically important reservoir of resistance genes (resistome, yet prior studies indicate that the true diversity of gut-associated resistomes has been underestimated. To deeply characterize the pediatric gut-associated resistome, we created metagenomic recombinant libraries in an Escherichia coli host using fecal DNA from 22 healthy infants and children (most without recent antibiotic exposure, and performed functional selections for resistance to 18 antibiotics from eight drug classes. Resistance-conferring DNA fragments were sequenced (Illumina HiSeq 2000, and reads assembled and annotated with the PARFuMS computational pipeline. Resistance to 14 of the 18 antibiotics was found in stools of infants and children. Recovered genes included chloramphenicol acetyltransferases, drug-resistant dihydrofolate reductases, rRNA methyltransferases, transcriptional regulators, multidrug efflux pumps, and every major class of beta-lactamase, aminoglycoside-modifying enzyme, and tetracycline resistance protein. Many resistance-conferring sequences were mobilizable; some had low identity to any known organism, emphasizing cryptic organisms as potentially important resistance reservoirs. We functionally confirmed three novel resistance genes, including a 16S rRNA methylase conferring aminoglycoside resistance, and two tetracycline-resistance proteins nearly identical to a bifidobacterial MFS transporter (B. longum s. longum JDM301. We provide the first report to our knowledge of resistance to folate-synthesis inhibitors conferred by a predicted Nudix hydrolase (part of the folate synthesis pathway. This functional metagenomic survey of gut-associated resistomes, the largest of its kind to date, demonstrates that fecal resistomes of healthy children are far more diverse than previously suspected, that clinically relevant resistance genes are present even without recent selective

  20. The dual influences of age and obstetric history on fecal continence in parous women.

    LENUS (Irish Health Repository)

    Eogan, Maeve

    2011-02-01

    To assess whether women who underwent forceps delivery were more likely than those who delivered either normally (spontaneous vaginal delivery [SVD]) or by cesarean to experience deterioration in fecal continence as they aged.

  1. Comparing wastewater chemicals, indicator bacteria concentrations, and bacterial pathogen genes as fecal pollution indicators

    Science.gov (United States)

    Haack, S.K.; Duris, J.W.; Fogarty, L.R.; Kolpin, D.W.; Focazio, M.J.; Furlong, E.T.; Meyer, M.T.

    2009-01-01

    The objective of this study was to compare fecal indicator bacteria (FIB) (fecal coliforms, Escherichia coli [EC], and enterococci [ENT]) concentrations with a wide array of typical organic wastewater chemicals and selected bacterial genes as indicators of fecal pollution in water samples collected at or near 18 surface water drinking water intakes. Genes tested included esp (indicating human-pathogenic ENT) and nine genes associated with various animal sources of shiga-toxin-producing EC (STEC). Fecal pollution was indicated by genes and/or chemicals for 14 of the 18 tested samples, with little relation to FIB standards. Of 13 samples with Society of Agronomy, Crop Science Society of America, and Soil Science Society of America. All rights reserved.

  2. [Occurrence of gastrointestinal parasites in fecal samples of cats in Andradina City, São Paulo].

    Science.gov (United States)

    Coelho, Willian Marinho Dourado; do Amarante, Alessandro Francisco Talamini; de Soutello, Ricardo Velludo Gomes; Meireles, Marcelo Vasconcelos; Bresciani, Katia Denise Saraiva

    2009-01-01

    The purpose of this study was to verify the occurrence of gastrointestinal parasites in fecal samples from cats of the Andradina city, SP. This work was carried out from March to November of 2007, and used 51 cats delivered to the Center of Zoonoses Control of that city. Techniques of Willis and Faust were used in the fecal examination and resulted in detection of Ancylostoma spp. in 96.1% of the animals; Toxocara spp. in 43.1%; Cystoisospora spp. in 43.1%; Dipylidium caninum in 21.6% and Giardia spp. in 5.9% samples. Cryptosporidium spp. oocysts were detected in 3.9% fecal samples by the use of malachite green negative stain. There was no significant association between the occurrence of endoparasites and consistency of fecal samples. The results confirm that these cats represent important hosts of parasites, some of those with high zoonotic potential.

  3. Alterations in fecal microbiota composition by probiotic supplementation in healthy adults

    DEFF Research Database (Denmark)

    Kristensen, Nadja B; Bryrup, Thomas; Allin, Kristine H

    2016-01-01

    references of relevant papers. Search terms included healthy adult, probiotic, bifidobacterium, lactobacillus, gut microbiota, fecal microbiota, intestinal microbiota, intervention, and (clinical) trial. RCTs of solely probiotic supplementation and placebo in healthy adults that examined alteration...

  4. Prospective regenerative medicine therapies for obstetric trauma-induced fecal incontinence.

    Science.gov (United States)

    Parmar, Nina; Kumar, Lalit; Emmanuel, Anton; Day, Richard M

    2014-01-01

    Fecal incontinence is a major public health issue that has yet to be adequately addressed. Obstetric trauma and injury to the anal sphincter muscles are the most common cause of fecal incontinence. New therapies are emerging aimed at repair or regeneration of sphincter muscle and restoration of continence. While regenerative medicine offers an attractive option for fecal incontinence there are currently no validated techniques using this approach. Although many challenges are yet to be resolved, the advent of regenerative medicine is likely to offer disruptive technologies to treat and possibly prevent the onset of this devastating condition. This article provides a review on regenerative medicine approaches for treating fecal incontinence and a critique of the current landscape in this area.

  5. Application of enteric viruses for fecal pollution source tracking in environmental waters

    Science.gov (United States)

    Microbial source tracking (MST) tools are used to identify sources of fecal pollution for accurately assessing public health risk and implementing best management practices (BMPs). This review focuses on the potential of enteric viruses for MST applications. Following host infect...

  6. Application of fecal calprotectin and myeloperoxidase in evaluation of disease activity of ulcerative colitis

    Institute of Scientific and Technical Information of China (English)

    柏明见

    2013-01-01

    Objective To explore the clinical value of fecal calprotectin and myeloperoxidase in evaluation of ulcerative colitis(UC) activity.Methods Specimens of serum and feces over the same period were collected from

  7. Relief of fecal incontinence by sacral nerve stimulation linked to focal brain activation

    DEFF Research Database (Denmark)

    Lundby, Lilli; Møller, Arne; Buntzen, Steen;

    2011-01-01

    This study aimed to test the hypothesis that sacral nerve stimulation affects afferent vagal projections to the central nervous system associated with frontal cortex activation in patients with fecal incontinence....

  8. Predicting Fecal Indicator Bacteria Concentrations in the South Fork Broad River Watershed Using Virtual Beach

    Science.gov (United States)

    Virtual Beach (VB) is a decision support tool that constructs site-specific statistical models to predict fecal indicator bacteria (FIB) at recreational beaches. Although primarily designed for making decisions regarding beach closures or issuance of swimming advisories based on...

  9. Differential Decomposition of Bacterial and Viral Fecal Indicators in Common Human Pollution Types

    Science.gov (United States)

    Understanding the decomposition of microorganisms associated with different human fecal pollution types is necessary for proper implementation of many water qualitymanagement practices, as well as predicting associated public health risks. Here, thedecomposition of select cultiva...

  10. Differential Decay of Bacterial and Viral Fecal Indicators in Common Human Pollution Sources

    Science.gov (United States)

    Understanding the decomposition of different human fecal pollution sources is necessary for proper implementation of many water quality management practices, as well as predicting associated public health risks. Here, the decay of select cultivated and molecular indicators of fe...

  11. Fecal sterols, seasonal variability, and probable sources along the ring of cenotes, Yucatan, Mexico.

    Science.gov (United States)

    Arcega-Cabrera, F; Velázquez-Tavera, N; Fargher, L; Derrien, M; Noreña-Barroso, E

    2014-11-01

    Rapid development in Yucatan has had a dramatic impact on the environment, especially the water supply. Groundwater is the only source of water in Yucatan, since surface water is virtually absent due to the karstic nature of the soil. The ring of cenotes (RC) is a geological feature which functions as a source of water and as nodes in the underground river system that canalizes water towards the coast. Numerous productive and domestic activities take place around the RC in the absence of wastewater treatment or sewage systems. Consequently, a number of researchers have hypothesized that pollutants could migrate from the land surface to the underlying aquifer and, eventually, to the coast. Therefore, the present study investigates the relationship among sources of fecal sterols and their levels in cenotes, using the expected levels of fecal sterols obtained by a spatial analysis of the sources and a Pollution Source Index. Accordingly, expected levels are compared with the detected levels of fecal sterols in 5 areas around the RC. Regarding levels, observed during a sampling campaign carried out along the RC during September 2011 (rainy season) and May 2012 (dry season), varied from low to high concentrations of sterols (0.5-2396.42 μg g(-1)) and fecal sterols (0.3-1690.18 μg g(-1)). These concentrations showed no relationship between neighboring cenotes, where similar fecal sterol concentrations or gradients were expected. When comparing expected fecal sterols levels with the detected ones, only two of the five analyzed areas concur, suggesting that no clear relationship exists among sources and fecal sterols levels at the regional scale. Multivariate analysis showed that fecal sterols were associated with sterols and fine grain particulates during the rainy season, which suggests co-transport. During the dry season, fecal sterols associated with fine grain particulate and organic matter, which indicates a change to a deposition phenomenon. These findings

  12. Fecal sterols, seasonal variability, and probable sources along the ring of cenotes, Yucatan, Mexico

    Science.gov (United States)

    Arcega-Cabrera, F.; Velázquez-Tavera, N.; Fargher, L.; Derrien, M.; Noreña-Barroso, E.

