Epidemiology and microbiology of Shiga toxin-producing Escherichia coli other than serogroup O157 in England, 2009-2013

A comprehensive computational study to explore promising natural bioactive compounds targeting glycosyltransferase MurG in Escherichia coli for potential drug development

Peptidoglycan is a carbohydrate with a cross-linked structure that protects the cytoplasmic membrane of bacterial cells from damage. The mechanism of peptidoglycan biosynthesis involves the main synthesizing enzyme glycosyltransferase MurG, which is known as a potential target for antibiotic therapy. Many MurG inhibitors have been recognized as MurG targets, but high toxicity and drug-resistant Escherichia coli strains remain the most important problems for further development. In addition, the discovery of selective MurG inhibitors has been limited to the synthesis of peptidoglycan-mimicking compounds. The present study employed drug discovery, such as virtual screening using molecular docking, drug likeness ADMET proprieties predictions, and molecular dynamics (MD) simulation, to identify potential natural products (NPs) for Escherichia coli. We conducted a screening of 30,926 NPs from the NPASS database. Subsequently, 20 of these compounds successfully passed the potency, pharmacokinetic, ADMET screening assays, and their validation was further confirmed through molecular docking. The best three hits and the standard were chosen for further MD simulations up to 400 ns and energy calculations to investigate the stability of the NPs-MurG complexes. The analyses of MD simulations and total binding energies suggested the higher stability of NPC272174. The potential compounds can be further explored in vivo and in vitro for promising novel antibacterial drug discovery.

Shedding and exclusion from childcare in children with Shiga toxin-producing Escherichia coli, 2018-2022

Excluding children with Shiga toxin-producing Escherichia coli (STEC) from childcare until microbiologically clear of the pathogen, disrupts families, education, and earnings. Since PCR introduction, non-O157 STEC serotype detections in England have increased. We examined shedding duration by serotype and transmission risk, to guide exclusion advice. We investigated STEC cases aged <6 years, residing in England and attending childcare, with diarrhoea onset or sample date from 31 March 2018 to 30 March 2022. Duration of shedding was the interval between date of onset or date first positive specimen and earliest available negative specimen date. Transmission risk was estimated from proportions with secondary cases in settings attended by infectious cases. There were 367 cases (STEC O157 n = 243, 66.2%; STEC non-O157 n = 124, 33.8%). Median shedding duration was 32 days (IQR 20-44) with no significant difference between O157 and non-O157; 2% (n = 6) of cases shed for ≥100 days. Duration of shedding was reduced by 17% (95% CI 4-29) among cases reporting bloody diarrhoea. Sixteen settings underwent screening; four had secondary cases (close contacts' secondary transmission rate = 13%). Shedding duration estimates were consistent with previous studies (median 31 days, IQR 17-41). Findings do not warrant guidance changes regarding exclusion and supervised return of prolonged shedders, despite serotype changes.

Genetic Characterization of Intimin Gene (eae) in Clinical Shiga Toxin-Producing Escherichia coli Strains from Pediatric Patients in Finland

Shiga toxin (Stx)-producing Escherichia coli (STEC) infections cause outbreaks of severe disease in children ranging from bloody diarrhea to hemolytic uremic syndrome (HUS). The adherent factor intimin, encoded by eae, can facilitate the colonization process of strains and is frequently associated with severe disease. The purpose of this study was to examine and analyze the prevalence and polymorphisms of eae in clinical STEC strains from pediatric patients under 17 years old with and without HUS, and to assess the pathogenic risk of different eae subtypes. We studied 240 STEC strains isolated from pediatric patients in Finland with whole genome sequencing. The gene eae was present in 209 (87.1%) strains, among which 49 (23.4%) were from patients with HUS, and 160 (76.6%) were from patients without HUS. O157:H7 (126, 60.3%) was the most predominant serotype among eae-positive STEC strains. Twenty-three different eae genotypes were identified, which were categorized into five eae subtypes, i.e., γ1, β3, ε1, θ and ζ3. The subtype eae-γ1 was significantly overrepresented in strains from patients aged 5-17 years, while β3 and ε1 were more commonly found in strains from patients under 5 years. All O157:H7 strains carried eae-γ1; among non-O157 strains, strains of each serotype harbored one eae subtype. No association was observed between the presence of eae/its subtypes and HUS. However, the combination of eae-γ1+stx2a was significantly associated with HUS. In conclusion, this study demonstrated a high occurrence and genetic variety of eae in clinical STEC from pediatric patients under 17 years old in Finland, and that eae is not essential for STEC-associated HUS. However, the combination of certain eae subtypes with stx subtypes, i.e., eae-γ1+stx2a, may be used as risk predictors for the development of severe disease in children.

Haemolytic uraemic syndrome in children England, Wales, Northern Ireland, and Ireland: A prospective cohort study

Haemolytic uraemic syndrome (HUS) caused by infection with Shiga toxin-producing Escherichia coli (STEC) is a relatively rare but potentially fatal multisystem syndrome clinically characterised by acute kidney injury. This study aimed to provide robust estimates of paediatric HUS incidence in England, Wales, Northern Ireland, and the Republic of Ireland by using data linkage and case reconciliation with existing surveillance systems, and to describe the characteristics of the condition. Between 2011 and 2014, 288 HUS patients were included in the study, of which 256 (89.5%) were diagnosed as typical HUS. The crude incidence of paediatric typical HUS was 0.78 per 100,000 person-years, although this varied by country, age, gender, and ethnicity. The majority of typical HUS cases were 1 to 4 years old (53.7%) and female (54.0%). Clinical symptoms included diarrhoea (96.5%) and/or bloody diarrhoea (71.9%), abdominal pain (68.4%), and fever (41.4%). Where STEC was isolated (59.3%), 92.8% of strains were STEC O157 and 7.2% were STEC O26. Comparison of the HUS case ascertainment to existing STEC surveillance data indicated an additional 166 HUS cases were captured during this study, highlighting the limitations of the current surveillance system for STEC for monitoring the clinical burden of STEC and capturing HUS cases.

