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None of 50 healthy individuals and only 2 of 50 hospitalized patients (with Acinetobacter anitratus elsewhere) yielded A. anitratus on enrichment from fecal samples.
We describe a procedure for preparing fecal samples for determination of volatile fatty acids (VFAs) by gas-liquid chromatography (GLC) and "high-performance" liquid chromatography (HPLC). The simple, one-step procedure involves only ultrafiltration through a membrane with a molecular-mass cutoff of 3000 Da. As revealed by the GLC chromatograms, ultrafiltration appears to be as effective as steam distillation in sample clean-up. It also enables higher, more reproducible analytical recoveries of long-chain VFAs. The VFA content of the filtrate can also be measured by HPLC. Use of the ion-exclusion mechanism completely resolves isobutyric acid and butyric acid on a cation-exchange column. The mean (+/- SD) percentage distribution values of VFAs (measured by GLC) from five healthy subjects were 56.0 +/- 3.5 (acetic acid), 17.0 +/- 5.3 (propionic acid), 2.9 +/- 1.5 (isobutyric acid), 18.8 +/- 5.8 (butyric acid), 2.3 +/- 1.2 (isovaleric acid), and 2.9 +/- 0.8 (valeric acid).
The prevalence of Cryptosporidium sp. and Giardia sp. in fecal samples collected from free-ranging white-tailed deer (Odocoileus virginianus) was determined for animals in Virginia and Mississippi. The 34 Virginia samples came from young of the year (< or =6 months of age) presented to the Wildlife Center of Virginia, and the 360 Mississippi samples came from animals (> or =6 months of age) collected from 42 different sites across the state. Cryptosporidial oocysts were detected in 8.8% and 5.0% and Giardia sp. cysts were detected in 2.9% and 1.1% of the samples from Virginia and Mississippi, respectively. Analysis of data by collection site was not possible because of the small number of samples from some sites. Therefore, collection sites in Mississippi were grouped by the stream basin in which they occurred. Binary logistic regression analysis indicated the probability of infection with Cryptosporidium sp. decreased with increasing age of animal in all positive stream basins except 1, in which the pattern was reversed. This is the first report of either Cryptosporidium sp. or Giardia sp. in free-ranging white-tailed deer. The role of white-tailed deer in the epidemiology of these parasites is unknown. However, this study demonstrates that white-tailed deer shed cysts and oocysts of both parasites in the environment and must be considered potential sources of contamination.
We have developed a rapid and sensitive microimmunodot blot assay, the antigen spot test (AST), for the detection of bovine coronavirus (BCV) antigen from neonatal calf fecal samples. The AST procedure can be completed in 3.5 h, whereas the previously reported immunodot blot assays require 10 to 12 h. Ninety-six samples can be tested per membrane, and 10 membranes (960 samples) may be processed by a single technologist in 1 working day. The effects of detergents, oxidizing chemicals, chaotropic agents, and enzyme substrates in improving the sensitivity and signal-to-noise ratio of the AST were studied. Finally, the sensitivity and specificity of AST for the detection of BCV antigen were compared to those of a sandwich enzyme-linked immunosorbant assay (ELISA) and a hemagglutination assay (HA). Of 347 field samples tested by all three methods, 94.2% were positive by AST, 91.4% were positive by ELISA, and 86.7% were positive by HA. The sensitivity of the AST was determined to be 100% compared to the results of the ELISA reference method. The specificity of the AST was 67%, which reflects a lower limit of detection of 10(4) viral particles per ml in a 10% fecal suspension.
The occurrence and the further spread of high-level glycopeptide-resistant, vanA-positive Enterococcus faecium strains outside of hospitals have been investigated. We could isolate such bacteria directly from thawing liquids of commercially produced frozen poultry (chickens, turkeys; no further data on previous feeding with avoparcin were available). In 5 of 13 samples of raw minced meat of pigs originating from 13 different butcher's shops, glycopeptide-resistant E. faecium (VanA type) could be detected after overnight broth cultivation of these samples. No glycopeptide-resistant enterococci could be isolated from meat samples of chickens that were fed without avoparcin. VanA type E. faecium strains were also identified in 12 fecal samples recovered from 100 nonhospitalized humans in the rural area of Saxony-Anhalt federal county. These results suggest a possible role of the food chain in the spread of glycopeptide-resistant E. faecium. Molecular typing (macrorestriction and multilocus enzyme analysis) reveal a wide dissemination of the vanA gene among strains of different ecological origins.