    2014-11-01

    Rapid development in Yucatan has had a dramatic impact on the environment, especially the water supply. Groundwater is the only source of water in Yucatan, since surface water is virtually absent due to the karstic nature of the soil. The ring of cenotes (RC) is a geological feature which functions as a source of water and as nodes in the underground river system that canalizes water towards the coast. Numerous productive and domestic activities take place around the RC in the absence of wastewater treatment or sewage systems. Consequently, a number of researchers have hypothesized that pollutants could migrate from the land surface to the underlying aquifer and, eventually, to the coast. Therefore, the present study investigates the relationship among sources of fecal sterols and their levels in cenotes, using the expected levels of fecal sterols obtained by a spatial analysis of the sources and a Pollution Source Index. Accordingly, expected levels are compared with the detected levels of fecal sterols in 5 areas around the RC. Regarding levels, observed during a sampling campaign carried out along the RC during September 2011 (rainy season) and May 2012 (dry season), varied from low to high concentrations of sterols (0.5-2396.42 μg g- 1) and fecal sterols (0.3-1690.18 μg g- 1). These concentrations showed no relationship between neighboring cenotes, where similar fecal sterol concentrations or gradients were expected. When comparing expected fecal sterols levels with the detected ones, only two of the five analyzed areas concur, suggesting that no clear relationship exists among sources and fecal sterols levels at the regional scale. Multivariate analysis showed that fecal sterols were associated with sterols and fine grain particulates during the rainy season, which suggests co-transport. During the dry season, fecal sterols associated with fine grain particulate and organic matter, which indicates a change to a deposition phenomenon. These findings indicate

  13. Comparison of GMT presto assay and Roche cobas® 4800 CT/NG assay for detection of Chlamydia trachomatis and Neisseria gonorrhoeae in dry swabs.

    Science.gov (United States)

    de Waaij, Dewi J; Dubbink, Jan Henk; Peters, Remco P H; Ouburg, Sander; Morré, Servaas A

    2015-11-01

    Urogenital Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) are the most prevalent bacterial STIs worldwide. Molecular tests are the standard for the detection of CT and NG, as these are difficult to culture. The recently introduced CE-IVD marked GMT Presto assay promises to be a valuable addition in CT and NG diagnostics. The advantage of the Presto assay is that it works on many PCR systems and the DNA can be isolated by any system.We compared the Presto assay to the widely used Roche cobas® 4800 CT/NG test for the detection of CT and NG in 612 vaginal and rectal dry collected swabs. Discrepant samples were tested by the TIB MOLBIOL Lightmix Kit 480 HT CT/NG assay. The alloyed gold standard was defined as two concurring Presto and cobas® 4800 results, or, with discrepant Presto and cobas® results, two concurring results of either test together with the Lightmix Kit 480 HT CT/NG assay. For the Presto assay,we observed 77 CT positive (13%) and 22 NG positive (3,6%) vaginal samples, and 41 CT positive (6,7%) and 11 NG positive (1,8%) rectal samples. For the cobas® 4800 assay,we observed 77 CT positive (13%) and 21NG positive (3,4%) vaginal samples, and 39 CT positive (6,4%) and 11 NG positive (1,8%) rectal samples. Ten CT samples were discrepant between Presto and cobas® 4800 CT/NG assays, while two NG samples were discrepant. CT sensitivity in both assays was 100% compared to the alloyed gold standard. The sensitivity was 100% for both vaginal and rectal dry swabs, underlining the suitability of these sample types for detection of CT and NG. The Presto assay is therefore valuable for molecular detection of CT and NG in dry vaginal and rectal swabs.

  14. Recombinant Bovine Growth Hormone Criticism Grows.

    Science.gov (United States)

    Gaard, Greta

    1995-01-01

    Discusses concerns related to the use of recombinant bovine growth hormone in the United States and other countries. Analyses the issue from the perspectives of animal rights, human health, world hunger, concerns of small and organic farmers, costs to the taxpayer, and environmental questions. A sidebar discusses Canadian review of the hormone.…

  15. Abnormal fibrillin metabolism in bovine Marfan syndrome.

    Science.gov (United States)

    Potter, K. A.; Hoffman, Y.; Sakai, L. Y.; Byers, P. H.; Besser, T. E.; Milewicz, D. M.

    1993-01-01

    Bovine Marfan syndrome is a disorder that closely resembles human Marfan syndrome in its clinical signs and pathological lesions. The similarities between the human and bovine diseases suggest that similar metabolic defects could be responsible. Although indirect immunofluorescent assays for fibrillin in skin biopsies did not distinguish affected cattle from control animals, cultures of skin fibroblasts of affected animals were distinguished from normal, unrelated control animals and normal half-siblings on the basis of fibrillin staining. After 72 to 96 hours in culture, stained with anti-fibrillin monoclonal antibody 201, hyperconfluent fibroblast cultures of affected cattle had less immunoreactive fibrillin than control cultures, and the staining pattern was granular rather than fibrillar. Under similar culture conditions, normal bovine aortic smooth muscle cells produced large amounts of immunoreactive fibrillin, but smooth muscle cells from a single affected cow showed markedly less fibrillin staining. In pulse-chase metabolic labeling experiments with [35S]cysteine, dermal fibroblasts from 6 affected calves, incorporated far less fibrillin into the extracellular matrix than control cells. These findings are similar to those reported in human Marfan syndrome, and they suggest that the bovine Marfan syndrome, like the human disorder, is caused by a mutation in fibrillin, leading to defective microfibrillar synthesis. Images Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 PMID:8456941

  16. Bovine viral diarrhea virus: biosecurity and control

    Science.gov (United States)

    This paper discusses the recommended procedures involved in setting up biosecurity and control programs designed to limit bovine viral diarrhea virus infections in beef cattle operations. For the purpose of these discussions, a working definition of a biosecurity plan was considered to be an organiz...

  17. Characterization of the bovine ampkgamma1 gene.

    Science.gov (United States)

    Benkel, Bernhard; Kollers, Sonja; Fries, Ruedi; Sazanov, Alexei; Yoshida, Erin; Valle, Edith; Davoren, Jon; Hickey, Donal

    2005-03-01

    AMP-activated protein kinase (AMPK) represents the mammalian form of the core component of a kinase cascade that is conserved between fungi, plants, and animals. AMPK plays a major role in protecting mammalian cells from metabolic stress by switching off biosynthetic pathways that require ATP and switching on ATP-regenerating pathways. In this report, we describe the isolation and characterization of the gene for the noncatalytic bovine gamma1 subunit of AMPK. The bovine ampkgamma1 (PRKAG1) gene spans in excess of 14 kb and is located at BTA 5q21-q22. It consists of 12 exons ranging in size from 38 b to 166 b, interspersed with 11 introns that range between 97 b and 6753 b in length. The coding region of the bovine gene shares 93% and 90% nucleotide sequence similarity with its human and rat counterparts, and the bovine AMPKgamma1 protein is 98% and 95% identical to its human and rat homologs, respectively, in amino acid sequence. SNP discovery using a cattle DNA panel revealed a number of polymorphisms that may be useful for the evaluation of ampkgamma1 as a candidate gene for energy metabolism-related production traits.

  18. Vaccination of cattle against bovine viral diarrhoea

    NARCIS (Netherlands)

    Oirschot, van J.T.; Bruschke, C.J.M.; Rijn, van P.A.

    1999-01-01

    This brief review describes types and quality (efficacy and safety) of bovine viral diarrhoea virus (BVDV) vaccines that are in the market or under development. Both conventional live and killed vaccines are available. The primary aim of vaccination is to prevent congenital infection, but the few va

  19. An unusual presentation of enzootic bovine leukosis.

    OpenAIRE

    Sparling, A M

    2000-01-01

    A 6-year-old, Holstein x Simmental cow diagnosed with pyelonephritis had increasing difficulty rising and became recumbent, despite treatment with antibiotics. A serological test for the bovine leukemia virus was positive; at necropsy, the left kidney and ureter and the myocardium showed lesions of lymphosarcoma, confirmed by histology.

  20. NUTRIENTS AND EPIGENETICS IN BOVINE CELLS

    Science.gov (United States)

    This is a chapter for a book titled “Livestock Epigenetics” edited by Dr. Hasan Khatib and published by Wiley-Blackwell. This chapter is focused on the research development in our laboratory in the area of interaction of nutrients and genomic phonotype in bovine cells. Briefly, the Research on nutri...