Whole-Genome Sequencing of Shiga Toxin-Producing Escherichia coli for Characterization and Outbreak Investigation

Shiga toxin-producing Escherichia coli (STEC) causes high frequencies of foodborne infections worldwide and has been linked to numerous outbreaks each year. Pulsed-field gel electrophoresis (PFGE) has been the gold standard for surveillance until the recent transition to whole-genome sequencing (WGS). To further understand the genetic diversity and relatedness of outbreak isolates, a retrospective analysis of 510 clinical STEC isolates was conducted. Among the 34 STEC serogroups represented, most (59.6%) belonged to the predominant six non-O157 serogroups. Core genome single nucleotide polymorphism (SNP) analysis differentiated clusters of isolates with similar PFGE patterns and multilocus sequence types (STs). One serogroup O26 outbreak strain and another non-typeable (NT) strain, for instance, were identical by PFGE and clustered together by MLST; however, both were distantly related in the SNP analysis. In contrast, six outbreak-associated serogroup O5 strains clustered with five ST-175 serogroup O5 isolates, which were not part of the same outbreak as determined by PFGE. The use of high-quality SNP analyses enhanced the discrimination of these O5 outbreak strains into a single cluster. In all, this study demonstrates how public health laboratories can more rapidly use WGS and phylogenetics to identify related strains during outbreak investigations while simultaneously uncovering important genetic attributes that can inform treatment practices.

Shiga Toxin Subtypes, Serogroups, Phylogroups, RAPD Genotypic Diversity, and Select Virulence Markers of Shiga-Toxigenic Escherichia coli Strains from Goats in Mid-Atlantic US

Understanding Shiga toxin subtypes in E. coli from reservoir hosts may give insight into their significance as human pathogens. The data also serve as an epidemiological tool for source tracking. We characterized Shiga toxin subtypes in 491 goat E. coli isolates (STEC) from the mid-Atlantic US region (stx1 = 278, stx2 = 213, and stx1/stx2 = 95). Their serogroups, phylogroups, M13RAPD genotypes, eae (intimin), and hly (hemolysin) genes were also evaluated. STEC-positive for stx1 harbored Stx1c (79%), stx1a (21%), and stx a/c (4%). Those positive for Stx2 harbored stx2a (55%) and Stx2b (32%), while stx2a/stx2d and stx2a/stx2b were each 2%. Among the 343 STEC that were serogrouped, 46% (n = 158) belonged to O8, 20% (n = 67) to 076, 12% (n = 42) to O91, 5% (n = 17) to O5, and 5% (n = 18) to O26. Less than 5% belonged to O78, O87, O146, and O103. The hly and eae genes were detected in 48% and 14% of STEC, respectively. Most belonged to phylogroup B1 (73%), followed by D (10%), E (8%), A (4%), B2 (4%), and F (1%). M13RAPD genotyping revealed clonality of 091, O5, O87, O103, and O78 but higher diversity in the O8, O76, and O26 serogroups. These results indicate goat STEC belonged to important non-O157 STEC serogroups, were genomically diverse, and harbored Shiga toxin subtypes associated with severe human disease.

Prevalence and Characterization of Shiga Toxin Producing Escherichia coli Isolated from Animal Feed in Croatia

A survey on prevalence and number of Shiga toxin-producing Escherichia (E.) coli (STEC) in animal feed was carried out over a period of nine years in the Republic of Croatia. A total of 1688 feed samples were collected from feed factories and poultry farms. Analysis included two standard procedures: sample enrichment and (a) immunomagnetic separation and plating on two selective media; or (b) plating on two selective media. Confirmation of STEC included morphological examination, biochemical tests, serotyping, and polymerase chain reaction. Morphological and biochemical characterization revealed 629 E. coli strains. Further serological screening method revealed 78 STEC and EPEC serotypes, while only 27 strains were confirmed as STEC with PCR. All positive samples (1.6%) originated from poultry farms and contained combination of virulence genes: eaeA, stx1, and/or stx2. Since the presence of stx (especially stx2) and eae are identified as risk factors for development of severe diseases in humans, results of this survey indicate that avian sources of STEC infections might be one of those "undefined sources" of human illnesses. Further research is necessary for evaluation of risks posed by contaminated feed, poultry, and environment.

Network-wide analysis of the Serosep EntericBio Gastro Panel 2 for the detection of enteric pathogens in Public Health Wales microbiology laboratories

Introduction. A retrospective data analysis of 34 months (spanning 2016-2020) of 961573 diagnostic results obtained before and after nucleic acid amplification testing (NAAT) implementation, across the Public Health Wales microbiology network.Hypothesis / Gap Statement. This is the first network-wide analysis of the implementation of enteric NAAT in diagnostic microbiology.Aim. To assess the outcome of replacing microscopy and bacterial culture with NAAT as the primary test in the diagnosis of: Campylobacter spp., Salmonella sp., Shigella spp., Shiga toxin-producing Escherichia coli (STEC), Cryptosporidium spp. and Giardia duodenalis infections.Methodology. Following NAAT introduction, bacterial culture was performed as a secondary test, to provide further information from NAAT positive samples for epidemiological purposes. Primary detection rates and overall bacterial culture rates were calculated for each target pathogen using both testing regimes (Stage I) including a comparison of in-patient and out-patient diagnoses (Stage II).Results. Stage I analysis showed that the primary detection rate significantly increased for Campylobacter spp. (P<0.0001), Salmonella sp. (P=0.0151), Shigella spp. (P<0.0001), STEC (P<0.0001), Cryptosporidium spp. (P<0.0001) and Giardia duodenalis (P<0.0001) when using NAAT compared to microscopy or bacterial culture. A significant decrease was seen in the overall rate of Campylobacter spp. isolation by bacterial culture (P<0.0001), whilst other targets remained unaffected. Stage II analysis showed that NAAT positive out-patient samples were more likely to be supplemented by a positive bacterial culture than NAAT positive in-patient samples for Campylobacter spp. (P<0.0001), Salmonella sp. (P=0.0004) and STEC (P=0.0039). However, Shigella spp. was more frequently isolated from NAAT positive in-patient samples (P=0.0005). A notable increase was seen for G. duodenalis detection from in-patient samples (P=0.0002). Reference laboratory data showed the NAAT assay can detect at least 53 serotypes of STEC but may not be able to detect some of the rarer species of Cryptosporidium seen in human infections.Conclusion. The implementation of NAAT has significantly increased the primary detection rate of all target enteric pathogens in Wales and information gleaned previously from direct culture is largely unaffected.

Interventions for Shiga toxin-producing Escherichia coli gastroenteritis and risk of hemolytic uremic syndrome: A population-based matched case control study

Background

The role of antibiotics in the treatment of Shiga toxin-producing Escherichia coli (STEC) infection is controversial.

