Applicability of a multiplex PCR to detect O26, O45, O103, O111, O121, O145, and O157 serogroups of Escherichia coli in cattle feces1

Antimicrobial resistance and public and animal health risks associated with pathogenic Escherichia coli isolated from calves

We aimed to determine the antimicrobial susceptibility profile of pathogenic Escherichia coli strains isolated from fecal samples of calves and buffalo calves (2008-2013), in Minas Gerais, Brazil, as well as the frequency of O157 gene and strains carrying extended-spectrum beta-lactamases (ESBL) and mobile colistin resistance (mcr) genes. E. coli strains (n=518) were tested for susceptibility against ten antimicrobials. Tetracycline was the antimicrobial with the highest resistance rate (382/518), followed by ampicillin (321/518), sulfamethoxazole/trimethoprim (312/518), chloramphenicol (192/518), gentamicin (126/518), ciprofloxacin (148/518), cefazolin (89/518), colistin (54/518) and cefoxitin (34/518). Multidrug resistance (MDR) was observed in 381/518 isolates. No strain harbored mcr or O157 genes, whereas 19/99 were ESBL positive. The most prevalent pathotype and phylogroup were STEC and B1, respectively. Age, EHEC pathotype and resistance to aminoglycoside and cephem were significantly associated with MDR in the multivariate model. Overall, E. coli strains showed high rates of resistance to penicillin, tetracyclines and folate inhibitors, in addition to an alarming rate of MDR and ESBL-producing strains.

Study of the transfer of Shiga toxin-producing Escherichia coli during the slaughter of cattle using molecular typing combined with epidemiologic data

Investigation on the distribution and biological characteristics of Shiga-toxin producing Escherichia coli (STEC) during beef processing is essential for in-plant critical control points and food safety risk assessment. Serogroups and subtypes of stx genes of STEC strains isolated from beef processing lines were first investigated. Identification to cross-contamination among different sampling sites was further conducted by combining multilocus sequence typing (MLST) with the previous distribution and characterization data. The PCR-positive rate for STEC in 435 samples from two slaughter plants in China was 14.3% and the isolation rate for the 62 PCR positive and the entire set of 435 samples were 26% and 3.68% respectively. The existence of serotype O157:H7 (33%) and serogroups O121 (42%) and O26 (21%) as well as the high detection rate of high pathogenic gene stx2a (68%) in these serogroups indicated potential risk to the safety of beef. Traceability analysis showed that hide plays a critical role in cross-contamination between feces, lairage pens and post-washing carcasses from a molecular perspective. Intervening measures revolves around de-hiding should be involved in the in-plant safety control policy according to the tracing analysis.

Risk factors for diarrheagenic Escherichia coli infection in children aged 6-24 months in peri-urban community, Nairobi, Kenya

Escherichia coli commonly inhabits the gut of humans and animals as part of their microbiota. Though mostly innocuous, some strains have virulence markers that make them pathogenic. This paper presents results of a cross-sectional epidemiological study examining prevalence of diarrheagenic E. coli (DEC) pathotypes in stool samples of asymptomatic healthy children (n = 540) in Dagoretti South subcounty, Nairobi, Kenya. E. coli was cultured and pathotyped using PCR to target specific virulence markers associated with Shiga-toxin, enteropathogenic, enterotoxigenic, enteroaggregative, entero-invasive and diffusely adherent E. coli. Overall prevalence of DEC pathotypes was 20.9% (113/540) with enteropathogenic E. coli being the most prevalent (34.1%), followed by enteroaggregative E. coli (23.5%) and Shiga-toxin producing E. coli (22.0%) among positive samples. We found evidence of co-infection with multiple pathotypes in 15% of the positive samples. Our models indicated that at the household level, carriage of DEC pathotypes in children was associated with age group [12-18 months] (OR 1.78; 95%CI 1.03-3.07; p = 0.04), eating matoke (mashed bananas) (OR 2.32; 95%CI 1.44-3.73; p = 0.001) and pulses/legumes (OR 1.74; 95%CI 1.01-2.99; p = 0.046) while livestock ownership or contact showed no significant association with DEC carriage (p>0.05). Our findings revealed significant prevalence of pathogenic DEC circulating among presumptive healthy children in the community. Since there has been no previous evidence of an association between any food type and DEC carriage, unhygienic handling, and preparation of matoke and pulses/legumes could be the reason for significant association with DEC carriage. Children 12-18 months old are more prone to DEC infections due to exploration and hand-to-mouth behavior. A detailed understanding is required on what proportion of positive cases developed severe symptomatology as well as fatal outcomes. The co-infection of pathotypes in the rapidly urbanizing environment needs to be investigated for hybrid or hetero-pathotype circulation that have been implicated in previous infection outbreaks.

Evaluation of a Lactococcus lactis-based dried fermentation product administered through drinking water on nursery pig growth performance, fecal Escherichia coli virulence genes and pathotypes, antibiotic usage, and mortality

A total of 34,749 pigs were used in two experiments to evaluate the effects of a postbiotic dried fermentation product (DFP) administered through drinking water on nursery pig growth performance, antibiotic injection frequency, morbidity, mortality, fecal consistency, and characterization of fecal Escherichia coli. The DFP is composed of bioactive molecules derived from Lactococcus lactis. In Exp. 1, 350 barrows (DNA Line 200 × 400; initial body weight [BW] 6.1 ± 0.01 kg) were used in a 42-d study with five pigs per pen and 35 pens per treatment. The DFP was supplied for 14 d at a target dosage of 24 mg/kg BW using a water medicator at a 1:128 dilution. On days 7 and 14, fecal samples were collected for dry matter (DM) and to determine, by a multiplex polymerase chain reaction (PCR) assay, prevalence of 11 virulence genes characteristic of E. coli pathotypes. There was no evidence (P > 0.10) for differences for growth, incidence of diarrhea, number of antibiotic injections, removals, or fecal DM. On both fecal collection days, E. coli virulence genes were present with day 7 samples positive for genes that encode for hemolysins (hlyA, exhA), intimin (eae), and enteroaggregative heat-stable enterotoxin (astA). Prevalence of enterotoxin genes (elt, estA, estB, astA) increased on day 14, but DFP had no effects on the prevalence of any of the virulence genes. A total of 32 out of 72 E. coli isolates were identified as enterotoxigenic pathotype and all except one were from day 14 fecal samples. Fourteen isolates were positive for F4 fimbria and one isolate was positive for F4 and F18 fimbriae. In Exp. 2, 34,399 nursery pigs (initially 5.6 kg) were used in 20 nursery barns with 10 barns per treatment (control or DFP). The target dosage of the DFP for the first 14 d was 35 mg/kg BW. Following the 14-d supplementation period, pigs continued to be monitored for approximately 31 d. There was no evidence (P > 0.05) for the DFP to influence the overall percentage of pigs that died or growth performance. From days 0 to 14, providing the DFP reduced (P < 0.05) the percentage of pigs that were euthanized. However, providing the DFP increased (P < 0.05) the overall percentage of pigs that were euthanized and total mortality. For the number of antibiotic injections (treatment interventions), providing the DFP reduced the number of injections for the common period (P < 0.001) and overall (P = 0.002). These results indicate that the DFP did not influence growth performance but providing the DFP in Exp. 2 led to increased total nursery pig mortality.

Shiga Toxin-Producing Escherichia coli (STEC) Associated with Calf Mortality in Uruguay

In Uruguay, the mortality of dairy calves due to infectious diseases is high. Escherichia coli is a natural inhabitant of the intestinal microbiota, but can cause several infections. The aim of the work was to characterize E. coli isolates from intestinal and extraintestinal origin of dead newborn calves. Using PCR, virulence gene characteristics of pathogenic E. coli were searched. The pathogenic E. coli were molecularly characterized and the phylogroup, serogroup and the Stx subtype were determined. Antibiotic susceptibility was determined using the Kirby-Bauer disk diffusion method and plasmid-mediated quinolone resistance (PMQR) genes with PCR. Finally, clonal relationships were inferred using PFGE. Gene characteristics of the Shiga toxin-producing E. coli (STEC), Enteropathogenic E. coli (EPEC) and Necrotoxigenic E. coli (NTEC) were identified. The prevalence of the iucD, afa8E, f17, papC, stx1, eae and ehxA genes was high and no f5, f41, saa, sfaDE, cdtIV, lt, sta or stx2 were detected. The prevalence of STEC gene stx1 in the dead calves stood out and was higher compared with previous studies conducted in live calves, and STEC LEE+ (Enterohemorrhagic E. coli (EHEC)) isolates with stx1/eae/ehxA genotypes were more frequently identified in the intestinal than in the extraintestinal environment. E. coli isolates were assigned to phylogroups A, B1, D and E, and some belonged to the O111 serogroup. stx1a and stx1c subtypes were determined in STEC. A high prevalence of multi-resistance among STEC and qnrB genes was determined. The PFGE showed a high diversity of pathogenic strains with similar genetic profiles. It can be speculated that EHEC (stx1/eae/ehxA) could play an important role in mortality. The afa8E, f17G1 and papC genes could also have a role in calf mortality. Multidrug resistance defies disease treatment and increases the risk of death, while the potential transmissibility of genes to other species constitutes a threat to public health.

