A scoping review on the prevalence of Shiga-toxigenic Escherichia coli in wild animal species

Epidemiology and antimicrobial resistance profiles of pathogenic Escherichia coli from commercial swine and poultry abattoirs and farms in South Africa: A One Health approach

Pathogenic Escherichia coli (PEC) are important foodborne bacteria that can cause severe illness in humans. The PECs thrive within the intestines of humans as well as animals and may contaminate multiple ecosystems, including food and water, via faecal transmission. Abattoir and farm employees are at high risk of PEC exposure, which could translate to community risk through person-to-person contact. To determine the epidemiology and resistome of PECs in Gauteng and Limpopo provinces of South Africa, 198 swine faecal samples, 220 poultry cloacal swabs, 108 human hand swabs, 11 run-off water samples from abattoirs and farms were collected from four swine and five poultry commercial abattoirs and two swine farms. One effluent sample each was collected from four wastewater treatment plants (WWTP) and a tertiary hospital setting. Phenotypic and genotypic techniques were used including polymerase chain reaction, pulsed-field gel electrophoresis (PFGE) and whole genome sequencing (WGS). Results showed EHEC and EPEC prevalence was 4.1 % (22/542) and 20.8 % (113/542), respectively, with the O26 serogroup detected the most in PEC isolates. According to the PFGE dendrogram, isolates from poultry, human hand swabs and run-off water clustered together. Diverse virulence factors such as the novel stx2k subtype and eae genes were detected among the 36 representative PEC isolates according to WGS. The results showed that 66.7 % (24/36) of sequenced PECs presented with multi-drug resistance (MDR) to β-lactamase 13.9 % (5/36), aminoglycoside 61.1 % (22/36), tetracycline 41.7 % (15/36) and quinolones 38.9 % (14/36). No colistin nor carbapenem resistance was detected. Sequence types (STs) associated with MDR in this study were: ST752, ST189, ST206, ST10, ST48 and ST38. The findings highlight the threat of zoonotic pathogens to close human contacts and the need for enhanced surveillance to mitigate the spread of MDR foodborne PECs.

Occurrence, antibiotic resistance and molecular characterisation of Shiga toxin-producing Escherichia coli isolated from broiler chickens in Tunisia

1. Shiga toxin-producing Escherichia coli (STEC) strains are associated with disease outbreaks which cause a public health problem. The aim of this study was to determine the frequency of STEC strains, their virulence factors, phylogenetic groups and antimicrobial resistance profiles in broiler chickens.2. A total of 222 E.coli isolates were collected from the caecum of chickens intended to be slaughtered. Antibiotic susceptibility was tested against 21 antimicrobial agents and ESBL phenotype was assessed by double-disk synergy test. The presence of STEC virulence genes stx1, stx2,eaeA and ehxA was detected by PCR. The identification of STEC serogroups was realised by PCR amplification. Additive virulence genes, phylogenetic groups and integrons were examined among the STEC isolates.3. Out of 222 E.coli isolates, 72 (32%) were identified as STEC strains and the most predominant serogroups were O103, O145 and O157. Shiga toxin gene 1 (stx1) was found in 84.7% (61/72) of the STEC strains, and eae and stx2 were detected in 38.8% and 13.8%, respectively. The ESBL phenotype was documented in 48.6% (35/72) of isolates. Most of the isolates (90.3%) carried class 1 integron with the gene cassette encoding resistance to trimethoprim (dfrA) and streptomycin (aadA) in 31.9% of the isolates. Class 2 integron was identified in 36.1% of isolates.4. Broilers can be considered as a reservoir of STEC strains which have high virulence factors and integrons that might be transmitted to other chickens, environments and humans. It is important to undertake surveillance and efficient control measures in slaughterhouses and farms to control measures of STEC bacteria.

