Longitudinal study of Escherichia coli O157:H7 in a beef cattle feedlot and role of high-level shedders in hide contamination

A review of the role of epigenetic studies for intramuscular fat deposition in beef cattle

Intramuscular fat (IMF) deposition profoundly influences meat quality and economic value in beef cattle production. Meanwhile, contemporary developments in epigenetics have opened new outlooks for understanding the molecular basics of IMF regulation, and it has become a key area of research for world scholars. Therefore, the aim of this paper was to provide insight and synthesis into the intricate relationship between epigenetic mechanisms and IMF deposition in beef cattle. The methodology involves a thorough analysis of existing literature, including pertinent books, academic journals, and online resources, to provide a comprehensive overview of the role of epigenetic studies in IMF deposition in beef cattle. This review summarizes the contemporary studies in epigenetic mechanisms in IMF regulation, high-resolution epigenomic mapping, single-cell epigenomics, multi-omics integration, epigenome editing approaches, longitudinal studies in cattle growth, environmental epigenetics, machine learning in epigenetics, ethical and regulatory considerations, and translation to industry practices from perspectives of IMF deposition in beef cattle. Moreover, this paper highlights DNA methylation, histone modifications, acetylation, phosphorylation, ubiquitylation, non-coding RNAs, DNA hydroxymethylation, epigenetic readers, writers, and erasers, chromatin immunoprecipitation followed by sequencing, whole genome bisulfite sequencing, epigenome-wide association studies, and their profound impact on the expression of crucial genes governing adipogenesis and lipid metabolism. Nutrition and stress also have significant influences on epigenetic modifications and IMF deposition. The key findings underscore the pivotal role of epigenetic studies in understanding and enhancing IMF deposition in beef cattle, with implications for precision livestock farming and ethical livestock management. In conclusion, this review highlights the crucial significance of epigenetic pathways and environmental factors in affecting IMF deposition in beef cattle, providing insightful information for improving the economics and meat quality of cattle production.

Identification of Contamination Sources and Assessment of Risk Factors Associated with the Occurrence of Escherichia coli O157:H7 on Small-scale Cow-calf Operations in Oklahoma and Louisiana

Escherichia coli O157:H7 is a human pathogen that exists as part of the commensal microflora of cattle and is shed in animal feces. Little is known about the effect of management practices on its occurrence and transmission on small-scale cow-calf operations. Identification of risk factors associated with farm practices could help implement effective measures to control E. coli O157:H7. This study quantified the risk of E. coli O157:H7 occurrence associated with cow-calf farm practices using risk modeling. Management practices of small-scale cow-calf operations in OK and LA were assessed through survey-based research. Fecal, water, sediments and water-trough-swab samples were collected to determine the incidence of E. coli O157:H7, and potential on-farm contamination sources and risk factors identified. Association between the occurrence of pathogen and farm practices was determined using two risk assessment models (I and II). Model I determined the association of E. coli O157:H7 occurrence with water source, water container, feed, cattle breed, and herd density, while Model II determined its association with farm cleanliness. For both models, logistic regression was followed using a two-step approach, univariable and multivariable analysis. In OK and LA, E. coli O157:H7 was present in 5.8% and 8.8% fecal, 4.4% and 9.4% water, 10.3% and 9.6% sediments, and 1.5% and 10.6% water-trough-swab samples, respectively. In Model I, univariable analysis identified water container and feed, whereas multivariable analysis identified feed as a significant risk factor. In Model II, the univariable analysis found cleanliness of cattle-contact areas, such as, alleyways, water-trough, chute and equipment, to be a significant risk factor. In multivariable analysis, only the cleanliness of water-trough was identified to be a significant risk factor. Results from the study could aid in the development of on-farm best management practices for the reduction of E. coli O157:H7.

Phenolic Compounds in Bacterial Inactivation: A Perspective from Brazil

Phenolic compounds are natural substances that are produced through the secondary metabolism of plants, fungi, and bacteria, in addition to being produced by chemical synthesis. These compounds have anti-inflammatory, antioxidant, and antimicrobial properties, among others. In this way, Brazil represents one of the most promising countries regarding phenolic compounds since it has a heterogeneous flora, with the presence of six distinct biomes (Cerrado, Amazon, Atlantic Forest, Caatinga, Pantanal, and Pampa). Recently, several studies have pointed to an era of antimicrobial resistance due to the unrestricted and large-scale use of antibiotics, which led to the emergence of some survival mechanisms of bacteria to these compounds. Therefore, the use of natural substances with antimicrobial action can help combat these resistant pathogens and represent a natural alternative that may be useful in animal nutrition for direct application in food and can be used in human nutrition to promote health. Therefore, this study aimed to (i) evaluate the phenolic compounds with antimicrobial properties isolated from plants present in Brazil, (ii) discuss the compounds across different classes (flavonoids, xanthones, coumarins, phenolic acids, and others), and (iii) address the structure-activity relationship of phenolic compounds that lead to antimicrobial action.

Reduction of Pathogens in Feces and Lymph Nodes Collected from Beef Cattle Fed Lactobacillus salivarius (L28), Lactobacillus acidophilus (NP51) and Propionibacterium freudenreichii (NP28), Commercially Available Direct-Fed Microbials

The purpose of the study was to evaluate the prevalence and concentration of foodborne pathogens in the feces and peripheral lymph nodes (PLNs) of beef cattle when supplemented with direct-fed microbials (DFMs) in feedlots. Fecal samples were collected from the pen floors over a 5-month period at three different feedlots in a similar geographical location in Nebraska, where each feed yard represented a treatment group: (i.) control: no supplement, (ii.) Bovamine Defend: supplemented with NP51 and NP24 at a target dose of 9 log₁₀CFU/g/head/day, and (iii.) Probicon: supplemented with L28 at a target dose of 6 log₁₀CFU/g/head/day. Each fecal sample was tested for the prevalence of E. coli O157:H7 and Salmonella, and concentration of E. coli O157:H7, Enterobacteriaceae and Clostridium perfringens. Cattle were harvested and PLNs were collected on the harvest floor. Real-time Salmonella PCR assays were performed for each PLN sample to determine Salmonella presence. The cattle supplemented with both DFMs had reduced foodborne pathogens in fecal samples, but feces collected from the pens housing the cattle supplemented with Probicon consistently had significantly less E. coli O157:H7 and Salmonella prevalence as well as a lower C. perfringens concentration. While DFMs do not eliminate foodborne pathogens in fecal shedding and PLNs, the use of DFMs as a pre-harvest intervention allows for an effective way to target multiple pathogens reducing the public health risks and environmental dissemination from cattle.

Super Shedding in Enteric Pathogens: A Review

Super shedding occurs when a small number of individuals from a given host population shed high levels of a pathogen. Beyond this general definition, various interpretations of the shedding patterns have been proposed to identify super shedders, leading to the description of the super shedding phenomenon in a wide range of pathogens, in particular enteric pathogens, which are of considerable interest. Several underlying mechanisms may explain this observation, including factors related to the environment, the gut microbiota, the pathogen itself (i.e., genetic polymorphism), and the host (including immune factors). Moreover, data suggest that the interplay of these parameters, in particular at the host-pathogen-gut microbiota interface, is of crucial importance for the determination of the super shedding phenotype in enteric pathogens. As a phenomenon playing an important role in the epidemics of enteric diseases, the evidence of super shedding has highlighted the need to develop various control strategies.

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.

Characterization of Escherichia coli harboring colibactin genes (clb) isolated from beef production and processing systems

Certain strains of Escherichia coli possess and express the toxin colibactin (Clb) which induces host mutations identical to the signature mutations of colorectal cancer (CRC) that lead to tumorigenic lesions. Since cattle are a known reservoir of several Enterobacteriaceae including E. coli, this study screened for clb amongst E. coli isolated from colons of cattle-at-harvest (entering beef processing facility; n = 1430), across the beef processing continuum (feedlot to finished subprimal beef; n = 232), and in ground beef (n = 1074). Results demonstrated that clb⁺E. coli were present in cattle and beef. Prevalence of clb⁺E. coli from colonic contents of cattle and ground beef was 18.3% and 5.5%, respectively. clb⁺E. coli were found susceptible to commonly used meat processing interventions. Whole genome sequencing of 54 bovine and beef clb⁺ isolates showed clb occurred in diverse genetic backgrounds, most frequently in phylogroup B1 (70.4%), MLST 1079 (42.6%), and serogroup O49 (40.7%).