Objectives

To evaluate the association between treatment (antibiotics, antidiarrheal agents, and probiotics) for STEC infection and hemolytic uremic syndrome (HUS) development.

Patients and methods

We performed a population-based matched case-control study using the data from the National Epidemiological Surveillance of Infectious Diseases (NESID) between January 1, 2017 and December 31, 2018. We identified all patients with STEC infection and HUS as cases and matched patients with STEC infection without HUS as controls, with a case-control a ratio of 1:5. Further medical information was obtained by a standardized questionnaire. Multivariable conditional logistic regression model was used.

Results

7760 patients with STEC infection were registered in the NESID. 182 patients with HUS and 910 matched controls without HUS were selected. 90 patients with HUS (68 children and 22 adults) and 371 patients without HUS (266 children and 105 adults) were included in the main analysis. The matched ORs of any antibiotics and fosfomycin for HUS in children were 0.56 (95% CI 0.32–0.98), 0.58 (0.34–1.01). The matched ORs for HUS were 2.07 (1.07–4.03), 0.86 (0.46−1.61) in all ages treated with antidiarrheal agent and probiotics.

Conclusions

Antibiotics, especially fosfomycin, may prevent the development of HUS in children, while use of antidiarrheal agents should be avoided.

Shiga toxin-producing Escherichia coli diagnosed by Stx PCR: assessing the public health risk of non-O157 strains

BACKGROUND

The implementation by diagnostic laboratories in England of polymerase chain reaction (PCR) to screen faecal specimens for Shiga toxin-producing Escherichia coli (STEC) has resulted in a significant increase in notifications mainly due to non-O157 strains. The purpose of this study was to develop an approach to public health risk assessment that prioritizes follow-up to cases caused by haemolytic uraemic syndrome (HUS) associated E. coli (HUSEC) strains and minimizes unnecessary actions.

METHODS

Epidemiological and microbiological data were prospectively collected from 1 November 2013 to 31 March 2017 and used to compare three risk assessment approaches.

RESULTS

A history of HUS/bloody diarrhoea/age under 6 years and faecal specimens positive for stx-predicted HUSEC with a diagnostic accuracy of 84% (95% CI; 81-88%). STEC isolated by Gastrointestinal Bacteria Reference Unit (GBRU) and stx2 and eae positive predicted HUSEC with a diagnostic accuracy of 99% (95% CI; 98-100%). Risk assessment combining these two tests predicts the most efficient use of resources, predicting that 18% (97/552) of cases would be eligible for follow-up at some stage, 16% (86/552) following local stx PCR results, 1% (7/552) following GBRU results of stx2 and eae status and 0.7% (4/552) following whole-genome sequencing. Follow-up could be stopped in 78% (76/97) of these cases, 97% (74/76) following second stage risk assessment.

CONCLUSIONS

This three-stage risk assessment approach prioritizes follow-up to HUSEC and minimizes unnecessary public health actions. We developed it into the algorithm for public health actions included in the updated PHE Guidance for management of STEC published in August 2018.

Diversity of Non-O157 Shiga Toxin-Producing Escherichia coli Isolated from Cattle from Central and Southern Chile

Simple Summary

Cattle are the main reservoir of Shiga toxin-producing E. coli (STEC), foodborne pathogens that cause severe disease and outbreaks. However, not all STEC cause human illnesses or have the same virulence potential. Characterizing strains isolated worldwide allows insights into how strains spread and which isolates have a more significant risk potential. This study described STEC isolation rates from cattle in Chile and characterized 30 isolates. We obtained 93 STEC isolates from 56/446 (12.6%) fecal cattle samples. Then, 30 non-O157 STEC isolates were selected for complete characterization; we found isolates of 16 different sequence types and 17 serotypes. One isolate was resistant to tetracycline and carried resistance genes against the drug. Surveyed virulence genes (n = 31) were present from 13% to 100% of isolates, and one isolate carried 26/31 virulence genes. Most isolates (90%; 27/30) carried the stx2 gene, which is frequently linked to strains causing severe disease. A phylogenetic reconstruction demonstrated that isolates clustered based on serotypes, independent of their geographical origin (Central or Southern Chile). These results indicate that cattle in Chile carry a wide diversity of STEC potentially pathogenic for humans based on the presence of virulence genes.

Abstract

Cattle are the main reservoir of Shiga toxin-producing Escherichia coli (STEC), one of the world’s most important foodborne pathogens. The pathogen causes severe human diseases and outbreaks. This study aimed to identify and characterize non-O157 STEC isolated from cattle feces from central and southern Chile. We analyzed 446 cattle fecal samples and isolated non-O157 STEC from 12.6% (56/446); a total of 93 different isolates were recovered. Most isolates displayed β-glucuronidase activity (96.8%; 90/93) and fermented sorbitol (86.0%; 80/93), whereas only 39.8% (37/93) were resistant to tellurite. A subgroup of 30 representative non-O157 STEC isolates was selected for whole-genome sequencing and bioinformatics analysis. In silico analysis showed that they grouped into 16 different sequence types and 17 serotypes; the serotypes most frequently identified were O116:H21 and O168:H8 (13% each). A single isolate of serotype O26:H11 was recovered. One isolate was resistant to tetracycline and carried resistance genes tet(A) and tet(R); no other isolate displayed antimicrobial resistance or carried antimicrobial resistance genes. The intimin gene (eae) was identified in 13.3% (4/30) of the genomes and 90% (27/30) carried the stx2 gene. A phylogenetic reconstruction demonstrated that the isolates clustered based on serotypes, independent of geographical origin. These results indicate that cattle in Chile carry a wide diversity of STEC potentially pathogenic for humans based on the presence of critical virulence genes.

