Genomic Characteristics of Stx2e-Producing Escherichia coli Strains Derived from Humans, Animals, and Meats

Excess A-subunits of Shiga toxin 2a are produced in enterohemorrhagic Escherichia coli

Shiga toxins (Stx) produced by Shiga toxin-producing Escherichia coli (STEC) and enterohemorrhagic E. coli (EHEC) are ribosome-inactivating AB5 proteins that consist of one enzymatic active A-subunit (StxA) and a pentamer of non-covalently linked B-subunits (StxB). The description of Stx as an AB5 protein and the observation that A-subunits without their corresponding B-subunits also intoxicate eukaryotic cells, led to the question whether A- and B-subunits are produced in the bacteria in a 1:5 ratio or whether the A-subunit of the clinically most prominent subtype Stx2a is transcribed in excess revealing free A-subunits released in the bacterial environment. The aim of this study was therefore, to investigate the genetic and protein-based background for this observation in six Stx2a-encoding STEC and EHEC wildtype strains. For this purpose, transcriptional analysis of the Stx2a subunit genes, stxA2a and stxB2a, was performed by quantitative real-time PCR in one foodborne O113:H21 STEC isolate (strain TS18/08) and five HUS-associated EHEC strains with the serotypes O157:H7/H- (HUSEC003, HUSEC004), O103:H- (HUSEC008), O26:H11 (HUSEC018), and O104:H4 (LB226692). Contrary to the hypothesis that the A- and B-subunit genes are expressed in a ratio of 1:5 comparable to the holotoxin structure or in a ratio of 1:1 based on the operon structure, the results showed that stxA2a was expressed 1.90 ± 0.55-times stronger than the gene encoding the B-subunit, possibly indicating the presence of free A-subunits. In addition, strain-specific differences regarding the mRNA fold-changes of the A-subunit gene were observed. By use of native polyacrylamide gel electrophoresis and subsequent Western blot analysis, those single A-subunits were indeed detected in the culture supernatants of all six strains. To investigate whether the transcription ratios between A- and B-subunits observed are in a similar range as the amount of subunit proteins present after translation, a quantitative ELISA specific for StxA2a and StxB2a was established. Quantification of the subunits on protein level by use of ELISA revealed that the subunit ratio of StxA2a:StxB2a is 1.10 ± 0.20 for the strains HUSEC003, HUSEC004 and HUSEC008, but 4.63 ± 0.31 for the strains TS18/08, LB226692, and HUSEC018. The results of this study demonstrated that on both, the transcriptional and the translational level, the established 1:5 subunit ratio is not present in all investigated strains. In addition, the ratios observed after translation indicate that in some strains StxA2a subunits are even produced in higher amounts than B-subunits.

Occurrence of Multiple stx1 Genes and Rare Genomic Variation in stx1 Shiga Toxin-Producing Escherichia coli

Shiga toxin-producing Escherichia coli are important foodborne pathogens. There are several subtypes of the Shiga toxin Stx known, with Stx2 (a-o) being more diverse than Stx1 (a, c, d). Multiple occurrences of stx2 genes as well as combinations of stx1 and stx2 have been reported. However, there is a lack of knowledge on the occurrence of multiple stx1 genes in STEC strains. Here, we report two strains from food and animal feces which show genomic variations in the stx1 operon. The first strain harbors stx1a and stx1c genes, and the second strain shows an inactive stx1 operon due to an insertion in the stxA1a subunit gene. The screening of publicly available complete genome sequences of STEC revealed further strains harboring multiple stx1 genes, indicating that those strains also occur in human infections. This should be kept in mind when applying routine diagnostic methods like PCR, that do not detect multiple occurrences of stx1 genes of the same subtype. Moreover, the impact on the severity of human infections due to multiple stx1 genes has not been investigated well.

Hybrid strains of enterotoxigenic/Shiga toxin-producing Escherichia coli, United Kingdom, 2014-2023