Escherichia coli Strains Isolated from American Bison (Bison bison) Showed Uncommon Virulent Gene Patterns and Antimicrobial Multi-Resistance

E. coli is considered one of the most important zoonotic pathogens worldwide. Highly virulent and antimicrobial-resistant strains of E. coli have been reported in recent years, making it essential to understand their ecological origins. In this study, we analyzed the characteristics of E. coli strains present in the natural population of American bison (Bison bison) in Mexico. We sampled 123 individuals and determined the presence of E. coli using standard bacteriological methods. The isolated strains were characterized using molecular techniques based on PCR. To evaluate the diversity of E. coli strains in this population, we analyzed 108 suggestive colonies from each fecal sample. From a total of 13,284 suggestive colonies, we isolated 33 E. coli strains that contained at least one virulence gene. The virotypes of these strains were highly varied, including strains with atypical patterns or combinations compared to classical pathotypes, such as the presence of escV, eae, bfpB, and ial genes in E. coli strain LMA-26-6-6, or stx2, eae, and ial genes in E. coli strain LMA-16-1-32. Genotype analysis of these strains revealed a previously undescribed phylogenetic group. Serotyping of all strains showed that serogroups O26 and O22 were the most abundant. Interestingly, strains belonging to these groups exhibited different patterns of virulence genes. Finally, the isolated E. coli strains demonstrated broad resistance to antimicrobials, including various beta-lactam antibiotics.

Draft genome sequence of a Shiga toxin-producing Escherichia coli strain from deer meat showing an IS-element integration in the B-subunit of the Shiga toxin Stx2b gene

Shiga toxin-producing Escherichia coli (STEC) are important food-borne pathogens. Here we report sequence data of the STEC strain BfR-EC-18960, which has integrated IS elements in the B-subunit of the Shiga toxin Stx2b gene. The strain was isolated from deer meat at a local butchery in Germany in 2021.

Impressive pan-genomic diversity of E. coli from a wild animal community near urban development reflects human impacts

Human and domesticated animal waste infiltrates global freshwater, terrestrial, and marine environments, widely disseminating fecal microbes, antibiotics, and other chemical pollutants. Emerging evidence suggests that guts of wild animals are being invaded by our microbes, including Escherichia coli, which face anthropogenic selective pressures to gain antimicrobial resistance (AMR) and increase virulence. However, wild animal sources remain starkly under-represented among genomic sequence repositories. We sequenced whole genomes of 145 E. coli isolates from 55 wild and 13 domestic animal fecal samples, averaging 2 (ranging 1-7) isolates per sample, on a preserve imbedded in a human-dominated landscape in California Bay Area, USA, to assess AMR, virulence, and pan-genomic diversity. With single nucleotide polymorphism analyses we predict potential transmission routes. We illustrate the usefulness of E. coli to aid our understanding of and ability to surveil the emergence of zoonotic pathogens created by the mixing of human and wild bacteria in the environment.

Detection and Characterization of Zoonotic Pathogens in Game Meat Hunted in Northwestern Italy

Wildlife can represent a reservoir of zoonotic pathogens and a public health problem. In the present study, we investigated the spread of zoonotic pathogens (Salmonella spp., Yersinia enterocolitica, Listeria monocytogenes, Shiga-toxin-producing Escherichia coli (STEC), and hepatitis E virus (HEV)) considering the presence of virulence and antibiotic resistance genes in game meat from animals hunted in northwest Italy. During two hunting seasons (2020 to 2022), samples of liver and/or muscle tissue were collected from chamois (n = 48), roe deer (n = 26), deer (n = 39), and wild boar (n = 35). Conventional microbiology and biomolecular methods were used for the detection, isolation, and characterization of the investigated pathogens. Two L. monocytogenes serotype IIa strains were isolated from wild boar liver; both presented fosfomycin resistance gene and a total of 22 virulence genes were detected and specified in the text. Eight Y. enterocolitica biotype 1A strains were isolated from chamois (2), wild boar (5), and deer (1) liver samples; all showed streptogramin and beta-lactam resistance genes; the virulence genes found were myfA (8/8 strains), ymoA (8/8), invA (8/8), ystB (8/8), and ail (4/8). Our data underscore the potential role of wildlife as a carrier of zoonotic and antibiotic-resistant pathogens in northwest Italy and a food safety risk for game meat consumers.