The objective of this study was to describe the circulation of caliciviruses in the West Central region of Brazil and its correlation with children's gender and age, as well as with the year and months of the sample collection. Reverse transcriptase-polymerase chain reaction was performed to detect the human calicivirus genome in 1006 fecal samples that were collected in Goiânia (n = 696) and Brasília (n = 310). Viral RNA was detected in 8.6% of the samples. No significant difference in viral prevalence was found regarding gender, age or year of the sample. However, it was observed that in Goiânia, there is a higher incidence of caliciviruses from September to March. The analysis employing three primer pairs demonstrated that the Ni/E3 or JV12/13 primer pairs, which detect norovirus (NoV), detected 41 positive samples while the 289/290 primer pair, which detects NoV or sapovirus, detected the remaining 46 samples. Calicivirus circulates in the West Central region of Brazil and for better detection of this virus it is important to use more than one primer pair. Also, we conclude that the seasonality presented by this virus is related to higher humidity in the period.
Surveillance cultures for vancomycin-resistant enterococci (VRE) are time-consuming and expensive for the laboratory to perform. Therefore, we investigated the use of PCR as an alternative method of detecting and identifying VRE directly in fecal samples. PCR primers directed to vanA, vanB, vanC1, vanC2, and enterococcal ligase genes were used to detect and identify VRE in fecal material obtained by rectal or perirectal swabbing. Although PCR-inhibitory substances were present in DNA prepared directly from the swabs, the inhibitory substances could be reduced by processing the nucleic acid with two commercially available DNA preparation columns. Fecal material from 333 swabs was cultured on several selective agar media before and after broth enrichment. DNA was extracted from the fecal material and was analyzed by PCR. By using all four primer sets, only 59 (67.8%) of the samples were positive for vanA. However, after retesting the negative samples with only the vanA primer set, 77 (88.5%) of 87 specimens that were culture positive for Enterococcus faecium containing vanA were positive by PCR. One specimen was PCR positive for the vanA gene but culture negative for enterococci. The specificity of the vanA assay was 99.6%. PCR analysis of enrichment broth samples with all four primers sets after 15 to 18 h of incubation detected 74 (85.1%) of the 87 culture-positive specimens. The specificity of the vanA assay after the enrichment step was 100%. No vanB-containing enterococci were recovered by culture. Since 16 samples can be tested by PCR in 4 h (including electrophoresis), identification of VRE is possible within 8 h of specimen submission at a cost of approximately $10.12/assay. Thus, PCR may be a cost-effective alternative to culture for surveillance of VRE in some hospitals.
An automated PCR with fluorescent probes (molecular beacons) detected Mycobacterium avium subsp. paratuberculosis in bovine feces. When the PCR was compared with culture in testing 41 fecal samples, kappa scores of 0.94 to 0.96, a sensitivity of 93 to 96%, and a specificity of 92% were obtained. Results were quantitated by using a standard curve derived from a plasmid containing IS900. A minimum quantity of 1.7 x 10(-4) pg of DNA, correlating to 1 to 8 CFU, was detected.
Clostridium difficile is one of the most frequent causes of nosocomial gastrointestinal disease. Risk factors include prior antibiotic therapy, bowel surgery, and the immunocompromised state. Direct fecal analysis for C. difficile toxin B by tissue culture cytotoxin B assay (CBA), while only 60 to 85% sensitive overall, is a common laboratory method. We have used 1,003 consecutive, nonduplicate fecal samples to compare six commercially available immunoassays (IA) for C. difficile detection with CBA: Prima System Clostridium difficile Tox A and VIDAS Clostridium difficile Tox A II, which detect C. difficile toxin A; Premier Cytoclone A/B and Techlab Clostridium difficile Tox A/B, which detect toxins A and B; and ImmunoCard Clostridium difficile and Triage Micro C. difficile panels, which detect toxin A and a species-specific antigen. For all tests, Triage antigen was most sensitive (89.1%; negative predictive value [NPV] = 98.7%) while ImmunoCard was most specific (99.7%; positive predictive value [PPV] = 95.0%). For toxin tests only, Prima System had the highest sensitivity (82.2%; NPV = 98.0%) while ImmunoCard had the highest specificity (99.7%; PPV = 95.0%). Hematopoietic stem cell transplant (HSCT) patients contributed 44.7% of all samples tested, and no significant differences in sensitivity or specificity were noted between HSCT and non-HSCT patients. IAs, while not as sensitive as direct fecal CBA, produce reasonable predictive values, especially when both antigen and toxin are detected. They also offer significant advantages over CBA in terms of turnaround time and ease of use.