Variations of the Escherichia coli population in the digestive tract of broilers

We explored the between-group and temporal variations in the intestinal Escherichia coli populations of broilers under experimental conditions, taking both antimicrobial resistance and virulence into consideration. Four replicates of 45 commercial chicks were reared in four animal facilities. On their first day of life (Day 0), they were orally inoculated with two extended-spectrum-cephalosporin-resistant (ESCR) E. coli (2.72 log₁₀ CFU of a bla _CMY-2- and 2.55 log₁₀ CFU of a bla _CTX-M-carrying E. coli). Faecal samples were then collected weekly and caecal samples were obtained from birds sacrificed on Days 21 or 42. The total, ESC-, ciprofloxacin- and gentamicin-resistant E. coli populations were enumerated on MacConkey (MC) and MC-supplemented media, and eight virulence-associated genes (VAGs) (iroN, iutA, iss, ompT, hlyF, vat, frz_orf4 , and fyuA) were sought by PCR on isolates obtained on MC agar. The results showed significant between-group differences in the size of the resistant sub-populations and the presence of VAGs. Contrary to bla _CTX-M-positive strains, bla _CMY-positive strains persisted up to Day 42, but represented only a minor fraction of the total E. coli population. The ESC-, gentamicin- and ciprofloxacin-resistant populations decreased over time. Isolates obtained during the first week contained a mean of 5.1 VAGs. The percentages of some VAG profiles differed between faecal isolates on Day 41 and caecal isolates on Day 42. The fluctuations or differences between E. coli isolates according to group, age, and faecal or caecal origin need to be considered when designing experimental protocols and seeking to improve colibacillosis control. RESEARCH HIGHLIGHTS Temporal variations in the intestinal E. coli populations of broilers was studied. The antibiotic-resistant populations decreased over time. Virulence profiles differed between faecal isolates on Day 41 and caecal isolates on Day 42. Strains with the highest numbers of virulence genes were present during the first days.

Associations Between Season, Processing Plant, and Hide Cleanliness Scores with Prevalence and Concentration of Major Shiga Toxin-Producing Escherichia coli on Beef Cattle Hides

The objectives of this study were (1) to estimate the prevalence and concentration of the seven major Shiga toxin-producing Escherichia coli (STEC) serogroups (O26, O45, O103, O111, O121, O145, and O157), collectively called STEC-7, on cattle hides collected in different seasons and beef processing plants; and (2) to determine associations of season, plant, and hide cleanliness scores with the prevalence and concentration of STEC-7. A total of 720 hide surface samples (240/season) were collected over three seasons (summer and fall 2015 and spring 2016) from beef cattle carcasses in four commercial processing plants in the United States. Samples were subjected to selective culture and spiral plating methods. Overall model-adjusted mean prevalence (95% confidence interval) was 0.3% (0.03-2.3%) for STEC O26; 0.05% (<0.01-8.5%) for STEC O45; 0.2% (0.02-1.9%) for STEC O103; 0.05% (<0.01-8.5%) for STEC O145; and 3.1% (0.6-15.2%) for STEC O157. Four percent of hide samples were enumerable for STEC O157; mean concentration (standard deviation) = 2.1 (0.7) log₁₀ colony-forming units (CFUs)/100 cm². No samples were enumerable for non-O157 STEC. Hide-on prevalence of STEC O157 and STEC non-O157 (specifically of STEC O103) was higher in summer and spring, respectively. Across seasons and plants, the most common STEC non-O157 serogroups in this study (O26 and O103) were associated with a higher prevalence of STEC O157. Season and plant played a role in prevalence and concentration of STEC in beef cattle hides, varying by serogroup. Tailoring mitigation strategies at the plant can be challenging and processors would benefit from supplementary preharvest interventions to reduce overall contamination pressure at the plant, especially in fall and spring months when hide-on prevalence of STEC non-O157 is higher.

Socially engaged calves are more likely to be colonised by VTEC O157:H7 than individuals showing signs of poor welfare

In cattle herds, the transmission and persistence of VTEC O157:H7 (a serotype of verotoxin-producing Escherichia coli – known for its life threatening complications in humans) is dependent on a small proportion of cattle who become colonised and shed high numbers of the bacteria. Reducing the proportion of these animals is considered key for decreasing the prevalence of VTEC O157:H7. In this study, observations of calf behaviour and animal-based welfare indicators were used to explore individual risk factors and underlying drivers of colonisation in Swedish dairy calves. Interdependencies between variables led to three different approaches being used to visualize and explore the associations. Combining the results of all methods revealed similar patterns and suggest that healthy animals, actively grooming and interacting with others calves in the group have a higher risk of colonisation than small dairy calves in poor condition (diarrhoea, poor ruminal fill, poor body condition score and nasal discharge). This lends no support to the hypothesis that reduced welfare is a risk factor for VTEC O157:H7, but implies that individual differences in calf behaviour affect oral exposure to the bacteria so driving the risk of colonisation. This new finding has important implications for understanding of VTEC O157:H7 transmission within farms.

Supershed Escherichia coli O157:H7 Has Potential for Increased Persistence on the Rectoanal Junction Squamous Epithelial Cells and Antibiotic Resistance

Supershedding cattle shed Escherichia coli O157:H7 (O157) at ≥ 104 colony-forming units/g feces. We recently demonstrated that a supershed O157 (SS-O157) strain, SS-17, hyperadheres to the rectoanal junction (RAJ) squamous epithelial (RSE) cells which may contribute to SS-O157 persistence at this site in greater numbers, thereby increasing the fecal O157 load characterizing the supershedding phenomenon. In order to verify if this would be the signature adherence profile of any SS-O157, we tested additional SS-O157 isolates (n = 101; each from a different animal) in the RSE cell adherence assay. Similar to SS-17, all 101 SS-O157 exhibited aggregative adherence on RSE cells, with 56% attaching strongly (>10 bacteria/cell; hyperadherent) and 44% attaching moderately (1-10 bacteria/cells). Strain typing using Polymorphic Amplified Typing Sequences (PATS) analysis assigned the 101 SS-O157 into 5 major clades but not to any predominant genotype. Interestingly, 69% of SS-O157 isolates were identical to human O157 outbreak strains based on pulsed field gel electrophoresis profiles (CDC PulseNet Database), grouped into two clades by PATS distinguishing them from remaining SS-O157, and were hyperadherent on RSE cells. A subset of SS-O157 isolates (n = 53) representing different PATS and RSE cell adherence profiles were analyzed for antibiotic resistance (AR). Several SS-O157 (30/53) showed resistance to sulfisoxazole, and one isolate was resistant to both sulfisoxazole and tetracycline. Minimum inhibitory concentration (MIC) tests confirmed some of the resistance observed using the Kirby-Bauer disk diffusion test. Each SS-O157 isolate carried at least 10 genes associated with AR. However, genes directly associated with AR were rarely amplified: aac (3)-IV in 2 isolates, sul2 in 3 isolates, and tetB in one isolate. The integrase gene, int, linked with integron-based AR acquisition/transmission, was identified in 92% of SS-O157 isolates. Our results indicate that SS-O157 isolates could potentially persist longer at the bovine RAJ but exhibit limited resistance towards clinical antibiotics.

