Escherichia coli O157:H7: animal reservoir and sources of human infection

Occurrence of Coliform and Escherichia coli Contamination and Absence of Escherichia coli O157:H7 on Romaine Lettuce from Retail Stores in the Upper Midwest

A total of 720 whole, romaine lettuce heads were purchased from retail locations in the Upper Midwest and assessed for coliform and Escherichia coli contamination and for the presence of E. coli O157:H7. During a 16-month period (August 2010 through December 2011), coliform and E. coli counts were enumerated on Petrifilm, and the presence of E. coli O157:H7 and the virulence gene eae was evaluated by real-time PCR (qPCR). Over half (400 of 720) of the lettuce samples were processed with an immunomagnetic separation step before the qPCR assay. All retail lettuce samples were negative for E. coli O157:H7 when tested with the R.A.P.I.D. LT qPCR targeting a region of the O-antigen, and only two (0.28%) were positive for the eae gene when tested with LightCycler qPCR. On Petrifilm, coliform counts of most lettuce samples (96.4%) were between <10(1) and 10(3) CFU/g, and E. coli counts for nearly all lettuce samples (98.2%) were <10(1) CFU/g. No seasonal trend in coliform and E. coli counts was observed throughout the examination period nor was a difference in coliform counts observed between packaged and nonpackaged lettuce heads. These results contribute to the limited recorded data and understanding of microbial contamination of whole romaine lettuce heads purchased from retail locations, specifically revealing the absence of E. coli O157:H7 and low levels of contamination with coliforms and other E. coli strains.

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.

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.

Impact of Infection Dose and Previous Serum Antibodies against the Locus of Enterocyte Effacement Proteins on Escherichia coli O157:H7 Shedding in Calves following Experimental Infection

Escherichia coli O157:H7 is the main causative agent of haemolytic uremic syndrome. Cattle are the main reservoir of these bacteria, and have been shown to develop immune response to colonization. Our aim was to investigate the faecal shedding pattern of E. coli O157:H7 in calves challenged intragastrically with either 10⁸ or 10¹⁰ CFU, as well as the ability of specific preexisting antibodies to reduce shedding of the pathogen. Shedding was analysed by direct counting as well as enrichment of rectoanal mucosal swabs. Statistical analysis was performed using a linear model for repeated measures with and without the inclusion of preexisting antibodies against the carboxy-terminal fraction of intimin-γ (γ-intimin C280) as a covariable. Results suggest that there is a statistical difference in the area under the shedding curves between both doses for 14 as well as 28 days after challenge (p = 0.0069 and 0.0209, resp.). This difference is increased when the prechallenge antibodies are taken into account (p = 0.0056 and 0.0185). We concluded that the bacterial dose influences shedding on calves experimentally challenged and that preexisting antibodies against E. coli O157:H7 γ-intimin C280 could partially reduce faecal excretion.

Escherichia coli O157:H7--Discerning Facts from Fiction: An Integrated Research and Extension Project for Multiple Audiences

The O157:H7 (EcO157) epidemiology of Shiga-toxin-producing Escherichia coli (STEC) in cattle is complex, and myths about pre-harvest control are perpetuated. The objectives of this project were to identify perpetuated misinformation and inform four audiences about evidence-based risks and pre-harvest control of EcO157 by addressing: (i) EcO157 epidemiology and pre-harvest control; (ii) how food safety policy is created; and (iii) how to present accurate information about EcO157. An environmental scan using a daily Internet search helped identify themes for education. A literature review of pre-harvest control measures contributed to the development of educational materials (fact sheets, website, web presentations and conferences). Conference 1 was a webinar with 315 registrants, 10 countries including 41 US states and four Canadian provinces. Most participants felt confident in using their new knowledge, more than half felt confident enough to answer EcO157 questions from the public and many would recommend the recorded version of the webinar to colleagues. Conference 2 was live in the Washington, DC, area with most participants employed by the US government. All agreed that they better understood pre-harvest control, how food safety policy was made, and were confident they could create an effective message about STEC pre-harvest control. Videos were posted and received 348 Internet visitors within 2 months. Conference 3 was a webinar with a live audience and Twitter feeds, targeting people who give nutrition advice. Almost all ranked the programme good to excellent and relevant to their work. About 25% indicated that they would share: 'grass-fed beef is not safer than grain-fed', 25% would share information on effectiveness of cattle vaccines, and 14% would share information on message mapping. Across all conferences, major changes in knowledge included the following: there is no additional risk of EcO157 shedding from grain-fed versus grass-fed cattle, pre-harvest vaccination is efficacious, and production systems (pasture versus confinement) do not affect EcO157 shedding rates.

Optimizing the Protection of Cattle against Escherichia coli O157:H7 Colonization through Immunization with Different Combinations of H7 Flagellin, Tir, Intimin-531 or EspA

Enterohemorrhagic Escherichia coli (EHEC) are important human pathogens, causing hemorrhagic colitis and hemolytic uraemic syndrome in humans. E. coli O157:H7 is the most common serotype associated with EHEC infections worldwide, although other non-O157 serotypes cause life-threatening infections. Cattle are a main reservoir of EHEC and intervention strategies aimed at limiting EHEC excretion from cattle are predicted to lower the risk of human infection. We have previously shown that immunization of calves with recombinant versions of the type III secretion system (T3SS)-associated proteins EspA, intimin and Tir from EHEC O157:H7 significantly reduced shedding of EHEC O157 from experimentally-colonized calves, and that protection could be augmented by the addition of H7 flagellin to the vaccine formulation. The main aim of the present study was to optimize our current EHEC O157 subunit vaccine formulations by identifying the key combinations of these antigens required for protection. A secondary aim was to determine if vaccine-induced antibody responses exhibited cross-reactive potential with antigens from other EHEC serotypes. Immunization with EspA, intimin and Tir resulted in a reduction in mean EHEC O157 shedding following challenge, but not the mean proportion of calves colonized. Removal of Tir resulted in more prolonged shedding compared with all other groups, whereas replacement of Tir with H7 flagellin resulted in the highest levels of protection, both in terms of reducing both mean EHEC O157 shedding and the proportion of colonized calves. Immunization of calves with recombinant EHEC O157 EspA, intimin and Tir resulted in the generation of antibodies capable of cross-reacting with antigens from non-O157 EHEC serotypes, suggesting that immunization with these antigens may provide a degree of cross-protection against other EHEC serotypes. Further studies are now required to test the efficacy of these vaccines in the field, and to formally test the cross-protective potential of the vaccines against other non-O157 EHEC.

Recent advances in adherence and invasion of pathogenic Escherichia coli

PURPOSE OF REVIEW

Colonization of the host epithelia by pathogenic Escherichia coli is influenced by the ability of the bacteria to interact with host surfaces. Because the initial step of an E. coli infection is to adhere, invade, and persist within host cells, some strategies used by intestinal and extraintestinal E. coli to infect host cell are presented.

RECENT FINDINGS

This review highlights recent progress understanding how extraintestinal pathogenic E. coli strains express specific adhesins or invasins that allow colonization of the urinary tract or the meninges, while intestinal E. coli strains are able to colonize different regions of the intestinal tract using other specialized adhesins or invasins. Finally, evaluation of different diets and environmental conditions regulating the colonization of these pathogens is discussed.