OBJECTIVE: To determine sources and amounts of variation in a kinetics ELISA (KELA) and results of culture of fecal samples for Mycobacterium avium subsp paratuberculosis (MAP) in repeated tests of individual cows. ANIMALS: 112 cows on 6 commercial dairy farms in New York. PROCEDURE: A nonrandom longitudinal study was conducted from January 2001 to March 2002. A KELA was performed monthly, and MAP culture was performed bimonthly. Cow- and herd-level data were collected. The KELA and culture results were analyzed by use of models that corrected for clustering within herds and repeated measures on cows. RESULTS: Cows of second or higher lactation had increased KELA values, compared with values for first-lactation cows. Cows had lowest KELA values during the first 15 days in milk; KELA values increased until 60 days in milk and then stabilized. Moderate and heavy shedders had significantly higher KELA values than culture-negative cows, and KELA values of shedders progressively increased over time. On average, the KELA value was significantly increased 132 days after a cow was first detected to be a moderate shedder and 236 days after a cow was first detected to be a low shedder. CONCLUSIONS AND CLINICAL RELEVANCE: Analysis suggests that KELA results vary on a cow-level on the basis of lactation number and stage of lactation. High KELA values indicate heavy fecal shedding, but the KELA is not useful in identifying low and moderate shedders that can require up to 236 days to have a significant increase in KELA value.
A protocol was developed for the analysis of volatile short chain fatty acids in microsamples of feces, short chain fatty acid (SCFA) extraction was from fecal samples using ethanol incorporating n-hexanoic acid as an internal standard. The SCFAs were converted to pentafluorobenzyl esters with alpha-2,3,4,5,6-pentafluorotoluene and analyzed on a gas-liquid chromatograph equipped with an electron capture detector. One hundred milligrams of sample was routinely used but analysis could be carried out on 20 mg of sample.
In an attempt to detect rotavirus and adenovirus prevalence among other enteropathogens (bacteria and parasites) in diarrhoea, three hundred fecal samples originating from children living in Goiânia city (Goiás state, Brazil) were analysed. Rotavirus was found to be the only pathogen in 47 cases, and associated with other infectious agents in 21 cases. 97.0% positive samples of rotavirus showed an electrophoretic pattern characteristic of subgroup II. Adenovirus was found in 7 cases, and associated with other microorganisms in 1 case. Three methods were applied for virological analyses: enzyme immunoassay for rotavirus and adenovirus (EIARA), polyacrylamide gel electrophoresis (PAGE) and immunoelectron microscopy (IEM). The concordance among the three methods was 92.8%, PAGE and EIARA agreed in 95.8%, and IEM and EIARA agreed in 100.0%.
Genes encoding the CMY-2, CTX-M-14, and SHV-12 beta-lactamases were detected in three of five Escherichia coli isolates from fecal samples from healthy chickens which showed resistance or diminished susceptibility to extended-spectrum cephalosporins. A -42 mutation at the promoter region of the ampC gene was detected in the other two isolates.
By an immunomagnetic-bead (IMB) separation technique, isolation of Helicobacter pylori from gastrointestinal and fecal samples of gnotobiotic mice infected with the microorganism was tried. The isolation rate of H. pylori from stomach samples after IMB separation was not higher than that of direct culture of the samples. After IMB separation of feces, H. pylori was detectable by PCR, although H. pylori was not culturable.