Low to Zero Concentrations of Airborne Bacterial Pathogens and Indicator E. coli in Proximity to Beef Cattle Feedlots in Imperial Valley, California

This study characterized the effect of distance from beef cattle feedlots, environmental factors, and climate on the occurrence of airborne bacterial indicators and pathogens. Three hundred air samples were collected over 6 months from five feedlots, with each air sample comprising 6000 L of air. Air samples were processed onto TSB-enriched air filters, qPCR-screened, and then qPCR-confirmed for suspect positive colonies of E. coli O157, non-O157-Shiga-toxin-producing E. coli (STEC), Salmonella, and E. coli. Direct enumeration of E. coli was also collected. Although no bacterial pathogens were qPCR-confirmed for the 300 samples, E. coli was detected in 16.7% (50/300) of samples, with an overall mean concentration of 0.17 CFU/6000 L air. Logistic regression analyses revealed a higher odds of E. coli for samples in close proximity compared to >610 m (2000 ft) distance from feedlots, along with significant associations with meteorological factors, sampling hour of day, and the presence of a dust-generating activity such as plowing a field or nearby vehicular traffic. The lack of bacterial pathogen detection suggests airborne deposition from nearby feedlots may not be a significant mechanism of leafy green bacterial pathogen contamination; the result of our study provides data to inform future revisions of produce-safety guidance.

A systematic review and meta-analysis of published literature on prevalence of non-O157 Shiga toxin-producing Escherichia coli serogroups (O26, O45, O103, O111, O121, and O145) and virulence genes in feces, hides, and carcasses of pre- and peri-harvest cattle worldwide

OBJECTIVE

The objective of this study was to summarize peer-reviewed literature on the prevalence and concentration of non-O157 STEC (O26, O45, O103, O111, O121, and O145) serogroups and virulence genes (stx and eae) in fecal, hide, and carcass samples in pre- and peri-harvest cattle worldwide, using a systematic review of the literature and meta-analyses.

DATA SYNTHESIS

Seventy articles were eligible for meta-analysis inclusion; data from 65 articles were subjected to random-effects meta-analysis models to yield fecal prevalence estimates. Meta-regression models were built to explore variables contributing to the between-study heterogeneity.

RESULTS

Worldwide pooled non-O157 serogroup, STEC, and EHEC fecal prevalence estimates (95% confidence interval) were 4.7% (3.4-6.3%), 0.7% (0.5-0.8%), and 1.0% (0.8-1.1%), respectively. Fecal prevalence estimates significantly differed by geographic region (P < 0.01) for each outcome classification. Meta-regression analyses identified region, cattle type, and specimen type as factors that contribute to heterogeneity for worldwide fecal prevalence estimates.

CONCLUSIONS

The prevalence of these global foodborne pathogens in the cattle reservoir is widespread and highly variable by region. The scarcity of prevalence and concentration data for hide and carcass matrices identifies a large data gap in the literature as these are the closest proxies for potential beef contamination at harvest.

Differential Survival of Non-O157 Shiga Toxigenic Escherichia coli in Simulated Cattle Feedlot Runoff

Environmental survival time is important when evaluating adverse health outcomes from foodborne pathogens. Although outbreaks associated with manure-impacted irrigation or runoff water are relatively infrequent, their broad scope, regulatory importance, and severe health outcomes highlight the need to better understand the environmental survival of manure-borne pathogens. Shiga toxigenic Escherichia coli (STEC) are excreted in feces and persist in the environment until they die or recolonize a new host. Surface waters contaminated with manure-borne STEC can infect humans through drinking and recreational water use or irrigated crops that are minimally cooked. In this study, manure-impacted water microcosms mimicking beef cattle feedlot runoff were used to assess survival of STEC strains representing seven STEC serotypes (O26, O45, O103, O111, O121, O145, and O157) and persistence of target O antigen genes. Microcosms were sampled over the course of 1 year, and the entire experiment was repeated in a second year. Culture and polymerase chain reaction (PCR)-based techniques were used for detection and enumeration. Serotype-specific survival results were observed. Both STEC O26 and O45 declined slowly and remained culturable at 24 months. In contrast, STEC O121 and O145 decreased rapidly (-0.84 and -1.99 log10 abundance per month, respectively) and were unculturable by months 4 and 5, but detectable by PCR for a mean of 4.5 and 8.3 months, respectively. STEC O103, O111, and O157 remained culturable for a mean of 11.6, 5.5, and 15 months and detectable by PCR for a mean of 12, 13.8, and 18.6 months after inoculation, respectively. Results document that some STEC serotypes have the biological potential to survive in manure-impacted waters for extended periods of time when competing microflora are eliminated. Serotype-specific differences in survival of target bacteria and persistence of target genes were observed in this sample set, with STEC O26 and O45 strains appearing the most robust in these microcosm studies.

Shiga Toxin-Producing Escherichia coli in Wheat Grains: Detection and Isolation by Polymerase Chain Reaction and Culture Methods

Shiga toxin-producing Escherichia coli (STEC) are major foodborne pathogens and seven serogroups, O26, O45, O103, O111, O121, O145, and O157, often called top-7 STEC, account for the majority of the STEC-associated human illnesses in the United States. Two Shiga toxins, Shiga toxins 1 and 2, encoded by stx1 and stx2 genes, are major virulence factors that are involved in STEC infections. Foodborne STEC infections have been linked to a variety of foods of both animal and plant origin, including products derived from cereal grains. In recent years, a few STEC outbreaks have been linked to contaminated wheat flour. The microbiological quality of the wheat grains is a major contributor to the safety of wheat flour. The objective of the study was to utilize polymerase chain reaction (PCR)- and culture-based methods to detect and isolate STEC in wheat grains. Wheat grain samples (n = 625), collected from different regions of the United States, were enriched in modified buffered peptone water with pyruvate (mBPWp) or E. coli (EC) broth, and they were then subjected to PCR- and culture-based methods to detect and isolate STEC. Wheat grains enriched in EC broth yielded more samples positive for stx genes (1.6% vs. 0.32%) and STEC serogroups (5.8% vs. 2.4%) than mBPWp. The four serogroups of top-7 detected and isolated were O26, O45, O103, and O157 and none of the isolates was positive for the Shiga toxin genes. A total of five isolates that carried the stx2 gene were isolated and identified as serogroups O8 (0.6%) and O130 (0.2%). The EC broth was a better medium to enrich wheat grains than mBPWp for the detection and isolation of STEC. The overall prevalence of virulence genes and STEC serogroups in wheat grains was low. The stx2-positive serogroups isolated, O8 and O130, are not major STEC pathogens and have only been implicated in sporadic infections in animals and humans.

Analysis of drug sensitivity of Escherichia Coli O157H7

Sensitive and rapid tests of Escherichia coli drug sensitivity is very important for health of human and animals. An E. coli immunosensor was built based on electrochemical detection and immune detection technologies, through pretreating screen-printed electrodes, and analyzing the optimal reaction concentration of antigen antibody binding with the AC impedance method. Based on the detection system combining the immunosensor and electrochemical workstation, tests were carried out to measure the accuracy of E. coli concentration and drug sensitivity, and error of the detection system was calibrated in accordance with data from the electrochemical workstation. E. coli O157:H7 can be detected in the range of 10³ cfu/ml ~ 10¹² cfu/ml, and the detection error controlled within 5%. Results from the electrochemical workstation and those from the detection device were consistent, and both demonstrated a greater inhibitory effect of antibiotics on E. coli than on Bacillus subtilis. The electrochemical detection system is highly efficient and accurate, and could be widely applied to E. coli drug sensitivity tests in clinical medicine.

Identification, Shiga toxin subtypes and prevalence of minor serogroups of Shiga toxin-producing Escherichia coli in feedlot cattle feces

Shiga toxin-producing Escherichia coli (STEC) are foodborne pathogens that cause illnesses in humans ranging from mild to hemorrhagic enteritis with complications of hemolytic uremic syndrome and even death. Cattle are a major reservoir of STEC, which reside in the hindgut and are shed in the feces, a major source of food and water contaminations. Seven serogroups, O26, O45, O103, O111, O121, O145 and O157, called ‘top-7’, are responsible for the majority of human STEC infections in North America. Additionally, 151 serogroups of E. coli are known to carry Shiga toxin genes (stx). Not much is known about fecal shedding and prevalence and virulence potential of STEC other than the top-7. Our primary objectives were to identify serogroups of STEC strains, other than the top-7, isolated from cattle feces and subtype stx genes to assess their virulence potential. Additional objective was to develop and validate a novel multiplex PCR assay to detect and determine prevalence of six serogroups, O2, O74, O109, O131, O168, and O171, in cattle feces. A total of 351 strains, positive for stx gene and negative for the top-7 serogroups, isolated from feedlot cattle feces were used in the study. Of the 351 strains, 291 belonged to 16 serogroups and 60 could not be serogrouped. Among the 351 strains, 63 (17.9%) carried stx1 gene and 300 (82.1%) carried stx2, including 12 strains positive for both. The majority of the stx1 and stx2 were of stx1a (47/63; 74.6%) and stx2a subtypes (234/300; 78%), respectively, which are often associated with human infections. A novel multiplex PCR assay developed and validated to detect six serogroups, O2, O74, O109, O131, O168, and O171, which accounted for 86.9% of the STEC strains identified, was utilized to determine their prevalence in fecal samples (n = 576) collected from a commercial feedlot. Four serogroups, O2, O109, O168, and O171 were identified as the dominant serogroups prevalent in cattle feces. In conclusion, cattle shed in the feces a number of STEC serogroups, other than the top-7, and the majority of the strains isolated possessed stx2, particularly of the subtype 2a, suggesting their potential risk to cause human infections.