Epidemiological investigations identified an outbreak of Shiga toxin-producing Escherichia coli serotype O26:H11 associated with pre-packed sandwiches

In October 2019, public health surveillance systems in Scotland identified an increase in the number of reported infections of Shiga toxin-producing Escherichia coli (STEC) O26:H11 involving bloody diarrhoea. Ultimately, across the United Kingdom (UK) 32 cases of STEC O26:H11 stx1a were identified, with the median age of 27 years and 64% were male; six cases were hospitalised. Among food exposures there was an association with consuming pre-packed sandwiches purchased at outlets belonging to a national food chain franchise (food outlet A) [odds ratio (OR) = 183.89, P < 0.001]. The common ingredient identified as a component of the majority of the sandwiches sold at food outlet A was a mixed salad of Apollo and Iceberg lettuce and spinach leaves. Microbiological testing of food and environmental samples were negative for STEC O26:H11, although STEC O36:H19 was isolated from a mixed salad sample taken from premises owned by food outlet A. Contamination of fresh produce is often due to a transient event and detection of the aetiological agent in food that has a short-shelf life is challenging. Robust, statistically significant epidemiological analysis should be sufficient evidence to direct timely and targeted on-farm investigations. A shift in focus from testing the microbiological quality of the produce to investigating the processes and practices through the supply chain and sampling the farm environment is recommended.

Association between Shiga Toxin-Producing Escherichia coli O157:H7 stx Gene Subtype and Disease Severity, England, 2009-2019

Signs and symptoms of Shiga toxin–producing Escherichia coli (STEC) serogroup O157:H7 infection range from mild gastrointestinal to bloody diarrhea and hemolytic uremic syndrome (HUS). We assessed the association between Shiga toxin gene (stx) subtype and disease severity for »3,000 patients with STEC O157:H7 in England during 2009–2019. Odds of bloody diarrhea, HUS, or both, were significantly higher for patients infected with STEC O157:H7 possessing stx2a only or stx2a combined with other stx subtypes. Odds of severe signs/symptoms were significantly higher for isolates encoding stx2a only and belonging to sublineage Ic and lineage I/II than for those encoding stx2a only and belonging to sublineage IIb, indicating that stx2a is not the only driver causing HUS. Strains of STEC O157:H7 that had stx1a were also significantly more associated with severe disease than strains with stx2c only. This finding confounds public health risk assessment algorithms based on detection of stx2 as a predictor of severe disease.

Shiga Toxin-Associated Hemolytic Uremic Syndrome: Specificities of Adult Patients and Implications for Critical Care Management

Shiga toxin-producing Escherichia coli-associated hemolytic uremic syndrome (STEC-HUS) is a form of thrombotic microangiopathy secondary to an infection by an enterohemorrhagic E. coli. Historically considered a pediatric disease, its presentation has been described as typical, with bloody diarrhea at the forefront. However, in adults, the clinical presentation is more diverse and makes the early diagnosis hazardous. In this review, we review the epidemiology, most important outbreaks, physiopathology, clinical presentation and prognosis of STEC-HUS, focusing on the differential features between pediatric and adult disease. We show that the clinical presentation of STEC-HUS in adults is far from typical and marked by the prevalence of neurological symptoms and a poorer prognosis. Of note, we highlight knowledge gaps and the need for studies dedicated to adult patients. The differences between pediatric and adult patients have implications for the treatment of this disease, which remains a public health threat and lack a specific treatment.

Outbreak of Shiga toxin-producing Escherichia coli O157 linked with consumption of a fast-food product containing imported cucumbers, United Kingdom, August 2020

BACKGROUND

In August 2020, an outbreak of Shiga toxin-producing Escherichia coli (STEC) O157:H7 occurred in the United Kingdom. Whole genome sequencing revealed that these cases formed a genetically distinct cluster.

METHODS

Hypotheses generated from case interviews were tested in analytical studies, and results informed environmental sampling and food chain analysis. A case-case study used non-outbreak 'comparison' STEC cases; a case-control study used a market research panel to recruit controls.

RESULTS

A total of 36 cases were identified; all cases reported symptom onset between August 3 and August 16, 2020. The majority of cases (83%) resided in the Midlands region of England and in Wales. A high proportion of cases reported eating out, with one fast-food restaurant chain mentioned by 64% (n = 23) of cases. Both the case-case study (adjusted odds ratio (aOR) 31.8, 95% confidence interval (CI) 1.6-624.9) and the case-control study (aOR 9.19, 95% CI 1.0-82.8) revealed statistically significant results, showing that the consumption of a specific fast-food product was independently associated with infection.

CONCLUSIONS

Consumption of a specific fast-food product was a likely cause of this outbreak. The only ingredient specific to the product was cucumbers. The supply of cucumbers was immediately halted, and no further cases have been identified.

Epidemiological investigation of recurrent outbreaks of haemolytic uraemic syndrome caused by Shiga toxin-producing Escherichia coli serotype O55:H7 in England, 2014-2018

Recurrent outbreaks of haemolytic uraemic syndrome (HUS) caused by Shiga toxin-producing Escherichia coli (STEC) serotype O55:H7 occurred in England between 2014 and 2018. We reviewed the epidemiological evidence to identify potential source(s) and transmission routes of the pathogen, and to assess the on-going risk to public health. Over the 5-year period, there were 43 confirmed and three probable cases of STEC O55:H7. The median age of cases was 4 years old (range 6 months to 69 years old) and over half of all cases were female (28/46, 61%). There were 36/46 (78.3%) symptomatic cases, and over half of all cases developed HUS (25/46, 54%), including two fatal cases. No common food or environmental exposures were identified, although the majority of cases lived in rural or semi-rural environments and reported contact with both wild and domestic animals. This investigation informed policy on the clinical and public health management of HUS caused by STEC other than serotype O157:H7 (non-O157 STEC) in England, including comprehensive testing of all household contacts and household pets and more widespread use of polymerase chain reaction assays for the rapid diagnosis of STEC-HUS.

Molecular Characterization of the Enterohemolysin Gene (ehxA) in Clinical Shiga Toxin-Producing Escherichia coli Isolates

Shiga toxin (Stx)-producing Escherichia coli (STEC) is an important foodborne pathogen with the ability to cause bloody diarrhea (BD) and hemolytic uremic syndrome (HUS). Little is known about enterohemolysin-encoded by ehxA. Here we investigated the prevalence and diversity of ehxA in 239 STEC isolates from human clinical samples. In total, 199 out of 239 isolates (83.26%) were ehxA positive, and ehxA was significantly overrepresented in isolates carrying stx_2a + stx_2c (p < 0.001) and eae (p < 0.001). The presence of ehxA was significantly associated with BD and serotype O157:H7. Five ehxA subtypes were identified, among which, ehxA subtypes B, C, and F were overrepresented in eae-positive isolates. All O157:H7 isolates carried ehxA subtype B, which was related to BD and HUS. Three ehxA groups were observed in the phylogenetic analysis, namely, group Ⅰ (ehxA subtype A), group Ⅱ (ehxA subtype B, C, and F), and group Ⅲ (ehxA subtype D). Most BD- and HUS-associated isolates were clustered into ehxA group Ⅱ, while ehxA group Ⅰ was associated with non-bloody stool and individuals ≥10 years of age. The presence of ehxA + eae and ehxA + eae + stx₂ was significantly associated with HUS and O157:H7 isolates. In summary, this study showed a high prevalence and the considerable genetic diversity of ehxA among clinical STEC isolates. The ehxA genotypes (subtype B and phylogenetic group Ⅱ) could be used as risk predictors, as they were associated with severe clinical symptoms, such as BD and HUS. Furthermore, ehxA, together with stx and eae, can be used as a risk predictor for HUS in STEC infections.