The diversity of the predominant bacteria in the human gastrointestinal tract was studied by using 16S rRNA-based approaches. PCR amplicons of the V6 to V8 regions of fecal 16S rRNA and ribosomal DNA (rDNA) were analyzed by temperature gradient gel electrophoresis (TGGE). TGGE of fecal 16S rDNA amplicons from 16 individuals showed different profiles, with some bands in common. Fecal samples from two individuals were monitored over time and showed remarkably stable profiles over a period of at least 6 months. TGGE profiles derived from 16S rRNA and rDNA amplicons showed similar banding patterns. However, the intensities of bands with similar mobilities differed in some cases, indicating a different contribution to the total active fraction of the prominent fecal bacteria. Most 16S rRNA amplicons in the TGGE pattern of one subject were identified by cloning and sequence analysis. Forty-five of the 78 clones matched 15 bands, and 33 clones did not match any visible band in the TGGE pattern. Nested PCR of amplified 16S rDNA indicated preferential amplification of a sequence corresponding to 12 of the 33 nonmatching clones with similar mobilities in TGGE. The sequences matching 15 bands in the TGGE pattern showed 91.5 to 98.7% homology to sequences derived from different Clostridium clusters. Most of these were related to strains derived from the human intestine. The results indicate that the combination of cloning and TGGE analysis of 16S rDNA amplicons is a reliable approach to monitoring different microbial communities in feces.
To investigate the occurrence of the flavonoid-degrading bacterium Eubacterium ramulus in the human intestinal tract, an oligonucleotide probe designated S-S-E.ram-0997-a-A-18 was designed and validated, with over 90 bacterial strains representing the dominant described human fecal flora. Application of S-S-E. ram-0997-a-A-18 to fecal samples from 20 subjects indicated the presence of E. ramulus in each individual tested in numbers from 4.4 x 10(7) to 2.0 x 10(9) cells/g of fecal dry mass. Six fecal E. ramulus isolates were recognized by S-S-E.ram-0997-a-A-18 but exhibited different band patterns when analyzed by randomly amplified polymorphic DNA.
Replica plating can be used for the detection of antibiotic resistance in normal flora. We have evaluated this application of the replica plating method by comparing it with a five-colony method. The replica plating method uses a single plate for each antibiotic, with a concentration just above that for borderline resistance. By the five-colony method, five colonies per sample were picked, chosen to represent all different colony morphologies present, and MICs were determined by a standard agar dilution method. The gram-negative, aerobic floras of 131 fecal samples were screened for resistance to ampicillin, cefuroxime, nalidixic acid, trimethoprim, sulfamethoxazole, and tetracycline by both methods. The rate of resistance detection by the two methods did not differ statistically for any of the antibiotics tested. The breakpoint concentrations used for the replica plates in the study gave results similar to those produced by the agar dilution method and the breakpoint values of the National Committee for Clinical Laboratory Standards and can thus be recommended. As the only currently used resistance detection method, replica plating facilitates an exact determination of the percentage of resistant colonies/total number of colonies (between 1 and 100%) in a sample. This revealed an uneven distribution, with only 23% of the samples having resistance frequencies in the range of 10 to 85%; usually, the resistant flora either was a small minority or was very dominant in samples with resistance. This phenomenon was present for all of the antibiotics.
The high sensitivity of PCR compared to the difficulties of fecal culture in sheep prompted the development of PCR protocols for detection of Mycobacterium avium subsp. paratuberculosis DNA in sheep feces. Although the PCR itself is well developed, and does not pose large technical problems, concentrating the bacteria from samples that may contain low numbers of bacilli using practical methods is still the main difficulty for the use of this technique. In this study, we describe an extraction protocol for the concentration and purification of M. avium subsp. paratuberculosis DNA from fecal samples and we compare it with other methods. The diagnostic performance of the freeze-boiling method was evaluated using a reference method [Vet. Rec. 134 (1994) 95] on fecal samples from a group of selected sheep from different flocks of known individual serological, pathological, and cultural paratuberculosis status. Using, as a reference, a combination of results in those conventional methods, the freeze-boiling PCR protocol showed a sensitivity of 94.1%, and a specificity of 92.3%.