Molecular assessment of antimicrobial resistance and virulence in multi drug resistant ESBL-producing Escherichia coli and Klebsiella pneumoniae from food fishes, Assam, India

The present study investigated the prevalence of Extended-Spectrum Beta Lactamase (ESBL) -producing E. coli and K. pneumoniae from the food fishes in retail markets in Assam, India. A total of 54 ESBL-producing E. coli and 12 K. pneumoniae isolates were recovered from 79 fish samples and were analyzed for antimicrobial resistance genes (ARGs) and virulence genes. E. coli isolates were categorized as multi drug resistant with resistance up to 12 different antibiotics with multiple antibiotic resistances (MAR) index ranging from 0.26 to 0.63. In E. coli, 100% resistance to cefotaxime along with 6% resistance to ceftazidime (third-generation cephalosporins) was observed. Moreover, 85% of the E. coli isolates were resistant to cefepime, a fourth-generation cephalosporin. K. pneumoniae showed resistance to 11 different antibiotics with MAR index value ranging from 0.21 to 0.57. All K. pneumoniae isolates showed 100% resistance to cefotaxime, 67% resistance to ceftazidime and 75% resistance to cefepime. Molecular characterization of ARGs revealed the presence of CTX-M group 1(CTX-M-15) in almost all E. coli isolates (98%, n = 53) and 100% in K. pneumoniae. A combination of uniplex and multiplex PCRs revealed fewer ARGs in E. coli isolates, with each isolate carrying 3 to 5 genes (tetA, dfrA1, sul1, sul2, qnrB, qnrS, aac(6')-Ib-cr). Majority of the E. coli were assigned to low-virulence phylogroup B1 and A while 8% of them belonged to pathogenic phylogroup D. 31 unique genetic profiles were identified for E. coli isolates by Pulsed-Field Gel Electrophoresis (PFGE) typing. K. pneumoniae isolates were highly diverse with 11 unique genetic profiles and a substantial ARG profile (bla_TEM, bla_SHV, bla_OXA-1-like, tetA, strA, strB, dfrA1, sul1, sul2, qnrB, qnrS, aac(6')-Ib-cr, oqxA, oqxB). The frequency of ARGs ranged between 4 and 11. All K. pneumoniae isolates belonged to capsular serotype with wzi gene. Virulence gene iutA was prominent in all isolates while ybtS and kfu were confirmed in two isolates. Our findings raise concerns that fishes bought for consumption may serve as potential reservoirs of AMR genes and pose serious threat to public health. The study emphasizes the need for extensive surveillance of resistant strains in aquaculture and related settings, their in-depth analysis of population structure and transmission dynamics.

Polymerase Chain Reaction-Based Prevalence of Serogroups of Escherichia coli Known to Carry Shiga Toxin Genes in Feces of Finisher Pigs

Shiga toxin-producing Escherichia coli (STEC) are major foodborne pathogens and seven serogroups, O26, O45, O103, O111, O121, O145, and O157, that account for the majority of the STEC-associated illness in humans. Similar to cattle, swine also harbor STEC and shed them in the feces and can be a source of human STEC infections. Information on the prevalence of STEC in swine feces is limited. Therefore, our objective was to utilize polymerase chain reaction (PCR) assays to determine prevalence of major virulence genes and serogroups of STEC. Fecal samples (n = 598), collected from finisher pigs within 3 weeks before marketing in 10 pig flows located in 8 states, were included in the study. Samples enriched in E. coli broth were subjected to a real-time PCR assay targeting three virulence genes, Shiga toxin 1 (stx1), Shiga toxin 2 (stx2), and intimin (eae), which encode for Shiga toxins 1 and 2, and intimin, respectively. A novel PCR assay was designed and validated to detect serogroups, O8, O20, O59, O86, O91, O100, O120, and O174, previously reported to be commonly present in swine feces. In addition, enriched fecal samples positive for Shiga toxin genes were subjected to a multiplex PCR assay targeting O26, O45, O103, O104, O111, O121, O145, and O157 serogroups implicated in human clinical infections. Of the 598 fecal samples tested by real-time PCR, 25.9%, 65.1%, and 67% were positive for stx1, stx2, and eae, respectively. The novel eight-plex PCR assay indicated the predominant prevalence of O8 (88.6%), O86 (35.5%), O174 (24.1%), O100 (20.2%), and O91 (15.6%) serogroups. Among the seven serogroups relevant to human infections, three serogroups, O121 (17.6%), O157 (14%), and O26 (11%) were predominant. PCR-based detection indicated high prevalence of Shiga toxin genes and serogroups that are known to carry Shiga toxin genes, including serogroups commonly prevalent in cattle feces and implicated in human infections and in edema disease in swine.

Multiplex PCR Assays for the Detection of One Hundred and Thirty Seven Serogroups of Shiga Toxin-Producing Escherichia coli Associated With Cattle

Escherichia coli carrying prophage with genes that encode for Shiga toxins are categorized as Shiga toxin-producing E. coli (STEC) pathotype. Illnesses caused by STEC in humans, which are often foodborne, range from mild to bloody diarrhea with life-threatening complications of renal failure and hemolytic uremic syndrome and even death, particularly in children. As many as 158 of the total 187 serogroups of E. coli are known to carry Shiga toxin genes, which makes STEC a major pathotype of E. coli. Seven STEC serogroups, called top-7, which include O26, O45, O103, O111, O121, O145, and O157, are responsible for the majority of the STEC-associated human illnesses. The STEC serogroups, other than the top-7, called “non-top-7” have also been associated with human illnesses, more often as sporadic infections. Ruminants, particularly cattle, are principal reservoirs of STEC and harbor the organisms in the hindgut and shed in the feces, which serves as a major source of food and water contaminations. A number of studies have reported on the fecal prevalence of top-7 STEC in cattle feces. However, there is paucity of data on the prevalence of non-top-7 STEC serogroups in cattle feces, generally because of lack of validated detection methods. The objective of our study was to develop and validate 14 sets of multiplex PCR (mPCR) assays targeting serogroup-specific genes to detect 137 non-top-7 STEC serogroups previously reported to be present in cattle feces. Each assay included 7–12 serogroups and primers were designed to amplify the target genes with distinct amplicon sizes for each serogroup that can be readily identified within each assay. The assays were validated with 460 strains of known serogroups. The multiplex PCR assays designed in our study can be readily adapted by most laboratories for rapid identification of strains belonging to the non-top-7 STEC serogroups associated with cattle.

Potential risk-factors affecting Salmonella sp. and Escherichia coli occurrence and distribution in Midwestern United States swine feed mills

AIM

This study aimed to evaluate the patterns and potential risk factors associated with the occurrence of Salmonella sp. and Escherichia coli in selected United States swine feed mills.

METHODS AND RESULTS

A total of 405 samples were collected during fall 2018, spring and summer 2019 from selected sites including floors, equipment, shoes and feed in six feed mills in the US Midwest region. Each sample was analysed for the presence of Salmonella and E. coli with culture methods and confirmed by PCR. A survey regarding production volumes, hygiene practices and microbial testing capabilities was conducted in each facility All mills had at least one sampling site positive for either Salmonella or E. coli. Of the 405 samples, 4·7, and 14·1% were positive for Salmonella sp., and E. coli respectively. Sites with higher percentages of positive samples were the receiving, manufacturing, and control area floors. The survey responses indicated that the age of the mill might be a risk factor for bacterial contamination: the older the facility, the higher the number of positive samples. Other risk factors evaluated, such as the production capacity, did not appear to relate to bacterial prevalence.

CONCLUSION

The data documents the presence of E. coli and Salmonella in selected US swine feed mills, and an association between E. coli occurrence and number of ingredient suppliers to feed mill.

SIGNIFICANCE AND IMPACT OF THE STUDY

This information could be used to understand risk factors affecting the occurrence of Salmonella sp. and E. coli in feed mills and help implement monitoring and mitigation strategies for public health.

Single-Cell-Based Digital PCR Detection and Association of Shiga Toxin-Producing Escherichia coli Serogroups and Major Virulence Genes

Escherichia coli serogroups O157, O26, O45, O103, O111, O121, and O145, when carrying major virulence genes, the Shiga toxin genes stx ₁ and stx ₂ and the intimin gene eae, are important foodborne pathogens. They are referred to as the "top 7" Shiga toxin-producing E. coli (STEC) serogroups and were declared by the USDA as adulterants to human health. Since top 7 serogroup-positive cattle feces and ground beef can also contain nonadulterant E. coli strains, regular PCR cannot confirm whether the virulence genes are carried by adulterant or nonadulterant E. coli serogroups. Thus, traditional gold-standard STEC detection requires bacterial isolation and characterization, which are not compatible with high-throughput settings and often take a week to obtain a definitive result. In this study, we demonstrated that the partition-based multichannel digital PCR (dPCR) system can be used to detect and associate the E. coli serogroup-specific gene with major virulence genes and developed a single-cell-based dPCR approach for rapid (within 1 day) and accurate detection and confirmation of major STEC serogroups in high-throughput settings. Major virulence genes carried by each of the top 7 STEC serogroups were detected by dPCR with appropriately diluted intact bacterial cells from pure cultures, culture-spiked cattle feces, and culture-spiked ground beef. Furthermore, from 100 randomly collected, naturally shed cattle fecal samples, 3 O103 strains carrying eae and 2 O45 strains carrying stx ₁ were identified by this dPCR assay and verified by the traditional isolation method. This novel and rapid dPCR assay is a culture-independent, high-throughput, accurate, and sensitive method for STEC detection and confirmation.