Introduction. Diarrhoeagenic Escherichia coli (DEC) pathotypes are defined by genes located on mobile genetic elements, and more than one definitive pathogenicity gene may be present in the same strain. In August 2022, UK Health Security Agency (UKHSA) surveillance systems detected an outbreak of hybrid Shiga toxin-producing E. coli/enterotoxigenic E. coli (STEC-ETEC) serotype O101:H33 harbouring both Shiga toxin (stx) and heat-stable toxin (st).Gap statement. These hybrid strains of DEC are a public health concern, as they are often associated with enhanced pathogenicity. However, little is known about their epidemiology, clinical significance and associated public health burden.Aim. The aim of this study was to describe the microbiology, epidemiology and genomic analysis of this novel hybrid serotype in the context of the STEC-ETEC strains in the UKHSA archive.Methodology. From 2014 to 2023, STEC isolated from faecal specimens testing positive for STEC by PCR were sequenced on the NextSeq 1000 short read platform and a subset were selected for long read nanopore sequencing. Genomes were analysed to determine serotype, stx subtype, DEC pathogenicity genes and antimicrobial resistance determinants.Results. There were 162 STEC-ETEC strains isolated between 2014 and 2023, of which 117/162 were human clinical isolates and 45 were of food or animal origin. An average of 16 STEC-ETEC strains were identified each year, exhibiting a range of different stx subtypes, the most common profiles being stx2g,st (n=65, 40%) and stx2a,st (n=48, 30%). The most common sequence types were ST329 and ST200 (n=24 each), and the most frequently detected serotype was O187:H28 (n=25). Nine cases of genetically linked STEC-ETEC O101:H33, stx1a,st were detected between 8 August and 21 September 2022. Although the temporal and geographical distribution of the cases was characteristic of a foodborne outbreak, the contaminated vehicle was not identified.Conclusions. Phylogenetic analysis and long-read sequencing of the outbreak strain provided insight into the stepwise acquisition of st and stx and the evolutionary history of STEC-ETEC pathotypes. The integration of epidemiological data and whole-genome sequencing for routine surveillance of gastrointestinal pathogens is key to understanding the emergence of zoonotic hybrid DEC pathotypes and monitoring foodborne threats to public health.

Characterization of Escherichia coli strains producing Shiga Toxin 2f subtype from domestic Pigeon

Shiga toxin-producing Escherichia coli (STEC) can cause mild diarrhea even severe hemolytic uremic syndrome (HUS). Shiga toxin (Stx) is the primary virulence factor. Two Stx types and several subtypes have been identified. STEC strains encoding stx2f (Stx2f-STECs) are frequently identified from pigeons. Stx2f was initially considered to be associated with mild symptoms, more recently Stx2f-STECs have been isolated from HUS cases, indicating their pathogenic potential. Here, we investigated the prevalence of Stx2f-STECs among domestic pigeons in two regions in China, characterized the strains using whole-genome sequencing (WGS), and assessed the Stx2f transcriptions. Thirty-two Stx2f-STECs (4.36%) were culture-positive out of 734 fecal samples (one strain per sample). No other stx subtype-containing strain was isolated. Four serotypes and two sequence types were determined, and a novel sequence type ST15057 was identified. All strains harbored the E. coli attaching and effacing gene eae. Two types of Stx2f prophages were assigned. Stx2f-STECs showed variable Stx transcription levels induced by mitomycin C. Whole genome single-nucleotide polymorphism (wgSNP) analysis revealed different genetic backgrounds between pigeon-derived strains and those from diarrheal or HUS patients. In contrast, pigeon-derived Stx2f-STECs from diverse regions exhibited genetic similarity. Our study reports the prevalence and characteristics of Stx2f-STECs from pigeons in China. The pigeon-derived strains might pose low public health risk.

Phenotypic and Genotypic Characterization of Escherichia coli and Salmonella spp. Isolates from Pigs at Slaughterhouse and from Commercial Pork Meat in Portugal

Background: Foodborne diseases are a serious public health concern, and food-producing animals are a major source of contamination. Methods: The present study analysed Escherichia coli and Salmonella spp. isolated from faecal samples of 100 fattening pigs and from 52 samples of pork meat. Results: The results showed that the majority of the analysed meat samples were considered satisfactory in terms of microbiological quality (92.3% for E. coli and 94.2% for Salmonella spp.). Salmonella spp. was identified in 5.8% of the meat samples, whereas E. coli was detected in 89.5% of all samples (69.2% in meat and 100% in faecal samples). Furthermore, 1.9% of the faecal samples contained Shiga-toxin-producing E. coli and 3.9% contained enterotoxigenic E. coli. All sequenced isolates presented virulence genes for extraintestinal pathogenic E. coli. Moreover, 75.0% of E. coli isolates from meat and 71.8% from faeces samples showed antibiotic resistance, with 40.7% and 51.4%, respectively, being multidrug-resistant (MDR). The most prevalent resistances were to tetracycline, ampicillin, and sulfamethoxazole, and one E. coli isolate showed resistance to extended-spectrum β-lactamase. Conclusions: This study highlights the role of pigs as a potential source of human contamination and the importance of a One Health approach to ensure food safety and to promote public health.