SUMMARY

Discovery of new interactions between pathogenic E. coli and the host epithelial cells unravels the need for more mechanistic studies that can provide new clues regarding how to combat these infections.

The epidemiology, microbiology and clinical impact of Shiga toxin-producing Escherichia coli in England, 2009-2012

Between 1 January 2009 and 31 December 2012 in England, a total of 3717 cases were reported with evidence of Shiga toxin-producing E. coli (STEC) infection, and the crude incidence of STEC infection was 1·80/100 000 person-years. Incidence was highest in children aged 1-4 years (7·63/100 000 person-years). Females had a higher incidence of STEC than males [rate ratio (RR) 1·24, P < 0·001], and white ethnic groups had a higher incidence than non-white ethnic groups (RR 1·43, P < 0·001). Progression to haemolytic uraemic syndrome (HUS) was more frequent in females and children. Non-O157 STEC strains were associated with higher hospitalization and HUS rates than O157 STEC strains. In STEC O157 cases, phage type (PT) 21/28, predominantly indigenously acquired, was also associated with more severe disease than other PTs, as were strains encoding stx2 genes. Incidence of STEC was over four times higher in people residing in rural areas than urban areas (RR 4·39, P < 0·001). Exposure to livestock and/or their faeces was reported twice as often in cases living in rural areas than urban areas (P < 0·001). Environmental/animal contact remains an important risk factor for STEC transmission and is a significant driver in the burden of sporadic STEC infection. The most commonly detected STEC serogroup in England was O157. However, a bias in testing methods results in an unquantifiable under-ascertainment of non-O157 STEC infections. Implementation of PCR-based diagnostic methods designed to detect all STEC, to address this diagnostic deficit, is therefore important.

Whole-genome sequencing for national surveillance of Shiga toxin-producing Escherichia coli O157

BACKGROUND

National surveillance of gastrointestinal pathogens, such as Shiga toxin-producing Escherichia coli O157 (STEC O157), is key to rapidly identifying linked cases in the distributed food network to facilitate public health interventions. In this study, we used whole-genome sequencing (WGS) as a tool to inform national surveillance of STEC O157 in terms of identifying linked cases and clusters and guiding epidemiological investigation.

METHODS

We retrospectively analyzed 334 isolates randomly sampled from 1002 strains of STEC O157 received by the Gastrointestinal Bacteria Reference Unit at Public Health England, Colindale, in 2012. The genetic distance between each isolate, as estimated by WGS, was calculated and phylogenetic methods were used to place strains in an evolutionary context.

RESULTS

Estimates of linked clusters representing STEC O157 outbreaks in England and Wales increased by 2-fold when WGS was used instead of traditional typing techniques. The previously unidentified clusters were often widely geographically distributed and small in size. Phylogenetic analysis facilitated identification of temporally distinct cases sharing common exposures and delineating those that shared epidemiological and temporal links. Comparison with multi locus variable number tandem repeat analysis (MLVA) showed that although MLVA is as sensitive as WGS, WGS provides a more timely resolution to outbreak clustering.

CONCLUSIONS

WGS has come of age as a molecular typing tool to inform national surveillance of STEC O157; it can be used in real time to provide the highest strain-level resolution for outbreak investigation. WGS allows linked cases to be identified with unprecedented specificity and sensitivity that will facilitate targeted and appropriate public health investigations.

Suppression of Escherichia coli O157:H7 by Dung Beetles (Coleoptera: Scarabaeidae) using the lowbush blueberry agroecosystem as a model system

Wildlife as a source of microbial contamination is a food safety concern. Deer feces (scat) have been determined as a point source for Escherichia coli O157:H7 contamination of fresh produce. The ecological role of the scooped scarab (Onthophagus hecate (Panzer)), a generalist dung beetle species common in Maine blueberry fields, was explored as a biological control agent and alternatively as a pathogen vector between deer scat and food. A large-scale field survey of wildlife scat indicated that pathogenic E. coli O157:H7 was present, albeit at a low prevalence (1.9% of samples, n = 318), in the Maine lowbush blueberry agroecosystem. A manipulative field experiment verified that, should contact occur between deer scat and blueberry plants and fruit during the summer, contamination with E. coli O157:H7 can occur and persist for more than 72 h. For both the positive control and an experimental scat inoculation treatment, the levels of the bacterial population decreased over time, but at different rates (treatment x time interaction: F (1.9,18.8) = 358.486, P < 0.0001). The positive control inoculation, which resulted in a higher initial E. coli level on fruit, decayed at a faster rate than inoculation of fruit via scat in the experimental treatment. We conducted 2 laboratory studies to elucidate aspects of dung beetle feeding ecology as it relates to suppression of E. coli O157:H7 from deer scat to lowbush blueberry fruit. In both experiments, dung beetles buried the same amount of scat whether or not the scat was inoculated with the pathogen (F(1,6) = 0.001; P = 0.999 and (F (2,17) = 4.10, P = 0.147). Beetles feeding on E. coli inoculated deer scat were not found to vector the pathogen to fruit. In two studies, beetles lowered the amount of pathogenic E. coli persisting in soils compared to soils without beetles (F (2,9) = 7.757; P = 0.05 and F (2,17) = 8.0621, P = 0.004). Our study suggests that the dung beetle species, Onthophagus hecate, has the potential to contribute to the suppression of E. coli O157:H7 in agricultural landscapes.

Genetic characterization of Escherichia coli isolated from cattle carcasses and feces in Mexico state

Meat of bovine origin is one of the major vehicles in the transmission of verotoxigenic Escherichia coli (VTEC) to human consumers. This pathogen can produce serious human illness, including bloody diarrhea and hemolytic uremic syndrome. The aim of the current study was to characterize E. coli isolates (mainly VTEC strains) belonging to several serotypes in samples from cattle carcasses and feces of three municipal slaughter plants from Mexico State. The genetic diversity and molecular relatedness among the isolates was evaluated with multiple-locus variable-number tandem repeat analysis (MLVA). To our knowledge, and with the exception of E. coli O157:H7, this is the first time that serotypes analyzed here have been subtyped by MLVA in Mexico. MLVA typing grouped the 37 strains from this study into 30 distinct genotypes, 26 of which were unique. These findings indicate that cattle carcasses and feces from slaughter plants in Mexico are a source of VTEC that are genetically diverse in terms of serotypes and virulence profiles. The presence of these pathogens in carcasses indicates the high probability of the spread of VTEC strains during slaughter and processing.

The unexhausted potential of E. coli

E. coli's hardiness, versatility, broad palate and ease of handling have made it the most intensively studied and best understood organism on the planet. However, research on E.coli has primarily examined it as a model organism, one that is abstracted from any natural history. But E. coli is far more than just a microbial lab rat. Rather, it is a highly diverse organism with a complex, multi-faceted niche in the wild. Recent studies of 'wild' E. coli have, for example, revealed a great deal about its presence in the environment, its diversity and genomic evolution, as well as its role in the human microbiome and disease. These findings have shed light on aspects of its biology and ecology that pose far-reaching questions and illustrate how an appreciation of E. coli's natural history can expand its value as a model organism.