Evaluation of Bactericidal Effects of Phenyllactic Acid on Escherichia coli O157:H7 and Salmonella Typhimurium on Beef Meat

Bactericidal effects of various concentrations of phenyllactic acid on Shiga toxin-producing Escherichia coli (STEC), including E. coli O157:H7, O26:H11, O103:H2, and O121:H19, and on Salmonella Typhimurium DT104 in pure culture and microplates assays were studied. Beef cuts were surface sprayed with phenyllactic acid or lactic acid for inactivation of E. coli O157:H7 and Salmonella Typhimurium. The 1.5% phenyllactic acid inactivated all inoculated E. coli O157:H7, O26:H11, O103:H2, and O121:H19 and Salmonella Typhimurium DT104 (>6-log reduction) within 1 min of contact at 21°C, whereas 1.5% lactic acid did not result in microbial reduction. Microplate assays (for STEC and Salmonella Typhimurium DT104 at 10 to 100 CFU per well) indicated that concentrations of 0.25% phenyllactic acid or 0.25% lactic acid inhibited the growth of STEC and Salmonella Typhimurium DT104 incubated at 37°C for 24 h. Treatment of beef with 1.5% lactic acid or 1.5% phenyllactic acid reduced E. coli O157:H7 by 0.22 and 0.38 log CFU/cm², respectively, within 5 min and reduced Salmonella Typhimurium DT104 by 0.12 and 0.86 log CFU/cm², respectively. When meat treated with 1.5% phenyllactic acid was frozen at -20°C, inactivation of E. coli O157 and Salmonella Typhimurium DT104 was enhanced by 1.06 and 1.46 log CFU/cm², respectively. Thus, treatment of beef with 1.5% phenyllactic acid significantly reduced the population of E. coli O157:H7 and Salmonella.

A one-year longitudinal study of enterohemorrhagic Escherichia coli O157 fecal shedding in a beef cattle herd

Bovines are the primary reservoir of enterohemorrhagic Escherichia coli (EHEC) O157:H7 and the main source of its transmission to humans. Here, we present a one-year longitudinal study of fecal shedding of E. coli O157. E. coli O157 obtained from recto-anal mucosal samples were characterized by multiplex PCR. The E. coli O157 prevalence ranged from 0.84% in July to 15.25% in November. The confinement within pens resulted in prevalence of 11%. Most animals (61.86%; 75/118) shed E. coli O157 at least in one sampling occasion. Of the positive animals, 82.19%, 16.44%, and 1.37% were stx positive on one, two and three sampling occasions, respectively. All the E. coli O157 isolated strains carried the genes eae and rfb_O157, whereas 11%, 33% and 56% contained stx₁, stx₂ and stx₁/stx₂, respectively. The stx₁/stx₂ and stx₂ types were significantly higher during the grazing and finishing periods, respectively, in comparison with the rearing and grazing periods. The presence of stx_2a subtype was evident in four isolates, whereas stx_2c was present in at least seven. However, both subtypes were present simultaneously in two isolates. The stx₁/stx_2c, stx₁/stx_2d and stx₁/stx_2NT genotypes occurred in 24, 2 and 15 isolates, respectively. The simultaneous occurrence of stx₁ and stx_2c significantly increased during grazing. Some cases of within-pen and between-pen transmission occurred throughout the study. Contagion levels during in-field grazing were higher than during permanent confinement in the pens. Thus, the individual patterns of shedding varied depending on the proportion of animals shedding the bacteria within pens and the time of shedding.

Distribution of the stx1 and stx2 genes in Escherichia coli isolated from milk cattle according to season, age, and production scale in southwestern region of Goiás, Brazil

ABSTRACT This study determined the distribution of stx1 and stx2 genes in Escherichia coli isolated from dairy herds with regard to animal age, season, and farm production-scale, and analyzed the phylogenetic distribution of the groups A, B1, B2, and D of 276 isolates of bovine feces Shiga toxin-producing E. coli (STEC). The stx1 profile was the most common, detected in 20.4% (202/990) of the isolates, followed by stx2 (4.54%, 45/990) and stx1+stx2 (2.92%, 29/990). The stx1 gene was detected more frequently in calves than in adult animals. In the dry season (winter), the presence of stx1+stx2 profile in cattle feces was higher than in the rainy season (summer), while no significant changes were observed between seasons for the stx1 and stx2 profiles. The most predominant phylogenetic groups in adult animals were B1, A, and D, while groups A and B1 prevailed in calves. Our data highlight the importance of identifying STEC reservoirs, since 7.5% of the tested isolates were positive for stx2, the main profile responsible for the hemolytic-uremic syndrome (HUS). Moreover, these microorganisms are adapted to survive even in hostile environments and can contaminate the food production chain, posing a significant risk to consumers of animal products.

An investigation of shedding and super-shedding of Shiga toxigenic Escherichia coli O157 and E. coli O26 in cattle presented for slaughter in the Republic of Ireland

Shiga toxigenic Escherichia coli (STEC) are an important group of pathogens and can be transmitted to humans from direct or indirect contact with cattle faeces. This study investigated the shedding of E. coli O157 and O26 in cattle at the time of slaughter and factors associated with super-shedding (SS) animals. Rectoanal mucosal swab (RAMS) samples were collected from cattle (n = 1,317) at three large Irish commercial beef abattoirs over an 18 month period, and metadata were collected at the time of sampling regarding farm of origin, animal age, breed and gender. RAMS swabs were examined for the presence and numbers of E. coli O157 and O26 using a previously developed quantitative real-time PCR protocol. Samples positive by PCR were culturally examined and isolates analysed for the presence of stx subtypes, eae and phylogroup. Any samples with counts >10⁴  CFU/swab of STEC O157 or O26 were deemed to be super-shedders. Overall, 4.18% (55/1,317) of RAMS samples were positive for STEC O157, and 2.13% (28/1,317) were classified as STEC O157 SS. For STEC O26, 0.76% (10/1,317) of cattle were positive for STEC O26, and 0.23% (3/1,317) were classified as super-shedders. Fewer STEC shedders and SS were noted among older animals (>37 months). There was a seasonal trend observed for STEC O157, with the highest prevalence of shedding and SS events in the autumn (August to October). The majority of E. coli O157 (50/55) isolates had stx2 and were eae positive, with no significant difference between SS and low shedders (LS). Interestingly, all STEC O26 (n = 10) were eae negative and had varied stx profiles. This study demonstrates that, while the overall shedding rates are relatively low in cattle at slaughter, among positive animals there is a high level of SS, which may pose a higher risk of cross-contamination during slaughter.

Detection and Quantification of Seven Major Serogroups of Shiga Toxin-Producing Escherichia coli on Hides of Cull Dairy, Cull Beef, and Fed Beef Cattle at Slaughter†

Dehiding during beef cattle processing can introduce fecal contaminants, including Shiga toxin-producing Escherichia coli (STEC), from hides onto carcass surfaces, creating the potential for contaminated beef. Fecal shedding of major STEC serogroups (O26, O45, O103, O111, O121, O145, and O157; STEC-7) may differ among cattle populations, yet no study has been conducted to isolate STEC-7 on hides of multiple cattle types on the same production days at the same processing plant. Our objective was to estimate and compare prevalence and concentrations of STEC-7 on hides of cull dairy, cull beef, and fed beef cattle from the same date and processing plant. Overall, 1,500 cattle hides were sponge sampled from cull dairy ( n = 500), cull beef ( n = 500) and fed beef cattle ( n = 500) over 10 processing days. To determine prevalence, samples were subjected to an immunomagnetic separation culture method, and presumptive STEC isolates were tested by PCR for serogroup and major virulence genes. A spiral plate method was used to enumerate STEC-7 from hide samples. Data were analyzed with linear mixed models. All STEC-7 serogroups except O121 were detected and quantified on cattle hides in this study population. Slightly more fed beef hides (77 of 500; 15.4%) and cull beef hides (76 of 500; 15.2%) were positive for at least one STEC-7 strain compared with cull dairy hides (57 of 500; 11.4%), but cattle type was not significantly associated ( P = 0.19) with STEC-7 prevalence. Fed beef hides had a significantly higher prevalence ( P < 0.05) of STEC O103, O145, and O157 serogroups than did either of the other cattle types. The highest proportions of quantifiable samples were for STEC O145 (32 of 1,500 samples; 2.1%) and O157 (31 of 1,500 samples; 2.1%) serogroups, with the majority of concentrations at 3 to 5 and 2 to 4 log CFU/100 cm² of hide, respectively. Results indicate that hide contamination with some major STEC serogroups differs significantly among cattle types at harvest, even within the same day and location.