Prevalence of Shiga Toxin-Producing Escherichia coli O157 in Wild Scottish Deer with High Human Pathogenic Potential

Shiga toxin-producing E. coli (STEC) infections associated with wildlife are increasing globally, highlighting many 'spillover' species as important reservoirs for these zoonotic pathogens. A human outbreak of STEC serogroup O157 in 2015 in Scotland, associated with the consumption of venison meat products, highlighted several knowledge gaps, including the prevalence of STEC O157 in Scottish wild deer and the potential risk to humans from wild deer isolates. In this study, we undertook a nationwide survey of wild deer in Scotland and determined that the prevalence of STEC O157 in wild deer is low 0.28% (95% confidence interval = 0.06-0.80). Despite the low prevalence of STEC O157 in Scottish wild deer, identified isolates were present in deer faeces at high levels (>104 colony forming units/g faeces) and had high human pathogenic potential based on whole genome sequencing and virulence gene profiling. A retrospective epidemiological investigation also identified one wild deer isolate from this study as a possible source of a Scottish human outbreak in 2017. These results emphasise the importance of food hygiene practices during the processing of wild deer carcasses for human consumption.

Shiga toxin-producing Escherichia coli (STEC) and atypical enteropathogenic E. coli (aEPEC) in Swedish retail wheat flour

Wheat flour has been identified as the source of multiple outbreaks of gastrointestinal disease caused by shiga toxin-producing Escherichia coli (STEC). We have investigated the presence and genomic characteristics of STEC and related atypical enteropathogenic E. coli (aEPEC) in 200 bags of Swedish-produced retail wheat flour, representing 87 products and 25 brands. Samples were enriched in modified tryptone soya broth (mTSB) and screened with real-time PCR targeting stx₁, stx₂ and eae, and the serogroups O157, O121 and O26. Isolation was performed by immunomagnetic separation (IMS) for suspected STEC/aEPEC O157, O121 and O26, and by screening pools of colonies for other STEC. Real-time PCR after enrichment revealed 12 % of samples to be positive for shiga toxin genes (stx₁ and/or stx₂) and 11 % to be positive for intimin (eae). Organic production, small-scale production or whole grain did not significantly influence shiga toxin gene presence or absence in a generalized linear mixed model analysis. Eight isolates of STEC were recovered, all of which were intimin-negative. Multiple serotype/sequence type/shiga toxin subtype combinations that have also been found in flour samples in other European countries were recovered. Most STEC types recovered were associated with sporadic cases of STEC among humans in Sweden, but no types known to have caused outbreaks or severe cases of disease (i.e. haemolytic uraemic syndrome) were found. The most common finding was O187:H28 ST200 with stx_2g, with possible links to cervid hosts. Wildlife associated with crop damage is a plausible explanation for at least some of the surprisingly high frequency of STEC in wheat flour.

Shiga Toxin-Producing Escherichia coli in Faecal Samples from Wild Ruminants

Wildlife can harbour Shiga toxin-producing Escherichia coli (STEC). In the present study, STEC in faecal samples from red deer (n = 106) and roe deer (n = 95) were characterised. All isolates were non-O157 strains. In red deer, STEC were detected in 17.9% (n = 19) of the isolates, and the eae/stx_2b virulence profile was detected in two isolates (10.5%). One STEC strain harboured stx_1a (5.3%) and eighteen STEC strains harboured stx₂ (94.7%). The most prevalent stx₂ subtypes were stx_2b (n = 12; 66.7%), stx_2a (n = 3; 16.7%), and stx_2g (n = 2; 11.1%). One isolate could not be subtyped (NS) with the applied primers (5.6%). The most widely identified serotypes were O146:H28 (n = 4; 21%), O146:HNM (n = 2; 10.5%), O103:H7 (n = 1; 5.3%), O103:H21 (n = 1; 5.3%), and O45:HNM (n = 1; 5.3%). In roe deer, STEC were detected in 16.8% (n = 16) of the isolates, and the eae/stx_2b virulence profile was detected in one isolate (6.3%). Two STEC strains harboured stx_1a (12.5%), one strain harboured stx_1NS/stx_2b (6.3%), and thirteen strains harboured stx₂ (81.3%). The most common subtypes were stx_2b (n = 8; 61.5%), stx_2g (n = 2; 15.4%), non-typeable subtypes (NS) (n = 2; 15.4%), and stx_2a (n = 1; 7.7%). Serotype O146:H28 (n = 5; 31.3%) was identified. The study demonstrated that the zoonotic potential of STEC strains isolated from wildlife faeces should be monitored in the context of the 'One Health' approach which links human health with animal and environmental health.