Prevalence of carriage of Shiga toxin-producing Escherichia coli serotypes O157:H7, O26:H11, O103:H2, O111:H8, and O145:H28 among slaughtered adult cattle in France

The main pathogenic enterohemorrhagic Escherichia coli (EHEC) strains are defined as Shiga toxin (Stx)-producing E. coli (STEC) belonging to one of the following serotypes: O157:H7, O26:H11, O103:H2, O111:H8, and O145:H28. Each of these five serotypes is known to be associated with a specific subtype of the intimin-encoding gene (eae). The objective of this study was to evaluate the prevalence of bovine carriers of these “top five” STEC in the four adult cattle categories slaughtered in France. Fecal samples were collected from 1,318 cattle, including 291 young dairy bulls, 296 young beef bulls, 337 dairy cows, and 394 beef cows. A total of 96 E. coli isolates, including 33 top five STEC and 63 atypical enteropathogenic E. coli (aEPEC) isolates, with the same genetic characteristics as the top five STEC strains except that they lacked an stx gene, were recovered from these samples.O157:H7 was the most frequently isolated STEC serotype. The prevalence of top five STEC (all serotypes included) was 4.5% in young dairy bulls, 2.4% in young beef bulls, 1.8% in dairy cows, and 1.0% in beef cows. It was significantly higher in young dairy bulls (P<0.05) than in the other 3 categories. The basis for these differences between categories remains to be elucidated. Moreover,simultaneous carriage of STEC O26:H11 and STEC O103:H2 was detected in one young dairy bull. Lastly, the prevalence of bovine carriers of the top five STEC, evaluated through a weighted arithmetic mean of the prevalence by categories, was estimated to 1.8% in slaughtered adult cattle in France.

Evolutionary adaptation of an AraC-like regulatory protein in Citrobacter rodentium and Escherichia species

The evolution of pathogenic bacteria is a multifaceted and complex process, which is strongly influenced by the horizontal acquisition of genetic elements and their subsequent expression in their new hosts. A well-studied example is the RegA regulon of the enteric pathogen Citrobacter rodentium. The RegA regulatory protein is a member of the AraC/XylS superfamily, which coordinates the expression of a gene repertoire that is necessary for full pathogenicity of this murine pathogen. Upon stimulation by an exogenous, gut-associated signal, namely, bicarbonate ions, RegA activates the expression of a series of genes, including virulence factors, such as autotransporters, fimbriae, a dispersin-like protein, and the grlRA operon on the locus of enterocyte effacement pathogenicity island. Interestingly, the genes encoding RegA homologues are distributed across the genus Escherichia, encompassing pathogenic and nonpathogenic subtypes. In this study, we carried out a series of bioinformatic, transcriptional, and functional analyses of the RegA regulons of these bacteria. Our results demonstrated that regA has been horizontally transferred to Escherichia spp. and C. rodentium. Comparative studies of two RegA homologues, namely, those from C. rodentium and E. coli SMS-3-5, a multiresistant environmental strain of E. coli, showed that the two regulators acted similarly in vitro but differed in terms of their abilities to activate the virulence of C. rodentium in vivo, which evidently was due to their differential activation of grlRA. Our data indicate that RegA from C. rodentium has strain-specific adaptations that facilitate infection of its murine host. These findings shed new light on the development of virulence by C. rodentium and on the evolution of virulence-regulatory genes of bacterial pathogens in general.

Comparison of recto-anal mucosal swab and faecal culture for the detection of Escherichia coli O157 and identification of super-shedding in a mob of Merino sheep

We compared the use of recto-anal mucosal swab (RAMS) culture and faecal culture for the detection of E. coli O157 in a mob of Merino sheep. Fifty Merino wethers and maiden ewes housed in indoor pens were sampled on five occasions. We detected E coli O157 in 32% (16/50) of sheep, with weekly prevalence ranging from 4% (2/50) to 16% (8/50). Overall, 12·5% (2/16) were detected by RAMS culture only, and 37·5% (6/16) were detected by faecal culture only. The level of agreement between the two sampling methods was moderate [kappa statistic = 0·583, 95% confidence interval (CI) 0·460-0·707]. The relative sensitivities of RAMS and faecal culture were 67% (95% CI 41-86) and 57% (95% CI 34-77), respectively. We identified four super-shedding sheep using direct faecal culture. Although the majority of culture-positive sheep were detected at one sampling point only, 3/4 super-shedding sheep were culture-positive at two sampling points, and 1/4 was culture-positive at four sampling points. Persistent culture positivity may indicate sheep that could be considered 'super-shedders' at some point. The use of immunomagnetic separation further improved the rate of detection of E. coli O157, which was isolated from 1/34 animals that were previously negative by enrichment culture alone. A significant difference between sampling weeks was detected for both faecal (P = 0·021) and RAMS (P = 0·006), with the prevalence at the mid-point of sampling (week 4) significantly (P < 0·05) higher than at the beginning or end of the study. Study conditions (penned sheep) might have been responsible for the high prevalence and the epidemic pattern of infection observed, and could serve as a future model for studies of E. coli O157 transmission, shedding and super-shedding in sheep.

Development of colloidal gold immunochromatographic signal-amplifying system for ultrasensitive detection of Escherichia coli O157:H7 in milk

A colloidal gold immunochromatographic signal-amplifying test strip with a sandwich format was successfully developed to detect Escherichia coli O157:H7.

Perspectives on super-shedding of Escherichia coli O157:H7 by cattle

Escherichia coli O157:H7 is a foodborne pathogen that causes illness in humans worldwide. Cattle are the primary reservoir of this bacterium, with the concentration and frequency of E. coli O157:H7 shedding varying greatly among individuals. The term "super-shedder" has been applied to cattle that shed concentrations of E. coli O157:H7 ≥ 10⁴ colony-forming units/g feces. Super-shedders have been reported to have a substantial impact on the prevalence and transmission of E. coli O157:H7 in the environment. The specific factors responsible for super-shedding are unknown, but are presumably mediated by characteristics of the bacterium, animal host, and environment. Super-shedding is sporadic and inconsistent, suggesting that biofilms of E. coli O157:H7 colonizing the intestinal epithelium in cattle are intermittently released into feces. Phenotypic and genotypic differences have been noted in E. coli O157:H7 recovered from super-shedders as compared to low-shedding cattle, including differences in phage type (PT21/28), carbon utilization, degree of clonal relatedness, tir polymorphisms, and differences in the presence of stx2a and stx2c, as well as antiterminator Q gene alleles. There is also some evidence to support that the native fecal microbiome is distinct between super-shedders and low-shedders and that low-shedders have higher levels of lytic phage within feces. Consequently, conditions within the host may determine whether E. coli O157:H7 can proliferate sufficiently for the host to obtain super-shedding status. Targeting super-shedders for mitigation of E. coli O157:H7 has been proposed as a means of reducing the incidence and spread of this pathogen to the environment. If super-shedders could be easily identified, strategies such as bacteriophage therapy, probiotics, vaccination, or dietary inclusion of plant secondary compounds could be specifically targeted at this subpopulation. Evidence that super-shedder isolates share a commonality with isolates linked to human illness makes it imperative that the etiology of this phenomenon be characterized.

Lessons learned from a textbook outbreak: EHEC-O157:H7 infections associated with the consumption of raw meat products, June 2012, Limburg, Belgium

BACKGROUND

On 5 June 2012 several enterohemorrhagic Escherichia coli, EHEC, O157:H7 infections were reported to the public health authorities of Limburg.