Shiga Toxin-Producing Escherichia coli Strains from Romania: A Whole Genome-Based Description

The zoonotic Shiga toxin-producing Escherichia coli (STEC) group is unanimously regarded as exceptionally hazardous for humans. This study aimed to provide a genomic perspective on the STEC recovered sporadically from humans and have a foundation of internationally comparable data. Fifty clinical STEC isolates, representing the culture-confirmed infections reported by the STEC Reference Laboratory between 2016 and 2023, were subjected to whole-genome sequencing (WGS) analysis and sequences were interpreted using both commercial and public free bioinformatics tools. The WGS analysis revealed a genetically diverse population of STEC dominated by non-O157 serogroups commonly reported in human STEC infections in the European Union. The O26:H11 strains of ST21 lineage played a major role in the clinical disease resulting in hospitalisation and cases of paediatric HUS in Romania surpassing the O157:H7 strains. The latter were all clade 7 and mostly ST1804. Notably, among the Romanian isolates was a stx2a-harbouring cryptic clade I strain associated with a HUS case, stx2f- and stx2e-positive strains, and hybrid strains displaying a mixture of intestinal and extraintestinal virulence genes were found. As a clearer picture emerges of the STEC strains responsible for infections in Romania, further surveillance efforts are needed to uncover their prevalence, sources, and reservoirs.

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.

Do asymptomatic STEC-long-term carriers need to be isolated or decolonized? New evidence from a community case study and concepts in favor of an individualized strategy

Asymptomatic long-term carriers of Shigatoxin producing Escherichia coli (STEC) are regarded as potential source of STEC-transmission. The prevention of outbreaks via onward spread of STEC is a public health priority. Accordingly, health authorities are imposing far-reaching restrictions on asymptomatic STEC carriers in many countries. Various STEC strains may cause severe hemorrhagic colitis complicated by life-threatening hemolytic uremic syndrome (HUS), while many endemic strains have never been associated with HUS. Even though antibiotics are generally discouraged in acute diarrheal STEC infection, decolonization with short-course azithromycin appears effective and safe in long-term shedders of various pathogenic strains. However, most endemic STEC-strains have a low pathogenicity and would most likely neither warrant antibiotic decolonization therapy nor justify social exclusion policies. A risk-adapted individualized strategy might strongly attenuate the socio-economic burden and has recently been proposed by national health authorities in some European countries. This, however, mandates clarification of strain-specific pathogenicity, of the risk of human-to-human infection as well as scientific evidence of social restrictions. Moreover, placebo-controlled prospective interventions on efficacy and safety of, e.g., azithromycin for decolonization in asymptomatic long-term STEC-carriers are reasonable. In the present community case study, we report new observations in long-term shedding of various STEC strains and review the current evidence in favor of risk-adjusted concepts.

Characteristics of Shiga Toxin-Producing Escherichia coli Circulating in Asymptomatic Food Handlers

Shiga toxin-producing Escherichia coli (STEC) is a foodborne zoonotic pathogen that causes diarrhea, hemorrhagic colitis (HC), and hemolytic uremic syndrome (HUS) worldwide. Since the infection can be asymptomatic, the circulation of STEC in some asymptomatic carriers, especially in healthy-food-related professionals, is not yet well understood. In this study, a total of 3987 anal swab samples from asymptomatic food handlers were collected, and ten swabs recovered STEC strains (0.251%). Of the ten STEC isolates, seven serotypes and eight sequence types (ST) were determined using whole genome sequencing (WGS). Two stx1 subtypes (stx1a and stx1c) and four stx2 subtypes (stx2a, stx2b, stx2d, and stx2e) were detected. Seven different insertion sites were found in fourteen Stx prophages, and the dmsB and yfhL were the newly identified insertion sites. The ten strains showed the variable Stx transcription levels after the mitomycin C induction. The whole-genome phylogeny indicated that the strains from the asymptomatic food handlers were genetically distant from the strains of HUS patients. The STEC isolates circulating in asymptomatic carriers might pose a low potential to cause disease.

Enterohemorrhagic Escherichia coli O157:H7 - Xuzhou City, Jiangsu Province, China, 2001-2021

What is already known about this topic?

The largest and longest outbreak of diarrhea, which was complicated with hemolytic uremic syndrome (HUS) caused by enterohemorrhagic Escherichia coli (EHEC) O157:H7, occurred in Xuzhou City and its adjacent areas from 1999 to 2000 in China.