Prevalence and Implications of Shiga Toxin-Producing E. coli in Farm and Wild Ruminants

Shiga-toxin-producing Escherichia coli (STEC) is a food-borne pathogen that causes human gastrointestinal infections across the globe, leading to kidney failure or even death in severe cases. E. coli are commensal members of humans and animals' (cattle, bison, and pigs) guts, however, may acquire Shiga-toxin-encoded phages. This acquisition or colonization by STEC may lead to dysbiosis in the intestinal microbial community of the host. Wildlife and livestock animals can be asymptomatically colonized by STEC, leading to pathogen shedding and transmission. Furthermore, there has been a steady uptick in new STEC variants representing various serotypes. These, along with hybrids of other pathogenic E. coli (UPEC and ExPEC), are of serious concern, especially when they possess enhanced antimicrobial resistance, biofilm formation, etc. Recent studies have reported these in the livestock and food industry with minimal focus on wildlife. Disturbed natural habitats and changing climates are increasingly creating wildlife reservoirs of these pathogens, leading to a rise in zoonotic infections. Therefore, this review comprehensively surveyed studies on STEC prevalence in livestock and wildlife hosts. We further present important microbial and environmental factors contributing to STEC spread as well as infections. Finally, we delve into potential strategies for limiting STEC shedding and transmission.

Human-Borne Pathogens: Are They Threatening Wild Great Ape Populations?

Climate change and anthropic activities are the two main factors explaining wild great ape habitat reduction and population decline. The extent to which human-borne infectious diseases are contributing to this trend is still poorly understood. This is due to insufficient or fragmented knowledge on the abundance and distribution of current wild great ape populations, the difficulty obtaining optimal biological samples for diagnostic testing, and the scarcity of pathogen typing data of sufficient quality. This review summarises current information on the most clinically relevant pathogens of viral, bacterial, parasitic, and fungal nature for which transmission from humans to wild great apes is suspected. After appraising the robustness of available epidemiological and/or molecular typing evidence, we attempt to categorise each pathogen according to its likelihood of truly being of human origin. We further discuss those agents for which anthroponotic transmission is more likely. These include two viral (Human Metapneumovirus and Respiratory Syncytial Virus), one bacterial (diarrhoeagenic Escherichia coli), and two parasitic (Cryptosporidium spp. and Giardia duodenalis) pathogens. Finally, we identify the main drawbacks impairing research on anthroponotic pathogen transmission in wild great apes and propose research lines that may contribute to bridging current knowledge gaps.

The Population Genetics, Virulence, and Public Health Concerns of Escherichia coli Collected From Rats Within an Urban Environment

The co-existence of rats and humans in urban environments has long been a cause for concern regarding human health because of the potential for rats to harbor and transmit disease-causing pathogens. Here, we analyze whole-genome sequence (WGS) data from 41 Escherichia coli isolates collected from rat feces from 12 locations within the city of Chicago, IL, United States to determine the potential for rats to serve as a reservoir for pathogenic E. coli and describe its population structure. We identified 25 different serotypes, none of which were isolated from strains containing significant virulence markers indicating the presence of Shiga toxin-producing and other disease-causing E. coli. Nor did the E. coli isolates harbor any particularly rare stress tolerant or antimicrobial resistance genes. We then compared the isolates against a public database of approximately 100,000 E. coli and Shigella isolates of primarily food, food facility, or clinical origin. We found that only one isolate was genetically similar to genome sequences in the database. Phylogenetic analyses showed that isolates cluster by serotype, and there was little geographic structure (e.g., isolation by distance) among isolates. However, a greater signal of isolation by distance was observed when we compared genetic and geographic distances among isolates of the same serotype. This suggests that E. coli serotypes are independent lineages and recombination between serotypes is rare.