The effect of transportation and lairage on faecal shedding and carcass contamination with Escherichia coli O157 and O26 in very young calves in New Zealand

The effect of transportation and lairage on the faecal shedding and post-slaughter contamination of carcasses with Escherichia coli O157 and O26 in young calves (4-7-day-old) was assessed in a cohort study at a regional calf-processing plant in the North Island of New Zealand, following 60 calves as cohorts from six dairy farms to slaughter. Multiple samples from each animal at pre-slaughter (recto-anal mucosal swab) and carcass at post-slaughter (sponge swab) were collected and screened using real-time PCR and culture isolation methods for the presence of E. coli O157 and O26 (Shiga toxin-producing E. coli (STEC) and non-STEC). Genotype analysis of E. coli O157 and O26 isolates provided little evidence of faecal-oral transmission of infection between calves during transportation and lairage. Increased cross-contamination of hides and carcasses with E. coli O157 and O26 between co-transported calves was confirmed at pre-hide removal and post-evisceration stages but not at pre-boning (at the end of dressing prior to chilling), indicating that good hygiene practices and application of an approved intervention effectively controlled carcass contamination. This study was the first of its kind to assess the impact of transportation and lairage on the faecal carriage and post-harvest contamination of carcasses with E. coli O157 and O26 in very young calves.

Corn-Based Distillers' Grains in Diets for Feedlot Cattle Are Associated with the Burden of Escherichia coli O157 in Feces

Inclusion of distillers' grains (DGs) has been associated with increased prevalence of Escherichia coli O157:H7 in cattle housed in research settings. Our objective was to quantify the relationship between inclusion of DGs in commercial feedlot rations and the burden of E. coli O157. A convenience sample of 10 feedlots was enrolled based on DG use in finishing diets; 1 cohort included 5 feedlots in which DGs were greater than 15% of the dietary dry matter and the other cohort consisted of 5 feedlots at a concentration less than 8%. Sampling occurred at each feedlot on four occasions at ∼6-week intervals. At each feedlot visit, 4 pens of cattle within 3 weeks of slaughter were selected and 24 freshly voided fecal pats were sampled. Ten-gram samples were enriched in 90 mL of modified tryptic soy broth with novobiocin (20 mg/L) for 14 h at 42°C. Enrichments were subjected to immunomagnetic separation, plating onto chromogenic agar with novobiocin (5 mg/L) and potassium tellurite (2.5 mg/L), incubation for 18 h at 37°C, and latex agglutination of morphologically typical colonies. E. coli O157 was recovered from 16.7% of 3840 samples. Adjusted prevalence was 14.3% after controlling for within-feedlot and within-pen clustering. Prevalence during each sampling period was 19.9% (round 1), 21.0% (round 2), 14.1% (round 3), and 11.7% (round 4). Prevalence varied between cohorts, but this difference varied over time (p = 0.06). Among those with greater than 15% of the diet as DGs, prevalence was greater than those with less than 8% inclusion for all rounds of sampling (p < 0.01). Averaged across time, prevalence was 23.9% and 9.4% for those with greater than 15% and those with less than 8% of DGs, respectively. While observational, these data provide real-world support of reports of increased E. coli O157:H7 burden associated with DG use in cattle diets.

The prevalence of Escherichia coli O157:H7 fecal shedding in feedlot pens is affected by the water-to-cattle ratio: A randomized controlled trial

Escherichia coli O157:H7 fecal shedding in feedlot cattle is common and is a public health concern due to the risk of foodborne transmission that can result in severe, or even fatal, disease in people. Despite a large body of research, few practical and cost-effective farm-level interventions have been identified. In this study, a randomized controlled trial was conducted to assess the effect of reducing the level of water in automatically refilling water-troughs on fecal shedding of E. coli O157:H7 in feedlot cattle. Pens in a feedlot in the Texas Panhandle were randomly allocated as control (total number: 17) or intervention (total number: 18) pens. Fecal samples (2,759 in total) were collected both at baseline and three weeks after the intervention, and tested for the presence of E. coli O157:H7 using immunomagnetic bead separation and selective culture. There was a strong statistical association between sampling date and the likelihood of a fecal sample testing positive for E. coli O157:H7. Pen was also a strong predictor of fecal prevalence. Despite accounting for this high level of clustering, a statistically significant association between reduced water levels in the trough and increased prevalence of E. coli O157:H7 in the feces was observed (Odds Ratio = 1.6; 95% Confidence Interval: 1.2–2.0; Likelihood Ratio Test: p = 0.02). This is the first time that such an association has been reported, and suggests that increasing water-trough levels may be effective in reducing shedding of E. coli O157:H7 in cattle feces, although further work would be needed to test this hypothesis. Controlling E. coli O157:H7 fecal shedding at the pre-harvest level may lead to a reduced burden of human foodborne illness attributed to this pathogen in beef.

Enterohaemorrhagic and other Shiga toxin-producing Escherichia coli (STEC): Where are we now regarding diagnostics and control strategies?

Escherichia coli comprises a highly diverse group of Gram-negative bacteria and is a common member of the intestinal microflora of humans and animals. Generally, such colonization is asymptomatic; however, some E. coli strains have evolved to become pathogenic and thus cause clinical disease in susceptible hosts. One pathotype, the Shiga toxigenic E. coli (STEC) comprising strains expressing a Shiga-like toxin is an important foodborne pathogen. A subset of STEC are the enterohaemorrhagic E. coli (EHEC), which can cause serious human disease, including haemolytic uraemic syndrome (HUS). The diagnosis of EHEC infections and the surveillance of STEC in the food chain and the environment require accurate, cost-effective and timely tests. In this review, we describe and evaluate tests now in routine use, as well as upcoming test technologies for pathogen detection, including loop-mediated isothermal amplification (LAMP) and whole-genome sequencing (WGS). We have considered the need for improved diagnostic tools in current strategies for the control and prevention of these pathogens in humans, the food chain and the environment. We conclude that although significant progress has been made, STEC still remains an important zoonotic issue worldwide. Substantial reductions in the public health burden due to this infection will require a multipronged approach, including ongoing surveillance with high-resolution diagnostic techniques currently being developed and integrated into the routine investigations of public health laboratories. However, additional research requirements may be needed before such high-resolution diagnostic tools can be used to enable the development of appropriate interventions, such as vaccines and decontamination strategies.

The impact of the bovine faecal microbiome on Escherichia coli O157:H7 prevalence and enumeration in naturally infected cattle

AIMS

The objective of this study was to determine if the faecal microbiome has an association with Escherichia coli O157:H7 prevalence and enumeration.

METHODS AND RESULTS

Pyrosequencing analysis of faecal microbiome was performed from feedlot cattle fed one of three diets: (i) 94 heifers fed low concentrate (LC) diet, (ii) 142 steers fed moderate concentrate (MC) diet, and (iii) 132 steers fed high concentrate (HC) diet. A total of 322 585 OTUs were calculated from 2,411,122 high-quality sequences obtained from 368 faecal samples. In the LC diet group, OTUs assigned to the orders Clostridiales and RF39 (placed within the class Mollicutes) were positively correlated with both E. coli O157:H7 prevalence and enumeration. In the MC diet group, OTUs assigned to Prevotella copri were positively correlated with both E. coli O157:H7 prevalence and enumeration, whereas OTUs assigned to Prevotella stercorea were negatively correlated with both E. coli O157:H7 prevalence and enumeration. In both the MC diet group and the HC diet group, OTUs assigned to taxa placed within Clostridiales were both positively and negatively correlated with both E. coli O157:H7 prevalence and enumeration. However, all correlations were weak. In both the MC diet group and the HC diet group, stepwise linear regression through backward elimination analyses indicated that these OTUs were significantly correlated (P < 0·001) with prevalence or enumeration, explaining as much as 50% of variability in E. coli O157:H7 prevalence or enumeration.