What is added by this report?

According to surveillance results from 2001 to 2021, there was a significant decrease in the isolation rate of O157:H7, and cattle and sheep remained the primary hosts. However, non-Shiga toxin-producing O157:H7 emerged as the dominant strain, with stx2+stx1- strains following closely behind.

What are the implications for public health practice?

National surveillance of O157:H7 effectively serves as an early warning system and guidance for assessing the intensity and trend of disease epidemics. It is crucial to raise awareness of the public health risks associated with Shiga toxin-producing E. coli.

Identification and Genomic Characterization of Escherichia albertii in Migratory Birds from Poyang Lake, China

Escherichia albertii is an emerging zoonotic foodborne enteropathogen leading to human gastroenteritis outbreaks. Although E. albertii has been isolated from birds which have been considered as the potential reservoirs of this bacterium, its prevalence in migratory birds has rarely been described. In this study, E. albertii in migratory birds from Poyang Lake was investigated and characterized using whole genome sequencing. Eighty-one fecal samples from nine species of migratory birds were collected and 24/81 (29.6%) tested PCR-positive for E. albertii-specific genes. A total of 47 isolates was recovered from 18 out of 24 PCR-positive samples. All isolates carried eae and cdtB genes. These isolates were classified into eight E. albertii O-genotypes (EAOgs) (including three novel EAOgs) and three E. albertii H-genotypes (EAHgs). Whole genome phylogeny separated migratory bird-derived isolates into different lineages, some isolates in this study were phylogenetically closely grouped with poultry-derived or patient-derived strains. Our findings showed that migratory birds may serve as an important reservoir for heterogeneous E. albertii, thereby acting as potential transmission vehicles of E. albertii to humans.

Pre-treatment with phages achieved greater protection of mice against infection with Shiga toxin-producing Escherichia coli than post-treatment

Shiga toxin-producing Escherichia coli (STEC) is a group of pathogen that can cause various diseases in both humans and animals, such as watery diarrhea, hemorrhagic colitis, and uremia syndrome. Due to the serious situation of antibiotic resistance, phage therapy is considered to have a great potential in combating bacterial diseases. In this study, three phages (NJ-10, NJ-20, and NJ-38) with strong abilities to lyse virulent STEC strain CVCC193 cells in vitro were isolated. Subsequently, the therapeutic effects of the three phages were investigated in mice infected with CVCC193 cells. The results showed that the survival rates of mice injected with the phages at 3 h after challenge with CVCC193 cells were 40%-50%, while the survival rates of mice injected with the phages at 24 h before challenge were 80%-100%, indicating that pre-treatment with phages had better therapeutic effects than post-treatment. Pathological changes, bacterial loads in different organs, and serum levels of inflammatory factors of the infected mice were also detected. The results showed that the mice injected with the phages at 3 h after or 24 h before challenge with CVCC193 cells had significantly decreased organ lesions, bacterial loads, and serum levels of inflammatory factors as compared to infected mice without phage treatment. These results suggested that phages NJ-10, NJ-20, and NJ-38 can potentially protect against STEC infections.

High Prevalence and Persistence of Escherichia coli Strains Producing Shiga Toxin Subtype 2k in Goat Herds

Shiga toxin (Stx)-producing Escherichia coli (STEC) is a zoonotic pathogen with the ability to cause severe diseases like hemorrhagic colitis (HC) and hemolytic uremic syndrome (HUS). Shiga toxin (Stx) is the key virulence factor in STEC and can be classified into two types, Stx1 and Stx2, and different subtypes. Stx2k is a newly reported Stx2 subtype in E. coli strains from diarrheal patients, animals, and raw meats exclusively in China so far. To understand the reservoir of Stx2k-producing E. coli (Stx2k-STEC), we investigated Stx2k-STEC strains in goat herds and examined their genetic characteristics using whole-genome sequencing. A total of 448 STEC strains were recovered from 2,896 goat fecal samples, and 37.95% (170/448) were Stx2k-STEC. Stx2k-STEC strains of serotype O93:H28 and sequence type 4038 (ST4038) were the most predominant and were detected over several years. Notably, 55% of Stx2k-STEC strains carried the heat-labile toxin (LT)-encoding gene (elt) defining enterotoxigenic E. coli (ETEC), thereby exhibiting the hybrid STEC/ETEC pathotype. Stx2k-converting prophage genomes clustered into four groups and exhibited high similarity within each group. Strains from patients, raw meat, sheep, and goats were intermixed distributed in the phylogenetic tree, indicating the risk for cross-species spread of Stx2k-STEC and pathogenic potential for humans. Further studies are required to investigate the Stx2k-STEC strains in other reservoirs and to understand the mechanism of persistence in these hosts.