Nanopore-Based Surveillance of Zoonotic Bacterial Pathogens in Farm-Dwelling Peridomestic Rodents

The effective control of rodent populations on farms is crucial for food safety, as rodents are reservoirs and vectors for several zoonotic pathogens. Clear links have been identified between rodents and farm-level outbreaks of pathogens throughout Europe and Asia; however, comparatively little research has been devoted to studying the rodent–agricultural interface in the USA. Here, we address this knowledge gap by metabarcoding bacterial communities of rodent pests collected from Minnesota and Wisconsin food animal farms. We leveraged the Oxford Nanopore MinION sequencer to provide a rapid real-time survey of putative zoonotic foodborne pathogens, among others. Rodents were live trapped (n = 90) from three dairy and mixed animal farms. DNA extraction was performed on 63 rodent colons along with 2 shrew colons included as outgroups in the study. Full-length 16S amplicon sequencing was performed. Our farm-level rodent-metabarcoding data indicate the presence of multiple foodborne pathogens, including Salmonella spp., Campylobacter spp., Staphylococcus aureus, and Clostridium spp., along with many mastitis pathogens circulating within five rodent species (Microtus pennsylvanicus, Mus musculus, Peromyscus leucopus, Peromyscus maniculatus, and Rattus norvegicus) and a shrew (Blarina brevicauda). Interestingly, we observed a higher abundance of enteric pathogens (e.g., Salmonella) in shrew feces compared to the rodents analyzed in our study. Knowledge gained from our research efforts will directly inform and improve farm-level biosecurity efforts and public health interventions to reduce future outbreaks of foodborne and zoonotic disease.

Free-ranging red deer (Cervus elaphus) as carriers of potentially zoonotic Shiga toxin-producing Escherichia coli

Shiga toxin‐producing E. coli (STEC) are zoonotic foodborne pathogens of outmost importance and interest has been raised in recent years to define the potential zoonotic role of wildlife in STEC infection. This study aimed to estimate prevalence of STEC in free‐ranging red deer (Cervus elaphus) living in areas with different anthropisation levels and describe the characteristics of strains in order to evaluate the potential risk posed to humans. Two‐hundred one deer faecal samples collected in 2016–2018 from animals of Central Italian Alps were examined by bacteriological analysis and PCR screening of E. coli colonies for stx1, stx2 and eae genes. STEC strains were detected in 40 (19.9%) deer, with significantly higher prevalence in offspring than in yearlings. Whole genome analysis was performed to characterise a subset of 31 STEC strains. The most frequently detected serotype was O146:H28 (n = 10, 32.3%). Virulotyping showed different stx subtypes combinations, with stx2b‐only (n = 15, 48.4%) being the most prevalent. All STEC lacked the eae gene but harbored additional virulence genes, particularly adhesins, toxins and/or other colonisation factors also described in STEC isolated from disease in humans. The most frequently detected genes were astA (n = 22, 71%), subAB (n = 21, 68%), iha (n = 26, 83.9%) and lpfA (n = 24, 77%). Four hybrid STEC/Enterotoxigenic E. coli strains were also identified. According to the most recent paradigm for pathogenicity assessment of STEC issued by the European Food Safety Authority, our results suggest that red deer are carriers of STEC strains that may have zoonotic potential, regardless of the anthropisation levels. Particular attention should be drawn to these findings while handling and preparing game meat. Furthermore, deer may release STEC in the environment, possibly leading to the contamination of soil and water sources.

