Bovine Feces Research Articles

Phylogenetic analysis of Bacteroidales 16S rRNA gene sequences from human and animal effluents and assessment of ruminant faecal pollution by real‐time PCR

The aims of this study were to evaluate the host-specific distribution of Bacteroidales 16S rRNA gene sequences from human- and animal-related effluents and faeces, and to define a ruminant-specific marker. Bacteroidales 16S rRNA gene clone libraries were constructed from samples of effluent (sewage, bovine manure and pig slurry) and faeces (human, bovine, pig and wild bird), using PCR primers targeting order Bacteroidales. The phylogenetic analysis revealed six main distinct human-, bovine-, pig- and wild bird-specific clusters. From the bovine-specific cluster II, we designed a ruminant-specific marker, Rum-2-Bac, and this showed 97% sensitivity (n=30) and 100% specificity (n=40) when tested by TaqMan real-time PCR. Average concentrations of this marker in bovine and sheep faeces and in bovine manure were 8.2+/-0.5, 8.4+/-1.3 and 7+/-0.5 log10 copies per gram, respectively. It was also quantified in samples of runoff water impacted by bovine manure, with average concentrations of 5.1+/-0.3 log10 copies per millilitre water. Our results confirmed that some members of Bacteroidales isolated from effluents and faeces had host-specific distributions. Identification of a bovine-specific cluster made it possible to design a reliable ruminant-specific marker. The host-specific distribution of Bacteroidales sequences from effluents mirrored the host-specific distribution of sequences observed in individual faeces. This efficient new ruminant-specific Bacteroidales 16S rRNA marker represents a useful addition to the microbial source tracking toolbox.

Development of novel IC-ELISA as a primary high throughput screening for various estrogen molecules

An indirect competitive enzyme-linked immunosorbent assay (IC-ELISA) has been developed for detecting estrogen molecules in environmental samples. For generating anti-estrogen monoclonal antibody (mAb), BALB/c mice were immunized with 17-estra-diol (E2)-BSA and 5760 hybridoma cell lines were established. Through the optimization processes, a mAb(4BSA-e 3C11) and estriol(E3)-BSA were finally selected as a primary antibody and a coating antigen, respectively. The IC50 value for a standard estrogen (17β-E2) was 6.26 ng mL− and the detection range (20–80% B/B0) was 0.01–377.92ng mL−. The developed IC-ELISA showed some cross-reactivities (CRs) to various estrogen analogues, such as estrone (E1) (1.79%), E3(77.34%), 16-epiestriol(27.54%) and 16 keto-17β-E2(2.02%). On the other hand, the assay showed a negligible CRs to other steroid hormones (CR5<0.063%), suggesting the specificity of the assay to estrogen molecules. For assay validation, the developed IC-ELISA was compared side by side with high performance liquid chromatography (HPLC), which showed no significant difference in their performances between the two methods. The sensitivity of our IC-ELISA was approximately 100 fold higher than that of HPLC. The estrogen contents (Estrogen Equivalent Concentrations; EEC) in field samples were determined using the IC-ELISA, including swine sewage effluents (7.043 ± 0.023 ng-EEC mL−1), bovine feces (0.013±0.001 ng-EEC mL−1), and avian feces (0.017±0.001 ng-EEC mL−). Conclusively, we have developed an IC-ELISA that is highly sensitive to estrogens as well as can detect various estrogen analogues at the same time. This assay can be used as a primary screening for a large number of field samples before the instrumental analysis that is laborintensive and time-consuming.

Performance Assessment PCR-Based Assays Targeting Bacteroidales Genetic Markers of Bovine Fecal Pollution

There are numerous PCR-based assays available to characterize bovine fecal pollution in ambient waters. The determination of which approaches are most suitable for field applications can be difficult because each assay targets a different gene, in many cases from different microorganisms, leading to variation in assay performance. We describe a performance evaluation of seven end-point PCR and real-time quantitative PCR (qPCR) assays reported to be associated with either ruminant or bovine feces. Each assay was tested against a reference collection of DNA extracts from 247 individual bovine fecal samples representing 11 different populations and 175 fecal DNA extracts from 24 different animal species. Bovine-associated genetic markers were broadly distributed among individual bovine samples ranging from 39 to 93%. Specificity levels of the assays spanned 47.4% to 100%. End-point PCR sensitivity also varied between assays and among different bovine populations. For qPCR assays, the abundance of each host-associated genetic marker was measured within each bovine population and compared to results of a qPCR assay targeting 16S rRNA gene sequences from Bacteroidales. Experiments indicate large discrepancies in the performance of bovine-associated assays across different bovine populations. Variability in assay performance between host populations suggests that the use of bovine microbial source-tracking applications will require a priori characterization at each watershed of interest.