Detection of pathogenic Escherichia coli on potentially contaminated beef carcasses using cassette PCR and conventional PCR

BACKGROUND

Over a one year period, swabs of 820 beef carcasses were tested for the presence of Shiga toxin-producing Escherichia coli by performing Polymerase Chain Reaction (PCR) in a novel technology termed "cassette PCR", in comparison to conventional liquid PCR. Cassette PCR is inexpensive and ready-to-use. The operator need only add the sample and press "go". Cassette PCR can simultaneously test multiple samples for multiple targets. Carcass swab samples were first tested for the presence of STEC genes (O157, eae, stx1 and stx2). Samples were considered to be pathogenic if positive for eae plus stx1 and/or stx2. For samples scored as pathogenic, further testing screened for 6 additional high frequency O-antigens (O26, O45, O103, O111, O121, and O145).

RESULTS

Of the 820 samples, 41% were pathogenic and 30% were O157 positive. Of these, 19% of samples were positive for O157 and carried potentially pathogenic E. coli (eae plus stx1 and/or stx2). Of all samples identified as carrying pathogenic E. coli, 18.9, 38.8, 41.4, 0, 36.1, and 4.1% respectively were positive for O26, O45, O103, O111, O121, and O145. To validate cassette PCR testing, conventional PCR using STEC primers was performed on each of the 820 samples. Only 148 of 3280 cassette PCR tests were discordant with conventional PCR results. However, further fractional testing showed that 110 of these 148 PCRs reflected low numbers of E. coli in the enrichment broth and could be explained as due to Poisson limiting dilution of the template, affecting both cassette PCR and conventional PCR. Of the remaining 38 discordant tests, 27 initial capillary PCRs and 10 initial conventional tests were nominally discordant between cassette and conventional PCR, perhaps reflecting human/technical error on both sides of the comparison.

CONCLUSIONS

Contaminated beef carcass swabs were often complex, likely harboring more than one strain of pathogenic E. coli. Cassette PCR had 98.8% concordance with parallel conventional PCR for detection of STEC genes. This indicates that cassette PCR is highly reliable for detecting multiple pathogens in beef carcass swabs from processing plants.

Application of lab-on-a-chip multiplex cassette PCR for the detection of enterohemorrhagic Escherichia coli

Background

Fast molecular detection methods benefit from ready-to-run lab-on-a-chip molecular assays with minimum preparation time. Detection efficiency of such methods can improve if multiple targets are detected simultaneously per given reaction. Detection of food pathogens, i.e. Escherichia coli (E. coli), is generally performed in two stages with the detection of multiple targets in each stage.With simultaneous testing, screening for pathogens is fast and efficient.

Results

In this study, we show the application of multiplex PCR performed on a ready-made cassette to detect 10 targets each for eight samples known to harbor E. coli. In cassette PCR, the aluminum cassette (38.6 mm × 31.4 mm) contains 10 trenches having a total of 50 capillaries with microliter volumes of desiccated acrylamide gels holding all reagents required for the PCR including internal positive and negative controls. The gel contains LCGreen dye to detect double stranded DNA. Fluorescence monitoring allows the detection of the amplified products by melt curve analysis. In this application, each of the five capillaries in a given trench contains two of the primer sets for the detection of 10 targets in pathogenic E. coli, namely, O157, Eae, Stx1, Stx2 and six O-antigen genes. Primer specificity was confirmed. Each trench tests one sample. Eight minimally processed enriched beef carcass swab samples were analyzed for parallel detection of 10 targets within 1 h and 15 min. Samples were delivered to the capillaries by capillary forces thereby hydrating the gels. Multiplex cassette PCR results were confirmed with conventional multiplex PCRs performed in a commercial real-time PCR system.

Conclusions

Cassette PCR technology is ideally suited to multi-target detection of pathogens in food products. The cassette performs multiple PCR reactions in parallel, with multiplex detection of targets within each reaction unit. Cassette PCR/ melt curve analysis results for the simultaneous detection of 10 targets of pathogenic E.coli in beef carcass swab samples were confirmed with a conventional real-time PCR/ melt curve analysis as well as with agarose gel electrophoresis. Although designed for the detection of E. coli, this multiplex cassette PCR technique can be applied to any other assay where the fast detection of multiple targets is required.

Detection, Prevalence, and Pathogenicity of Non-O157 Shiga Toxin-Producing Escherichia coli from Cattle Hides and Carcasses

Cattle are a major reservoir for Shiga toxin-producing Escherichia coli (STEC) and harbor these bacteria in the intestinal tract. The prevalence, concentration, and STEC serogroup isolated in cattle varies between individuals. Hide removal at slaughter serves as a major point of carcass contamination and ultimately beef products. Certain STEC serogroups, such as O26, O45, O103, O111, O121, O145, and O157, containing the intestinal adherence factor intimin, pose a large economic burden to food producers because of testing and recalls. Human infection with STEC can cause illnesses ranging from diarrhea to hemorrhagic colitis and hemolytic uremic syndrome, and is commonly acquired through ingestion of contaminated foods, often beef products. Previously, most studies focused on O157 STEC, but there is growing recognition of the importance of non-O157 STEC serogroups. This review summarizes detection methods, prevalence, and methods for prediction of pathogenicity of non-O157 STEC from cattle hides and carcasses. A synthesis of procedures is outlined for general non-O157 STEC and targeted detection of specific STEC serogroups. Standardization of sample collection and processing procedures would allow for more robust comparisons among studies. Presence of non-O157 STEC isolated from cattle hides and carcasses and specific factors, such as point of sample collection and season, are summarized. Also, factors that might influence STEC survival on these surfaces, such as the microbial population on hides and microbial adherence genes, are raised as topics for future investigation. Finally, this review gives an overview on studies that have used genetic and cell-based methods to identify specific phenotypes of non-O157 STEC strains isolated from cattle to assess their risk to human health.

Presence of Shiga Toxin-Producing Escherichia coli (STEC) in Fresh Beef Marketed in 13 Regions of ITALY (2017)

The aim of this study was to determine the prevalence of Shiga toxin-producing Escherichia coli in fresh beef marketed in 2017 in 13 regions of Italy, to evaluate the potential risk to human health. According to the ISO/TS 13136:2012 standard, 239 samples were analysed and nine were STEC positive, from which 20 strains were isolated. The STEC-positive samples were obtained from Calabria (n = 1), Campania (n = 1), Lazio (n = 2), Liguria (n = 1), Lombardia (n = 1) and Veneto (n = 3). All STEC strains were analysed for serogroups O26, O45, O55, O91, O103, O104, O111, O113, O121, O128, O145, O146 and O157, using Real-Time PCR. Three serogroups were identified amongst the 20 strains: O91 (n = 5), O113 (n = 2), and O157 (n = 1); the O-group for each of the 12 remaining STEC strains was not identified. Six stx subtypes were detected: stx1a, stx1c, stx2a, stx2b, stx2c and stx2d. Subtype stx2c was the most common, followed by stx2d and stx2b. Subtype stx2a was identified in only one eae-negative strain and occurred in combination with stx1a, stx1c and stx2b. The presence in meat of STEC strains being potentially harmful to human health shows the importance, during harvest, of implementing additional measures to reduce contamination risk.

Bayesian estimation of sensitivity and specificity of culture- and PCR-based methods for the detection of six major non-O157 Escherichia coli serogroups in cattle feces

Non-O157 Shiga toxin-producing Escherichia coli (non-O157 STEC, O26, O45, O103, O111, O121, and O145) are foodborne pathogens of public health importance. Culture and PCR-based methods have been developed for the detection of these serogroups in cattle feces. The objectives of this study were to evaluate diagnostic sensitivity and specificity of PCR- and culture-based methods for the detection of the six non-O157 serogroups, and to estimate their true prevalence in cattle feces, using a Bayesian latent class modeling approach that accounts for conditional dependence among the three methods. A total of 576 fecal samples collected from the floor of pens of finishing feedlot cattle during summer 2013 were used. Fecal samples, suspended in E. coli broth, were enriched and subjected to three detection methods: culture (involving immunomagnetic separation with serogroup specific beads and plating on a selective medium), conventional (cPCR), and multiplex quantitative PCR (mqPCR) assays. Samples were considered serogroup positive if the sample or the recovered isolate tested positive by PCR for an O gene of interest; neither Shiga toxin (stx) nor intimin (eae) genes were assessed. Prior information on the performance of the three methods was elicited from three subject experts. Culture was generally the least sensitive and most specific of the 3 tests across serogroups, mqPCR was generally the most sensitive test and cPCR more specific than mqPCR. Sensitivity analysis indicated that posterior inferences on test performance and prevalence were susceptible to prior specification in cases where few or no detections present in the data for selected combinations of diagnostic methods (i.e. extreme category problem). Our results characterize performance of detection methods and true prevalence of non-O157 serogroups, thus informing necessary adjustments for test bias in risk modeling.