METHODS

We performed a case-control study, a trace back/forward investigation and compared strains isolated from human cases and food samples. A case was defined as anyone with a laboratory-confirmed E. coli O157:H7-infection in North-East Limburg from May 30 2012 till July 15 2012. Family members with bloody diarrhea were also included as cases. E. coli O157 was isolated by culture and the presence of the virulence genes was verified using (q)PCR. Isolates were genotyped and compared by Pulsed Field Gel Electrophoresis (PFGE) and insertion sequence 629-printing (IS629-printing).

RESULTS

The outbreak involved 24 cases, of which 17 were laboratory-confirmed. Five cases developed Hemolytic Uremic Syndrome (HUS) and fifteen were hospitalized. Cases reported a significantly higher consumption of "steak tartare", a raw meat product (OR 48.12; 95% CI; 5.62- 416.01). Cases were also more likely to buy meat-products at certain butcheries (OR 11.67; 95% CI; 1.41 - 96.49). PFGE and IS629-printing demonstrated that the vtx1a vtx2a eae ehxA positive EHEC O157:H7 strains isolated from three meat products and all seventeen human stool samples were identical. In a slaughterhouse, identified by the trace-back investigation, a carcass infected with a different EHEC strain was found and confiscated.

CONCLUSION

We present a well described and effectively investigated foodborne outbreak associated with meat products. Our main recommendations are the facilitation and acceleration of the outbreak detection and the development of a communication plan to reaches all persons at risk.

MESH

Foodborne diseases, Shiga-toxigenic Escherichia coli, Enterohemorrhagic Escherichia coli, Meat products, Case control studies, Electrophoresis, Gel, Pulsed-Field.

Geographically distinct Escherichia coli O157 isolates differ by lineage, Shiga toxin genotype, and total shiga toxin production

While the differential association of Escherichia coli O157 genotypes with animal and human hosts has recently been well documented, little is known about their distribution between countries and how this might affect regional disease rates. Here, we used a 48-plex single nucleotide polymorphism (SNP) assay to segregate 148 E. coli O157 isolates from Australia, Argentina, and the United States into 11 SNP lineages. We also investigated the relationship between SNP lineages, Shiga toxin (Stx) gene profiles, and total Stx production. E. coli O157 isolates clearly segregated into SNP lineages that were differentially associated with each country. Of the 11 SNP lineages, seven were detected among isolates from a single country, two were detected among isolates from all three countries, and another two were detected only among U.S. and Argentinean isolates. A number of Australian (30%) and Argentinean (14%) isolates were associated with novel, previously undescribed SNP lineages that were unique to each country. Isolates within SNP lineages that were strongly associated with the carriage of stx2a produced comparatively more Stx on average than did those lacking the stx2a subtype. Furthermore, the proportion of isolates in stx2a-associated SNP lineages was significantly higher in Argentina and the United States than Australia (P < 0.05). This study provides evidence for the geographic divergence of E. coli O157 and for a prominent role of stx2a in total Stx production. These results also highlight the need for more comprehensive studies of the global distribution of E. coli O157 lineages and the impacts of regionally predominant E. coli O157 lineages on the prevalence and severity of disease.

Longitudinal Characterization of Escherichia coli in Healthy Captive Non-Human Primates

The gastrointestinal (GI) tracts of non-human primates (NHPs) are well known to harbor Escherichia coli, a known commensal of human beings and animals. While E. coli is a normal inhabitant of the mammalian gut, it also exists in a number of pathogenic forms or pathotypes, including those with predisposition for the GI tract as well as the urogenital tract. Diarrhea in captive NHPs has long been a problem in both zoo settings and research colonies, including the Como Zoo. It is an animal welfare concern, as well as a public health concern. E. coli has not been extensively studied; therefore, a study was performed during the summer of 2009 in collaboration with a zoo in Saint Paul, MN, which was previously experiencing an increased incidence and severity of diarrhea among their NHP collection. Fresh fecal samples were collected weekly from each member of the primate collection, between June and August of 2009, and E. coli were isolated. A total of 33 individuals were included in the study, representing eight species. E. coli isolates were examined for their genetic relatedness, phylogenetic relationships, plasmid replicon types, virulence gene profiles, and antimicrobial susceptibility profiles. A number of isolates were identified containing virulence genes commonly found in several different E. coli pathotypes, and there was evidence of clonal transmission of isolates between animals and over time. Overall, the manifestation of chronic diarrhea in the Como Zoo primate collection is a complex problem whose solution will require regular screening for microbial agents and consideration of environmental causes. This study provides some insight toward the sharing of enteric bacteria between such animals.

Pathogen reduction in minimally managed composting of bovine manure

Spread of manure pathogens is of considerable concern due to use of manure for land application. In this study, the effects of four static pile treatment options for bovine manure on die-off of a generic Escherichia coli, E. coli O157:H7 surrogate, Salmonella Senftenberg, Salm. Typhimurium, and Listeria monocytogenes were evaluated. Bovine manure spiked with these bacteria were placed in cassettes at the top, middle, and bottom sections of four static pile treatments that reflect minimal changes in pile construction with and without straw. Temperatures were monitored continuously during the 28 day self-heating period. E. coli and salmonellae were reduced from 8 to 9 log10 CFU g(-1) to undetectable levels (<1.77 log10 MPN g(-1)) at 25-30 cm depths within 7 days in all pile sections except for the manure-only pile in which 3-4 logs of reduction were obtained. No L. monocytogenes initially present at 6.62 log10 CFU g(-1) were recovered from straw-amended piles after 14 days, in contrast with manure-only treatment in which this pathogen was recovered even at 28 days. Decline of target bacterial populations corresponded to exposure to temperatures above 45°C for more than 3 days and amendments of manure with straw to increase thermophilic zones. Use of straw to increase aeration, self-heating capacity, and heat retention in manure piles provides producers a minimal management option for composting that enhances pathogen die-off and thereby reduces risk of environmental spread when manure is applied to land.

Insertion/deletion-based approach for the detection of Escherichia coli O157:H7 in freshwater environments

Enterohemorrhagic Escherichia coli O157:H7 is responsible for many outbreaks of gastrointestinal illness and hemolytic uremic syndrome worldwide. Monitoring this pathogen in food and water supplies is an important public health issue. Highly conserved genetic markers, which are characteristic for specific strains, can provide direct identification of target pathogens. In this study, we examined a new detection strategy for pathogenic strains of E. coli O157:H7 serotype based on a conserved signature insertion/deletion (CSI) located in the ybiX gene using TaqMan-probe-based quantitative PCR (qPCR). The qPCR assay was linear from 1.0 × 10(2) to 1.0 × 10(7) genome copies and was specific to O157:H7 when tested against a panel of 15 non-O157:H7 E. coli. The assay also maintained detection sensitivity in the presence of competing E. coli K-12, heterologous nontarget DNA spiked in at a 1000-fold and 800-fold excess of target DNA, respectively, demonstrating the assay's ability to detect E. coli O157:H7 in the presence of high levels of background DNA. This study thus validates the use of strain-specific CSIs as a new class of diagnostic marker for pathogen detection.