Genetic diversity and pathogenic potential of Shiga toxin-producing Escherichia coli (STEC) derived from German flour

Shiga toxin-producing Escherichia coli (STEC) can cause severe human illness, which are frequently linked to the consumption of contaminated beef or dairy products. However, recent outbreaks associated with contaminated flour and undercooked dough in the United States and Canada, highlight the potential of plant based food as transmission routes for STEC. In Germany STEC has been isolated from flour, but no cases of illness have been linked to flour. In this study, we characterized 123 STEC strains isolated from flour and flour products collected between 2015 and 2019 across Germany. In addition to determination of serotype and Shiga toxin subtype, whole genome sequencing (WGS) was used for isolates collected in 2018 to determine phylogenetic relationships, sequence type (ST), and virulence-associated genes (VAGs). We found a high diversity of serotypes including those frequently associated with human illness and outbreaks, such as O157:H7 (stx2c/d, eae), O145:H28 (stx2a, eae), O146:H28 (stx2b), and O103:H2 (stx1a, eae). Serotypes O187:H28 (ST200, stx2g) and O154:H31 (ST1892, stx1d) were most prevalent, but are rarely linked to human cases. However, WGS analysis revealed that these strains, as well as, O156:H25 (ST300, stx1a) harbour high numbers of VAGs, including eae, nleB and est1a/sta1. Although STEC-contaminated flour products have yet not been epidemiologically linked to human clinical cases in Germany, this study revealed that flour can serve as a vector for STEC strains with a high pathogenic potential. Further investigation is needed to determine the sources of STEC contamination in flour and flour products particularly in regards to these rare serotypes.

The Role of Peridomestic Rodents as Reservoirs for Zoonotic Foodborne Pathogens

Although rodents are well-known reservoirs and vectors for a number of zoonoses, the functional role that peridomestic rodents serve in the amplification and transmission of foodborne pathogens is likely underappreciated. Clear links have been identified between commensal rodents and outbreaks of foodborne pathogens throughout Europe and Asia; however, comparatively little research has been devoted to studying this relationship in the United States. In particular, regional studies focused on specific rodent species and their foodborne pathogen reservoir status across the diverse agricultural landscapes of the United States are lacking. We posit that both native and invasive species of rodents associated with food-production pipelines are likely sources of seasonal outbreaks of foodborne pathogens throughout the United States. In this study, we review the evidence that identifies peridomestic rodents as reservoirs for foodborne pathogens, and we call for novel research focused on the metagenomic communities residing at the rodent-agriculture interface. Such data will likely result in the identification of new reservoirs for foodborne pathogens and species-specific demographic traits that might underlie seasonal enteric disease outbreaks. Moreover, we anticipate that a One Health metagenomic research approach will result in the discovery of new strains of zoonotic pathogens circulating in peridomestic rodents. Data resulting from such research efforts would directly inform and improve upon biosecurity efforts, ultimately serving to protect our food supply.

Distribution of Novel Og Types in Shiga Toxin-Producing Escherichia coli Isolated from Healthy Cattle

Shiga toxin-producing Escherichia coli (STEC) is an important foodborne pathogen. Although most cases of STEC infection in humans are due to O157 and non-O157 serogroups, there are also reports of infection with STEC strains that cannot be serologically classified into any O serogroup (O-serogroup untypeable [OUT]). Recently, it has become clear that even OUT strains can be subclassified based on the diversity of O-antigen biosynthesis gene cluster (O-AGC) sequences. Cattle are thought to be a major reservoir of STEC strains belonging to various serotypes; however, the internal composition of OUT STEC strains in cattle remains unknown. In this study, we screened 366 STEC strains isolated from healthy cattle by using multiplex PCR kits including primers that targeted novel O-AGC types (Og types) found in OUT E. coli and Shigella strains in previous studies. Interestingly, 94 (25.7%) of these strains could be classified into 13 novel Og types. Genomic analysis revealed that the results of the in silico serotyping of novel Og-type strains were perfectly consistent with those of the PCR experiment. In addition, it was revealed that a dual Og8+OgSB17-type strain carried two types of O-AGCs from E. coli O8 and Shigella boydii type 17 tandemly inserted at the locus, with both antigens expressed on the cell surface. The results of this comprehensive analysis of cattle-derived STEC strains may help improve our understanding of the strains circulating in the environment. Additionally, the DNA-based serotyping systems used in this study could be used in future epidemiological studies and risk assessments of other STEC strains.