IMPORTANCE Strains of the recently reported Stx2k-STEC have been circulating in a variety of sources over time in China. Here, we show a high prevalence of Stx2k-STEC in goat herds. More than half of the strains were of the hybrid STEC/ETEC pathotype. Stx2k-STEC strains of predominant serotypes have been widespread in the goat herds over several years. Stx2k-converting prophages have exhibited a high level of similarity across geographical regions and time and might be maintained and transmitted horizontally. Given that goat-derived Stx2k-STEC strains share similar genetic backbones with patient-derived strains, the high prevalence of Stx2k-STEC in goats suggests that there is a risk of cross-species spread and that these strains may pose pathogenetic potential to humans. Our study thus highlights the need to monitor human Stx2k-STEC infections in this region and, by extension, in other geographic locations.

Comparative Genomics of Shiga Toxin-Producing Escherichia coli Strains Isolated from Pediatric Patients with and without Hemolytic Uremic Syndrome from 2000 to 2016 in Finland

Shiga toxin-producing Escherichia coli (STEC) infection can cause mild to severe illness, such as nonbloody or bloody diarrhea, and the fatal hemolytic uremic syndrome (HUS). The molecular mechanism underlying the variable pathogenicity of STEC infection is not fully defined so far. Here, we performed a comparative genomics study on a large collection of clinical STEC strains collected from STEC-infected pediatric patients with and without HUS in Finland over a 16-year period, aiming to identify the bacterial genetic factors that can predict the risk to cause HUS and poor renal outcome. Of 240 STEC strains included in this study, 52 (21.7%) were from pediatric patients with HUS. Serotype O157:H7 was the main cause of HUS, and Shiga toxin gene subtype stx2a was significantly associated with HUS. Comparative genomics and pangenome-wide association studies identified a number of virulence and accessory genes overrepresented in HUS-associated STEC compared to non-HUS STEC strains, including genes encoding cytolethal distending toxins, type III secretion system effectors, adherence factors, etc. No virulence or accessory gene was significantly associated with risk factors for poor renal outcome among HUS patients assessed in this study, including need for and duration of dialysis, presence and duration of anuria, and leukocyte counts. Whole-genome phylogeny and multiple-correspondence analysis of pangenomes could not separate HUS STEC from non-HUS STEC strains, suggesting that STEC strains with diverse genetic backgrounds may independently acquire genetic elements that determine their varied pathogenicity. Our findings indicate that nonbacterial factors, i.e., characteristics of the host immunity, might affect STEC virulence and clinical outcomes.

IMPORTANCE Shiga toxin-producing Escherichia coli (STEC) is a serious public health burden worldwide which causes outbreaks of gastrointestinal diseases and the fatal hemolytic uremic syndrome (HUS) characterized by the triad of mechanical hemolytic anemia, thrombocytopenia, and acute renal failure. Understanding the mechanism underlying the disease severity and patient outcome is of high importance. Using comparative genomics on a large collection of clinical STEC strains from STEC-infected patients with and without HUS, our study provides a reference of STEC genetic factors/variants that can be used as predictors of the development of HUS, which will aid risk assessment at the early stage of STEC infection. Additionally, our findings suggest that nonbacterial factors may play a primary role in the renal outcome in STEC-infected patients with HUS; further studies are needed to validate this.

Genomic Characterization of Escherichia coli O8 Strains Producing Shiga Toxin 2l Subtype

Shiga toxin-producing Escherichia coli (STEC) can cause diseases ranging from mild diarrhea to fatal extra-intestinal hemolytic uremic syndrome (HUS). Shiga toxin (Stx) is the key virulence factor in STEC, two Stx types (Stx1 and Stx2) and several subtypes varying in sequences, toxicity, and host specificity have been identified. Stx2l is a newly-designated subtype related to human disease but lacks thorough characterization. Here, we identified Stx2l from five STEC strains (Stx2l-STECs) recovered from raw mutton and beef in China. Whole-genome sequencing (WGS) was used to characterize the Stx2l-STECs in this study together with Stx2l-STECs retrieved from public databases. Our study revealed that all the analyzed Stx2l-STEC strains belonged to the same serogroup O8. Multilocus sequencing typing (MLST) showed two sequence types (ST88 and ST23) among these strains. Stx2l-converting prophages from different sources shared a highly similar structure and sequence. Single-nucleotide polymorphism (SNP)-based analysis revealed genetic relatedness between the human-derived and food-derived strains belonging to ST23. To conclude, our study supported the designation of Stx2l and demonstrated diverse host range and geographical distribution of Stx2l-STECs.Stx2l-STEC strains from different sources showed a high genetic similarity with an identical O8 serogroup. Further studies are needed to investigate the epidemiological trait and pathogenic potential of Stx2l-STEC strains.