Bloom of resident antibiotic-resistant bacteria in soil following manure fertilization

The increasing prevalence of antibiotic-resistant bacteria is a global threat to public health. Agricultural use of antibiotics is believed to contribute to the spread of antibiotic resistance, but the mechanisms by which many agricultural practices influence resistance remain obscure. Although manure from dairy farms is a common soil amendment in crop production, its impact on the soil microbiome and resistome is not known. To gain insight into this impact, we cultured bacteria from soil before and at 10 time points after application of manure from cows that had not received antibiotic treatment. Soil treated with manure contained a higher abundance of β-lactam-resistant bacteria than soil treated with inorganic fertilizer. Functional metagenomics identified β-lactam-resistance genes in treated and untreated soil, and indicated that the higher frequency of resistant bacteria in manure-amended soil was attributable to enrichment of resident soil bacteria that harbor β-lactamases. Quantitative PCR indicated that manure treatment enriched the blaCEP-04 gene, which is highly similar (96%) to a gene found previously in a Pseudomonas sp. Analysis of 16S rRNA genes indicated that the abundance of Pseudomonas spp. increased in manure-amended soil. Populations of other soil bacteria that commonly harbor β-lactamases, including Janthinobacterium sp. and Psychrobacter pulmonis, also increased in response to manure treatment. These results indicate that manure amendment induced a bloom of certain antibiotic-resistant bacteria in soil that was independent of antibiotic exposure of the cows from which the manure was derived. Our data illustrate the unintended consequences that can result from agricultural practices, and demonstrate the need for empirical analysis of the agroecosystem.

Daily variations in Escherichia coli O157 shedding patterns in a cohort of dairy heifers at pasture

Escherichia coli O157 is a human pathogen carried asymptomatically by cattle and shed in their faeces. Infection can occur from the consumption of contaminated beef or by direct contact. Large variations of E. coli O157 shedding in cattle exist and vary in the number of cattle positive for E. coli O157 and the amount of bacteria (c.f.u./g faeces) shed by positive animals. To investigate E. coli O157 shedding and super-shedding (>104 c.f.u./g) we used daily sampling over two 8-day periods; in January 2013 (n = 12) and February 2013 (n = 21). Samples were tested by direct faecal culture for enumeration and by immunomagnetic separation to detect lower levels of shedding. We identified three patterns of shedding, similar to previously observed descriptions: intermittent, transient and consistent. The most commonly observed pattern was intermittent shedding and variation in the level of shedding could be large. This extreme variation is demonstrated by a heifer from which E. coli O157 could be not detected one day, was super-shedding E. coli O157 the next and was detected as shedding >100 c.f.u./g the following day. Recto-anal mucosal swab testing did not predict super-shedding in this cohort of heifers. The variable individual patterns of shedding suggest that a common mechanism of infection may not operate within such a herd when considering previously described patterns and the inferred mechanisms. The sporadic and intermittent nature of shedding is a challenge to identifying risk factors and potential intervention strategies.

Risk Factors for Shiga Toxin-Producing Escherichia coli- Associated Human Diseases

We have reviewed the risk factors for the occurrence of Shiga toxin-producing Escherichia coli (STEC)-associated human diseases. The analysis of STEC surveillance data and trends shows differences in frequency and severity of the illnesses across countries, whereas the economic and social costs for the affected families, the community, and the health system are better estimated in developed countries. The occurrence of STEC infections is determined by the interaction of the pathogen, the reservoirs, and the biological, cultural, and behavioral aspects of the host. The main risk factors identified in earlier case-control and population-based studies were dietary behaviors and beef consumption. However, in recent years, other risky exposures have also emerged, like the consumption of raw vegetables and sprouts, working or camping in rural areas, visiting farms, and person-to-person transmission. Epidemiological changes have also been determined by the intensification of cattle production, the increase in centralized food production and distribution, and the growth in the volume of international trade of foods. The main lessons learned from recent large outbreaks are knowledge of virulence determinants of new pathogenic strains, recognition of new vehicles of infection, development of new methodologies for detecting STEC in foods and humans, improvement in food regulations and hygiene guidelines, new therapeutic approaches in the treatment of infected patients, establishment of continuous educational programs for food consumers, and enhanced cooperation and teamwork of regional and international networks.

Biofilm formation protects Escherichia coli against killing by Caenorhabditis elegans and Myxococcus xanthus

Enteric bacteria, such as Escherichia coli, are exposed to a variety of stresses in the nonhost environment. The development of biofilms provides E. coli with resistance to environmental insults, such as desiccation and bleach. We found that biofilm formation, specifically production of the matrix components curli and cellulose, protected E. coli against killing by the soil-dwelling nematode Caenorhabditis elegans and the predatory bacterium Myxococcus xanthus. Additionally, matrix-encased bacteria at the air-biofilm interface exhibited ∼40-fold-increased survival after C. elegans and M. xanthus killing compared to the non-matrix-encased cells that populate the interior of the biofilm. To determine if nonhost Enterobacteriaceae reservoirs supported biofilm formation, we grew E. coli on media composed of pig dung or commonly contaminated foods, such as beef, chicken, and spinach. Each of these medium types provided a nutritional environment that supported matrix production and biofilm formation. Altogether, we showed that common, nonhost reservoirs of E. coli supported the formation of biofilms that subsequently protected E. coli against predation.

Future perspectives, applications and challenges of genomic epidemiology studies for food-borne pathogens: A case study of Enterohemorrhagic Escherichia coli (EHEC) of the O157:H7 serotype

The shiga-toxin (Stx)-producing human pathogen Escherichia coli serotype O157:H7 is a highly pathogenic subgroup of Stx-producing E. coli (STEC) with food-borne etiology and bovine reservoir. Each year in the U. S., approximately 100,000 patients are infected with enterohemorrhagic E. coli (EHEC) of the O157:H7 serotype. This food-borne pathogen is a global public health threat responsible for widespread outbreaks of human disease. Since its initial discovery in 1982, O157:H7 has rapidly become the dominant EHEC serotype in North America. Hospitalization rates among patients as high as 50% have been reported for severe outbreaks of human disease. Symptoms of disease can rapidly deteriorate and progress to life-threatening complications such as Hemolytic Uremic Syndrome (HUS), the leading cause of kidney failure in children, or Hemorrhagic Colitis. In depth understanding of the genomic diversity that exists among currently circulating EHEC populations has broad applications for improved molecular-guided biosurveillance, outbreak preparedness, diagnostic risk assessment, and development of alternative toxin-suppressing therapeutics.

Characterization of rumen bacterial strains isolated from enrichments of rumen content in the presence of propolis

Propolis presents many biological properties, including antibacterial activities, and has been proposed as an additive in ruminant nutrition. Twenty bacterial strains, previously isolated from enrichments of Brazilian cow rumen contents in the presence of different propolis extracts (LLOS), were characterized using phenotyping and 16S rRNA identification. Seven strains were assigned to Streptococcus sp., most likely S. bovis, and were all degrading starch. One amylolytic lactate-utilizing strain of Selenomonas ruminantium was also found. Two strains of Clostridium bifermentans were identified and showed proteolytic activity. Two strains were assigned to Mitsuokella jalaludinii and were saccharolytic. One strain belonged to a Bacillus species and seven strains were affiliated with Escherichia coli. All of the 20 strains were able to use many sugars, but none of them were able to degrade the polysaccharides carboxymethylcellulose and xylans. The effect of three propolis extracts (LLOS B1, C1 and C3) was tested on the in vitro growth of four representative isolates of S. bovis, E. coli, M. jalaludinii and C. bifermentans. The growth of S. bovis, E. coli and M. jalaludinii was not affected by the three propolis extracts at 1 mg ml(-1). C. bifermentans growth was completely inhibited at this LLOS concentration, but this bacterium was partially resistant at lower concentrations. LLOS C3, with the lower concentration of phenolic compounds, was a little less inhibitory than B1 and C1 on this strain.