Comparative genomic analysis of a Shiga toxin-producing Escherichia coli (STEC) O145:H25 associated with a severe pediatric case of hemolytic uremic syndrome in Davidson County, Tennessee, US

Background

Shiga toxin-producing E. coli (STECs) are foodborne pathogens associated with bloody diarrhea and hemolytic uremic syndrome (HUS). Although the STEC O157 serogroup accounts for the highest number of infections, HUS-related complications and deaths, the STEC non-O157, as a group, accounts for a larger proportion of STEC infections and lower HUS cases. There is limited information available on how to recognize non-O157 serotypes associated with severe disease. The objectives of this study were to describe a patient with STEC non-O157 infection complicated with HUS and to conduct a comparative whole genome sequence (WGS) analysis among the patient’s STEC clinical isolate and STEC O157 and non-O157 strains.

Results

The STEC O145:H25 strain EN1I-0044-2 was isolated from a pediatric patient with diarrhea, HUS and severe neurologic and cardiorespiratory complications, who was enrolled in a previously reported case-control study of acute gastroenteritis conducted in Davidson County, Tennessee in 2013. The strain EN1I-0044-2 genome sequence contained a chromosome and three plasmids. Two of the plasmids were similar to those present in O145:H25 strains whereas the third unique plasmid EN1I-0044-2_03 shared no similarity with other STEC plasmids, and it carried 23 genes of unknown function. Strain EN1I-0044-2, compared with O145:H25 and O157 serogroup strains shared chromosome- and plasmid-encoded virulence factors, including Shiga toxin, LEE type III secretion system, LEE effectors, SFP fimbriae, and additional toxins and colonization factors.

Conclusions

A STEC O145:H25 strain EN1I-0044-2 was isolated from a pediatric patient with severe disease, including HUS, in Davidson County, TN. Phylogenetic and comparison WGS analysis provided evidence that strain EN1I-0044-2 closely resembles O145:H25, and confirmed an independent evolutionary path of STEC O145:H25 and O145:H28 serotypes. The strain EN1I-0044-2 virulence make up was similar to other O145:H25 and O157 serogroups. It carried stx2 and the LEE pathogenicity island, and additional colonization factors and enterotoxin genes. A unique feature of strain EN1I-0044-2 was the presence of plasmid pEN1I-0044-2_03 carrying genes with functions to be determined. Further studies will be necessary to elucidate the role that newly acquired genes by O145:H25 strains play in pathogenesis, and to determine if they may serve as genetic markers of severe disease.

Incubation Period of Shiga Toxin-Producing Escherichia coli

Shiga toxin–producing Escherichia coli are pathogenic bacteria found in the gastrointestinal tract of humans. Severe infections could lead to life-threatening complications, especially in young children and the elderly. Understanding the distribution of the incubation period, which is currently inconsistent and ambiguous, can help in controlling the burden of disease. We conducted a systematic review of outbreak investigation reports, extracted individual incubation data and summary estimates, tested for heterogeneity, classified studies into subgroups with limited heterogeneity, and undertook a meta-analysis to identify factors that may contribute to the distribution of the pathogen’s incubation period. Twenty-eight studies were identified for inclusion in the review (1 of which included information on 2 outbreaks), and the resulting I² value was 77%, indicating high heterogeneity. Studies were classified into 5 subgroups, with the mean incubation period ranging from 3.5 to 8.1 days. The length of the incubation period increased with patient age and decreased by 7.2 hours with every 10% increase in attack rate.

Antimicrobial resistance profiles of diarrhoeagenic Escherichia coli isolated from travellers returning to the UK, 2015-2017

Introduction. Diarrhoeagenic Escherichia coli (DEC) are difficult to distinguish from non-pathogenic commensal E. coli using traditional culture methods. The implementation of PCR targeting specific virulence genes characteristic of the five DEC pathotypes, has improved the detection of DEC in faecal specimens from patients with symptoms of gastrointestinal disease.Aim. Antimicrobial resistance (AMR) profiles of 660 strains of DEC isolated between 2015 and 2017 from UK travellers reporting symptoms of gastrointestinal disease were reviewed to look for evidence of emerging AMR associated with travellers' diarrhoea.Methodology. All isolates of DEC were sequenced, and sequence type, serotype, pathotype markers and AMR profiles were derived from the genome data.Results. A travel history was provided for 54.1 % (357/660) of cases, of which 77.0 % (275/357) reported travel outside the UK within 7 days of onset of symptoms, and 23.0 % (82/357) reported no travel in that time frame. Of the 660 strains of DEC in this study, 265 (40.2 %) samples were identified as EAEC, 48 (7.3 %) as EIEC, 61 (9.2 %) were ETEC and 286 (43.3 %) were EPEC. EPEC caused the highest percentage of infections in children (40.6 %) whilst the highest proportion of cases reporting recent travel were infected with ETEC (86.1 %). There were 390/660 (59.0 %) isolates resistant to at least one antimicrobial on the panel tested (EIEC, 81.3 %; ETEC, n=65.6 %; EAEC, n=73.2 %; EPEC, 40.9 %) and 265/660 (40.2 %) were multidrug-resistant (EIEC, 33.3 %; ETEC, 32.8 %; EAEC, 56.2 %; EPEC, 28.0 %). Genes conferring resistance to the beta-lactams and fluroquinolones were highest in the EAEC pathotype, 56.6 and 60.7%, respectively.Conclusions. Increasing MDR, along with resistance to the fluroquinolones and the third-generation cephalosporins, in DEC causing travellers' diarrhoea provides further evidence for the need to restrict the use of antimicrobial agents and continuous monitoring.