CONCLUSIONS

Individual colonic bacterial species have little impact on E. coli O157:H7 shedding but collectively groups of bacteria were strongly associated with pathogen shedding.

SIGNIFICANCE AND IMPACT OF THE STUDY

Bacterial groups in the bovine colon may impact faecal shedding of the zoonotic pathogen E. coli O157:H7, and manipulation of the intestinal microbiota to alter these bacteria may reduce shedding of this pathogen and foodborne illnesses.

Host mechanisms involved in cattle Escherichia coli O157 shedding: a fundamental understanding for reducing foodborne pathogen in food animal production

The host mechanisms involved in Escherichia coli O157 super-shedding in cattle is largely unknown. In this study, the comparison of transcriptomes of intestinal tissues between super-shedders (SS) and cattle negative for E. coli O157 (NS) was performed, aiming to identify genes that are potentially associated with super-shedding. In total, 16,846 ± 639 (cecum) to 18,137 ± 696 (distal jejunum) were expressed throughout the intestine, with the expressed genes associated with immune functions more pronounced in the small intestine. In total, 351 differentially expressed (DE) genes were identified throughout the intestine between SS and NS, with 101 being up-regulated and 250 down-regulated in SS. Functional analysis revealed DE genes were involved in increased T-cell responses and cholesterol absorption in the distal jejunum and descending colon, and decreased B-cell maturation in the distal jejunum of SS. RNA-Seq based SNP discovery revealed that the mutations in seven DE genes involved in leukocyte activation and cholesterol transportation were associated with E. coli O157 shedding. Our findings suggest that T-cell responses and cholesterol metabolism in the intestinal tract may be associated with super-shedding phenomenon, and the SNPs in the DE genes are possibly associated with the observed gene expression difference between SS and NS.

Persistence of Escherichia coli O157:H7 and Total Escherichia coli in Feces and Feedlot Surface Manure from Cattle Fed Diets with and without Corn or Sorghum Wet Distillers Grains with Solubles

Feeding corn wet distillers grains with solubles (WDGS) to cattle can increase the load of Escherichia coli O157:H7 in feces and on hides, but the mechanisms are not fully understood. The objective of these experiments was to examine a role for the persistence of E. coli O157:H7 in the feces and feedlot pen surfaces of cattle fed WDGS. In the first study, feces from steers fed 0, 20, 40, or 60% corn WDGS were inoculated with E. coli O157:H7. The E. coli O157:H7 numbers in feces from cattle fed 0% corn WDGS rapidly decreased (P < 0.05), from 6.28 to 2.48 log CFU/g of feces by day 14. In contrast, the E. coli O157:H7 numbers in feces from cattle fed 20, 40, and 60% corn WDGS were 4.21, 5.59, and 6.13 log CFU/g of feces, respectively, on day 14. A second study evaluated the survival of E. coli O157:H7 in feces from cattle fed 0 and 40% corn WDGS. Feces were collected before and 28 days after the dietary corn was switched from high-moisture corn to dry-rolled corn. Within dietary corn source, the pathogen persisted at higher concentrations (P < 0.05) in 40% corn WDGS feces at day 7 than in 0% WDGS. For 40% corn WDGS feces, E. coli O157:H7 persisted at higher concentrations (P < 0.05) at day 7 in feces from cattle fed high-moisture corn (5.36 log CFU/g) than from those fed dry-rolled corn (4.27 log CFU/g). The percentage of WDGS had no effect on the E. coli O157:H7 counts in feces from cattle fed steam-flaked corn-based diets containing 0, 15, and 30% sorghum WDGS. Greater persistence of E. coli O157:H7 on the pen surfaces of animals fed corn WDGS was not demonstrated, although these pens had a higher prevalence of the pathogen in the feedlot surface manure after the cattle were removed. Both or either the greater persistence and higher numbers of E. coli O157:H7 in the environment of cattle fed WDGS may play a part in the increased prevalence of E. coli O157:H7 in cattle by increasing the transmission risk.

Reducing Foodborne Pathogen Persistence and Transmission in Animal Production Environments: Challenges and Opportunities

Preharvest strategies to reduce zoonotic pathogens in food animals are important components of the farm-to-table food safety continuum. The problem is complex; there are multiple pathogens of concern, multiple animal species under different production and management systems, and a variety of sources of pathogens, including other livestock and domestic animals, wild animals and birds, insects, water, and feed. Preharvest food safety research has identified a number of intervention strategies, including probiotics, direct-fed microbials, competitive exclusion cultures, vaccines, and bacteriophages, in addition to factors that can impact pathogens on-farm, such as seasonality, production systems, diet, and dietary additives. Moreover, this work has revealed both challenges and opportunities for reducing pathogens in food animals. Animals that shed high levels of pathogens and predominant pathogen strains that exhibit long-term persistence appear to play significant roles in maintaining the prevalence of pathogens in animals and their production environment. Continued investigation and advancements in sequencing and other technologies are expected to reveal the mechanisms that result in super-shedding and persistence, in addition to increasing the prospects for selection of pathogen-resistant food animals and understanding of the microbial ecology of the gastrointestinal tract with regard to zoonotic pathogen colonization. It is likely that this continued research will reveal other challenges, which may further indicate potential targets or critical control points for pathogen reduction in livestock. Additional benefits of the preharvest reduction of pathogens in food animals are the reduction of produce, water, and environmental contamination, and thereby lower risk for human illnesses linked to these sources.

Spiral Plating Method To Quantify the Six Major Non-O157 Escherichia coli Serogroups in Cattle Feces

Cattle are a major reservoir of the six major Shiga toxin-producing non-O157 Escherichia coli (STEC) serogroups (O26, O45, O103, O111, O121, and O145) responsible for foodborne illnesses in humans. Besides prevalence in feces, the concentrations of STEC in cattle feces play a major role in their transmission dynamics. A subset of cattle, referred to as super shedders, shed E. coli O157 at high concentrations (≥4 log CFU/g of feces). It is not known whether a similar pattern of fecal shedding exists for non-O157. Our objectives were to initially validate the spiral plating method to quantify the six non-O157 E. coli serogroups with pure cultures and culture-spiked fecal samples and then determine the applicability of the method and compare it with multiplex quantitative PCR (mqPCR) assays for the quantification of the six non-O157 E. coli serogroups in cattle fecal samples collected from commercial feedlots. Quantification limits of the spiral plating method were 3 log, 3 to 4 log, and 3 to 5 log CFU/mL or CFU/g for individual cultures, pooled pure cultures, and cattle fecal samples spiked with pooled pure cultures, respectively. Of the 1,152 cattle fecal samples tested from eight commercial feedlots, 122 (10.6%) and 320 (27.8%) harbored concentrations ≥4 log CFU/g of one or more of the six serogroups of non-O157 by spiral plating and mqPCR methods, respectively. A majority of quantifiable samples, detected by either spiral plating (135 of 137, 98.5%) or mqPCR (239 of 320, 74.7%), were shedding only one serogroup. Only one of the quantifiable samples was positive for a serogroup carrying Shiga toxin (stx1) and intimin (eae) genes; 38 samples were positive for serogroups carrying the intimin gene. In conclusion, the spiral plating method can be used to quantify non-O157 serogroups in cattle feces, and our study identified a subset of cattle that was super shedders of non-O157 E. coli. The method has the advantage of quantifying non-O157 STEC, unlike mqPCR that quantifies serogroups only.

Prevalence of Escherichia coli O157:H7 in beef cattle at slaughter and beef carcasses at retail shops in Ethiopia

Background

There is paucity of information regarding the epidemiology of Escherichia coli O157: H7 in developing countries. In this study, we investigated the occurrence of E. coli O157: H7 associated with beef cattle at processing plants and at retail shops in Ethiopia.

Methods

Various samples were collected from beef cattle at slaughter/processing plants, carcass at retail shops and humans at health centers. E. coli O157: H7 was isolated, identified and characterized for antimicrobial resistance, using standard microbiological methods.