Spatiotemporal Variability in Microbial Quality of Western US Agricultural Water Supplies: A Multistate Study

In 2011, the US Congress passed the Food Safety Modernization Act, which tasks the US Food and Drug Administration to establish microbiological standards for agricultural water. However, little data are available for the microbiological quality of surface water irrigation supplies. During the 2015 irrigation season, we conducted a baseline study on the microbial water quality of large irrigation districts in California ( = 2) and Washington ( 4). Monthly samples ( 517) were analyzed for bacterial indicators (fecal coliforms, enterococci, and ) and pathogens ( spp., O157, and non-O157 Shiga toxin-producing [STEC]). Although there was a high degree of variability (μ ± SD = 59.13 ± 106.0), only 11% of samples (56/517) exceeded 126 colony-forming units (CFU) 100 mL, and only six samples exceeded 410 CFU 100 mL. Two volumes of water were collected for pathogen analysis (1 L and 10 L); prevalence of in 10-L samples (68149) was nearly double of that found in 1-L samples (132/517). We found STEC during ∼9% of sampling events (58/517); serotypes O26 and O45 were the most common at 31 and 26%, respectively. Pathogens were not associated with exceedance of the regulatory threshold, yet the odds of detecting increased approximately threefold (odds ration [O.R.] = 3.14, 0.0001) for every log increase in turbidity. Microbiological outcomes were highly district-specific, suggesting drivers of water quality vary across spatiotemporal scales. The true risk of contamination of produce from irrigation water supplies remains unknown, along with the optimal monitoring strategy to improve food safety.

Multi-Year Persistence of Verotoxigenic Escherichia coli (VTEC) in a Closed Canadian Beef Herd: A Cohort Study

In this study, fecal samples were collected from a closed beef herd in Alberta, Canada from 2012 to 2015. To limit serotype bias, which was observed in enrichment broth cultures, Verotoxigenic Escherichia coli (VTEC) were isolated directly from samples using a hydrophobic grid-membrane filter verotoxin immunoblot assay. Overall VTEC isolation rates were similar for three different cohorts of yearling heifers on both an annual (68.5 to 71.8%) and seasonal basis (67.3 to 76.0%). Across all three cohorts, O139:H19 (37.1% of VTEC-positive samples), O22:H8 (15.8%) and O?(O108):H8 (15.4%) were among the most prevalent serotypes. However, isolation rates for serotypes O139:H19, O130:H38, O6:H34, O91:H21, and O113:H21 differed significantly between cohort-years, as did isolation rates for some serotypes within a single heifer cohort. There was a high level of VTEC serotype diversity with an average of 4.3 serotypes isolated per heifer and 65.8% of the heifers classified as "persistent shedders" of VTEC based on the criteria of >50% of samples positive and ≥4 consecutive samples positive. Only 26.8% (90/336) of the VTEC isolates from yearling heifers belonged to the human disease-associated seropathotypes A (O157:H7), B (O26:H11, O111:NM), and C (O22:H8, O91:H21, O113:H21, O137:H41, O2:H6). Conversely, seropathotypes B (O26:NM, O111:NM) and C (O91:H21, O2:H29) strains were dominant (76.0%, 19/25) among VTEC isolates from month-old calves from this herd. Among VTEC from heifers, carriage rates of vt1, vt2, vt1+vt2, eae, and hlyA were 10.7, 20.8, 68.5, 3.9, and 88.7%, respectively. The adhesin gene saa was present in 82.7% of heifer strains but absent from all of 13 eae+ve strains (from serotypes/intimin types O157:H7/γ1, O26:H11/β1, O111:NM/θ, O84:H2/ζ, and O182:H25/ζ). Phylogenetic relationships inferred from wgMLST and pan genome-derived core SNP analysis showed that strains clustered by phylotype and serotype. Further, VTEC strains of the same serotype usually shared the same suite of antibiotic resistance and virulence genes, suggesting the circulation of dominant clones within this distinct herd. This study provides insight into the diverse and dynamic nature of VTEC populations within groups of cattle and points to a broad spectrum of human health risks associated with these E. coli strains.

Occurrence and characterization of seven major Shiga toxin-producing Escherichia coli serotypes from healthy cattle on cow-calf operations in South Africa

Cattle are a major reservoir of Shiga toxin-producing Escherichia coli. This study investigated the occurrence of seven major STEC serogroups including O157, O145, O103, O121, O111, O45 and O26 among 578 STEC isolates previously recovered from 559 cattle. The isolates were characterized for serotype and major virulence genes. Polymerase chain reaction revealed that 41.7% (241/578) of isolates belonged to STEC O157, O145, O103, O121, O45 and O26, and 33 distinct serotypes. The 241 isolates corresponded to 16.5% (92/559) of cattle that were STEC positive. The prevalence of cattle that tested positive for at least one of the six serogroups across the five farms was variable ranging from 2.9% to 43.4%. Occurrence rates for individual serogroups were as follows: STEC O26 was found in 10.2% (57/559); O45 in 2.9% (16/559); O145 in 2.5% (14/559); O157 in 1.4% (8/559); O121 in 1.1% (6/559); and O103 in 0.4% (2/559). The following proportions of virulence genes were observed: stx1, 69.3% (167/241); stx2, 96.3% (232/241); eaeA, 7.1% (17/241); ehxA, 92.5% (223/241); and both stx1 and stx2, 62.2% (150/241) of isolates. These findings are evidence that cattle in South Africa carry STEC that belong to six major STEC serogroups commonly incriminated in human disease. However, only a subset of serotypes associated with these serogroups were clinically relevant in human disease. Most STEC isolates carried stx1, stx2 and ehxA but lacked eaeA, a major STEC virulence factor in human disease.

Spatial and temporal variability of bacterial indicators and pathogens in six California reservoirs during extreme drought

California has one of the largest systems of surface water reservoirs in the world, providing irrigation water to California's agriculturally productive Central Valley. Irrigation water is recognized as a vehicle for the microbial contamination of raw produce and must be monitored according to new federal regulation. The purpose of this study was to further understanding of the variability of fecal indicator bacteria (Escherichia coli and fecal coliforms) and pathogens (E. coli O157:H7 (O157), non-O157 Shiga toxin-producing E. coli (STEC) and Salmonella) along both horizontal and vertical profiles within California reservoirs. Monthly sampling was conducted in six reservoirs located in the foothills of the Western Sierra Nevada during the summer irrigation season and extreme drought conditions of 2014 (n = 257). Concentrations of fecal indicator bacteria were highly variable between reservoirs (p < 0.05) and along the horizontal profile (p < 0.001) from upstream to downstream, with higher concentrations typically found outside of the reservoirs than within. Though many of the reservoirs were thermally stratified, bacterial concentrations were not associated with water temperature (p > 0.05) or any one particular depth strata (p < 0.05). However, prevalence of Salmonella and STEC (16/70 and 9/70 respectively) was higher in the deep strata than in mid or surface layers. We found no statistical association between samples collected downstream of reservoirs and those from the reservoirs themselves. Continued monitoring and modeling of both bacterial indicators and enteric pathogens are critical to our ability to estimate the risk of surface irrigation water supplies and make appropriate management decisions.

A new integrated approach to analyze bulk tank milk and raw milk filters for the presence of the E. coli serogroups frequently associated with VTEC status

We optimized a combination of microbiological and molecular methods to quickly identify the presence of the O157 and the six non-O157 serogroups (O26, O45, O103, O111, O121 and O145) most frequently associated with VTEC status, at herd level. The lower detection limit of this methodology is 10¹CFU/ml for each of the serogroups tested. We tested 67 bulk tank milk (BTM) and raw milk filters (RMF) derived from dairy herds located in Lombardy and Trentino Alto Adige. We identified 3 positive samples and 20 positive samples out of 67 respectively in the BTM and RMF. Interestingly, several samples showed positivity for more than one serogroups at the same time. We also identified the presence of E. coli O45 and O121 for the first time in raw milk and raw milk filters. Once screened the seven serogroups of interest in our samples, we evaluated the real pathogenicity of our positive, non-O157 samples through two parallel molecular biology methods: virulence gene research by PCR, and HRMA and sequencing. The most frequently isolated serogroups in milk were O157 (2.64%), O103 (2.11%), and O145 (1.06%), while in RMF the frequencies were, respectively 14.92%, 4.48%, and 2.98%. Moreover, this is the first published report in Italy of positive recovery of O45 and O121 serogroups in milk and milk filters. The new diagnostic approach proposed investigate the presence of the O157 and big six non-O157 serogroups at farm level and not to identify VTEC hazard only once the product is processed and/or is ready to be consumed.

Virulence genes, Shiga toxin subtypes, major O-serogroups, and phylogenetic background of Shiga toxin-producing Escherichia coli strains isolated from cattle in Iran

The aim of this study was to investigate the virulence potential of the isolated bovine STEC for humans in Iran. In this study a collection of STEC strains (n = 50) had been provided via four stages, including sampling from feces of cattle, E. coli isolation, molecular screening of Shiga toxin (stx) genes, and saving the STEC strains from various geographical areas in Iran. The STEC isolates were subjected to stx-subtyping, O-serogrouping, and phylo-grouping by conventional polymerase chain reaction (PCR). Occurrence of stx1 (52%) and stx2 (64%) was not significantly different (p = 0.1), and 16% of isolates carried both stx1 and stx2, simultaneously. In addition, 36% and 80% of the isolates were positive for eae and ehxA, respectively. Molecular subtyping showed that stx1a (52%), stx2a (44%), stx2c (44%), and stx2d (30%) were the most prevalent subtypes; two combinations stx2a/stx2c and stx2c/stx2d coexisted in 18% and 10% of STEC strains, respectively. Three important non-O157 serogroups, including O113 (20%), O26 (12%), and O111 (10%), were predominant, and none of the isolates belonged to O157. Importantly, one O26 isolate carried stx1, stx2, eae and ehxA and revealed highly virulent stx subtypes. Moreover, all the 21 serogrouped strains belonged to the B1 phylo-type. Our study highlights the significance of non-O157 STEC strains carrying highly pathogenic virulence genes in cattle population as the source of this pathogen in Iran. Since non-O157 STEC strains are not routinely tried in most diagnostic laboratories, majority of the STEC-associated human infections appear to be overlooked in the clinical settings.