Lyophilization Prior to Direct DNA Extraction from Bovine Feces Improves the Quantification of Escherichia coli O157:H7 and Campylobacter jejuni

Lyophilization was used to concentrate bovine feces prior to DNA extraction and analysis using real-time PCR. Lyophilization significantly improved the sensitivity of detection compared to that in fresh feces and was associated with reliable quantification of both Escherichia coli O157:H7 and Campylobacter jejuni bacteria present in feces at concentrations ranging between 2 log(10) and 6 log(10) CFU g(-)(1).

Effect of Daily Temperature Fluctuation during the Cool Season on the Infectivity of Cryptosporidium parvum

The present work calculated the rate of inactivation of Cryptosporidium parvum oocysts attributable to daily oscillations of low ambient temperatures. The relationship between air temperature and the internal temperature of bovine feces on commercial operations was measured, and three representative 24-h thermal regimens in the approximately 15 degrees C, approximately 25 degrees C, and approximately 35 degrees C ranges were chosen and emulated using a thermocycler. C. parvum oocysts suspended in deionized water were exposed to the temperature cycles, and their infectivity in mice was tested. Oral inoculation of 10(3) treated oocysts per neonatal BALB/c mouse (approximately 14 times the 50% infective dose) resulted in time- and temperature-dependent reductions in the proportion of infected mice. Oocysts were completely noninfectious after 14 24-h cycles with the 30 degrees C regimen and after 70 24-h cycles with the 20 degrees C regimen. In contrast, oocysts remained infectious after 90 24-h cycles with the 10 degrees C regimens. The estimated numbers of days needed for a 1-log(10) reduction in C. parvum oocyst infectivity were 4.9, 28.7, and 71.5 days for the 30, 20, and 10 degrees C thermal regimens, respectively. The loss of infectivity of oocysts induced by these thermal regimens was due in part to partial or complete in vitro excystation.

DNA extraction from bovine faeces: current status and future trends

There is an increasing interest in the detection and enumeration of micro-organisms pathogenic for human and present in bovine faeces. This interest is because pollution of the environment by animal faeces may affect the safety of food and of drinking or recreational water. Detection and quantification of microbial pathogens carried out using DNA extracted from the faecal matrix are affected by the quality and the quantity of the DNA extracts, which are critical factors that limit the accuracy and sensitivity of molecular studies. This review compares published methods on DNA extraction from bovine faeces, focusing on the extent to which the success of DNA amplification is affected by issues related to the faeces. Following a general discussion on the DNA extraction methods used for faeces, we focus particularly on issues related to the faecal environment itself. The objective is to identify information that can be used to improve the sensitivity of those PCR methods used after direct DNA extraction.

Efficiency of entomopathogenic fungi in the control of eggs and larvae of the horn fly Haematobia irritans (Diptera: Muscidae)

The present study assessed the pathogenic effect of isolates E9, IBCB425 and IBCB159 of the Metarhizium anisopliae fungus, JAB06, JAB07 and AM09 of Beauveria bassiana, IBCB133 and CB75 of Isaria fumosorosea (= Paecilomyces fumosoroseus) and CG189 and CG195 of Isaria farinosa (= Paecilomyces farinosus) against eggs and larvae of the horn fly Haematobia irritans. Eggs were inoculated with suspensions containing 10 6, 10 7 and 10 8 conidia ml −1 of the fungal isolates and observed after 48 h to determine viability. In the larvae study, eggs were allowed to hatch into fresh bovine feces that had been treated with 10 8, 10 7 or 10 6 conidia mg feces −1. In both studies, 5 days after initial procedures, all formed pupae were transferred to an incubator at 27 ± 0.5 °C until the emergence of the adult flies was complete. The M. anisopliae isolates did not cause the death of H. irritans eggs, but they did promote the death of larvae that hatched from treated eggs, and therefore increased the total mortality. Isolate E9 promoted 100% mortality of treated larvae at a concentration of 10 8 conidia ml −1. For the B. bassiana isolates, no activity was observed against insect eggs or larvae. Both I. fumosorosea isolates promoted significant mortality ( p < 0.05) of eggs at every concentration of conidia. Isolate CG195 of I. farinosa increased the mortality of larvae and pupae that hatched from treated eggs and promoted significant total mortality ( p < 0.05) of the insect at every concentration of conidia.