  1. Epidemiology and control of bovine ephemeral fever.

    Science.gov (United States)

    Walker, Peter J; Klement, Eyal

    2015-10-28

    Bovine ephemeral fever (or 3-day sickness) is an acute febrile illness of cattle and water buffaloes. Caused by an arthropod-borne rhabdovirus, bovine ephemeral fever virus (BEFV), the disease occurs seasonally over a vast expanse of the globe encompassing much of Africa, the Middle East, Asia and Australia. Although mortality rates are typically low, infection prevalence and morbidity rates during outbreaks are often very high, causing serious economic impacts through loss of milk production, poor cattle condition at sale and loss of traction power at harvest. There are also significant impacts on trade to regions in which the disease does not occur, including the Americas and most of Europe. In recent years, unusually severe outbreaks of bovine ephemeral fever have been reported from several regions in Asia and the Middle East, with mortality rates through disease or culling in excess of 10-20%. There are also concerns that, like other vector-borne diseases of livestock, the geographic distribution of bovine ephemeral fever could expand into regions that have historically been free of the disease. Here, we review current knowledge of the virus, including its molecular and antigenic structure, and the epidemiology of the disease across its entire geographic range. We also discuss the effectiveness of vaccination and other strategies to prevent or control infection.

  2. DETECTION OF THE BOVINE VIRAL DIARRHEA ANTIBODIES

    Directory of Open Access Journals (Sweden)

    I. V. Goraichuk

    2013-06-01

    Full Text Available Bovine viral diarrhea is a widespread infection of cattle that has a wide range of clinical symptoms in domestic and wild ruminants. It is a major problem in cattle and causes significant economic losses in the cattle industry. The virus infects bovines of all ages and causes both immunosuppression and reproductive, respiratory and digestive disorders. Persistently infected cattle are the main factor in transmission of the disease between and among herds. Comparative results of antibodies presence received by two methods of enzymoimmunoassay and virus neutralization test are given in the paper. During the work, 1010 samples of blood serum of cattle from three farms in the Kharkiv region were selected and analyzed. Bovine viral diarrhea virus concerning antibodies were found by enzymoimmunoassay in 704 samples (69.7% using commercial kit and in 690 samples (68.3% using in house method. After results clarification by virus neutralization test, bovine viral diarrhea antibodies were found in 712 samples (70.5%. Immunoenzyme analysis is recommended for mass screening of cattle for viral diarrhea occurrence. The results confirm that the sensitivity immunoenzyme analysis satisfies the requirements of the diagnostic methods. Using the neutralization reaction of viruses as the «gold standard» of serological methods, it is appropriate to clarify the results of immunoenzyme analysis. Since the results contain a signi ficant number of false positive results, it is necessary to carry out comprehensive studies using both serological and molecular genetics methods.

  3. Transmission of new bovine prion to mice

    NARCIS (Netherlands)

    Baron, T.G.M.; Biacabe, A.G.; Bencsik, A.; Langeveld, J.P.M.

    2006-01-01

    We previously reported that cattle were affected by a prion disorder that differed from bovine spongiform encephalopathy (BSE) by showing distinct molecular features of disease-associated protease-resistant prion protein (PrPres). We show that intracerebral injection of such isolates into C57BL/6 mi

  4. Aortic reconstruction with bovine pericardial grafts

    Directory of Open Access Journals (Sweden)

    Silveira Lindemberg Mota

    2003-01-01

    Full Text Available INTRODUCTION: Glutaraldehyde-treated crimped bovine pericardial grafts are currently used in aortic graft surgery. These conduits have become good options for these operations, available in different sizes and shapes and at a low cost. OBJECTIVE:To evaluate the results obtained with bovine pericardial grafts for aortic reconstruction, specially concerning late complications. METHOD: Between January 1995 and January 2002, 57 patients underwent different types of aortic reconstruction operations using bovine pericardial grafts. A total of 29 (50.8% were operated on an urgent basis (mostly acute Stanford A dissection and 28 electively. Thoracotomy was performed in three patients for descending aortic replacement (two patients and aortoplasty with a patch in one. All remaining 54 underwent sternotomy, cardiopulmonary bypass and aortic resection. Deep hypothermia and total circulatory arrest was used in acute dissections and arch operations. RESULTS: Hospital mortality was 17.5%. Follow-up was 24.09 months (18.5 to 29.8 months confidence interval and complication-free actuarial survival curve was 92.3% (standard deviation ± 10.6. Two patients lately developed thoracoabdominal aneurysms following previous DeBakey II dissection and one died from endocarditis. One "patch" aortoplasty patient developed local descending aortic pseudoaneurysm 42 months after surgery. All other patients are asymptomatic and currently clinically evaluated with echocardiography and CT scans, showing no complications. CONCLUSION: Use of bovine pericardial grafts in aortic reconstruction surgery is adequate and safe, with few complications related to the conduits.

  5. Molecular biology of bovine viral diarrhea virus

    Science.gov (United States)

    Bovine viral diarrhea viruses (BVDV) are arguably the most important viral pathogen of ruminants worldwide and can cause severe economic loss. Clinical symptoms of the disease caused by BVDV range from subclinical to severe acute hemorrhagic syndrome, with the severity of disease being strain depend...

  6. Pathogenesis of bovine spongiform encephalopathy in sheep

    NARCIS (Netherlands)

    Keulen, van L.J.M.; Vromans, M.E.W.; Dolstra, C.H.; Bossers, A.; Zijderveld, van F.G.

    2008-01-01

    The pathogenesis of bovine spongiform encephalopathy (BSE) in sheep was studied by immunohistochemical detection of scrapie-associated prion protein (PrPSc) in the gastrointestinal, lymphoid and neural tissues following oral inoculation with BSE brain homogenate. First accumulation of PrPSc was dete

  7. Pasteurella multocida and bovine respiratory disease.

    Science.gov (United States)

    Dabo, S M; Taylor, J D; Confer, A W

    2007-12-01

    Pasteurella multocida is a pathogenic Gram-negative bacterium that has been classified into three subspecies, five capsular serogroups and 16 serotypes. P. multocida serogroup A isolates are bovine nasopharyngeal commensals, bovine pathogens and common isolates from bovine respiratory disease (BRD), both enzootic calf pneumonia of young dairy calves and shipping fever of weaned, stressed beef cattle. P. multocida A:3 is the most common serotype isolated from BRD, and these isolates have limited heterogeneity based on outer membrane protein (OMP) profiles and ribotyping. Development of P. multocida-induced pneumonia is associated with environmental and stress factors such as shipping, co-mingling, and overcrowding as well as concurrent or predisposing viral or bacterial infections. Lung lesions consist of an acute to subacute bronchopneumonia that may or may not have an associated pleuritis. Numerous virulence or potential virulence factors have been described for bovine respiratory isolates including adherence and colonization factors, iron-regulated and acquisition proteins, extracellular enzymes such as neuraminidase, lipopolysaccharide, polysaccharide capsule and a variety of OMPs. Immunity of cattle against respiratory pasteurellosis is poorly understood; however, high serum antibodies to OMPs appear to be important for enhancing resistance to the bacterium. Currently available P. multocida vaccines for use in cattle are predominately traditional bacterins and a live streptomycin-dependent mutant. The field efficacy of these vaccines is not well documented in the literature.

  8. Proficiency test for antibiotics in bovine muscle

    NARCIS (Netherlands)

    Elbers, I.J.W.; Berendsen, B.J.A.; Pikkemaat, M.G.; Stolker, A.A.M.

    2010-01-01

    The aim of this proficiency study was to give laboratories the possibility to evaluate or demonstrate their competence for the analysis of antibiotics in bovine muscle, including the screening analysis. This study also provided an evaluation of the methods applied for screening and quantitative conf

  9. Aggregation and fibrillation of bovine serum albumin

    DEFF Research Database (Denmark)

    Holm, NK; Jespersen, SK; Thomassen, LV;

    2007-01-01

    The all-alpha helix multi-domain protein bovine serum albumin (BSA) aggregates at elevated temperatures. Here we show that these thermal aggregates have amyloid properties. They bind the fibril-specific dyes Thioflavin T and Congo Red, show elongated although somewhat worm-like morphology...