Animal Reservoirs of Shiga Toxin-Producing Escherichia coli

Shiga toxin-producing Escherichia coli (STEC) strains have been detected in a wide diversity of mammals, birds, fish, and several insects. Carriage by most animals is asymptomatic, thus allowing for dissemination of the bacterium in the environment without detection. Replication of the organism may occur in the gastrointestinal tract of some animals, notably ruminants. Carriage may also be passive or transient, without significant amplification of bacterial numbers while in the animal host. Animals may be classified as reservoir species, spillover hosts, or dead-end hosts. This classification is based on the animal's ability to (i) transmit STEC to other animal species and (ii) maintain STEC infection in the absence of continuous exposure. Animal reservoirs are able to maintain STEC infections in the absence of continuous STEC exposure and transmit infection to other species. Spillover hosts, although capable of transmitting STEC to other animals, are unable to maintain infection in the absence of repeated exposure. The large diversity of reservoir and spillover host species and the survival of the organism in environmental niches result in complex pathways of transmission that are difficult to interrupt.

Detection and source tracking of Escherichia coli, harboring intimin and Shiga toxin genes, isolated from the Little Bighorn River, Montana

The Little Bighorn River flows through the Crow Indian Reservation in Montana. In 2008, Escherichia coli concentrations as high as 7179 MPN/100 ml were detected in the river at the Crow Agency Water Treatment Plant intake site. During 2008, 2009, and 2012, 10 different serotypes of E. coli, including O157:H7, harboring both intimin and Shiga toxin genes were isolated from a popular swim site of the Little Bighorn River in Crow Agency. As part of a microbial source tracking study, E. coli strains were isolated from river samples as well as from manure collected from a large cattle feeding operation in the upper Little Bighorn River watershed; 23% of 167 isolates of E. coli obtained from the manure tested positive for the intimin gene. Among these manure isolates, 19 were identified as O156:H8, matching the serotype of an isolate collected from a river sampling site close to the cattle feeding area.

Life on the outside: role of biofilms in environmental persistence of Shiga-toxin producing Escherichia coli

Escherichia coli is a heterogeneous species that can be part of the normal flora of humans but also include strains of medical importance. Among pathogenic members, Shiga-toxin producing E. coli (STEC) are some of the more prominent pathogenic E. coli within the public sphere. STEC disease outbreaks are typically associated with contaminated beef, contaminated drinking water, and contaminated fresh produce. These water- and food-borne pathogens usually colonize cattle asymptomatically; cows will shed STEC in their feces and the subsequent fecal contamination of the environment and processing plants is a major concern for food and public safety. This is especially important because STEC can survive for prolonged periods of time outside its host in environments such as water, produce, and farm soil. Biofilms are hypothesized to be important for survival in the environment especially on produce, in rivers, and in processing plants. Several factors involved in biofilm formation such as curli, cellulose, poly-N-acetyl glucosamine, and colanic acid are involved in plant colonization and adherence to different surfaces often found in meat processing plants. In food processing plants, contamination of beef carcasses occurs at different stages of processing and this is often caused by the formation of STEC biofilms on the surface of several pieces of equipment associated with slaughtering and processing. Biofilms protect bacteria against several challenges, including biocides used in industrial processes. STEC biofilms are less sensitive than planktonic cells to several chemical sanitizers such as quaternary ammonium compounds, peroxyacetic acid, and chlorine compounds. Increased resistance to sanitizers by STEC growing in a biofilm is likely to be a source of contamination in the processing plant. This review focuses on the role of biofilm formation by STEC as a means of persistence outside their animal host and factors associated with biofilm formation.

Risk factors for Escherichia coli O157 shedding and super-shedding by dairy heifers at pasture

We undertook a longitudinal study within a cohort of 52 dairy heifers maintained under constant management systems and sampled weekly to investigate a comprehensive range of risk factors which may influence shedding or super-shedding of E. coli O157 (detected by direct faecal culture and immunomagnetic separation). E. coli O157 was detected from 416/933 (44.6%) samples (faeces and recto-anal mucosal swabs) and 32 (3.4%) samples enumerated at >10000 c.f.u./g. Weekly point prevalence ranged from 9.4% to 94.3%. Higher temperature (P < 0.001), rainfall (P = 0.02), relative humidity (P < 0.001), pasture growth (P = 0.013) and body score (P = 0.029) were positively associated with increased shedding. Higher rainfall (P < 0.001), hide contamination (P = 0.002) and increased faecal consistency (P = 0.023) were positively associated with super-shedding. Increased solar exposure had a negative effect on both shedding and super-shedding within bivariate analyses but in the final multivariate model for shedding demonstrated a positive effect (P = 0.017). Results suggest that environmental factors are important in E. coli O157 shedding in cattle.

Occurrence and characterization of Shiga toxin-producing Escherichia coli O157:H7 and other non-sorbitol-fermenting E. coli in cattle and humans in urban areas of Morogoro, Tanzania

Escherichia coli strains such as Shiga toxin-producing E. coli (STEC), enteropathogenic E. coli, enterotoxigenic, attaching, and effacing E. coli, and enteroinvasive E. coli cause diarrhea in humans. Although other serotypes exist, the most commonly reported STEC in outbreaks is O157:H7. A cross-sectional study was conducted to isolate and characterize non-sorbitol-fermenting (NSF) E. coli O157:H7 from urban and periurban livestock settings of Morogoro, Tanzania. Human stool, cattle feces, and soil and water samples were collected. Observations and questionnaire interview studies were used to gather information about cattle and manure management practices in the study area. E. coli were isolated on sorbitol MacConkey agar and characterized by conventional biochemical tests. Out of 1049 samples, 143 (13.7%) yielded NSF E. coli. Serological and antimicrobial tests and molecular typing were performed to NSF E. coli isolates. These procedures detected 10 (7%) pathogenic E. coli including STEC (n=7), enteropathogenic E. coli (EPEC) (n=2), and attaching and effacing E. coli (A/EEC) (n=1) strains. The STEC strains had the ability to produce VT1 and different VT2 toxin subtypes that caused cytopathic effects on Vero cells. The prevalence of STEC in cattle was 1.6%, out of which 0.9% was serotype O157:H7 and the overall prevalence of diarrheagenic E. coli in cattle was 2.2%. The serotypes O157:H7, O142:H34, O113:H21, O+:H-, O+:H16, and O25:H4 were identified. One ESBL-producing isolate showed the MLST type ST131. To our knowledge, this is the first finding in Tanzania of this recently emerged worldwide pandemic clonal group, causing widespread antimicrobial-resistant infections, and adds knowledge of the geographical distribution of ST131. Cattle manure was indiscriminately deposited within residential areas, and there was direct contact between humans and cattle feces during manure handling. Cattle and manure management practices expose humans, animals, and the environment to pathogenic E. coli and other manure-borne pathogens. Therefore, there is a need to improve manure management practices in urban and periurban areas to prevent pathogen spread and associated human health risks.