Recovery of antimicrobial-resistantEscherichia coliafter storage of bovine feces in Cary–Blair medium

The effect of storing bovine feces in Cary-Blair medium on the recovery of antimicrobial-resistant Escherichia coli was investigated. Feces from cattle at a research feedlot (n = 50) and at a commercial feedlot (n = 46) were processed immediately or after storage in Cary-Blair medium for 8 days at 5 degrees C. Total, ampicillin-resistant, and tetracycline-resistant E. coli were isolated. The number of total E. coli decreased slightly after storage (0.19 log units; p < 0.001), but storage of feces in Cary-Blair medium did not affect recovery of ampicillin- or tetracycline-resistant E. coli.

Susceptibilidade do besouro rola-bosta africano a reguladores de crescimento de insetos

Verificou-se a ação dos reguladores de crescimento de insetos (IGR), diflubenzuron e methoprene, sobre o besouro rola-bosta africano, Digitonthophagus gazella (Fabricius), um inimigo natural da mosca-dos-chifres, Haematobia irritans irritans (Linnaeus). Casais de besouros foram colocados em baldes contendo terra úmida e alimentados com fezes bovinas contendo 1, 0,5 ou 0,2ppm de diflubenzuron e 0,2ppm de methoprene. Os insetos e sua prole foram recuperados com o auxílio de armadilhas pitfall. Diflubenzuron e methoprene não afetaram a sobrevivência dos adultos inicialmente expostos, mas interferiram na produção de descendentes. Diflubenzuron, nas concentrações de 1 e 0,5ppm, também afetou a duração do ciclo de vida dos besouros. Nenhum dos IGRs alterou a razão sexual dos descendentes obtidos. As concentrações testadas de diflubenzuron mostraram-se moderadamente nocivas ao besouro enquanto methoprene a 0,2ppm mostrou ser pouco nocivo, segundo os critérios da International Organization for Biological Control.

THE DIRECT SALE OF RAW MILK: PREVALENCE OF PATHOGENS IN RAW MILK AND BOVINE FAECES COLLECTED IN FARMS WITHIN THE PROVINCE OF PESARO-URBINO

In the last years, direct sale of raw milk by vending machines has largely increased in several European Countries and Italy. As a consequence, adequate hygienic measures and correct consumer’s information is required in order to reduce any potential risk linked to this product. In the present study, the occurrence of pathogens (Salmonella spp., verocytotoxigenic E.coli, Campylobacter spp., Listeria monocytogenes, S.aureus) in raw milk and bovine faeces collected in 4 farms in the province of Pesaro-Urbino (Italy), between January 2007 and March 2009 has been investigated; 99.5% of milk samples resulted negative for the pathogens considered and complying with the regulation S. aureus limits. Campylobacter has been found in 0.44% of the samples, collected during summer, while only one sample resulted positive to a non-verocytotoxigenic E.coli O157. In respect to faeces, 62.6% of the samples resulted negative, 33.6% were contaminated by Campylobacter spp. (68% Campylobacter coli and 32% Campylobacter jejuni) and 3.8% by E.coli O157. No samples resulted positive for Salmonella spp. or Listeria monocytogenes. The results highlight the necessity of a strict plan of hygienic and sanitary controls, with particular attention to milking process hygiene and raw milk storage, to reduce the risk of contamination of the product.