  10. EVOLUTION AND RECOMBINATION OF BOVINE DNA REPEATS

    NARCIS (Netherlands)

    JOBSE, C; BUNTJER, JB; HAAGSMA, N; BREUKELMAN, HJ; BEINTEMA, JJ; LENSTRA, JA

    1995-01-01

    The history of the abundant repeat elements in the bovine genome has been studied by comparative hybridization and PCR. The Bov-A and Bov-B SINE elements both emerged just after the divergence of the Camelidae and the true ruminants. A 31-bp subrepeat motif in satellites of the Bovidae species cattl

  11. Concomitant infection of Neospora caninum and Bovine Herpesvirus type 5 in spontaneous bovine abortions

    Directory of Open Access Journals (Sweden)

    Maia S. Marin

    2013-11-01

    Full Text Available Bovine Herpesvirus type 5 (BoHV-5 has not been conclusively demonstrated to cause bovine abortion. Brain lesions produced by Neospora caninum and Bovine Herpesvirus type 1 (BoHV-1 exhibit common features. Therefore, careful microscopic evaluation and additional diagnostic procedures are required to achieve an accurate final etiological diagnosis. The aim of the present work was to investigate the occurrence of infections due to BoHV-1, BoHV-5 and N. caninum in 68 cases of spontaneous bovine abortions which showed microscopic lesions in the fetal central nervous system. This study allowed the identification of 4 (5.9% fetuses with dual infection by BoHV-5 and N. caninum and 33 (48.5% cases in which N. caninum was the sole pathogen identified. All cases were negative to BoHV-1. The results of this study provide evidence that dual infection by BoHV-5 and N. caninum occur during pregnancy in cattle; however, the role of BoHV-5 as a primary cause of bovine abortion needs further research. Molecular diagnosis of BoHV-5 and N. caninum confirmed the importance of applying complementary assays to improve the sensitivity of diagnosing bovine abortion.

  12. Human parvovirus 4 in nasal and fecal specimens from children, Ghana.

    Science.gov (United States)

    Drexler, Jan Felix; Reber, Ulrike; Muth, Doreen; Herzog, Petra; Annan, Augustina; Ebach, Fabian; Sarpong, Nimarko; Acquah, Samuel; Adlkofer, Julia; Adu-Sarkodie, Yaw; Panning, Marcus; Tannich, Egbert; May, Jürgen; Drosten, Christian; Eis-Hübinger, Anna Maria

    2012-10-01

    Nonparenteral transmission might contribute to human parvovirus 4 (PARV4) infections in sub-Saharan Africa. PARV4 DNA was detected in 8 (0.83%) of 961 nasal samples and 5 (0.53%) of 943 fecal samples from 1,904 children in Ghana. Virus concentrations ≤ 6-7 log(10) copies/mL suggest respiratory or fecal-oral modes of PARV4 transmission.

  13. Microbiota transplantation restores normal fecal bile acid composition in recurrent Clostridium difficile infection.

    Science.gov (United States)

    Weingarden, Alexa R; Chen, Chi; Bobr, Aleh; Yao, Dan; Lu, Yuwei; Nelson, Valerie M; Sadowsky, Michael J; Khoruts, Alexander

    2014-02-15

    Fecal microbiota transplantation (FMT) has emerged as a highly effective therapy for refractory, recurrent Clostridium difficile infection (CDI), which develops following antibiotic treatments. Intestinal microbiota play a critical role in the metabolism of bile acids in the colon, which in turn have major effects on the lifecycle of C. difficile bacteria. We hypothesized that fecal bile acid composition is altered in patients with recurrent CDI and that FMT results in its normalization. General metabolomics and targeted bile acid analyses were performed on fecal extracts from patients with recurrent CDI treated with FMT and their donors. In addition, 16S rRNA gene sequencing was used to determine the bacterial composition of pre- and post-FMT fecal samples. Taxonomic bacterial composition of fecal samples from FMT recipients showed rapid change and became similar to the donor after the procedure. Pre-FMT fecal samples contained high concentrations of primary bile acids and bile salts, while secondary bile acids were nearly undetectable. In contrast, post-FMT fecal samples contained mostly secondary bile acids, as did non-CDI donor samples. Therefore, our analysis showed that FMT resulted in normalization of fecal bacterial community structure and metabolic composition. Importantly, metabolism of bile salts and primary bile acids to secondary bile acids is disrupted in patients with recurrent CDI, and FMT corrects this abnormality. Since individual bile salts and bile acids have pro-germinant and inhibitory activities, the changes suggest that correction of bile acid metabolism is likely a major mechanism by which FMT results in a cure and prevents recurrence of CDI.

  14. Designing fecal microbiota transplant trials that account for differences in donor stool efficacy.

    Science.gov (United States)

    Olesen, Scott W; Gurry, Thomas; Alm, Eric J

    2017-01-01

    Fecal microbiota transplantation is a highly effective intervention for patients suffering from recurrent Clostridium difficile, a common hospital-acquired infection. Fecal microbiota transplantation's success as a therapy for C. difficile has inspired interest in performing clinical trials that experiment with fecal microbiota transplantation as a therapy for other conditions like inflammatory bowel disease, obesity, diabetes, and Parkinson's disease. Results from clinical trials that use fecal microbiota transplantation to treat inflammatory bowel disease suggest that, for at least one condition beyond C. difficile, most fecal microbiota transplantation donors produce stool that is not efficacious. The optimal strategies for identifying and using efficacious donors have not been investigated. We therefore examined the optimal Bayesian response-adaptive strategy for allocating patients to donors and formulated a computationally tractable myopic heuristic. This heuristic computes the probability that a donor is efficacious by updating prior expectations about the efficacy of fecal microbiota transplantation, the placebo rate, and the fraction of donors that produce efficacious stool. In simulations designed to mimic a recent fecal microbiota transplantation clinical trial, for which traditional power calculations predict [Formula: see text] statistical power, we found that accounting for differences in donor stool efficacy reduced the predicted statistical power to [Formula: see text]. For these simulations, using the heuristic Bayesian allocation strategy more than quadrupled the statistical power to [Formula: see text]. We use the results of similar simulations to make recommendations about the number of patients, the number of donors, and the choice of clinical endpoint that clinical trials should use to optimize their ability to detect if fecal microbiota transplantation is effective for treating a condition.

  15. Source tracking swine fecal waste in surface water proximal to swine concentrated animal feeding operations

    Science.gov (United States)

    Heaney, Christopher D.; Myers, Kevin; Wing, Steve; Hall, Devon; Baron, Dothula; Stewart, Jill R.

    2015-01-01

    Swine farming has gone through many changes in the last few decades, resulting in operations with a high animal density known as confined animal feeding operations (CAFOs). These operations produce a large quantity of fecal waste whose environmental impacts are not well understood. The purpose of this study was to investigate microbial water quality in surface waters proximal to swine CAFOs including microbial source tracking of fecal microbes specific to swine. For one year, surface water samples at up- and downstream sites proximal to swine CAFO lagoon waste land application sites were tested for fecal indicator bacteria (fecal coliforms, Escherichia coli and Enterococcus) and candidate swine-specific microbial source-tracking (MST) markers (Bacteroidales Pig-1-Bac, Pig-2-Bac, and Pig-Bac-2, and methanogen P23-2). Testing of 187 samples showed high fecal indicator bacteria concentrations at both up- and downstream sites. Overall, 40%, 23%, and 61% of samples exceeded state and federal recreational water quality guidelines for fecal coliforms, E. coli, and Enterococcus, respectively. Pig-1-Bac and Pig-2-Bac showed the highest specificity to swine fecal wastes and were 2.47 (95% confidence interval [CI] = 1.03, 5.94) and 2.30 times (95% CI = 0.90, 5.88) as prevalent proximal down- than proximal upstream of swine CAFOs, respectively. Pig-1-Bac and Pig-2-Bac were also 2.87 (95% CI = 1.21, 6.80) and 3.36 (95% CI = 1.34, 8.41) times as prevalent when 48 hour antecedent rainfall was greater than versus less than the mean, respectively. Results suggest diffuse and overall poor sanitary quality of surface waters where swine CAFO density is high. Pig-1-Bac and Pig-2-Bac are useful for tracking off-site conveyance of swine fecal wastes into surface waters proximal to and downstream of swine CAFOs and during rain events. PMID:25600418

  16. Fecal Kinetics and Digestibilities of Hays and Supplements Estimated by Marker Methods in the Horse

    OpenAIRE

    Hargreaves, Belinda Jane

    1998-01-01

    Fecal Kinetics and Digestibilities of Hays and Supplements Estimated by Marker Methods in the Horse by Belinda J. Hargreaves David S. Kronfeld, Chairman Department of Animal and Poultry Science (ABSTRACT) A marker model of fecal kinetics using chromic oxide (Cr) or ytterbium chloride (Yb) is being developed for grazing horses. The model consists of removal of feces at a constant rate from a single compartment, the prefecal mass. It was tested in experiments on stall-fed h...