Limitations of Immunomagnetic Separation for Detection of the Top Seven Serogroups of Shiga Toxin-Producing Escherichia coli

Shiga toxin-producing Escherichia coli (STEC) strains are foodborne pathogens that negatively impact human health and compromise food safety. Serogroup O157 is the most frequently isolated and studied STEC serogroup, but six others (O26, O45, O103, O111, O121, and O145) have also been identified as significant sources of human disease and collectively have been referred to as the "top six" pathogenic serogroups. Because detection methods for non-O157 serogroups are not yet refined, the objective of this study was to compare the effectiveness of immunomagnetic separation (IMS) for recovery of serogroup O157 isolates with that for each of the top six E. coli serogroups in pure and mixed cultures of STEC at 10³ to 10⁷ CFU/mL. After serogroup-specific IMS, DNA was extracted from cultured isolates to analyze the specificity of each IMS assay using conventional and quantitative PCR. In pure cultures, DNA copy number obtained after IMS was lower for O111 and O157 (P < 0.01) than for other serogroups. Based on quantitative PCR (qPCR) analyses, specificity was reduced for all IMS assays when STEC isolates were mixed at 7 log CFU/mL, although the O157 IMS assays recovered only O157 over a wider range of concentrations than did assays for non-O157 serogroups. At the lowest dilution tested, conventional PCR was specific for all serogroups except O121 and O145. For these two serogroups, no dilution tested recovered only O121 or O145 when evaluated with conventional PCR. Refinements to IMS assays, development of selective media, and determination of optimal enrichment times to reduce background microflora or competition among serogroups would be especially beneficial for recovery of O111, O121, and O145 serogroups to improve STEC detection and isolation.

Feedlot- and Pen-Level Prevalence of Enterohemorrhagic Escherichia coli in Feces of Commercial Feedlot Cattle in Two Major U.S. Cattle Feeding Areas

The objective of this study was to determine feedlot- and pen-level fecal prevalence of seven enterohemorrhagic Escherichia coli (EHEC) belonging to serogroups (O26, O45, O103, O111, O121, O145, and O157, or EHEC-7) in feces of feedlot cattle in two feeding areas in the United States. Cattle pens from four commercial feedlots in each of the two major U.S. beef cattle areas were sampled. Up to 16 pen-floor fecal samples were collected from each of 4-6 pens per feedlot, monthly, for a total of three visits per feedlot, from June to August, 2014. Culture procedures including fecal enrichment in E. coli broth, immunomagnetic separation, and plating on selective media, followed by confirmation through polymerase chain reaction (PCR) testing, were conducted. Generalized linear mixed models were fitted to estimate feedlot-, pen-, and sample-level fecal prevalence of EHEC-7 and to evaluate associations between potential demographic and management risk factors with feedlot and within-pen prevalence of EHEC-7. All study feedlots and 31.0% of the study pens had at least one non-O157 EHEC-positive fecal sample, whereas 62.4% of pens tested positive for EHEC O157; sample-level prevalence estimates ranged from 0.0% for EHEC O121 to 18.7% for EHEC O157. Within-pen prevalence of EHEC O157 varied significantly by sampling month; similarly within-pen prevalence of non-O157 EHEC varied significantly by month and by the sex composition of the pen (heifer, steer, or mixed). Feedlot management factors, however, were not significantly associated with fecal prevalence of EHEC-7. Intraclass correlation coefficients for EHEC-7 models indicated that most of the variation occurred between pens, rather than within pens, or between feedlots. Hence, the potential combination of preharvest interventions and pen-level management strategies may have positive food safety impacts downstream along the beef chain.

Nationwide investigation of Shiga toxin-producing Escherichia coli among cattle in Japan revealed the risk factors and potentially virulent subgroups

A nationwide study of Shiga toxin-producing Escherichia coli (STEC) was performed to determine the prevalence, characteristics and risk factors for fecal shedding of STEC among cattle in Japan. Information on rearing practices was also collected to identify risk factors for fecal shedding of STEC. STEC was isolated from 24·1% of samples (133/551) collected from 59·1% of farms (65/110). Bayesian clustering using the virulence marker profiles of the isolates subdivided the isolates into four genetically distinct groups, two of which corresponded to eae- or saa-positive STEC, which can cause severe disease in human. Both STEC groups exhibited characteristic phylogeny and virulence marker profiles. It is noteworthy that the tellurite resistance gene was not detected in all saa-positive STEC isolates, suggesting that the standard isolation method using tellurite might lead to an underestimation of the prevalence of saa-positive STEC. A multivariate logistic regression model using epidemiological information revealed a significantly (P < 0·01) high odds ratio on STEC fecal shedding in tie-stall housing and a low odds ratio in flat feed box and mechanical ventilation. Information on isolate characteristics of the two major pathotypes and risk factors in rearing practices will facilitate the development of preventative measures for STEC fecal shedding from cattle.

Competition during enrichment of pathogenicEscherichia colimay result in culture bias

Deadly outbreaks and illnesses due to Shiga toxin-producing Escherichia coli (STEC) occur worldwide; however, the cultivation methods required for adequate monitoring and traceback investigations are inefficient at best. Detection of STEC relies heavily on enrichment; yet no standard media or protocols exist. Furthermore, whether enrichment may bias detection of multiple STEC serogroups from complex samples is unknown. Thus, 14 STEC strains of serogroups O157 and the top six non-O157s (O26, O45, O103, O111, O121, and O145) were enriched in pairs for 6–78 h in broth and evaluated by quantitative polymerase chain reaction (qPCR). Here we show that a conventional 6-h enrichment protocol did not result in intra-species culture bias for the isolates tested. However, subsequent enrichments often produced biased cultures, with differences in the qPCR gene copy number ≥2 log10apparent in 12%, 38%, and 52% of competitions after 30, 54, and 78 h of consecutive enrichments, respectively. Some strains were able to prevail and (or) out-compete the opponent strain in 100% of competitions. Our results suggest that culture bias should be considered and (or) evaluated further due to the potential implications during routine pathogen screening and outbreak investigations.

Monitoring Seven Potentially Pathogenic Escherichia coli Serogroups in a Closed Herd of Beef Cattle from Weaning to Finishing Phases

The goal of this study was to monitor Shiga toxin-producing Escherichia coli (STEC) serogroups and virulence genes in cattle (n = 30) originating from a closed herd. Fecal samples were collected (1) at weaning, (2) upon arrival to a feedlot, (3) after 30 days on feed (DOF), and (4) after 135 DOF. DNA was extracted from feces for detection of virulence and serogroup genes by polymerase chain reaction (PCR) and immunomagnetic separation and pulsed-field gel electrophoresis (PFGE) were performed to collect and subtype STEC isolates. The prevalence of each serogroup measured by PCR from weaning to 135 DOF was 23.3-80.0% for O26, 33.3-46.7% for O45, 70.0-73.3% for O103, 36.7-86.7% for O111, 56.7-6.7% for O121, 26.7-66.7% for O145, and 66.7-90.0% for O157. Total fecal samples positive for virulence genes were 87.5% for ehxA, 85.8% for stx₁, 60.0% for stx₂, 52.5% for eae, and 44.2% for the autoagglutinating adhesion gene, saa. The prevalence of each serogroup and virulence gene tended to increase by 135 DOF, with the exception of O121, stx₂, and saa. The frequency of detection of some virulence genes was largely affected over time, most notably with saa and stx₂ decreasing, and eae increasing when cattle were transitioned to concentrate-based diets. PFGE analysis of O157 and O103 fecal isolates revealed dominant pulsotypes, but the presence of identical O103 isolates, which differed in virulence profiles. Overall, this study showed that fecal shedding of E. coli serogroups and virulence-associated genes are highly variable over time as cattle move from ranch to feedlot. To mitigate STEC, it is important to understand the factors affecting both prevalence of individual serogroups and the presence of virulence factors.

Development of 11-Plex MOL-PCR Assay for the Rapid Screening of Samples for Shiga Toxin-Producing Escherichia coli

Strains of Shiga toxin-producing Escherichia coli (STEC) are a serious threat to the health, with approximately half of the STEC related food-borne illnesses attributable to contaminated beef. We developed an assay that was able to screen samples for several important STEC associated serogroups (O26, O45, O103, O104, O111, O121, O145, O157) and three major virulence factors (eae, stx₁, stx₂) in a rapid and multiplexed format using the Multiplex oligonucleotide ligation-PCR (MOL-PCR) assay chemistry. This assay detected unique STEC DNA signatures and is meant to be used on samples from various sources related to beef production, providing a multiplex and high-throughput complement to the multiplex PCR assays currently in use. Multiplex oligonucleotide ligation-PCR (MOL-PCR) is a nucleic acid-based assay chemistry that relies on flow cytometry/image cytometry and multiplex microsphere arrays for the detection of nucleic acid-based signatures present in target agents. The STEC MOL-PCR assay provided greater than 90% analytical specificity across all sequence markers designed when tested against panels of DNA samples that represent different STEC serogroups and toxin gene profiles. This paper describes the development of the 11-plex assay and the results of its validation. This highly multiplexed, but more importantly dynamic and adaptable screening assay allows inclusion of additional signatures as they are identified in relation to public health. As the impact of STEC associated illness on public health is explored additional information on classification will be needed on single samples; thus, this assay can serve as the backbone for a complex screening system.