Phylogenetic analysis and characterization of Korean bovine viral diarrhea viruses

Thirty-six bovine viral disease viruses (BVDVs) were identified in bovine feces (n=16), brains (n=2), and aborted fetuses (n=18) in Korea. To reveal the genetic diversity and characteristics of these Korean strains, the sequences of their 5′-untranslated regions (5′-UTRs) were determined and then compared with published reference sequences. Neighbor-joining phylogenetic analysis revealed that most of the Korean viruses were of the BVDV subtypes 1a (n=17) or 2a (n=17). The remaining strains were of subtypes 1b (n=1) and 1n (n=1). This analysis indicates that the 1a and 2a BVDV subtypes are predominant and widespread in Korea. In addition, the prevalence of BVDV-2 was markedly higher in aborted fetuses than in other samples and was more often associated with reproductive problems and significant mortality in cattle.

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

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 μg ml −1 of ceftiofur. The cultures were incubated with 5 μg 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 μg ml −1 ceftiofur in broth cultures in less than 24 h; 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 β-lactams, and a nitrocefin assay showed β-lactamase activity in the 17 strains that metabolized ceftiofur. The results show that some β-lactamase-producing bacteria from the bovine fecal microflora are capable of transforming ceftiofur to metabolites lacking bactericidal activity.

Development and Application of a Fecal Antigen Diagnostic Sandwich ELISA for Estimating Prevalence of Fasciola gigantica in Cattle in Central Java, Indonesia

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.

Do microbial interactions and cultivation media decrease the accuracy of Salmonella surveillance systems and outbreak investigations?

Cultivation methods are commonly used in Salmonella surveillance systems and outbreak investigations, and consequently, conclusions about Salmonella evolution and transmission are highly dependent on the performance characteristics of these methods. Past studies have shown that Salmonella serotypes can exhibit different growth characteristics in the same enrichment and selective media. This could lead not only to biased conclusions about the dominant strain present in a sample with mixed Salmonella populations, but also to a low sensitivity for detecting a Salmonella strain in a sample with only a single strain present. The objective of this study was to determine whether cultivation media select preferentially for specific strains of Salmonella in heterogeneous cultures. In this study, four different Salmonella strains (one Salmonella Newport, two Salmonella Typhimurium, and one Salmonella Enteritidis) were competed in a broth-based experiment and a bovine fecal experiment with varied combinations and concentrations of each strain. In all experiments, the strain of Salmonella Newport was the most competitive, regardless of the starting concentration and cultivation protocol. One strain of Salmonella Typhimurium was rarely detected in competition, even when it was the only strain present in bovine feces. Overall, the probability of detecting a specific Salmonella strain had little to do with its starting concentration in the sample. The bias introduced by culture could be dramatically biasing Salmonella surveillance systems and hindering traceback investigations during Salmonella outbreaks. Future studies should focus on the microbiological explanations for this Salmonella interstrain variability, approaches for minimizing the bias, and estimations of the public health significance of this bias.

Detection and identification by PCR of Clostridium chauvoei in clinical isolates, bovine faeces and substrates from biogas plant

BackgroundClostridium chauvoei causes blackleg, an acute disease associated with high mortality in ruminants. The apparent primary port of entry is oral, during grazing on pasture contaminated by spores. Cases of blackleg can occur year after year on contaminated pastures. A method to determine the prevalence of C. chauvoei spores on pasture would be useful.The standard method for C. chauvoei detection is culture and biochemical identification, which requires a pure culture. In most muscle samples from cattle dead from blackleg the amount of C. chauvoei in samples is high and the bacterium can easily be cultured, although some samples may be contaminated. Detection by PCR would be faster and independent of contaminating flora.Digested residues from biogas plants provide an excellent fertiliser, but it is known that spore-forming baeria such as Clostridium spp. are not reduced by pasteurisation. The use of digested residues as fertiliser may contribute to the spread of C. chauvoei. Soil, manure and substrate from biogas plants are contaminated with other anaerobic bacteria which outgrow C. chauvoei. Therefore, detection by PCR is would be useful. This study applied a PCR-based method to detect of C. chauvoei in 25 muscle and blood samples, 114 manure samples, 84 soil samples and 33 samples from the biogas process.MethodsMuscle tissues from suspected cases of blackleg were analysed both by the standard culture method followed by biochemical identification and by PCR, with and without preculture. To investigate whether muscle tissue samples are necessary, samples taken by swabs were also investigated. Samples from a biogas plant and manure and soil from farms were analysed by culture followed by PCR. The farms had proven cases of blackleg. For detection of C. chauvoei in the samples, a specific PCR primer pair complementary to the spacer region of the 16S-23S rRNA gene was used.ResultsClostridium chauvoei was detected in 32% of muscle samples analysed by culture with identification by biochemical methods and in 56% of cases by culture in combination with PCR. Clostridium chauvoei was detected in 3 (out of 11) samples from the biogas plants collected before pasteurisation, but samples taken after pasteurisation and after digestion all tested negative. Clostridium chauvoei was not detected in any soil or silage samples and only one manure samples tested positive.ConclusionThe diagnostic method used for C. chauvoei was not applicable in estimating the risk of blackleg on particular pastures from manure or soil samples, but found to be highly useful for clinical samples.