Evaluation of chromogenic selective agar (CHROMagar STEC) for the direct detection of Shiga toxin-producing Escherichia coli from faecal specimens

Shiga toxin-producing Escherichia coli (STEC) are zoonotic pathogens that cause symptoms of severe gastrointestinal disease, including haemolytic uraemic syndrome (HUS), in humans. Currently in England, STEC serotypes other than O157:H7 are not cultured at the local hospital laboratories. The aim of this study was to evaluate the utility of CHROMagar STEC for the direct detection of STEC from faecal specimens in a diagnostic setting, compared to the current reference laboratory method using PCR targeting the Shiga-toxin gene (stx) to test multiple colonies cultured on MacConkey agar. Of the 292 consecutive faecal specimens submitted to the Gastrointestinal Bacterial Reference Unit that tested positive for stx by PCR, STEC could not be cultured on MacConkey agar or CHROMagar STEC from 87/292 (29.8 %). Of the 205 that were cultured, 106 (51.7 %) were detected on both MacConkey agar and CHROMagar STEC and 99 (48.3 %) were detected on MacConkey agar only. All 106 (100 %) isolates that grew on CHROMagar STEC had the ter gene cassette, known to be associated with resistance to tellurite, compared to 13/99 (13.1 %) that were not detected on CHROMagar STEC. CHROMagar STEC supported the growth of 36/40 (90 %) isolates harbouring stx2a or stx2d, the subtypes most frequently associated with progression to HUS. Of the 92 isolates harbouring eae, an important STEC virulence marker, 77 (83.7 %) grew on CHROMagar STEC. CHROMagar STEC is a useful selective media for the rapid, near-patient detection of STEC that have the potential to cause HUS.

Genetic diversity of the intimin gene (eae) in non-O157 Shiga toxin-producing Escherichia coli strains in China

Shiga toxin-producing Escherichia coli (STEC) is an important foodborne pathogen. The increasing incidence of non-O157 STEC has posed a great risk to public health. Besides the Shiga toxin (Stx), the adherence factor, intimin, coded by eae gene plays a critical role in STEC pathogenesis. In this study, we investigated the prevalence and polymorphisms of eae gene in non-O157 STEC strains isolated from different sources in China. Among 735 non-O157 STEC strains, eae was present in 70 (9.5%) strains. Eighteen different eae genotypes were identified in 62 eae-positive STEC strains with the nucleotide identities ranging from 86.01% to 99.97%. Among which, seven genotypes were newly identified in this study. The eighteen eae genotypes can be categorized into five eae subtypes, namely β1, γ1, ε1, ζ3 and θ. Associations between eae subtypes/genotypes and serotypes as well as origins of strains were observed in this study. Strains belonging to serotypes O26:H11, O103:H2, O111:H8 are associated with particular eae subtypes, i.e., β1, ε1, θ, respectively. Most strains from diarrheal patients (7/9, 77.8%) carried eae-β1 subtype, while most isolates from cattle (23/26, 88.5%) carried eae-ζ3 subtype. This study demonstrated a genetic diversity of eae gene in non-O157 STEC strains from different sources in China.

Virulence Profiling and Molecular Typing of Shiga Toxin-Producing E. coli (STEC) from Human Sources in Brazil

Since no recent data characterizing Shiga toxin-producing E. coli (STEC) from human infections in Brazil are available, the present study aimed to investigate serotypes, stx genotypes, and accessory virulence genes, and also to perform pulsed-field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST) of 43 STEC strains recovered from 2007 to 2017. Twenty-one distinct serotypes were found, with serotype O111:H8 being the most common. However, serotypes less frequently reported in human diseases were also found and included a hybrid STEC/ETEC O100:H25 clone. The majority of the strains carried stx1a as the sole stx genotype and were positive for the eae gene. Regarding the occurrence of 28 additional virulence genes associated with plasmids and pathogenicity islands, a diversity of profiles was found especially among the eae-harboring strains, which had combinations of markers composed of up to 12 distinct genes. Although PFGE analysis demonstrated genetic diversity between serotypes such as O157:H7, O111:H8, O26:H11, O118:H16, and O123:H2, high genetic relatedness was found for strains of serotypes O24:H4 and O145:H34. MLST allowed the identification of 17 distinct sequence types (STs) with ST 16 and 21 being the most common ones. Thirty-five percent of the strains studied were not typeable by the currently used MLST approach, suggesting new STs. Although STEC O111:H8 remains the leading serotype in Brazil, a diversity of other serotypes, some carrying virulence genes and belonging to STs incriminated as causing severe disease, were found in this study. Further studies are needed to determine whether they have any epidemiological relevance.

Shiga Toxin-Associated Hemolytic Uremic Syndrome: A Narrative Review

The severity of human infection by one of the many Shiga toxin-producing Escherichia coli (STEC) is determined by a number of factors: the bacterial genome, the capacity of human societies to prevent foodborne epidemics, the medical condition of infected patients (in particular their hydration status, often compromised by severe diarrhea), and by our capacity to devise new therapeutic approaches, most specifically to combat the bacterial virulence factors, as opposed to our current strategies that essentially aim to palliate organ deficiencies. The last major outbreak in 2011 in Germany, which killed more than 50 people in Europe, was evidence that an effective treatment was still lacking. Herein, we review the current knowledge of STEC virulence, how societies organize the prevention of human disease, and how physicians treat (and, hopefully, will treat) its potentially fatal complications. In particular, we focus on STEC-induced hemolytic and uremic syndrome (HUS), where the intrusion of toxins inside endothelial cells results in massive cell death, activation of the coagulation within capillaries, and eventually organ failure.