Results

At the processing plants E. coli O157: H7 was detected in 1.89% of fecal, 0.81% of intestinal mucosal swab, 0.54% of skin swab and 0.54% of carcass internal swab samples. At retail shops it was detected in 0.8% of carcass and 0.8% of cutting board swab samples, while all samples from utensils, hands from workers, and fecal and stool samples were negative. All isolates were resistant to Amoxicillin, moderately resistant to Cefoxitine and Nitrofurantoins but susceptible to other antimicrobials tested.

Conclusions

E. coli O157: H7 occurs at low prevalence in beef cattle, and the current sanitary dressing procedures in the processing plants and storage conditions in the retail shops are effective against E. coli O157: H7.

Changes in bacterial community composition of Escherichia coli O157:H7 super-shedder cattle occur in the lower intestine

Escherichia coli O157:H7 is a foodborne pathogen that colonizes ruminants. Cattle are considered the primary reservoir of E. coli O157:H7 with super-shedders, defined as individuals excreting > 10⁴E. coli O157:H7 CFU g^-1 feces. The mechanisms leading to the super-shedding condition are largely unknown. Here, we used 16S rRNA gene pyrosequencing to examine the composition of the fecal bacterial community in order to investigate changes in the bacterial microbiota at several locations along the digestive tract (from the duodenum to the rectal-anal junction) in 5 steers previously identified as super-shedders and 5 non-shedders. The overall bacterial community structure did not differ by E. coli O157:H7 shedding status; but several differences in the relative abundance of taxa and OTUs were noted between the two groups. The genus Prevotella was most enriched in the non-shedders while the genus Ruminococcus and the Bacteroidetes phylum were notably enriched in the super-shedders. There was greater bacterial diversity and richness in samples collected from the lower- as compared to the upper gastrointestinal tract (GI). The spiral colon was the only GI location that differed in terms of bacterial diversity between super-shedders and non-shedders. These findings reinforced linkages between E. coli O157:H7 colonization in cattle and the nature of the microbial community inhabiting the digestive tract of super-shedders.

Characterization of Enterohemorrhagic Escherichia coli on Veal Hides and Carcasses

Enterohemorrhagic Escherichia coli (EHEC) are Shiga toxin-producing E. coli associated with the most severe forms of foodborne illnesses. The U.S. Department of Agriculture, Food Safety and Inspection Service has identified a higher percentage of non-O157 EHEC compared with E. coli O157:H7-positive samples collected from veal trimmings than from products produced from other cattle slaughter classes. Therefore samples were collected from hides and preevisceration carcasses at five veal processors to assess E. coli O157:H7 and non-O157 EHEC contamination during bob veal and formula-fed veal dressing procedures. E. coli O157:H7 prevalence was measured by culture isolation and found to be on 20.3% of hides and 6.7% of carcasses. In contrast, a non-O157 EHEC molecular screening assay identified 90.3% of hides and 68.2% of carcasses as positive. Only carcass samples were taken forward to culture confirmation and 38.7% yielded one or more non-O157 EHEC isolates. The recovery of an EHEC varied by plant and sample collection date; values ranged from 2.1 to 87.8% among plants and from 4.2 to 64.2% within the same plant. Three plants were resampled after changes were made to sanitary dressing procedures. Between the two collection times at the three plants, hide-to-carcass transfer of E. coli O157:H7 and non-O157 EHEC was significantly reduced. All adulterant EHEC serogroups (O26, O45, O103, O111, O121, and O145) were isolated from veal carcasses as well as four other potentially pathogenic serogroups (O5, O84, O118, and O177). Bob veal was found to have a greater culture prevalence of E. coli O157:H7 and greater positive molecular screens for non-O157 EHEC than formula-fed veal (P < 0.05), but the percentage of culture-confirmed non-O157 EHEC was not different (P > 0.05) between the two types of calves. EHEC-O26, -O111, and -O121 were found more often in bob veal (P < 0.05), whereas EHEC-O103 was found more often in formula-fed veal (P < 0.05).

Curli Temper Adherence of Escherichia coli O157:H7 to Squamous Epithelial Cells from the Bovine Recto-Anal Junction in a Strain-Dependent Manner

Our recent studies have shown that intimin and the locus of enterocyte effacement-encoded proteins do not play a role in Escherichia coli O157:H7 (O157) adherence to the bovine recto-anal junction squamous epithelial (RSE) cells. To define factors that play a contributory role, we investigated the role of curli, fimbrial adhesins commonly implicated in adherence to various fomites and plant and human epithelial cells, in O157 adherence to RSE cells. Specifically, we examined (i) wild-type strains of O157; (ii) curli variants of O157 strains; (iii) isogenic curli deletion mutants of O157; and (iv) adherence inhibition of O157 using anti-curlin sera. Results of these experiments conducted under stringent conditions suggest that curli do not solely contribute to O157 adherence to RSE cells and in fact demonstrate a modulating effect on O157 adherence to RSE cells in contrast to HEp-2 cells (human epidermoid carcinoma of the larynx cells with HeLa contamination). The absence of curli and presence of blocking anti-curli antibodies enhanced O157-RSE cell interactions among some strains, thus alluding to a spatial, tempering effect of curli on O157 adherence to RSE cells when present. At the same time, the presence or absence of curli did not alter RSE cell adherence patterns of another O157 strain. These observations are at variance with the reported role of curli in O157 adherence to human cell lines such as HEp-2 and need to be factored in when developing anti-adherence modalities for preharvest control of O157 in cattle.

IMPORTANCE

This study demonstrated that O157 strains interact with epithelial cells in a host-specific manner. The fimbriae/adhesins that are significant for adherence to human cell lines may not have a role or may have a modulating role in O157 adherence to bovine cells. Targeting such adhesins may not prevent O157 attachment to bovine cells but instead may result in improved adherence. Hence, conducting host-specific evaluations is critical when selecting targets for O157 control strategies.

Heterogeneous shedding of influenza by human subjects and its implications for epidemiology and control

Heterogeneity of infectiousness is an important feature of the spread of many infections, with implications for disease dynamics and control, but its relevance to human influenza virus is still unclear. For a transmission event to occur, an infected individual needs to release infectious particles via respiratory symptoms. Key factors to take into account are virus dynamics, particle release in relation to respiratory symptoms, the amount of virus shed and, importantly, how these vary between infected individuals. A quantitative understanding of the process of influenza transmission is relevant to designing effective mitigation measures. Here we develop an influenza infection dynamics model fitted to virological, systemic and respiratory symptoms to investigate how within-host dynamics relates to infectiousness. We show that influenza virus shedding is highly heterogeneous between subjects. From analysis of data on experimental infections, we find that a small proportion (<20%) of influenza infected individuals are responsible for the production of 95% of infectious particles. Our work supports targeting mitigation measures at most infectious subjects to efficiently reduce transmission. The effectiveness of public health interventions targeted at highly infectious individuals would depend on accurate identification of these subjects and on how quickly control measures can be applied.

'Super' or just 'above average'? Supershedders and the transmission of Escherichia coli O157:H7 among feedlot cattle

Supershedders have been suggested to be major drivers of transmission of Escherichia coli O157:H7 (E. coli O157:H7) among cattle in feedlot environments, despite our relatively limited knowledge of the processes that govern periods of high shedding within an individual animal. In this study, we attempt a data-driven approach, estimating the key characteristics of high shedding behaviour, including effects on transmission to other animals, directly from a study of natural E. coli O157:H7 infection of cattle in a research feedlot, in order to develop an evidence-based definition of supershedding. In contrast to the hypothesized role of supershedders, we found that high shedding individuals only modestly increased the risk of transmission: individuals shedding over 10(3) cfu g(-1) faeces were estimated to pose a risk of transmission only 2.45 times greater than those shedding below that level. The data suggested that shedding above 10(3) cfu g(-1) faeces was the most appropriate definition of supershedding behaviour and under this definition supershedding was surprisingly common, with an estimated prevalence of 31.3% in colonized individuals. We found no evidence that environmental contamination by faeces of shedding cattle contributed to transmission over timescales longer than 3 days and preliminary evidence that higher stocking density increased the risk of transmission.