  17. Effects of Long Term Antibiotic Therapy on Human Oral and Fecal Viromes.

    Directory of Open Access Journals (Sweden)

    Shira R Abeles

    Full Text Available Viruses are integral members of the human microbiome. Many of the viruses comprising the human virome have been identified as bacteriophage, and little is known about how they respond to perturbations within the human ecosystem. The intimate association of phage with their cellular hosts suggests their communities may change in response to shifts in bacterial community membership. Alterations to human bacterial biota can result in human disease including a reduction in the host's resilience to pathogens. Here we report the ecology of oral and fecal viral communities and their responses to long-term antibiotic therapy in a cohort of human subjects. We found significant differences between the viral communities of each body site with a more heterogeneous fecal virus community compared with viruses in saliva. We measured the relative diversity of viruses, and found that the oral viromes were significantly more diverse than fecal viromes. There were characteristic changes in the membership of oral and fecal bacterial communities in response to antibiotics, but changes in fecal viral communities were less distinguishing. In the oral cavity, an abundance of papillomaviruses found in subjects on antibiotics suggests an association between antibiotics and papillomavirus production. Despite the abundance of papillomaviruses identified, in neither the oral nor the fecal viromes did antibiotic therapy have any significant impact upon overall viral diversity. There was, however, an apparent expansion of the reservoir of genes putatively involved in resistance to numerous classes of antibiotics in fecal viromes that was not paralleled in oral viromes. The emergence of antibiotic resistance in fecal viromes in response to long-term antibiotic therapy in humans suggests that viruses play an important role in the resilience of human microbial communities to antibiotic disturbances.

  18. 不同病程手足口病患者咽拭、肛拭配对标本肠道病毒检出率的比较%Comparison of enterovirus detection rates in paired specimens of throat swabs and anus swabs from patients in different phases of hand-foot-mouth disease

    Institute of Scientific and Technical Information of China (English)

    李颐; 居丽雯; 蒋露芳; 沈磊; 赵文良; 沈琦; 蔡明毅; 孟威; 姜庆五

    2013-01-01

    目的 比较不同病程手足口病患者咽拭、肛拭配对标本中肠道病毒的检出率.方法 采集2010年7月至2011年12月上海市儿童医院临床诊断手足口病患儿175例咽拭、肛拭配对标本,采用实时-PCR法进行柯萨奇病毒A组16型(CoxA16)、肠道病毒71型(EV71)和其他EV属检测,分析不同病程配对标本肠道病毒检出率.配对标本行McNemar检验.结果 175例患者的配对标本CoxA 16、EV71、其他EV属咽拭子阳性率分别为38.29%、20.57%和8.00%,肛拭子阳性率分别为44.00%、23.43%和13.14%.结果显示两种标本检测结果的差异均有统计学意义(均P<0.01).发病当天至发病后2d及4~11 d肛拭EV71阳性率均比咽拭阳性率高;发病后2~3d肛拭CoxA 16阳性率均比咽拭阳性率高;发病当天至发病后3d肛拭其他EV属阳性率均比咽拭阳性率高.对于EV71,咽拭标本在发病后3~11 d均可检出阳性,而CoxA 16、其他EV属在发病3d后都无法检出阳性.结论 肛拭标本总体阳性率高于咽拭标本.EV71在呼吸道带毒持续时间长于CoxA 16和其他EV属.在发病2d内肠道病毒在咽部繁殖扩增,此时病毒可通过呼吸道途径传播.%Objective To compare the detection rates of enterovirus in paired specimens of throat swabs and anus swabs from patients with different phases of hand-food-mouth disease (HFMD).Methods A total of 175 paired throat swabs and anus swabs from patients who were clinically diagnosed with HFMD in Children's Hospital of Shanghai from July 2010 to December 2011 were collected.Real-time reverse transcription polymerase chain reaction (RT-PCR) to detect Enterovirus 71 (EV71),Coxsackievirus group A type 16 (CoxA16) and other Enterovirus(EV) was performed.The detection rates of paired specimens within different phases of the disease were compared.Results Among the 175 pairs of specimens,the positive rates of CoxA16,EV71 and other EV in throat swabs were 38.29%,20.57% and 8.00

  19. Antibacterial activity of marine culturable bacteria collected from a global sampling of ocean surface waters and surface swabs of marine organisms

    DEFF Research Database (Denmark)

    Gram, Lone; Melchiorsen, Jette; Bruhn, Jesper Bartholin

    2010-01-01

    The purpose of the present study was to isolate marine culturable bacteria with antibacterial activity and hence a potential biotechnological use. Seawater samples (244) and 309 swab samples from biotic or abiotic surfaces were collected on a global Danish marine research expedition (Galathea 3...... surfaces was inhibitory. It was not possible to relate a specific kind of eukaryotic surface or a specific geographic location to a general high occurrence of antagonistic bacteria. Five hundred and nineteen strains representing all samples and geographic locations were identified on the basis of partial...

  20. Canine skin and conjunctival swab samples for the detection and quantification of Leishmania infantum DNA in an endemic urban area in Brazil.

    Directory of Open Access Journals (Sweden)

    Sidney de Almeida Ferreira

    Full Text Available BACKGROUND: We evaluated kDNA PCR/hybridization and quantitative real-time PCR (qPCR targeting the gene of DNA polymerase of Leishmania infantum for CVL diagnosis and assessment of parasite load in clinical samples obtained invasively and non-invasively. METHODOLOGY/PRINCIPAL FINDINGS: Eighty naturally infected dogs from an endemic urban area in Brazil were used. Animals were divided into two groups based on the presence or absence of CVL clinical sings. Skin biopsies, bone marrow, blood and conjunctival swabs samples were collected and submitted to L. infantum DNA detection. In addition, anti-Leishmania antibody titers were measured by Immunofluorescence antibody test. The symptomatic dogs had increased titers compared to asymptomatic dogs (P = 0.025. The frequencies of positive results obtained by kDNA PCR/hybridization for asymptomatic and symptomatic dogs, respectively, were as follows: right conjunctiva, 77.5% and 95.0%; left conjunctiva, 75.0% and 87.5%; skin, 45.0% and 75.0%; bone marrow, 50.0% and 77.5%; and blood, 27.5% and 22.5%. In both groups, the parasite load in the skin samples was the highest (P<0.0001. The parasite loads in the conjunctival swab and bone marrow samples were statistically equivalent within each group. The parasite burden in conjunctival swabs was higher in the dogs with clinical signs than in asymptomatic dogs (P = 0.028. This same relationship was also observed in the bone marrow samples (P = 0.002. No differences in amastigotes load in the skin were detected between the groups. CONCLUSIONS: The conjunctival swab is a suitable clinical sample for qualitative molecular diagnosis of CVL. The highest parasite burdens were detected in skin regardless of the presence of VL-associated clinical signs. The qPCR results emphasized the role of dogs, particularly asymptomatic dogs, as reservoirs for CVL because of the high cutaneous parasite loads. These results may help to explain the maintenance of high

  1. Multicenter evaluation of the LightCycler methicillin-resistant Staphylococcus aureus (MRSA) advanced test as a rapid method for detection of MRSA in nasal surveillance swabs.

    Science.gov (United States)

    Peterson, Lance R; Liesenfeld, Oliver; Woods, Christopher W; Allen, Stephen D; Pombo, David; Patel, Parul A; Mehta, Maitry S; Nicholson, Bradly; Fuller, DeAnna; Onderdonk, Andrew

    2010-05-01

    The rate of methicillin-resistant Staphylococcus aureus (MRSA) infection continues to rise in many health care settings. Rapid detection of MRSA colonization followed by appropriate isolation can reduce transmission and infection. We compared the performance of the new Roche LightCycler MRSA advanced test to that of the BD GeneOhm MRSA test and culture. Double-headed swabs were used to collect anterior nasal specimens from each subject. For both tests, DNA was extracted and real-time PCR was performed according to manufacturer's instructions. For culture, one swab of the pair was plated directly to CHROMagar MRSA. The swab paired with the BD GeneOhm MRSA test was also placed into an enrichment broth and then plated to CHROMagar MRSA. Colonies resembling staphylococci were confirmed as S. aureus by standard methods. Discrepant specimens had further testing with additional attempts to grow MRSA as well as sample amplicon sequencing. Agreement between results for the two swabs was 99.3% for those with valid results. A total of 1,402 specimens were tested using direct culture detection of MRSA as the gold standard; 187 were culture positive for MRSA. The LightCycler MRSA advanced test had relative sensitivity and specificity of 95.2% (95% confidence interval [CI]: 91.1% to 97.8%) and 96.4% (95% CI: 95.2% to 97.4%), respectively. The BD GeneOhm assay had relative sensitivity and specificity of 95.7% (95% CI: 91.7% to 98.1%) and 91.7% (95% CI: 90.0% to 93.2%), respectively. Following discrepancy analysis, the relative sensitivities of the LightCycler MRSA advanced test and the BD GeneOhm MRSA assay were 92.2 and 93.2%, respectively; relative specificities were 98.9 and 94.2%, respectively. Specificity was significantly better (Padvanced test. The sensitivity of direct culture was 80.4%. The LightCycler MRSA advanced test is a useful tool for sensitive and rapid detection of MRSA nasal colonization.