Influence of Season and Feedlot Location on Prevalence and Virulence Factors of Seven Serogroups of Escherichia coli in Feces of Western-Canadian Slaughter Cattle

Pooled feces collected over two years from 1749 transport trailers hauling western-Canadian slaughter cattle were analysed by PCR for detection of Escherichia coli serogroups O26, O45, O103, O111, O121, O145, and O157. Sequential immunomagnetic separation was then used to collect bacterial isolates (n = 1035) from feces positive for target serogroups. Isolated bacteria were tested by PCR to confirm serogroup and the presence of eae, ehxA, stx₁, and stx₂ virulence genes. Based on PCR screening, serogroup prevalence in feces ranged from 7.0% (O145) to 94.4% (O103) with at least 3 serogroups present in 79.5% of samples. Origin of cattle affected serogroup PCR prevalence and O157 was most prevalent in feces from south-west Alberta (P < 0.001). All serogroups demonstrated seasonal variations in PCR prevalence, with O26, O45, O103, O121, and O157 least prevalent (P < 0.001) in cooler winter months, while uncommon serogroups O111 and O145 increased in prevalence during winter (P < 0.001). However, isolates collected during winter were predominantly from serogroups O103 and O45. No seasonal variation was noted in proportion of isolates which were Shiga toxin containing E. coli (STEC; P = 0.18) or positive for Shiga toxin and eae (enterohemorrhagic E. coli; EHEC; P = 0.29). Isolates of serogroups O111, O145, and O157 were more frequently EHEC than were others, although 37.6–54.3% of isolates from other serogroups were also EHEC. Shiga-toxin genes present also varied by geographic origin of cattle (P < 0.05) in all serogroups except O157. As cattle within feedlots are sourced from multiple regions, locational differences in serogroup prevalence and virulence genes imply existence of selection pressures for E. coli and their virulence in western-Canadian cattle. Factors which reduce carriage or expression of virulence genes, particularly in non-O157 serogroups, should be investigated.

Multiplex Quantitative PCR Assays for the Detection and Quantification of the Six Major Non-O157 Escherichia coli Serogroups in Cattle Feces

Shiga toxin-producing Escherichia coli (STEC) serogroups O26, O45, O103, O111, O121, and O145, called non-O157 STEC, are important foodborne pathogens. Cattle, a major reservoir, harbor the organisms in the hindgut and shed them in the feces. Although limited data exist on fecal shedding, concentrations of non-O157 STEC in feces have not been reported. The objectives of our study were (i) to develop and validate two multiplex quantitative PCR (mqPCR) assays, targeting O-antigen genes of O26, O103, and O111 (mqPCR-1) and O45, O121, and O145 (mqPCR-2); (ii) to utilize the two assays, together with a previously developed four-plex qPCR assay (mqPCR-3) targeting the O157 antigen and three virulence genes (stx1, stx2, and eae), to quantify seven serogroups and three virulence genes in cattle feces; and (iii) to compare the three mqPCR assays to a 10-plex conventional PCR (cPCR) targeting seven serogroups and three virulence genes and culture methods to detect seven E. coli serogroups in cattle feces. The two mqPCR assays (1 and 2) were shown to be specific to the target genes, and the detection limits were 4 and 2 log CFU/g of pure culture-spiked fecal samples, before and after enrichment, respectively. A total of 576 fecal samples collected from a feedlot were enriched in E. coli broth and were subjected to quantification (before enrichment) and detection (after enrichment). Of the 576 fecal samples subjected, before enrichment, to three mqPCR assays for quantification, 175 (30.4%) were quantifiable (≥4 log CFU/g) for at least one of the seven serogroups, with O157 being the most common serogroup. The three mqPCR assays detected higher proportions of postenriched fecal samples (P > 0.01) as positive for one or more serogroups compared with cPCR and culture methods. This is the first study to assess the applicability of qPCR assays to detect and quantify six non-O157 serogroups in cattle feces and to generate data on fecal concentration of the six serogroups.

Pooling of Immunomagnetic Separation Beads Does Not Affect Detection Sensitivity of Six Major Serogroups of Shiga Toxin-Producing Escherichia coli in Cattle Feces

Shiga toxin-producing Escherichia coli (STEC) of the serogroups O26, O45, O103, O111, O121, and O145, often called non-O157 STEC, are foodborne pathogens. Cattle are asymptomatic reservoirs for STEC; the organisms reside in the hindgut and are shed in the feces, which serve as the source of food product contaminations. Culture-based detection of non-O157 STEC involves an immunomagnetic separation (IMS) step to capture the specific serogroups in complex matrices, such as feces. The IMS procedure is time consuming and labor intensive because of the need to subject each fecal sample to six individual beads. Therefore, our objective was to evaluate whether pooling of IMS beads affects sensitivity of non-O157 STEC detection compared with using individual IMS beads. The evaluation was done by comparing detection of serogroups in feces spiked with pure cultures (experiments 1 and 2) and from feces (n = 384) of naturally shedding cattle (experiment 3). In spiked fecal samples, detection with pools of three, four, six, or seven beads was similar to, or at times higher than, detection with individual IMS beads. In experiment 3, the proportions of fecal samples that tested positive for the six serogroups as detected by individual or pooled beads were similar. Based on noninferiority tests, detection with pooled beads was not substantially inferior to detection with individual beads (P > 0.05). In conclusion, the pooling of IMS beads is a better option for detection of STEC serogroups in fecal samples compared with individual beads because the procedure saves time and labor and has the prospect of a higher throughput.

Characterization of Shiga Toxigenic Escherichia coli O157 and Non-O157 Isolates from Ruminant Feces in Malaysia

Shiga toxigenic Escherichia coli (STEC) O157 and several other serogroups of non-O157 STEC are causative agents of severe disease in humans world-wide. The present study was conducted to characterize STEC O157 and non-O157 serogroups O26, O103, O111, O121, O45, and O145 in ruminants in Malaysia. A total of 136 ruminant feces samples were collected from 6 different farms in Peninsular Malaysia. Immunomagnetic beads were used to isolate E. coli O157 and non-O157 serogroups, while PCR was used for the detection and subtyping of STEC isolates. STEC O157:H7 was isolated from 6 (4%) feces samples and all isolates obtained carried stx 2c, eaeA-γ1, and ehxA. Non-O157 STEC was isolated from 2 (1.5%) feces samples with one isolate carrying stx 1a, stx 2a, stx 2c, and ehxA and the other carrying stx 1a alone. The presence of STEC O157 and non-O157 in a small percentage of ruminants in this study together with their virulence characteristics suggests that they may have limited impact on public health.

A Comparison of Culture- and PCR-Based Methods to Detect Six Major Non-O157 Serogroups of Shiga Toxin-Producing Escherichia coli in Cattle Feces

Culture-based methods to detect the six major non-O157 (O26, O45, O103, O111, O121 and O145) Shiga toxin-producing E. coli (STEC) are not well established. Our objectives of this study were to develop a culture-based method to detect the six non-O157 serogroups in cattle feces and compare the detection with a PCR method. Fecal samples (n = 576) were collected in a feedlot from 24 pens during a 12-week period and enriched in E. coli broth at 40° C for 6 h. Enriched samples were subjected to immunomagnetic separation, spread-plated onto a selective chromogenic medium, and initially pooled colonies, and subsequently, single colonies were tested by a multiplex PCR targeting six serogroups and four virulence genes, stx1, stx2, eae, and ehxA (culture method). Fecal suspensions, before and after enrichment, were also tested by a multiplex PCR targeting six serogroups and four virulence genes (PCR method). There was no difference in the proportions of fecal samples that tested positive (74.3 vs. 77.4%) for one or more of the six serogroups by either culture or the PCR method. However, each method detected one or more of the six serogroups in samples that were negative by the other method. Both culture method and PCR indicated that O26, O45, and O103 were the dominant serogroups. Higher proportions (P < 0.05) of fecal samples were positive for O26 (44.4 vs. 22.7%) and O121 (22.9 vs. 2.3%) serogroups by PCR than by the culture method. None of the fecal samples contained more than four serogroups. Only a small proportion of the six serogroups (23/640; 3.6%) isolated carried Shiga toxin genes. The culture method and the PCR method detected all six serogroups in samples negative by the other method, highlighting the importance of subjecting fecal samples to both methods for accurate detection of the six non-O157 STEC in cattle feces.