Genomic analysis of Shiga toxin-producing Escherichia coli from patients and asymptomatic food handlers in Japan

Shiga toxin-producing Escherichia coli (STEC) can cause severe gastrointestinal disease and colonization among food handlers. In Japan, STEC infection is a notifiable disease, and food handlers are required to undergo routine stool examination for STEC. However, the molecular epidemiology of STEC is not entirely known. We investigated the genomic characteristics of STEC from patients and asymptomatic food handlers in Miyagi Prefecture, Japan. Whole-genome sequencing (WGS) was performed on 65 STEC isolates obtained from 38 patients and 27 food handlers by public health surveillance in Miyagi Prefecture between April 2016 and March 2017. Isolates of O157:H7 ST11 and O26:H11 ST21 were predominant (n = 19, 29%, respectively). Non-O157 isolates accounted for 69% (n = 45) of all isolates. Among 48 isolates with serotypes found in the patients (serotype O157:H7 and 5 non-O157 serotypes, O26:H11, O103:H2, O103:H8, O121:H19 and O145:H28), adhesion genes eae, tir, and espB, and type III secretion system genes espA, espJ, nleA, nleB, and nleC were detected in 41 to 47 isolates (85–98%), whereas isolates with other serotypes found only in food handlers were negative for all of these genes. Non-O157 isolates were especially prevalent among patients younger than 5 years old. Shiga-toxin gene stx1a, adhesion gene efa1, secretion system genes espF and cif, and fimbrial gene lpfA were significantly more frequent among non-O157 isolates from patients than among O157 isolates from patients. The most prevalent resistance genes among our STEC isolates were aminoglycoside resistance genes, followed by sulfamethoxazole/trimethoprim resistance genes. WGS revealed that 20 isolates were divided into 9 indistinguishable core genomes (<5 SNPs), demonstrating clonal expansion of these STEC strains in our region, including an O26:H11 strain with stx1a+stx2a. Non-O157 STEC with multiple virulence genes were prevalent among both patients and food handlers in our region of Japan, highlighting the importance of monitoring the genomic characteristics of STEC.

Mapping of control measures to prevent secondary transmission of STEC infections in Europe during 2016 and revision of the national guidelines in Norway

In 2016, we reviewed preventive control measures for secondary transmission of Shiga-toxin producing Escherichia coli (STEC) in humans in European Union (EU)/European Free Trade Association (EEA) countries to inform the revision of the respective Norwegian guidelines which at that time did not accommodate for the varying pathogenic potential of STEC. We interviewed public health experts from EU/EEA institutes, using a semi-structured questionnaire. We revised the Norwegian guidelines using a risk-based approach informed by the new scientific evidence on risk factors for HUS and the survey results. All 13 (42%) participating countries tested STEC for Shiga toxin (stx) 1, stx2 and eae (encoding intimin). Five countries differentiated their control measures based on clinical and/or microbiological case characteristics, but only Denmark based their measures on routinely conducted stx subtyping. In all countries, but Norway, clearance was obtained with ⩽3 negative STEC specimens. After this review, Norway revised the STEC guidelines and recommended only follow-up of cases infected with high-virulent STEC (determined by microbiological and clinical information); clearance is obtained with three negative specimens. Implementation of the revised Norwegian guidelines will lead to a decrease of STEC cases needing follow-up and clearance, and will reduce the burden of unnecessary public health measures and the socioeconomic impact on cases. This review of guidelines could assist other countries in adapting their STEC control measures.

Phylogenetic context of Shiga toxin-producing Escherichia coli serotype O26:H11 in England

The increasing use of PCR for the detection of gastrointestinal pathogens in hospital laboratories in England has improved the detection of Shiga toxin-producing Escherichia coli (STEC), and the diagnosis of haemolytic uraemic syndrome (HUS). We aimed to analyse the microbiological characteristics and phylogenetic relationships of STEC O26:H11, clonal complex (CC) 29, in England to inform surveillance, and to assess the threat to public health. There were 502 STEC belonging to CC29 isolated between 2014 and 2019, of which 416 were from individual cases. The majority of isolates belonged to one of three major sequence types (STs), ST16 (n=37), ST21 (n=350) and ST29 (n=24). ST16 and ST29 were mainly isolated from cases reporting recent travel abroad. Within ST21, there were three main clades associated with domestic acquisition. All three domestic clades had Shiga toxin subtype gene (stx) profiles associated with causing severe clinical outcomes including STEC-HUS, specifically either stx1a, stx2a or stx1a/stx2a. Isolates from the same patient, same household or same outbreak with an established source for the most part fell within 5-SNP single linkage clusters. There were 19 5-SNP community clusters, of which six were travel-associated and one was an outbreak of 16 cases caused by the consumption of contaminated salad leaves. Of the remaining 12 clusters, 9/12 were either temporally or geographically related or both. Exposure to foodborne STEC O26:H11 ST21 capable of causing severe clinical outcomes, including STEC-HUS, is an emerging risk to public health in England. The lack of comprehensive surveillance of this STEC serotype is a concern, and there is a need to expand the implementation of methods capable of detecting STEC in local hospital settings.

Development and Validation of Shiga Toxin-Producing Escherichia coli Immunodiagnostic Assay

Shiga toxin (Stx)-producing Escherichia coli (STEC) and its subgroup enterohemorrhagic E. coli are important pathogens involved in diarrhea, which may be complicated by hemorrhagic colitis and hemolytic uremic syndrome, the leading cause of acute renal failure in children. Early diagnosis is essential for clinical management, as an antibiotic treatment in STEC infections is not recommended. Previously obtained antibodies against Stx1 and Stx2 toxins were employed to evaluate the sensitivity and specificity of the latex Agglutination test (LAT), lateral flow assay (LFA), and capture ELISA (cEIA) for STEC detection. The LAT (mAb Stx1 plus mAb stx2) showed 99% sensitivity and 97% specificity. Individually, Stx1 antibodies showed 95.5% and 94% sensitivity and a specificity of 97% and 99% in the cEIA and LFA assay, respectively. Stx2 antibodies showed a sensitivity of 92% in both assays and a specificity of 100% and 98% in the cEIA and LFA assay, respectively. These results allow us to conclude that we have robust tools for the diagnosis of STEC infections.

The epidemiology of Shiga toxin-producing Escherichia coli infections in the South East of England: November 2013-March 2017 and significance for clinical and public health

PURPOSE

This study describes the epidemiology of Shiga toxin-producing Escherichia coli (STEC) infections in a population in the South East of England.