  2. Fecal microbiota transplantation: effectiveness, complexities, and lingering concerns.

    Science.gov (United States)

    Pamer, E G

    2014-03-01

    The mammalian colon is home to a microbial ecosystem that enhances resistance to infection, stimulates mucosal immune defenses, synthesizes essential vitamins, and promotes caloric uptake by hydrolyzing complex carbohydrates. The bacterial populations inhabiting the gut are complex and vary between different individuals. Clinical and experimental studies reveal that the colonic microbiota can enhance or ameliorate intestinal and systemic inflammatory diseases. Because of its potential to enhance resistance to infection and to reduce inflammatory diseases, targeted manipulation of microbial populations is a growing focus of investigation. The most dramatic manipulation of the intestinal microbiota involves fecal microbiota transplantation (FMT) from healthy donors to individuals with specific diseases. Remarkable clinical effectiveness of FMT has been demonstrated for recurrent Clostridium difficile infection and ongoing studies are investigating FMT for other diseases. Transplantation of complex microbial populations to recipients likely triggers mucosal immune responses that, depending on the microbiota composition and the recipient's genotype, could range from pro- to anti-inflammatory. The impact of FMT on the recipient immune system is complex and unpredictable. Ongoing discovery of commensal microbes and investigations of their impact on the host will lead to the development of new probiotic agents and microbial consortia that will eventually replace FMT.

  3. Fecal microbiota transplantation in inflammatory bowel disease: beyond the excitement.

    Science.gov (United States)

    Ianiro, Gianluca; Bibbò, Stefano; Scaldaferri, Franco; Gasbarrini, Antonio; Cammarota, Giovanni

    2014-10-01

    The purpose of this article is to perform a systematic review of the literature on the use of fecal microbiota transplantation (FMT) in inflammatory bowel disease (IBD).There is an increasing interest of both physicians and patients in assessing the possible role of the FMT in the treatment of IBD.Electronic and manual bibliographic searches were performed to identify original reports in which subjects with IBD were treated with FMT. Because of the scarcity of studies with adequate sample size, case series and case reports were also considered. A critical appraisal of the clinical research evidence on the effectiveness, safety, and other parameters related to FMT was made. Data extraction was independently performed by 2 reviewers.We found a total of 31 publications on the use of FMT in IBD. The majority were case reports or case series, whereas 8 publications reported data from open-label trials including a very less number of patients. A total of 133 patients with IBD were managed with FMT. Of these, 57 subjects (43%) had a Clostridium difficile infection. A resolution or reduction of symptoms was reported in 80 of 113 (71%) patients with evaluable IBD. Moreover, FMT does not seem to provide the same safety profile showed for non-IBD individuals with C difficile infection.The available evidence is limited and weak. FMT has the potential to be somehow of help in managing patients with IBD, but considerable further efforts are necessary to make this procedure a valid option for these subjects.

  4. Distribution of Fecal Indicator Bacteria along the Malibu, California, Coastline

    Science.gov (United States)

    Izbicki, John

    2011-01-01

    Each year, over 550 million people visit California's public beaches. To protect beach-goers from exposure to waterborne disease, California state law requires water-quality monitoring for fecal indicator bacteria (FIB), such as enterococci and Escherichia coli (E. coli), at beaches having more than 50,000 yearly visitors. FIB are used to assess the microbiological quality of water because, although not typically disease causing, they are correlated with the occurrence of certain waterborne diseases. Tests show that FIB concentrations occasionally exceed U.S. Environmental Protection Agency (USEPA) public health standards for recreational water in Malibu Lagoon and at several Malibu beaches (Regional Water Quality Control Board, 2009). Scientists from the U.S. Geological Survey's (USGS) California Water Science Center are doing a study to identify the distribution and sources of FIB in coastal Malibu waters (fig. 1). The study methods were similar to those used in a study of FIB contamination on beaches in the Santa Barbara, California, area (Izbicki and others, 2009). This report describes the study approach and presents preliminary results used to evaluate the distribution and source of FIB in the Malibu area. Results of this study will help decision-makers address human health issues associated with FIB contamination in Malibu, and the methods used in this study can be used in other coastal areas affected by FIB contamination.

  5. Fecal microbiota transplantation broadening its application beyond intestinal disorders.

    Science.gov (United States)

    Xu, Meng-Que; Cao, Hai-Long; Wang, Wei-Qiang; Wang, Shan; Cao, Xiao-Cang; Yan, Fang; Wang, Bang-Mao

    2015-01-07

    Intestinal dysbiosis is now known to be a complication in a myriad of diseases. Fecal microbiota transplantation (FMT), as a microbiota-target therapy, is arguably very effective for curing Clostridium difficile infection and has good outcomes in other intestinal diseases. New insights have raised an interest in FMT for the management of extra-intestinal disorders associated with gut microbiota. This review shows that it is an exciting time in the burgeoning science of FMT application in previously unexpected areas, including metabolic diseases, neuropsychiatric disorders, autoimmune diseases, allergic disorders, and tumors. A randomized controlled trial was conducted on FMT in metabolic syndrome by infusing microbiota from lean donors or from self-collected feces, with the resultant findings showing that the lean donor feces group displayed increased insulin sensitivity, along with increased levels of butyrate-producing intestinal microbiota. Case reports of FMT have also shown favorable outcomes in Parkinson's disease, multiple sclerosis, myoclonus dystonia, chronic fatigue syndrome, and idiopathic thrombocytopenic purpura. FMT is a promising approach in the manipulation of the intestinal microbiota and has potential applications in a variety of extra-intestinal conditions associated with intestinal dysbiosis.

  6. Modulation of mice fecal microbiota by administration of casein glycomacropeptide

    Directory of Open Access Journals (Sweden)

    Qingsen Chen

    2012-12-01

    Full Text Available Casein glycomacropeptide (GMP is known to promote the in vitro growth of Bifidobacteria and Lactobacilli. In this paper, we used conven- tional culture techniques and fluorescent in situ hybridization (FISH techniques to investigate the effect of casein GMP on mice fecal microbiota. The population structure of the intestinal microbiota, including Lactobacillus, Bifidobacteria, Enterococcus, coliforms and Enterobacteriaceae, was tested and compared. After consecutive administration of casein GMP for 15 days, numbers of Lactobacillus and Bifidobacteria increased significantly (P<0.01, numbers of Enterobacteriaceae and Coliforms decreased significantly (P<0.05 while no significant changes were observed for Enterococcus. The detection limits of FISH technique were significantly lower (P<0.01 than the traditional culture method. These results suggested that consumption of casein GMP had a prebiotic effect on male BALB/c mice. Casein GMP helped establish a healthier intestinal microbiota. Additionally, FISH was proved to be a rapid and relatively low-cost detection method that can be used to further our understanding of human intestinal microbiota.

  7. Fecal contamination of wastewater treatment plants in Portugal.

    Science.gov (United States)

    Oliveira, Manuela; Serrano, Isa; Van Harten, Sofia; Bessa, Lucinda J; Bernardo, Fernando; da Costa, Paulo Martins

    2016-07-01

    Reutilization of effluents from wastewater treatment plants (WWTP) for non-potable applications is increasing due to the reduction of sustainable water resources. These products mostly come from municipal WWTP and also from slaughterhouses effluents. The microbiological certification of these products is mandatory before their discharge into the environment. This study evaluates if the treatment applied in WWTP to municipal waters or to poultry slaughterhouse effluents distributed over the Portuguese continental territory is efficient in reducing the microbiological risk associated with the reutilization of those wastewaters and sludges. Fecal indicators Escherichia coli and enterococci were evaluated in 42 and 24 wastewater samples from 14 municipal WWTP and 8 poultry slaughterhouse treatment plants, respectively, by the conventional culture method and a rapid Fluorescent in situ hybridization (FISH) technique. Bacterial enumeration in inflow water from most WWTP was rather high (generally >10(5) cells/ml), for both E. coli and Enterococcus spp., and the bacterial quantification by FISH was generally higher than enumeration by the conventional culture method. In both types of treatment plants studied, bacterial load from effluents and sludges was not statistically different from the inflows, indicating that the treatment applied seems to be equally unable to reduce the microbiological load of the effluents. These findings may jeopardize the safe reuse of treated wastewaters in agriculture and the quality of the water environment. Therefore, products like water, sewage sludge, and biosolids originated from the municipal and slaughterhouse WWTP studied should not be reutilized, and effluents treatment should be urgently reviewed.

  8. The Host Shapes the Gut Microbiota via Fecal MicroRNA.

    Science.gov (United States)

    Liu, Shirong; da Cunha, Andre Pires; Rezende, Rafael M; Cialic, Ron; Wei, Zhiyun; Bry, Lynn; Comstock, Laurie E; Gandhi, Roopali; Weiner, Howard L

    2016-01-13

    The host gut microbiota varies across species and individuals but is relatively stable over time within an individual. How the host selectively shapes the microbiota is largely unclear. Here, we show that fecal microRNA (miRNA)-mediated inter-species gene regulation facilitates host control of the gut microbiota. miRNAs are abundant in mouse and human fecal samples and present within extracellular vesicles. Cell-specific loss of the miRNA-processing enzyme, Dicer, identified intestinal epithelial cells (IEC) and Hopx-positive cells as predominant fecal miRNA sources. These miRNAs can enter bacteria, such as F. nucleatum and E. coli, specifically regulate bacterial gene transcripts, and affect bacterial growth. IEC-miRNA-deficient (Dicer1(ΔIEC)) mice exhibit uncontrolled gut microbiota and exacerbated colitis, and WT fecal miRNA transplantation restores fecal microbes and ameliorates colitis. These findings identify both a physiologic role by which fecal miRNA shapes the gut microbiota and a potential strategy for manipulating the microbiome.