Comparative Genomic Analysis of Escherichia coli O157:H7 Isolated from Super-Shedder and Low-Shedder Cattle

Cattle are the primary reservoir of the foodborne pathogen Escherichia coli O157:H7, with the concentration and frequency of E. coli O157:H7 shedding varying substantially among individual hosts. The term ''super-shedder" has been applied to cattle that shed ≥10(4) cfu E. coli O157:H7/g of feces. Super-shedders have been reported to be responsible for the majority of E. coli O157:H7 shed into the environment. The objective of this study was to determine if there are phenotypic and/or genotypic differences between E. coli O157:H7 isolates obtained from super-shedder compared to low-shedder cattle. From a total of 784 isolates, four were selected from low-shedder steers and six isolates from super-shedder steers (4.01-8.45 log cfu/g feces) for whole genome sequencing. Isolates were phage and clade typed, screened for substrate utilization, pH sensitivity, virulence gene profiles and Stx bacteriophage insertion (SBI) sites. A range of 89-2473 total single nucleotide polymorphisms (SNPs) were identified when sequenced strains were compared to E. coli O157:H7 strain Sakai. More non-synonymous SNP mutations were observed in low-shedder isolates. Pan-genomic and SNPs comparisons did not identify genetic segregation between super-shedder or low-shedder isolates. All super-shedder isolates and 3 of 4 of low-shedder isolates were typed as phage type 14a, SBI cluster 3 and SNP clade 2. Super-shedder isolates displayed increased utilization of galactitol, thymidine and 3-O-β-D-galactopyranosyl-D-arabinose when compared to low-shedder isolates, but no differences in SNPs were observed in genes encoding for proteins involved in the metabolism of these substrates. While genetic traits specific to super-shedder isolates were not identified in this study, differences in the level of gene expression or genes of unknown function may still contribute to some strains of E. coli O157:H7 reaching high densities within bovine feces.

A Farm Transmission Model for Salmonella in Pigs, Applicable to E.U. Member States

The burden of Salmonella entering pig slaughterhouses across the European Union is considered a primary food safety concern. To assist E.U. member states with the development of national control plans, we have developed a farm transmission model applicable to all member states. It is an individual-based stochastic susceptible-infected model that takes into account four different sources of infection of pigs (sows, feed, external contaminants such as rodents, and new stock) and various management practices linked to Salmonella transmission/protection (housing, flooring, feed, all-in-all-out production). A novel development within the model is the assessment of dynamic shedding rates. The results of the model, parameterized for two case study member states (one high and one low prevalence) suggest that breeding herd prevalence is a strong indicator of slaughter pig prevalence. Until a member state's' breeding herd prevalence is brought below 10%, the sow will be the dominant source of infection to pigs raised for meat production; below this level of breeding herd prevalence, feed becomes the dominant force of infection.

Prevalence and Level of Enterohemorrhagic Escherichia coli in Culled Dairy Cows at Harvest

The primary objective of this study was to determine the prevalence and level of enterohemorrhagic Escherichia coli (EHEC) O26, O45, O103, O111, O121, and O145 (collectively EHEC-6) plus EHEC O157 in fecal, hide, and preintervention carcass surface samples from culled dairy cows. Matched samples (n = 300) were collected from 100 cows at harvest and tested by a culture-based method and two molecular methods: NeoSEEK STEC (NS) and Atlas STEC EG2 Combo. Both the culture and NS methods can be used to discriminate among the seven EHEC types (EHEC-7), from which the cumulative prevalence was inferred, whereas the Atlas method can discriminate only between EHEC O157 and non-O157 EHEC, without discrimination of the serogroup. The EHEC-7 prevalence in feces, hides, and carcass surfaces was 6.5, 15.6, and 1.0%, respectively, with the culture method and 25.9, 64.9, and 7.0%, respectively, with the NS method. With the Atlas method, the prevalence of non-O157 EHEC was 29.1, 38.3, and 28.0% and that of EHEC O157 was 29.1, 57.0, and 3.0% for feces, hides, and carcasses, respectively. Only two samples (a hide sample and a fecal sample) originating from different cows contained quantifiable EHEC. In both samples, the isolates were identified as EHEC O157, with 4.7 CFU/1,000 cm(2) in the hide sample and 3.9 log CFU/g in the fecal sample. Moderate agreement was found between culture and NS results for detection of EHEC O26 (κ = 0.58, P < 0.001), EHEC O121 (κ = 0.50, P < 0.001), and EHEC O157 (κ = 0.40, P < 0.001). No significant agreement was observed between NS and Atlas results or between culture and Atlas results. Detection of an EHEC serogroup in fecal samples was significantly associated with detection of the same EHEC serogroup in hide samples for EHEC O26 (P = 0.001), EHEC O111 (P = 0.002), EHEC O121 (P < 0.001), and EHEC-6 (P = 0.029) based on NS detection and for EHEC O121 (P < 0.001) based on detection by culture. This study provides evidence that non-O157 EHEC are ubiquitous on hides of culled dairy cattle and that feces are an important source of non-O157 EHEC hide contamination.

"Preharvest" Food Safety for Escherichia coli O157 and Other Pathogenic Shiga Toxin-Producing Strains

Preharvest food safety refers to the concept of reducing the rates of contamination of unprocessed foods with food-borne disease pathogens in order to reduce human exposure and disease. This article addresses the search for effective preharvest food safety practices for application to live cattle to reduce both contamination of foods of bovine origin and environmental contamination resulting from cattle. Although this research has resulted in several practices that significantly decrease contamination by Escherichia coli O157, the effects are limited in magnitude and unlikely to affect the incidence of human disease without much wider application and considerably higher efficacy than is presently apparent. Infection of cattle with E. coli O157 is transient and seasonally variable, likely resulting from a complex web of exposures. It is likely that better identification of the true maintenance reservoir of this agent and related Shiga toxin-producing E. coli is required to develop more effective control measures for these important food- and waterborne disease agents.

Standardized Escherichia coli O157:H7 Exposure Studies in Cattle Provide Evidence that Bovine Factors Do Not Drive Increased Summertime Colonization

The increased summertime prevalence of cattle carriage of enterohemorrhagic Shiga toxin-producing Escherichia coli O157:H7 (STEC O157) is associated with the increased summertime incidence of human infection. The mechanism driving the seasonality of STEC O157 carriage among cattle is unknown. We conducted experimental challenge trials to distinguish whether factors extrinsic or intrinsic to cattle underlie the seasonality of STEC O157 colonization. Holstein steers (n = 20) exposed to ambient environmental conditions were challenged with a standardized pool of STEC O157 strains four times at 6-month intervals. The densities and durations of rectoanal junction mucosa (RAJ) colonization with STEC O157 were compared by season (winter versus summer), dose (10(9) CFU versus 10(7) CFU), and route of challenge (oral versus rectal). Following summer challenges, the RAJ STEC O157 colonization density was significantly lower (P = 0.016) and the duration was shorter (P = 0.052) than for winter challenges, a seasonal pattern opposite to that observed naturally. Colonization was unaffected by the challenge route, indicating that passage through the gastrointestinal microbiome did not significantly affect the infectious dose to the RAJ. A 2-log reduction of the challenge doses in the second-year trials was accompanied by similarly reduced RAJ colonization in both seasons (P < 0.001). These results refute the hypothesis that cattle are predisposed to STEC O157 colonization during the summer months, either due to intrinsic factors or indirectly due to gastrointestinal tract microbiome effects. Instead, the data support the hypothesis that the increased summertime STEC O157 colonization results from increased seasonal oral exposure to this pathogen.

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.

Saltelli Global Sensitivity Analysis and Simulation Modelling to Identify Intervention Strategies to Reduce the Prevalence of Escherichia coli O157 Contaminated Beef Carcasses

Introduction

Strains of Shiga-toxin producing Escherichia coli O157 (STEC O157) are important foodborne pathogens in humans, and outbreaks of illness have been associated with consumption of undercooked beef. Here, we determine the most effective intervention strategies to reduce the prevalence of STEC O157 contaminated beef carcasses using a modelling approach.