Comparative Transcriptomics of Shiga Toxin-Producing and Commensal Escherichia coli and Cytokine Responses in Colonic Epithelial Cell Culture Infections

Ingestion of Shiga toxin-producing Escherichia coli (STEC) can result in a range of illness severity from asymptomatic to hemorrhagic colitis and death; thus risk assessment of STEC strains for human pathogenicity is important in the area of food safety. Illness severity depends in part on the combination of virulence genes carried in the genome, which can vary between strains even of identical serotype. To better understand how core genes are regulated differently among strains and to identify possible novel STEC virulence gene candidates that could be added to the risk assessment repertoire, we used comparative transcriptomics to investigate global gene expression differences between two STEC strains associated with severe illness and a commensal E. coli strain during in vitro intestinal epithelial cell (IEC) infections. Additionally, we compared a wide array of concomitant cytokine levels produced by the IECs. The cytokine expression levels were examined for a pattern representing STEC pathogenicity; however, while one STEC strain appeared to elicit a proinflammatory response, infection by the other strain produced a pattern comparable to the commensal E. coli. This result may be explained by the significant differences in gene content and expression observed between the STEC strains. RNA-Seq analysis revealed considerable disparity in expression of genes in the arginine and tryptophan biosynthesis/import pathways between the STEC strains and the commensal E. coli strain, highlighting the important role some amino acids play in STEC colonization and survival. Contrasting differential expression patterns were observed for genes involved in respiration among the three strains suggesting that metabolic diversity is a strategy utilized to compete with resident microflora for successful colonization. Similar temporal expression results for known and putative virulence genes were observed in the STEC strains, revealing strategies used for survival prior to and after initial adherence to IECs. Additionally, three genes encoding hypothetical proteins located in mobile genetic elements were, after interrogation of a large set of E. coli genomes, determined to likely represent novel STEC virulence factors.

The population genetics of pathogenic Escherichia coli

Escherichia coli is a commensal of the vertebrate gut that is increasingly involved in various intestinal and extra-intestinal infections as an opportunistic pathogen. Numerous pathotypes that represent groups of strains with specific pathogenic characteristics have been described based on heterogeneous and complex criteria. The democratization of whole-genome sequencing has led to an accumulation of genomic data that render possible a population phylogenomic approach to the emergence of virulence. Few lineages are responsible for the pathologies compared with the diversity of commensal strains. These lineages emerged multiple times during E. coli evolution, mainly by acquiring virulence genes located on mobile elements, but in a specific chromosomal phylogenetic background. This repeated emergence of stable and cosmopolitan lineages argues for an optimization of strain fitness through epistatic interactions between the virulence determinants and the remaining genome.

Recent Updates on Outbreaks of Shiga Toxin-Producing Escherichia coli and Its Potential Reservoirs

Following infection with certain strains of Shiga toxin-producing Escherichia coli (STEC), particularly enterohemorrhagic ones, patients are at elevated risk for developing life-threatening extraintestinal complications, such as acute renal failure. Hence, these bacteria represent a public health concern in both developed and developing countries. Shiga toxins (Stxs) expressed by STEC are highly cytotoxic class II ribosome-inactivating proteins and primary virulence factors responsible for major clinical signs of Stx-mediated pathogenesis, including bloody diarrhea, hemolytic uremic syndrome (HUS), and neurological complications. Ruminant animals are thought to serve as critical environmental reservoirs of Stx-producing Escherichia coli (STEC), but other emerging or arising reservoirs of the toxin-producing bacteria have been overlooked. In particular, a number of new animal species from wildlife and aquaculture industries have recently been identified as unexpected reservoir or spillover hosts of STEC. Here, we summarize recent findings about reservoirs of STEC and review outbreaks of these bacteria both within and outside the United States. A better understanding of environmental transmission to humans will facilitate the development of novel strategies for preventing zoonotic STEC infection.