Escherichia coli O157:H7 strains isolated from environmental sources differ significantly in acetic acid resistance compared with human outbreak strains.

A number of studies on the influence of acid on Escherichia coli O157:H7 have shown considerable strain differences, but limited information has been reported to compare the acid resistance based on the different sources of E. coli O157:H7 isolates. The purpose of this study was to determine the survival of E. coli O157:H7 strains isolated from five sources (foods, bovine carcasses, bovine feces, water, and human) in 400 mM acetic acid solutions under conditions that are typical of acidified foods. The isolates from bovine carcasses, feces, and water survived acetic acid treatment at pH 3.3 and 30 degrees C significantly (P < or = 0.05) better than did any food or human isolates. However, resistance to acetic acid significantly increased as temperature decreased to 15 degrees C for a given pH, with little (P > or = 0.05) difference among the different isolation sources. All groups of E. coli O157:H7 strains showed more than 1.8- to 4.5-log reduction at pH 3.3 and 30 degrees C after 25 min. Significantly reduced (less than 1-log reduction) lethality for all E. coli O157:H7 strain mixtures was observed when pH increased to 3.7 or 4.3, with little difference in acetic acid resistance among the groups. The addition of glutamate to the acetic acid solution or anaerobic incubation provided the best protection compared with the above conditions for all groups of isolates. These results suggest that temperature, pH, and atmospheric conditions are key factors in establishing strategies for improving the safety of acidified foods.

Evaluation of the control of pathogen load by an anti-Salmonella bacterium in a herd of cattle with persistent Salmonella infection

To determine whether an anti-Salmonella bacterium is involved in control of pathogen load in persistently infected cattle herds. 24 Holstein calves experimentally infected and 39 Holstein cows naturally infected with Salmonella spp. An Escherichia coli (designated as P8E5) that possessed anti-Salmonella activity was isolated from Salmonella-negative bovine feces obtained from a herd with endemic Salmonella infection. In vitro analysis involved enumerating Salmonella enterica serovar Typhimurium coincubated with E coli P8E5. In vivo analysis involved coadministration of Salmonella spp and E coli P8E5 or an E coli control strain to neonatal Holstein calves. Fecal samples were collected on multiple days after inoculation, and quantitative PCR assay was performed by use of Salmonella-specific primers. E coli P8E5 reduced viability of Salmonella spp in vitro. Shedding of Salmonella organisms was diminished in calves administered E coli P8E5, whereas the control strain of E coli had no effect on shedding of Salmonella organisms. In this study, an E coli strain was identified that possessed bacteriocin-like activity and was able to decrease viability of Salmonella organisms in vitro and in vivo. Therefore, it is possible that this organism could be representative of native microbiota that dampen Salmonella spp in persistently infected cattle herds.