  9. Evaluation and Improved Use of Fecal Occult Blood Test in the Constipated Child.

    Science.gov (United States)

    Kilway, Denise M

    2016-01-01

    This quality improvement project examined the use of fecal occult blood test in the constipated child in a pediatric gastroenterology outpatient clinic. A retrospective chart review was completed on 100 children seen for an initial visit with the gastroenterology provider. The number of fecal occult blood tests performed and the child's coinciding symptoms were tallied and compared with the North American Society of Pediatric Gastroenterology, Hepatology, and Nutrition recommendations. An educational intervention was held with the pediatric gastroenterology providers consisting of a PowerPoint presentation summarizing aims of the quality improvement project and reviewing recommendations for use of fecal occult blood test in the constipated child. Pre- and post-intervention chart review data sets were compared. Results showed a 19.6% decrease in the use of fecal occult blood tests performed during the post-intervention timeframe. However, when used in conjunction with North American Society of Pediatric Gastroenterology, Hepatology, and Nutrition recommendations, the appropriateness of fecal occult blood test use increased by 71.4% in the post-intervention patients. Reviewing the recommendations with gastroenterology providers assisted in optimizing the meaningful use of fecal occult blood test, improving quality and safety of care for children seen in the pediatric gastroenterology outpatient clinic.

  10. Fecal calprotectin as a biomarker of inflammatory lesions of the small bowel seen by videocapsule endoscopy

    Directory of Open Access Journals (Sweden)

    Juan Egea-Valenzuela

    2015-04-01

    Full Text Available Introduction: The levels of calprotectin in the stools are proportional to neutrophil activity in the enteric lumen, so fecal calprotectin is a useful intestinal inflammatory biomarker. It is an extended tool as predictor of colonic pathology but there is scare evidence about its utility in the small bowel. Objective: To test the yield of fecal calprotectin to detect lesions in the small bowel. Material and methods: We have retrospectively included 71 patients sent for small bowel capsule endoscopy in study for suspected inflammatory bowel disease. All of them had a determination of fecal calprotectin and had been sent to colonoscopy with no findings. Patients have been divided in groups: A, fecal calprotectin 100 µg/g, and we have analyzed which of them presented inflammatory lesions in capsule endoscopy studies. Results: The rate of patients with signi ficative lesions was 1 out of 10 (10% in group A, 6 out of 24 (25% in group B, and 21 out of 34 (62% in group C. If we consider levels over 50 µg/g pathologic, fecal calprotectin presents sensitivity: 96%, specificity: 23%, NPV: 90% and PPV: 56%. If we consider levels over 100 µg/g pathologic these values are sensitivity: 75%, specificity: 67%, NPV: 79% and PPV: 62%. Conclusions: Fecal calprotectin has high sensitivity but not so good specificity for predicting small bowel lesions after a normal colonoscopy. In daily practice it will be more useful to establish in 100 µg/g the limit to indicate capsule endoscopy studies.

  11. Salmonella spp. fecal shedding detected by real-time PCR in competing endurance horses.

    Science.gov (United States)

    Fielding, C Langdon; Meier, Chloe A; Magdesian, K Gary; Pusterla, Nicola

    2013-09-01

    Fecal shedding of Salmonella spp. was recently documented in 8% of endurance horses presented to equine referral centers for colic. Previous studies have documented fecal shedding of Salmonella spp. in as few as 0.8% of the general horse population, although horses with colic appear to be at higher risk. Fecal Salmonella spp. shedding before and after endurance horse competitions has not been evaluated. Fecal samples were collected from 204 horses during three separate 100 mile endurance competitions. Following incubation in selenite broth, 289 fecal samples were tested by real-time PCR analysis for Salmonella spp. Only one post-race sample (0.5% tested positive for Salmonella spp. in this study and no pre-race sample was available from this horse. Results suggest that fecal shedding of Salmonella spp. is uncommon in endurance horses during competitions. Further research is needed to confirm and identify the source of Salmonella spp. infection in endurance horses with colic requiring treatment at referral centers.

  12. Virulence genotypes of Escherichia coli canine isolates from pyometra, cystitis and fecal origin.

    Science.gov (United States)

    Mateus, Luisa; Henriques, Sofia; Merino, Carolina; Pomba, Constança; Lopes da Costa, Luís; Silva, Elisabete

    2013-10-25

    Pyometra is the most common diestrual uterine disease of bitches. Escherichia coli is the most frequent bacterium isolated from the uterine content of pyometra uteri and it is associated with the most severe clinical signs, leading to endotoxemia and sepsis. In this study, canine E. coli isolates from pyometra (n=31), cystitis (n=23) and fecal (n=26) origin were compared regarding the prevalence of 23 potential virulence traits (15 virulence factor (VF) genes and 8 pathogenicity associated islands-PAIs), detected by PCR assays. Overall, there was a considerable overlap between pyometra, cystitis and fecal isolates regarding the phylogenetic grouping and virulence traits. Virulence traits more prevalent in pyometra than in cystitis and fecal isolates included two PAIs (PAI IV536 and PAI ICFT073) and three VF genes (sfa/focDE, fyuA and chuA). Regardless the isolates' origin, the average number of virulence traits per strain was higher in B2 than in the other phylogenetic groups (A, B1 and D). The prevalence of phylogenetic group B2 was significantly higher in pyometra (94%) than in cystitis (48%) and fecal (39%) isolates. In conclusion, pyometra isolates have a high potential of virulence and a broad virulence genotype, although being similar to a subset of cystitis and fecal isolates. This leads to the suggestion that cystitis and fecal isolates may be able to induce pyometra in receptive hosts.

  13. Temporary Fecal Diversion in the Management of Colorectal and Perianal Crohn’s Disease

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    Rudolf Mennigen

    2015-01-01

    Full Text Available Aim. To evaluate the results of temporary fecal diversion in colorectal and perianal Crohn’s disease. Method. We retrospectively identified 29 consecutive patients (14 females, 15 males; median age: 30.0 years, range: 18–76 undergoing temporary fecal diversion for colorectal (n=14, ileal (n=4, and/or perianal Crohn’s disease (n=22. Follow-up was in median 33.0 (3–103 months. Response to fecal diversion, rate of stoma reversal, and relapse rate after stoma reversal were recorded. Results. The response to temporary fecal diversion was complete remission in 4/29 (13.8%, partial remission in 12/29 (41.4%, no change in 7/29 (24.1%, and progress in 6/29 (20.7%. Stoma reversal was performed in 19 out of 25 patients (76% available for follow-up. Of these, the majority (15/19, 78.9% needed further surgical therapies for a relapse of the same pathology previously leading to temporary fecal diversion, including colorectal resections (10/19, 52.6% and creation of a definitive stoma (7/19, 36.8%. At the end of follow-up, only 4/25 patients (16% had a stable course without the need for further definitive surgery. Conclusion. Temporary fecal diversion can induce remission in otherwise refractory colorectal or perianal Crohn’s disease, but the chance of enduring remission after stoma reversal is low.

  14. Assessment of Fecal Contamination in Oklahoma Water Systems through the Use of Sterol Fingerprints

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    Yueming Lu

    2016-11-01

    Full Text Available Fecal contamination is a major concern for water quality management, since the fecal materials are associated with pathogens that can cause illness wherever water is used for recreational, drinking and aquaculture purposes. In order to monitor source(s of fecal contamination in Oklahoma water systems, sterol profiles were previously examined in rural and urban samples collected from the Illinois River Basin and the Norman Wastewater Treatment Plant (WWTP, respectively. Two distinctive, qualitatively and quantitatively, sterol fingerprints were recognized. Despite the effective removal of organic material by the Norman WWTP, human-derived sterol fingerprints, characterized by a predominance of fecal stanols such as coprostanol, were still significant in the output from the plant. The source of fecal material in the Illinois River samples (rural was defined as being characteristic of corn-feed chicken manure originating from surrounding feedlots through the principal component analysis (PCA of the sterol distributions and carbon compound specific isotope analysis of selected sterols (CSIA, δ13C. Thiosteranes, formed during sludge treatments, were also shown to be useful tracers for monitoring sludge application in agriculture fields. The results obtained were used to provide water management authorities with qualitative insights into the source of fecal material inputs into the environment.

  15. Multiple modes of water quality impairment by fecal contamination in a rapidly developing coastal area: southwest Brunswick County, North Carolina.