Phage Cocktail Targeting STEC O157:H7 Has Comparable Efficacy and Superior Recovery Compared with Enrofloxacin in an Enteric Murine Model

O157:H7 is the most important Shiga toxin-producing Escherichia coli (STEC) serotype in relation to public health. Given that antibiotics may contribute to the exacerbation of STEC-related disease and an increased frequency of antibiotic-resistant strains, bacteriophage (phage) therapy is considered a promising alternative. However, phage therapy targeting enteric pathogens is still underdeveloped with many confounding effects from the microbiota. Here we comprehensively compared the therapeutic efficacy of a phage cocktail with the antibiotic enrofloxacin in a mouse model of STEC O157:H7 EDL933 infection. Enrofloxacin treatment provided 100% survival and the phage cocktail treatment provided 90% survival. However, in terms of mouse recovery, the phage cocktail outperformed enrofloxacin in all measured outcomes. Compared with enrofloxacin treatment, phage treatment led to a faster elimination of enteric pathogens, decreased expression levels of inflammatory markers, increased weight gain, maintenance of a stable relative organ weight, and improved homeostasis of the gut microbiota. These results provide support for the potential of phage therapy to combat enteric pathogens and suggest that phage treatment leads to enhanced recovery of infected mice compared with antibiotics. IMPORTANCE With the increasing severity of antibiotic resistance and other adverse consequences, animal experiments and clinical trials investigating the use of phages for the control and prevention of enteric bacterial infections are growing. However, the effects of phages and antibiotics on organisms when treating intestinal infections have not been precisely studied. Here, we comprehensively compared the therapeutic efficacy of a phage cocktail to the antibiotic enrofloxacin in a mouse model of STEC O157:H7 EDL933 infection. We found that, despite a slightly lower protection rate, phage treatment contributed to a faster recovery of infected mice compared with enrofloxacin. These results highlight the potential benefits of phage therapy to combat enteric infections.

High prevalence and pathogenic potential of Shiga toxin-producing Escherichia coli strains in raw mutton and beef in Shandong, China

Shiga toxin-producing Escherichia coli (STEC) is a foodborne pathogen that can cause severe human diseases such as hemolytic uremic syndrome (HUS). Human STEC infections are frequently caused through consumption of contaminated foods, especially raw meats. This study aimed to investigate the prevalence of STEC in raw meats and to characterize the meat-derived STEC strains using whole genome sequencing. Our study showed that 26.6% of raw mutton, and 7.5% of raw beef samples were culture-positive for STEC. Thirteen serotypes were identified in 22 meat-derived isolates in this study, including the virulent serotypes O157:H7 and O26:H11. Seven Shiga toxin (Stx) subtypes were found in 22 isolates, of these, stx1c and stx1c + stx2b were predominant. The recently-reported stx2k subtype was found in three mutton-sourced isolates. A number of other virulence genes such as genes encoding intimin (eae), enterohemorrhagic E. coli (EHEC) hemolysin (ehxA), EHEC factor for adherence (efa1), heat-stable enterotoxin 1 (astA), type III secretion system effectors, were detected in meat-derived STEC strains. One mutton-sourced isolate was resistant to three antibiotics, i.e., tetracycline, chloramphenicol, and trimethoprim-sulfamethoxazole. Whole-genome phylogeny indicated the genomic diversity of meat-derived strains in this study. O157:H7 and O26:H11 isolates in this study were phylogenetically grouped together with strains from HUS patients, suggesting their pathogenic potential. To conclude, our study reported high STEC contaminations in retail raw meats, particularly raw mutton, genomic characterization indicated pathogenic potential of meat-derived STEC strains. These findings highlight the critical need for increased monitoring of STEC in retail raw meats in China.

•

High prevalence of Shiga toxin-producing E. coli (STEC) was detected in raw mutton, compared to beef.

•

Virulent serotypes O157:H7 and O26:H11 were found in meat-sourced STEC isolates.

•

Meat-sourced STEC isolates in the same region exhibited genetic diversity.