Fallow Deer (Dama dama) as a Reservoir of Shiga Toxin-Producing Escherichia coli (STEC)

Shiga toxin-producing Escherichia (E.) coli (STEC) are responsible for the outbreaks of serious diseases in humans. Only a few reports on fallow deer as a reservoir of foodborne pathogens have been published to date. The purpose of this study was to determine the occurrence of STEC strains in the fallow deer population in Poland. In all, 94 fallow deer swabs were tested. Polymerase chain reaction (PCR) was performed to detect the virulence profile of stx1, stx2 and eae or aggR genes, to identify the subtypes of stx1 and stx2 genes and to perform O and H serotyping. STEC and attaching and effacing (AE)-STEC were identified in 13 isolates (13.83%). The most hazardous virulence profile was detected in three strains, namely stx2d serotype O103:HNM, eae/stx1a serotype O26:HNM and eae/stx1a serotype O157:H7. The predominant stx gene was stx2, which was identified in 76.92% of isolates. E. coli O157 was detected in 4/94 (4.26%). Other E. coli serogroups, O26, O103, O111 and O145, were identified in 14/94 fallow deer (14.89%). The present findings suggest that fallow deer are carriers of STEC/AE-STEC that are potentially pathogenic to humans.

Shiga toxin-producing Escherichia coli isolates from red deer (Cervus elaphus), roe deer (Capreolus capreolus) and fallow deer (Dama dama) in Poland

Shiga toxin-producing Escherichia (E.) coli (STEC) pathogens are responsible for the outbreaks of serious diseases in humans, including haemolytic uraemic syndrome (HUS), bloody diarrhoea (BD) and diarrhoea (D), and they pose a significant public health concern. Wild ruminants are an important environmental reservoir of foodborne pathogens that can cause serious illnesses in humans and contaminate fresh products. There is a general scarcity of published data about wildlife as a reservoir of foodborne pathogens in Poland, which is why the potential epidemiological risk associated with red deer, roe deer and fallow deer as reservoirs of STEC/AE-STEC strains was evaluated in this study. The aim of the study was to investigate the prevalence of STEC strains in red deer (Cervus elaphus), roe deer (Capreolus capreolus) and fallow deer (Dama dama) populations in north-eastern Poland, and to evaluate the potential health risk associated with wild ruminants carrying STEC/AE-STEC strains. We examined 252 rectal swabs obtained from 134 roe deer (Capreolus capreolus), 97 red deer (Cervus elaphus) and 21 fallow deer (Dama dama) in north-eastern Poland. The samples were enriched in modified buffered peptone water. Polymerase chain reaction (PCR) assays were conducted to determine the virulence profile of stx1, stx2 and eae or aggR genes, to identify the subtypes of stx1 and stx2 genes, and to perform O and H serotyping. E. coli O157:H7 isolates were detected in the rectal swabs collected from 1/134 roe deer (0.75%) and 4/97 red deer (4.1%), and they were not detected in fallow deer (Dama dama). The remaining E. coli serogroups, namely O26, O103, O111 and O145 that belong to the "top five" non-O157 serogroups, were detected in 15/134 roe deer (11.19%), 18/97 red deer (18.56%) and 2/21 fallow deer (9.52%). STEC/AE-STEC strains were detected in 33 roe deer isolates (24.63%), 21 red deer isolates (21.65%) and 2 fallow deer isolates (9.52%). According to the most recent FAO/WHO report, stx2a and eae genes are the primary virulence traits associated with HUS, and these genes were identified in one roe deer isolate and one red deer isolate. Stx2 was the predominant stx gene, and it was detected in 78.79% of roe deer and in 71.43% of red deer isolates. The results of this study confirmed that red deer and roe deer in north-eastern Poland are carriers of STEC/AE-STEC strains that are potentially pathogenic for humans. This is the first report documenting the virulence of STEC/AE-STEC strains from wild ruminants in Poland.