    Science.gov (United States)

    Cahoon, Lawrence B; Hales, Jason C; Carey, Erin S; Loucaides, Socratis; Rowland, Kevin R; Toothman, Byron R

    2016-02-01

    Fecal contamination of surface waters is a significant problem, particularly in rapidly developing coastal watersheds. Data from a water quality monitoring program in southwest Brunswick County, North Carolina, gathered in support of a regional wastewater and stormwater management program were used to examine likely modes and sources of fecal contamination. Sampling was conducted at 42 locations at 3-4-week intervals between 1996 and 2003, including streams, ponds, and estuarine waters in a variety of land use settings. Expected fecal sources included human wastewater systems (on-site and central), stormwater runoff, and direct deposition by animals. Fecal coliform levels were positively associated with rainfall measures, but frequent high fecal coliform concentrations at times of no rain indicated other modes of contamination as well. Fecal coliform levels were also positively associated with silicate levels, a groundwater source signal, indicating that flux of fecal-contaminated groundwater was a mode of contamination, potentially elevating FC levels in impacted waters independent of stormwater runoff. Fecal contamination by failing septic or sewer systems at many locations was significant and in addition to effects of stormwater runoff. Rainfall was also linked to fecal contamination by central sewage treatment system failures. These results highlight the importance of considering multiple modes of water pollution and different ways in which human activities cause water quality degradation. Management of water quality in coastal regions must therefore recognize diverse drivers of fecal contamination to surface waters.

  16. Assessing Transmission of Salmonella to Bovine Peripheral Lymph Nodes upon Horn Fly Feeding.

    Science.gov (United States)

    Olafson, Pia Untalan; Brown, Tyson R; Lohmeyer, Kimberly H; Harvey, Roger B; Nisbet, David J; Loneragan, Guy H; Edrington, Thomas S

    2016-07-01

    Biting arthropods are implicated in the transdermal transmission of Salmonella to bovine peripheral lymph nodes, and such contamination can contribute to increased Salmonella prevalence in processed beef. Since horn flies can acquire Salmonella and then excrete the bacteria in their feces, on-animal fly infestations were conducted in this study to assess whether horn flies have a role in this bacterial transmission. Three Salmonella serotypes were used to assess fly acquisition from and excretion onto cattle. The results indicated that flies can acquire Salmonella from the hide, as assessed by recovery from homogenates of surfacesterilized flies, and that Salmonella persists for at least 5 days in the fly. Fly fecal excreta serves as a bacterial contaminant on the hide, and the overall mean probable estimate of the quantity shed was ≈10(5) most probable number per fly cage area. In 5 days, no transmission of the bacteria to bovine peripheral lymph nodes was evident, prompting an assessment of the effects of prolonged horn fly feeding on transmission. Three groups of animals were infested with flies that had consumed a blood meal containing Salmonella Senftenberg. After 5 days, the study was either terminated or the flies were removed and the cages replenished with unfed flies either once or twice over the course of an 11- or 19-day fly exposure period, respectively. A microlancet-inoculated positive-control animal was included in each group for comparison. The impact of prolonged horn fly feeding was evident, as 8% of lymph nodes cultured were positive from the 5-day exposure, whereas 50 and 42% were positive from 11- and 19-day exposures, respectively. Higher concentrations of Salmonella were recovered from fly-infested animals than from the microlancet-inoculated control, likely a result of repeated inoculations over time by flies versus a single introduction. The data described provide new insights into the transmission dynamics of Salmonella in cattle

  17. Fecal Collection and Stabilization Methods for Improved Fecal DNA Test for Colorectal Cancer in a Screening Setting

    Directory of Open Access Journals (Sweden)

    Francesca Maria Carozzi

    2013-01-01

    Full Text Available Early detection of CRC and adenomas reduces CRC-related mortality. The optimal screening test for CRC is still a subject of debate, and molecular stool sample analysis could provide a valid alternative to conventional methods in terms of compliance and practicability. Seven fecal DNA storage systems were evaluated in two successive phases. In the first phase of the study was selected the preservative buffer able to ensure the best human DNA recovery. In the second phase was evaluated human DNA stability, amplificability and integrity in DNA extracted from selected buffer. Results showed that the best performance was obtained in samples stored in 100 mM EDTA buffer and Genefec buffer. Likewise buffer addition yielded a significant increase in DNA stability and integrity without PCR inhibition, compared to the matched aliquots with no buffer added. Our study shows that samples collected in stabilization solution stabilize DNA so that intact nucleic acids, are more effectively detectable in the molecular assay. DNA buffer preservation and storage conditions could be useful to guarantee the most consistent yield in human DNA. Stabilization buffer addition to stool samples prior to transport presents an easily implemented solution that appears to be highly effective. Overall DNA extracted from faeces preserved in preservative buffer can feasibility been used for molecular analysis leading to an increase of assay sensitivity.

  18. Development of a multiplex real-time PCR for the simultaneous detection of herpes simplex and varicella zoster viruses in cerebrospinal fluid and lesion swab specimens.

    Science.gov (United States)

    Wong, Anita A; Pabbaraju, Kanti; Wong, Sallene; Tellier, Raymond

    2016-03-01

    Herpes simplex viruses (HSV) and varicella zoster virus (VZV) can have very similar and wide-ranging clinical presentations. Rapid identification is necessary for timely antiviral therapy, especially with infections involving the central nervous system, neonates, and immunocompromised individuals. Detection of HSV-1, HSV-2 and VZV was combined into one real-time PCR reaction utilizing hydrolysis probes. The assay was validated on the LightCycler(®) (Roche) and Applied Biosystems 7500 Real-Time PCR System (Thermo Fisher Scientific Inc.) to detect alphaherpesviruses in cerebral spinal fluid (CSF) and lesion swab specimens, respectively. Validation data on blood and tissue samples are also presented. The multiplex assay showed excellent sensitivity, specificity and reproducibility when compared to two singleplex real-time PCR assays for CSF samples and direct fluorescent antigen/culture for lesion swab samples. Implementation of the multiplex assay has facilitated improved sensitivity and accuracy as well as reduced turn-around-times and costs. The results from a large data set of 16,622 prospective samples tested between August 16, 2012 to February 1, 2014 at the Provincial Laboratory for Public Health (Alberta, Canada) are presented here.

  19. Microbial profiling of cpn60 universal target sequences in artificial mixtures of vaginal bacteria sampled by nylon swabs or self-sampling devices under different storage conditions.

    Science.gov (United States)

    Schellenberg, John J; Oh, Angela Yena; Hill, Janet E

    2017-05-01

    The vaginal microbiome is increasingly characterized by deep sequencing of universal genes. However, there are relatively few studies of how different specimen collection and sample storage and processing influence these molecular profiles. Here, we evaluate molecular microbial community profiles of samples collected using the HerSwab™ self-sampling device, compared to nylon swabs and under different storage conditions. In order to minimize technical variation, mixtures of 11 common vaginal bacteria in simulated vaginal fluid medium were sampled and DNA extracts prepared for massively parallel sequencing of the cpn60 universal target (UT). Three artificial mixtures imitating commonly observed vaginal microbiome profiles were easily distinguished and proportion of sequence reads correlated with the estimated proportion of the organism added to the artificial mixtures. Our results indicate that cpn60 UT amplicon sequencing quantifies the proportional abundance of member organisms in these artificial communities regardless of swab type or storage conditions, although some significant differences were observed between samples that were stored frozen and thawed prior to DNA extraction, compared to extractions from samples stored at room temperature for up to 7days. Our results indicate that an on-the-market device developed for infectious disease diagnostics may be appropriate for vaginal microbiome profiling, an approach that is increasingly facilitated by rapidly dropping deep sequencing costs.

  20. Dietary fiber supplementation for fecal incontinence: a randomized clinical trial.

    Science.gov (United States)

    Bliss, Donna Z; Savik, Kay; Jung, Hans-Joachim G; Whitebird, Robin; Lowry, Ann; Sheng, Xiaoyan

    2014-10-01

    Dietary fiber supplements are used to manage fecal incontinence (FI), but little is known about the fiber type to recommend or the level of effectiveness of such supplements, which appears related to the fermentability of the fiber. The aim of this single-blind, randomized controlled trial was to compare the effects of three dietary fiber supplements (carboxymethylcellulose [CMC], gum arabic [GA], or psyllium) with differing levels of fermentability to a placebo in community-living individuals incontinent of loose/liquid feces. The primary outcome was FI frequency; secondary outcomes included FI amount and consistency, supplement intolerance, and quality of life (QoL). Possible mechanisms underlying supplement effects were also examined. After a 14-day baseline, 189 subjects consumed a placebo or 16 g total fiber/day of one of the fiber supplements for 32 days. FI frequency significantly decreased after psyllium supplementation versus placebo, in both intent-to-treat and per-protocol mixed model analyses. CMC increased FI frequency. In intent-to-treat analysis, the number of FI episodes/week after supplementation was estimated to be 5.5 for Placebo, 2.5 for Psyllium, 4.3 for GA, and 6.2 for CMC. Only psyllium consumption resulted in a gel in feces. Supplement intolerance was low. QoL scores did not differ among groups. Patients with FI may experience a reduction in FI frequency after psyllium supplementation, and decreased FI frequency has been shown to be an important personal goal of treatment for patients with FI. Formation of a gel in feces appears to be a mechanism by which residual psyllium improved FI.