Molecular characterization of enterohemorrhagic E. coli O157 isolated from animal fecal and food samples in Eastern China

Objective. To elucidate the extent of food contamination by enterohemorrhagic Escherichia coli (EHEC) O157 in Eastern China. Methods. A total of 1100 food and animal fecal samples were screened for EHEC O157. Then, molecular characterization of each isolate was determined. Results. EHEC O157 was isolated as follows: pig feces, 4% (20/500); cattle feces, 3.3% (2/60); chicken feces, 1.43% (2/140); pork, 2.14% (3/140), milk, 1.67% (1/60); and chicken meat, 1.67% (1/60). The stx1, stx2, eae, and hlyA genes were present in 26.7% (8/30), 40% (12/30), 63.3% (19/30), and 50% (15/30) of the O157 isolates, respectively. Molecular typing showed that strains from fecal and food samples were clustered into the same molecular typing group. Furthermore, the isolates from pork and pig feces possessed the same characterization as the clinical strains ATCC35150 and ATCC43889. Biofilm formation assays showed that 53.3% of the EHEC O157 isolates could produce biofilm. However, composite analyses showed that biofilm formation of EHEC O157 was independent of genetic background. Conclusions. Animal feces, especially from pigs, serve as reservoirs for food contamination by EHEC O157. Thus, it is important to control contamination by EHEC O157 on farms and in abattoirs to reduce the incidence of foodborne infections in humans.

Changing plasmid types responsible for extended spectrum cephalosporin resistance in Escherichia coli O157:H7 in the United States, 1996-2009

Escherichia coli O157 is a major cause of foodborne illness. Plasmids are genetic elements that mobilize antimicrobial resistance determinants including bla_CMY β-lactamases that confer resistance to extended-spectrum cephalosporins (ESC). ESCs are important for treating a variety of infections. IncA/C plasmids are found among diverse sources, including cattle, the principal source of E. coli O157 infections in humans. IncI1 plasmids are common among E. coli and Salmonella from poultry and other avian sources. To broaden our understanding of reservoirs of bla_CMY, we determined the types of plasmids carrying bla_CMY among E. coli O157. From 1996 to 2009, 3742 E. coli O157 isolates were tested. Eleven (0.29%) were ceftriaxone resistant and had a bla_CMY-2-containing plasmid. All four isolates submitted before 2001 and a single 2001 isolate had bla_CMY encoded on IncA/C plasmids, while all five isolates submitted after 2001 and a single 2001 isolate had bla_CMY carried on IncI1 plasmids. The IncI1 plasmids were ST2, ST20, and ST23. We conclude that cephalosporin resistance among E. coli O157:H7 is due to plasmid-encoded bla_CMY genes and that plasmid types appear to have shifted from IncA/C to IncI1. This shift suggests either a change in plasmid type among animal reservoirs or that the organism has expanded into avian reservoirs. More analysis of human, retail meat, and food animal isolates is necessary to broaden our understanding of the antimicrobial resistance determinants of ESC resistance among E. coli O157.

Comparison of strand-specific transcriptomes of enterohemorrhagic Escherichia coli O157:H7 EDL933 (EHEC) under eleven different environmental conditions including radish sprouts and cattle feces

Background

Multiple infection sources for enterohemorrhagic Escherichia coli O157:H7 (EHEC) are known, including animal products, fruit and vegetables. The ecology of this pathogen outside its human host is largely unknown and one third of its annotated genes are still hypothetical. To identify genetic determinants expressed under a variety of environmental factors, we applied strand-specific RNA-sequencing, comparing the SOLiD and Illumina systems.

Results

Transcriptomes of EHEC were sequenced under 11 different biotic and abiotic conditions: LB medium at pH4, pH7, pH9, or at 15°C; LB with nitrite or trimethoprim-sulfamethoxazole; LB-agar surface, M9 minimal medium, spinach leaf juice, surface of living radish sprouts, and cattle feces. Of 5379 annotated genes in strain EDL933 (genome and plasmid), a surprising minority of only 144 had null sequencing reads under all conditions. We therefore developed a statistical method to distinguish weakly transcribed genes from background transcription. We find that 96% of all genes and 91.5% of the hypothetical genes exhibit a significant transcriptional signal under at least one condition. Comparing SOLiD and Illumina systems, we find a high correlation between both approaches for fold-changes of the induced or repressed genes. The pathogenicity island LEE showed highest transcriptional activity in LB medium, minimal medium, and after treatment with antibiotics. Unique sets of genes, including many hypothetical genes, are highly up-regulated on radish sprouts, cattle feces, or in the presence of antibiotics. Furthermore, we observed induction of the shiga-toxin carrying phages by antibiotics and confirmed active biofilm related genes on radish sprouts, in cattle feces, and on agar plates.

Conclusions

Since only a minority of genes (2.7%) were not active under any condition tested (null reads), we suggest that the assumption of significant genome over-annotations is wrong. Environmental transcriptomics uncovered hitherto unknown gene functions and unique regulatory patterns in EHEC. For instance, the environmental function of azoR had been elusive, but this gene is highly active on radish sprouts. Thus, NGS-transcriptomics is an appropriate technique to propose new roles of hypothetical genes and to guide future research.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-353) contains supplementary material, which is available to authorized users.

A mixture of Lactobacillus casei, Lactobacillus lactis, and Paenibacillus polymyxa reduces Escherichia coli O157:H7 in finishing feedlot cattle

A direct-fed microbial (DFM) containing Paenibacillus polymyxa, Lactobacillus casei, and Lactobacillus lactis was fed to cattle (n = 120) to determine impacts on shedding and survival of Escherichia coli O157:H7 in feces. Cattle were individually penned and fed diets containing 0 (control), 4 × 10(7) CFU (DFM-4), 8 × 10(7) CFU (DFM-8), or 1.2 × 10(8) CFU (DFM-12) lactobacilli per kg of dietary dry matter over 84-day fall-winter growing and 140-day spring-summer finishing periods. Fecal grab samples were collected from cattle at 28-day intervals, E. coli O157:H7 was detected by immunomagnetic separation, and isolates were compared by pulsed-field gel electrophoresis. During the growing period, feces negative for E. coli O157 from each dietary treatment were inoculated with 10(5) CFU/g nalidixic acid-resistant E. coli O157:H7 and were incubated at 4 and 22(u) C for 11 weeks. Fecal pH and fecal dry matter were measured on days 0, 1, 3, and 7 and weekly thereafter, with E. coli O157:H7 enumerated through dilution plating. Treatment with DFMs did not affect survival of E. coli O157:H7 in feces or fecal pH (P > 0.05). Only one steer was positive for E. coli O157:H7 during the growing period, but during the finishing period, DFM-8 and DFM-12 reduced the prevalence of E. coli O157:H7 in feces (P < 0.05). Feeding DFMs also reduced the frequency of individual steers shedding E. coli O157:H7 during finishing (P < 0.05), with control steers shedding E. coli O157:H7 up to four times, whereas DFM-12 steers shed E. coli O157:H7 a maximum of twice. Treatment with DFMs influenced pulsed-field gel electrophoresis profiles; steers that were fed DFM-8 and DFM-12 shed more diverse subtypes of E. coli O157:H7 than did control or DFM-4 steers. Because a companion study found linear improvement in performance with increasing dosage of DFMs in the first 28 days of the growing period, targeted use of DFM-12 during this time and for the final 1 or 2 weeks prior to slaughter may optimize performance and reduce E. coli O157:H7 while minimizing feed costs.