Summer and Winter Prevalence of Shiga Toxin-Producing Escherichia coli (STEC) O26, O45, O103, O111, O121, O145, and O157 in Feces of Feedlot Cattle

The United States Department of Agriculture Food Safety and Inspection Service has declared seven Shiga toxin-producing Escherichia coli (STEC) serogroups (O26, O45, O103, O111, O121, O145, and O157) as adulterants in raw, nonintact beef products. The objective of this study was to determine the prevalence of these seven serogroups and the associated virulence genes (Shiga toxin [stx1, stx2], and intimin [eae]) in cattle feces during summer (June-August 2013) and winter (January-March 2014) months. Twenty-four pen floor fecal samples were collected from each of 24 cattle pens, in both summer and winter months, at a commercial feedlot in the United States. Samples were subjected to culture-based detection methods that included enrichment, serogroup-specific immunomagnetic separation and plating on selective media, followed by a multiplex polymerase chain reaction for serogroup confirmation and virulence gene detection. A sample was considered STEC positive if a recovered isolate harbored an O gene, stx1, and/or stx2, and eae genes. All O serogroups of interest were detected in summer months, and model-adjusted prevalence estimates are as follows: O26 (17.8%), O45 (14.6%), O103 (59.9%), O111 (0.2%), O121 (2.0%), O145 (2.7%), and O157 (41.6%); however, most non-O157 isolates did not harbor virulence genes. The cumulative model-adjusted sample-level prevalence estimates of STEC O26, O103, O145, and O157 during summer (n=576) were 1.0, 1.6, 0.8, and 41.4%, respectively; STEC O45, O111, and O121 were not detected during summer months. In winter, serogroups O26 (0.9%), O45 (1.5%), O103 (40.2%), and O121 (0.2%) were isolated; however, no virulence genes were detected in isolates from cattle feces collected during winter (n=576). Statistically significant seasonal differences in prevalence were identified for STEC O103 and O157 (p<0.05), but data on other STEC were sparse. The results of this study indicate that although non-O157 serogroups were present, non-O157 STEC were rarely detected in feces from the feedlot cattle populations tested in summer and winter months.

Molecular Characterization of Enterotoxin-Producing Escherichia coli Collected in 2011-2012, Russia

Enterotoxin-producing Escherichia coli (ETEC) are one of the main causative agents of diarrhea in children especially in developing countries and travel diarrhoea in adults. Pathogenic properties of ETEC associated with their ability to produce a heat-stable (ST) and/or heat-labile (LT) enterotoxins, as well as adhesins providing bacterial adhesion to intestinal epithelial cells. This study presents the molecular characterization of the ETEC isolates collected from the Central and Far-Eastern regions of Russia in 2011–2012. It was shown that all ETEC under study (n=18) had the heat-labile enterotoxin-coding operon elt, and had no the genes of the heat-stable enterotoxin operon est. DNA sequencing revealed two types of nucleotide exchanges in the eltB gene coding subunit B of LT in isolates collected from Cherepovets city (Central region, Russia) and Vladivostok city (Far-East region, Russia). Only one ETEC strain carried genes cfaA, cfaB, cfaC and cfaD coding adhesion factor CFA/I. Expression of LT in four ETEC isolates in the agglutination reaction was detected using a latex test-system. The isolates were assigned to serogroups O142 (n = 6), О6 (n = 4), О25 (n = 5), О26 (n = 2), and O115 (n = 1). Genotyping showed that they belonged to an earlier described sequence-type ST4 (n = 3) as well as to 11 novel sequence-types ST1043, ST1312, ST3697, ST3707, ST3708, ST3709, ST3710, ST3755, ST3756, ST3757 and ST4509. The ETEC isolates displayed different levels of antimicrobial resistance. Eight isolates were resistant to only one drug, three isolates—to two drugs, one isolate—to three drugs, two isolates—to four antibacterials, and only one isolate to each of the five, six and ten antibacterials simultaneously. Genetic determinants of the resistance to beta-lactams and other classes of antibacterials on the ETEC genomes were identified. There are bla_TEM (n = 10), bla_CTX-M-15 (n = 1), class 1 integron (n = 3) carrying resistance cassettes to aminoglycosides and sulphonamides dfrA17-aadA5 and dfrA12-orfF-aadA2. One isolate ETEC_Ef-6 was found to be a multidrug-resistant (MDR) pathogen that carried both the beta-lactamase gene and class 1 integron. These data suggest the circulation of ETEC in Russia. Further investigations are necessary to study the spread of the revealed ETEC sequence types (STs) and serotypes. Their role in the etiology of diarrhea should be also estimated.

Virulence characterization and molecular subtyping of typical and atypical Escherichia coli O157:H7 and O157:H(-) isolated from fecal samples and beef carcasses in Mexico

The objective of the study was to characterize virulence genes and subtype Escherichia coli O157:H7 and O157:H( 2 ) isolates obtained from a vertically integrated feedlot slaughter plant in Mexico. A total of 1,695 samples were collected from feedlots, holding pens, colon contents, hides, and carcasses. E. coli O157:H7 detection and confirmation was carried out using conventional microbiology techniques, immunomagnetic separation, latex agglutination, and the BAX system. A total of 97 E. coli O157 strains were recovered and screened for key virulence and metabolic genes using multiplex and conventional PCR. Eighty-eight (91.72%) of the strains carried stx2, eae, and ehxA genes. Ten isolates (8.25%) were atypical sorbitol-fermenting strains, and nine were negative for the flicH7 gene and lacked eae, stx1, stx2, and ehxA. One sorbitol-positive strain carried stx2, eae, tir, toxB, and iha genes but was negative for stx1 and ehxA. Pulsed-field gel electrophoresis (PFGE) analysis yielded 49 different PFGE subtypes, showing a high genetic diversity; however, the majority of the typical isolates were closely related (80 to 90% cutoff). Atypical O157 isolates were not closely related within them or to typical E. coli O157:H7 isolates. Identical PFGE subtypes were found in samples obtained from colon contents, feedlots, holding pens, and carcasses. Isolation of a sorbitolfermenting E. coli O157 positive for a number of virulence genes is a novel finding in Mexico. These data showed that genetically similar strains of E. coli O157:H7 can be found at various stages of beef production and highlights the importance of preventing cross-contamination at the pre- and postharvest stages of processing.

Ocorrência de Escherichia coli O157:H7 e O26 sorbitol negativas em matadouro frigorífico de bovino e suscetibilidade a antimicrobianos

A carne bovina pode ser um meio de transmissão de Escherichia coli O157:H7 e de não-O157 para os humanos, que a ingerem mal cozida, sendo responsáveis por causarem doenças severas, como a síndrome hemolítico urêmica. A resistência bacteriana se tornou preocupante em relação à eficácia nos tratamentos das doenças, e tendo em vista tais aspectos este estudo teve os objetivos de verificar a ocorrência de E. coli O157:H7 e não-O157 em etapas do abate bovino, asssim como de avaliar a suscetibilidade dessas bactérias frente à ação de antimicrobianos. Foram colhidas em abatedouro bovino 21 amostras de superfície de mãos dos manipuladores, 21 de facas e 300 provenientes de 50 animais em seis pontos no fluxograma de abate. O isolamento foi realizado utilizando o ágar CT-SMAC e a caracterização dos sorotipos pela PCR. Houve uma ocorrência maior de E. coli O157:H7 (12,0%) nos animais, e menor ocorrência de E. coli O26 (8,0%) e de O113 (2,0%). E. coli O26 esteve presente em 9,52% das facas. A presença de E. coli não-O157 sorbitol negativa foi um fato inesperado devido ao método de isolamento utilizado. Todos os isolados de E. coli O157:H7 mostraram-se sensíveis à tetraciclina, cefepime, cefoxitina, ciprofloxacina e sulfazotrim, e 78,85% deles foram resistentes à cefalotina e 34,61% à ampicilina. Todas E. coli O26 foram sensíveis ao cefepime, cefoxitina e sulfazotrim, e 88,23% resistentes à tetraciclina e cefalotina e 82,35% à ampicilina. A multirresistência aos antibimicrobianos foi observada em todos os sorotipos, devendo, portanto, haver critérios no uso de antimicrobianos nos tratamentos para não se tornar um problema de saúde pública.

Fecal shedding of non-O157 serogroups of Shiga toxin-producing Escherichia coli in feedlot cattle vaccinated with an Escherichia coli O157:H7 SRP vaccine or fed a Lactobacillus-based direct-fed microbial

The objectives of this study were to determine whether fecal shedding of non-O157 Shiga toxin-producing Escherichia coli (STEC) in feedlot cattle was affected by the use of an E. coli O157:H7 vaccine or a direct-fed microbial (DFM) and whether the shedding of a particular non-O157 STEC serogroup within feces was associated with shedding of O157 or other non-O157 STEC serogroups. A total of 17,148 cattle in 40 pens were randomized to receive one, both, or neither (control) of the two interventions: a vaccine based on the siderophore receptor and porin proteins (E. coli SRP vaccine, two doses) and a DFM product (low-dose Bovamine). Fresh fecal samples (30 samples per pen) were collected weekly from pen floors for four consecutive weeks beginning approximately 56 days after study allocation. DNA extracted from enriched samples was tested for STEC O157 and non-O157 serogroups O26, O45, O103, O111, O121, and O145 and for four major virulence genes (stx1, stx2, eae, and ehxA) using an 11-gene multiplex PCR assay. Generalized linear mixed models were used to analyze the effects of treatments and make within-sample comparisons of the presence of O-serogroup-specific genes. Results of cumulative prevalence measures indicated that O157 (14.6%), O26 (10.5%), and O103 (10.3%) were the most prevalent STEC O serogroups. However, the vaccine, DFM, or both had no significant effect (P > 0.05) on fecal prevalence of the six non-O157 STEC serogroups in feedlot cattle. Within-sample comparisons of the presence of STEC serogroup-specific genes indicated that fecal shedding of E. coli O157 in cattle was associated with an increased probability (P < 0.05) of fecal shedding of STEC O26, O45, O103, and O121. Our study revealed that neither the E. coli O157:H7 vaccine, which reduced STEC O157 fecal shedding, nor the DFM significantly affected fecal shedding of non-O157 STEC serogroups, despite the fact that the most prevalent non-O157 STEC serogroups tended to occur concurrently with O157 STEC strains within fecal samples.