Method

A computational model simulated events and processes in the beef harvest chain. Information from empirical studies was used to parameterise the model. Variance-based global sensitivity analysis (GSA) using the Saltelli method identified variables with the greatest influence on the prevalence of STEC O157 contaminated carcasses. Following a baseline scenario (no interventions), a series of simulations systematically introduced and tested interventions based on influential variables identified by repeated Saltelli GSA, to determine the most effective intervention strategy.

Results

Transfer of STEC O157 from hide or gastro-intestinal tract to carcass (improved abattoir hygiene) had the greatest influence on the prevalence of contaminated carcases. Due to interactions between inputs (identified by Saltelli GSA), combinations of interventions based on improved abattoir hygiene achieved a greater reduction in maximum prevalence than would be expected from an additive effect of single interventions. The most effective combination was improved abattoir hygiene with vaccination, which achieved a greater than ten-fold decrease in maximum prevalence compared to the baseline scenario.

Conclusion

Study results suggest that effective interventions to reduce the prevalence of STEC O157 contaminated carcasses should initially be based on improved abattoir hygiene. However, the effect of improved abattoir hygiene on the distribution of STEC O157 concentration on carcasses is an important information gap—further empirical research is required to determine whether reduced prevalence of contaminated carcasses is likely to result in reduced incidence of STEC O157 associated illness in humans. This is the first use of variance-based GSA to assess the drivers of STEC O157 contamination of beef carcasses.

Comparison of methods for the enumeration of enterohemorrhagic Escherichia coli from veal hides and carcasses

The increased association of enterohemorrhagic Escherichia coli (EHEC) with veal calves has led the United States Department of Agriculture Food Safety and Inspection Service to report results of veal meat contaminated with the Top 7 serogroups separately from beef cattle. However, detection methods that can also provide concentration for determining the prevalence and abundance of EHEC associated with veal are lacking. Here we compared the ability of qPCR and a molecular based most probable number assay (MPN) to detect and enumerate EHEC from veal hides at the abattoir and the resulting pre-intervention carcasses. In addition, digital PCR (dPCR) was used to analyze select samples. The qPCR assay was able to enumerate total EHEC in 32% of the hide samples with a range of approximately 34 to 91,412 CFUs/100 cm² (95% CI 4-113,460 CFUs/100 cm²). Using the MPN assay, total EHEC was enumerable in 48% of the hide samples and ranged from approximately 1 to greater than 17,022 CFUs/100 cm² (95% CI 0.4–72,000 CFUs/100 cm²). The carcass samples had lower amounts of EHEC with a range of approximately 4–275 CFUs/100 cm² (95% CI 3–953 CFUs/100 cm²) from 17% of samples with an enumerable amount of EHEC by qPCR. For the MPN assay, the carcass samples ranged from 0.1 to 1 CFUs/100 cm² (95% CI 0.02–4 CFUs/100 cm²) from 29% of the samples. The correlation coefficient between the qPCR and MPN enumeration methods indicated a moderate relation (R² = 0.39) for the hide samples while the carcass samples had no relation (R² = 0.002), which was likely due to most samples having an amount of total EHEC below the reliable limit of quantification for qPCR. Interestingly, after enrichment, 81% of the hide samples and 94% of the carcass samples had a detectable amount of total EHEC by qPCR. From our analysis, the MPN assay provided a higher percentage of enumerable hide and carcass samples, however determining an appropriate dilution range and the limited throughput offer additional challenges.

Prevalence and concentration of Escherichia coli O157 in different seasons and cattle types processed in North America: A systematic review and meta-analysis of published research

Systematic review (SR) and meta-analyses (MA) methodologies were used to identify, critically evaluate and synthesize prevalence and concentration estimates for Escherichia coli O157 contamination along the beef production chain, and to illustrate differences based on cattle types and seasonality in North America from the scientific peer-reviewed literature. Four electronic databases were searched to identify relevant articles. Two independent reviewers performed all SR steps. Random effects MA models were used to estimate the pooled prevalence and concentration of E. coli O157 in feces, hides and carcasses of cattle processed in North America, including their seasonal estimates. The potential sources of between studies heterogeneity were identified using meta-regression and sub-group analysis. Results indicated differences in the fecal prevalence of E. coli O157 among cattle types: 10.68% (95% CI: 9.17-12.28%) in fed beef, 4.65% (95% CI: 3.37-6.10%) in adult beef, and 1.79% (95% CI: 1.20-2.48%) in adult dairy. Fed beef fecal prevalence was 10.65% (95% CI: 8.93-12.49%) during summer and 9.17% (95% CI: 5.24-13.98%) during the winter months. For adult beef, the fecal prevalence was 7.86% (95% CI: 5.43-10.66%) during summer, and 4.21% (95% CI: 1.95-7.13%) during winter. Among adult dairy, the fecal prevalence was 2.27% (95% CI: 1.5-3.18%) during summer, and 0.36% (95% CI: 0.09-0.74%) during winter. There was a significantly higher percentage of hides with E. coli O157 concentration ≥ 40 CFU/100 cm(2) on hides of fed beef sampled at the processing plant (23.81%; 95% CI: 14.79-34.15%) compared to those sampled at the feedlot (1.74%; 95% CI: 0.53-3.44%). Prevalence of E. coli O157 on carcass surfaces differed by season only at the post-evisceration stage, but decreased considerably through the subsequent processing stages. Country, study setting, detection method, hide swab area, and study design were identified as significant sources of heterogeneity among studies reporting prevalence of E. coli O157 along the beef production chain. The pooled prevalence and concentration estimates from this study provide a sound and reliable microbiological basis for risk assessment modeling of E. coli O157 and other pathogens in the food chain.

Longitudinal study of Escherichia coli O157 shedding and super shedding in dairy heifers

A longitudinal study was conducted to assess the methods available for detection of Escherichia coli O157 and to investigate the prevalence and occurrence of long-term shedding and super shedding in a cohort of Australian dairy heifers. Samples were obtained at approximately weekly intervals from heifers at pasture under normal management systems. Selective sampling techniques were used with the aim of identifying heifers with a higher probability of shedding or super shedding. Rectoanal mucosal swabs (RAMS) and fecal samples were obtained from each heifer. Direct culture of feces was used for detection and enumeration. Feces and RAMS were tested by enrichment culture. Selected samples were further tested retrospectively by immunomagnetic separation of enriched samples. Of 784 samples obtained, 154 (19.6%) were detected as positive using culture methods. Adjusting for selective sampling, the prevalence was 71 (15.6%) of 454. In total, 66 samples were detected as positive at >10(2) CFU/g of which 8 were >10(4) CFU/g and classed as super shedding. A significant difference was observed in detection by enriched culture of RAMS and feces. Dairy heifers within this cohort exhibited variable E. coli O157 shedding, consistent with previous estimates of shedding. Super shedding was detected at a low frequency and inconsistently from individual heifers. All detection methods identified some samples as positive that were not detected by any other method, indicating that the testing methods used will influence survey results.

Synchronization ofE. coliO157 shedding in a grass-fed beef herd: a longitudinal study

This study aims to describe in detail the temporal dynamics ofE. coliO157 shedding and risk factors for shedding in a grass-fed beef herd. During a 9-month period, 23 beef cows were sampled twice a week (58 sampling points) andE. coliO157 was enumerated from faecal samples. Isolates were screened by PCR for presence ofrfbE,stx1andstx2. The prevalence per sampling day ranged from 0% to 57%. This study demonstrates that many members of the herd were concurrently sheddingE. coliO157. Occurrence of rainfall (P< 0·01), feeding silage (P< 0·01) and lactating (P< 0·01) were found to be predictors of shedding. Moving cattle to a new paddock had a negative effect on shedding. This approach, based on short-interval sampling, confirms the known variability of shedding within a herd and highlights that high shedding events are rare.