Shiga toxin-producing Escherichia coli distribution and characterization in a pasture-based cow-calf production system

Shiga toxin-producing Escherichia coli (STEC) strains are commonly found in cattle gastrointestinal tracts. In this study, prevalence and distribution of E. coli virulence genes (stx1, stx2, hlyA, and eaeA) were assessed in a cow-calf pasture-based production system. Angus cows (n = 90) and their calves (n = 90) were kept in three on-farm locations, and fecal samples were collected at three consecutive times (July, August, and September 2011). After enrichment of samples, stx1, stx2, eaeA, and hlyA were amplified and detected with a multiplex PCR (mPCR) assay. Fecal samples positive for stx genes were obtained from 93.3% (84 of 90) of dams and 95.6% (86 of 90) of calves at one or more sampling times. Age class (dam or calf), spatial distribution of cattle (farm locations B, H, K), and sampling time influenced prevalence and distribution of virulence genes in the herd. From 293 stx-positive fecal samples, 744 E. coli colonies were isolated. Virulence patterns of isolates were determined through mPCR assay: stx1 was present in 41.9% (312 of 744) of the isolates, stx2 in 6.5% (48 of 744), eaeA in 4.2% (31 of 744), and hlyA in 2.4% (18 of 744). Prevalence of non-O157 STEC was high among the isolates: 33.8% (112 of 331) were STEC O121, 3.6% (12 of 331) were STEC O103, and 1.8% (6 of 331) were STEC O113. One isolate (0.3%) was identified as STEC O157. Repetitive element sequence-based PCR (rep-PCR) fingerprinting was used to study genetic diversity of stx-positive E. coli isolates. Overall, rep-PCR fingerprints were highly similar, supporting the hypothesis that strains are transmitted between animals but not necessarily from a dam to its calf. Highly similar STEC isolates were obtained at each sampling time, but isolates obtained from dams were more diverse than those from calves, suggesting that strain differences in transference may exist. Understanding the transfer of E. coli from environmental and animal sources to calves may aid in developing intervention strategies to reduce E. coli colonization of young cattle.

Molecular detection of nine clinically important non-O157 Escherichia coli serogroups from raw sheep meat in Chaharmahal-va-Bakhtiari province, Iran

STEC isolates and also stx-negative Escherichia coli isolates from sheep meat from the Chaharmahal-va-Bakhtiari province, Iran were analyzed for nine clinically important non-O157 serotypes by PCR. A total of 90 E. coli isolates were tested. Stx-positive and eae-positive E. coli isolates did not belong to the nine most clinically relevant non-O157 STECs. Of the 80 non-STEC isolates, two belonged to the O103 and two belonged to the O128 groups. Stx-negative E. coli O103 and O128 strains isolated have potential in acquiring stx genes and continuing into the digestive system of consumers. Further studies are needed to analyze virulence characteristics of these E. coli strains to determine their potential role in causing disease in humans. For the sake of public health, it is important to monitor and investigate non-O157 diarrheagenic E. coli strains in meat in order to control and prevent them.

Diverse antibiotic resistance genes in dairy cow manure

Application of manure from antibiotic-treated animals to crops facilitates the dissemination of antibiotic resistance determinants into the environment. However, our knowledge of the identity, diversity, and patterns of distribution of these antibiotic resistance determinants remains limited. We used a new combination of methods to examine the resistome of dairy cow manure, a common soil amendment. Metagenomic libraries constructed with DNA extracted from manure were screened for resistance to beta-lactams, phenicols, aminoglycosides, and tetracyclines. Functional screening of fosmid and small-insert libraries identified 80 different antibiotic resistance genes whose deduced protein sequences were on average 50 to 60% identical to sequences deposited in GenBank. The resistance genes were frequently found in clusters and originated from a taxonomically diverse set of species, suggesting that some microorganisms in manure harbor multiple resistance genes. Furthermore, amid the great genetic diversity in manure, we discovered a novel clade of chloramphenicol acetyltransferases. Our study combined functional metagenomics with third-generation PacBio sequencing to significantly extend the roster of functional antibiotic resistance genes found in animal gut bacteria, providing a particularly broad resource for understanding the origins and dispersal of antibiotic resistance genes in agriculture and clinical settings.

The increasing prevalence of antibiotic resistance among bacteria is one of the most intractable challenges in 21st-century public health. The origins of resistance are complex, and a better understanding of the impacts of antibiotics used on farms would produce a more robust platform for public policy. Microbiomes of farm animals are reservoirs of antibiotic resistance genes, which may affect distribution of antibiotic resistance genes in human pathogens. Previous studies have focused on antibiotic resistance genes in manures of animals subjected to intensive antibiotic use, such as pigs and chickens. Cow manure has received less attention, although it is commonly used in crop production. Here, we report the discovery of novel and diverse antibiotic resistance genes in the cow microbiome, demonstrating that it is a significant reservoir of antibiotic resistance genes. The genomic resource presented here lays the groundwork for understanding the dispersal of antibiotic resistance from the agroecosystem to other settings.

Prevalence and antimicrobial resistance of porcine O157 and non-O157 Shiga toxin-producing Escherichia coli from India

The aims of this study were to determine the prevalence of Shiga toxin-producing Escherichia coli (STEC) strains in pigs as a possible STEC reservoir in India as well as to characterize the STEC strains and to determine the antimicrobial resistance pattern of the strains. A total of 782 E. coli isolates from clinically healthy (n = 473) and diarrhoeic piglets (309) belonging to major pig-producing states of India were screened by the polymerase chain reaction (PCR) assay for the presence of virulence genes characteristic for STEC, that is, Shiga toxin-producing gene(s) (stx1, stx2), intimin (eae), enterohemolysin (hlyA) and STEC autoagglutinating adhesin (Saa). Overall STEC were detected in 113 (14.4%) piglets, and the prevalence of E. coli O157 and non-O157 STEC were 4 (0.5%) and 109 (13.9%), respectively. None of the O157 STEC isolates carried gene encoding for H7 antigen (fliCh7). The various combinations of virulence genes present in the strains studied were stx1 in 4.6%, stx1 in combination with stx2 gene in 5.1%, stx1 in combination with stx2 and ehxA in 0.6%, stx1 in combination with stx2 and eae in 0.2% and stx2 alone in 3.7%. All STEC isolates were found negative for STEC autoagglutinating adhesin (Saa). The number of STEC isolates which showed resistance to antimicrobials such as ampicillin, tetracycline, streptomycin, lincomycin, nalidixic acid, sulfadiazine, penicillin, gentamicin, kanamycin and ceftriaxone were 100, 99, 98, 97, 95, 94, 92, 88, 85 and 85, respectively. Ninety-seven isolates showed resistance to more than 2 antimicrobials, and 8 resistance groups (R1 to R8) were observed. This study demonstrates that pigs in India harbour both O157 and non-O157 STEC, and this may pose serious public health problems in future.