Reduction ofEscherichia coliO157:H7 in Cattle Drinking-Water bytrans-Cinnamaldehyde

Cattle serve as a major reservoir of E. coli O157:H7 and excrete the pathogen in feces. Environmental persistence of E. coli O157:H7 plays a vital role in its epidemiology on farms, and cattle water troughs are a demonstrated long-term reservoir of E. coli O157:H7 for animals. The objective of this study was to investigate the potential of low concentrations of trans-cinnamaldehyde for killing E. coli O157:H7 in cattle drinking-water. A five-strain mixture of E. coli O157:H7 was inoculated (at approximately 8.0 log colony-forming units [CFU]/mL) into 100 mL samples of well water containing 0, 0.03, 0.05, 0.07, or 0.1% trans-cinnamaldehyde. Additionally, water samples containing (1% w/v) bovine feces or feed were also included. The samples were incubated at 21 degrees , 8 degrees , or 4 degrees C for 7 days and tested for viable E. coli O157:H7 on days 0, 1, 3, 5, and 7. Triplicate samples of each treatment and control were included and the study was replicated twice. All concentrations of trans-cinnamaldehyde were effective in killing E. coli O157:H7 in water, but the magnitude of killing significantly increased with increase in trans-cinnamaldehyde concentration and storage temperature (p < 0.05). The presence of feed or feces in water decreased the antibacterial effect of trans-cinnamaldehyde on E. coli O157:H7 (p < 0.05). This study indicated that trans-cinnamaldehyde is effective in killing E. coli O157:H7 in cattle drinking-water, but detailed palatability studies on cattle intake of water containing the antimicrobial are needed.

Survival ofCampylobacterspp. in bovine faeces on pasture

To determine the survival on pasture of Campylobacter spp. naturally present in bovine faeces and compare this with a previously published study using laboratory-cultured Campylobacter spp. Ten freshly collected cow pats were deposited on pasture during summer, and Campylobacter spp. were enumerated by enrichment broth culture. The counts in three pats were below detection limits. Counts of Campylobacter spp. in the other seven pats fell below detection limits within 14 days. The geometric means of the counts up to 7 days produced a T(90) of 2.2 days. Characterization of Campylobacter spp. by PCR and pulsed field gel electrophoresis indicated the presence of at least six genotypes of Campylobacter jejuni, Campylobacter coli and Campylobacter lari. Campylobacter spp. naturally present in cow faeces exhibited a similar survival rate to that previously determined using laboratory-cultured strains. The highly variable counts of naturally occurring Campylobacter spp., and the predominance of lower counts, also support the earlier decision to use laboratory-cultured strains in survival experiments. This study reaffirms the short survival of Campylobacter spp. in cow faeces deposited on pasture. This information will be incorporated into a 'reservoir model' for Campylobacter spp. in cow pats on New Zealand pastures.

Selection, characterization, and application of DNA aptamers for the capture and detection of Salmonella enterica serovars

Sensitive and specific pre-analytical sample processing methods are needed to enhance our ability to detect and quantify food borne pathogens from complex food and environmental samples. In this study, DNA aptamers were selected and evaluated for the capture and detection of Salmonella enterica serovar. Typhimurium. A total of 66 candidate sequences were enriched against S. Typhimurium outer membrane proteins (OMPs) with counter-selection against Escherichia coli OMPs and lipopolysaccharides (LPS). Specificity of the selected aptamers was evaluated by gel-shift analysis against S. Typhimurium OMP. Five Salmonella-specific aptamer candidates were selected for further characterization. A dilution-to-extinction capture protocol using pure cultures of S. Typhimurium further narrowed the field to two candidates (aptamers 33 and 45) which showed low-end detection limits of 10–40 CFU. DNase protection assays applied to these aptamers confirmed sequence-specific binding to S. Typhimurium OMP preparations, while South-Western blot analysis combined with mass spectrometry identified putative membrane proteins as targets for aptamer binding. Aptamer 33 was bound to magnetic beads and used for the capture of S. Typhimurium seeded into whole carcass chicken rinse samples, followed by detection using quantitative real-time RT-PCR. In a pull-down assay format, detection limits were 10 1–10 2 CFU S. Typhimurium/9 mL rinsate, while in a recirculation format, detection limits were 10 2–10 3 CFU/25 mL rinsate. Reproducible detection at <10 1 S. typhimurium CFU/g was also achieved in spike-and-recovery experiments using bovine feces. The pull-down analysis using aptamer 33 was validated on 3 naturally infected chicken litter samples confirming their applicability in the field. This study demonstrates the applicability of Salmonella specific aptamers for pre-analytical sample processing as applied to food and environmental sample matrices.