METHODS

From 1 November 2013 to 31 March 2017 participating diagnostic laboratories reported Shiga toxin gene (stx) positive real-time PCR results to local public health teams. Stx positive faecal samples/isolates were referred to the Gastrointestinal Bacteria Reference Unit (GBRU) for confirmation by culture and typing by whole genome sequencing (WGS). Key clinical information was collected by public health teams.Results/Key findings. Altogether, 548 faecal specimens (420 were non-travel associated) were stx positive locally, 535 were submitted to the GBRU. STEC were isolated from 42 %, confirmed by stx PCR in 21 % and 37 % were PCR negative. The most common non-travel associated STEC serogroups were O157, O26, O146 and O91. The annualized incidence of confirmed STEC infections (PCR or culture) was 5.8 per 100 000. The ratio of O157 to non-O157 STEC serogroups was 1:7. The annualized incidence of non-O157 haemolytic uraemic syndrome-associated Escherichia coli (HUSEC) strains was 0.4 per 100 000. Bloody diarrhoea was reported by 58 % of cases infected with E. coli O157, 33 % of cases infected with non-O157 HUSEC strains and 12 % of other lower risk non-O157 strains. Overall, 76 % of non-O157 HUSEC isolates possessed the eae virulence gene.

CONCLUSIONS

HUSEC including serogroup O157 were uncommon and more likely to cause bloody diarrhoea than other STEC. The routine use of stx PCR testing can influence clinical management. Understanding the local epidemiology facilitates a proportionate public health response to STEC, based on clinical and microbiological characteristics including stx subtype(s).

Implementation of multiplex PCR diagnostics for gastrointestinal pathogens linked to increase of notified Shiga toxin-producing Escherichia coli cases in Norway, 2007-2017

The aim of this study was to investigate implementation of multiplex PCR assays (broad screening PCR) on the distribution and characteristics of notified Shiga toxin-producing Escherichia coli (STEC) cases in Norway, 2007-2017. We described STEC cases notified to the Norwegian Surveillance System for Communicable Diseases (MSIS), 2007-2017 and categorised cases as high-virulent, low-virulent or unclassifiable STEC infections based on guidelines for follow-up of STEC cases. We conducted descriptive analysis and time series analysis allowing for trends and seasonality, and calculated adjusted incidence rate ratios (aIRR) using negative binomial regression for laboratories with and without broad screening PCR. A total of 1458 STEC cases were notified to MSIS (2007-2017), median age 21 years, 51% female. Cases were categorised as having 475 (33%) high-virulent, 652 (45%) low-virulent, and 331 (23%) unclassifiable STEC infections. We observed a higher increasing monthly trend in cases (aIRR = 1.020; 95% CI 1.016-1.024) notified from laboratories with broad screening PCR (n = 4) compared to laboratories (n = 17) without (aIRR = 1.011; 95% CI 1.007-1.014). Notification of low-virulent STEC infections increased from laboratories with broad screening PCR. The increase in notified STEC cases was prominent in cases categorised with a low-virulent STEC infection and largely attributable to unselective screening methods. We recommend NIPH to maintain differentiated control measures for STEC cases to avoid follow-up of low-virulent STEC infections. We recommend microbiological laboratories in Norway to consider a more cost-effective broad screening PCR strategy that enables differentiation of high-virulent STEC infections.

Risk determinants for the development of typical haemolytic uremic syndrome in Belgium and proposition of a new virulence typing algorithm for Shiga toxin-producing Escherichia coli

In Belgium, it is mandatory to report Shiga toxin-producing Escherichia coli (STEC) infections to the health inspection authorities. To facilitate the decision making regarding infection control measures, information about the risk factors for the development of the haemolytic uremic syndrome (HUS) can be helpful. We performed statistical analyses on a dataset of 411 Belgian STEC strains. Demographic and clinical patient characteristics as well as phenotypical and genotypical STEC strain characteristics were taken into account. Multivariate logistic regression models indicated that age categories ⩽5, 6-12 and ⩾75; the stx2 gene; and the eae gene were significant HUS development risk determinants. The stx2a subtype had the highest risk (OR 29.6, 95% CI 7.0-125.1), while all stx1 subtypes encompassed a significant lower risk (OR 0.3, 95% CI 0.1-0.5). Presence of the stx1 gene without stx2 encompassed a lower risk than the combined presence of stx1 and stx2, or stx2 solely. Based on these results, we propose a new virulence typing algorithm that will enable the National Reference Centre to provide the physicians and health inspection authorities with a risk classification for the development of HUS. We believe this will contribute to a more efficient STEC infection control management in Belgium.

Factors in the emergence of serious human infections associated with highly pathogenic strains of shiga toxin-producing Escherichia coli

The appearance of highly pathogenic strains of Shiga toxin (Stx)-producingEscherichia. coli (STEC) has owed largely to the acquisition of Stx-encoding prophages by strains of E. coli that have pre-existing potential as enteric pathogens, such as atypical enteropathogenic E. coli (aEPEC) and enteroaggregative E. coli (EAEC). However, while high pathogenic potential is necessary, it is not sufficient for such strains to have a serious public health impact (i.e., large outbreaks, many cases of HUS, or both). To do so requires susceptible hosts and additional elements related to transmission, such as, socio-economic, societal, and lifestyle, factors. Two examples are discussed to illustrate this. The factors involved in the emergence of serious disease associated with E. coli O157:H7 in the 1980s probably included a massive increase in population exposure to this pathogen, likely as a result of the introduction of factory farming of cattle in the 1960s, and the development and wide patronage of fast food hamburger restaurants, and, potentially, waning immunity to intimin as a result of the reduction of incidence of enteropathogenic E. coli (EPEC) infection. In the devastating outbreak of Stx2-positiveEAEC O104:H4 in 2011, the wide distribution of the proposed vehicle of transmission, imported fenugreek seeds, was decisive in the exposure of a large population in Central Europe to this pathogen. Contributing factors likely included a preference for eating raw sprouts as a healthy food choice by the affected cases, many of whom were women. Low population levels of immunity to Stx2 probably contributed to the severe clinical outcome. A better understanding of the factors responsible for the emergence of potentially dangerous STEC pathogens as well as of extensive and serious disease associated with them can enhance public health strategies to respond to them.

Twenty-seven years of screening for Shiga toxin-producing Escherichia coli in a university hospital. Brussels, Belgium, 1987-2014

Objective

Since 1987 all fecal samples referred to the clinical microbiology laboratory of the UZ Brussel were screened for the presence of Shiga toxin-producing E. coli (STEC). In this study all STEC strains isolated over a period of 27 years (1987–2014) were reexamined to achieve deeper insight in the STEC infections in our patient population.

Methods

A total of 606 STEC strains from 604 patients were subjected to molecular methods for shiga toxin (stx) subtyping, detection of additional virulence genes, typing of the O-serogroups, and phylogenetic relatedness assessment of STEC O157:H7/H-.

Results

Since the introduction of PCR in 1991 the annual positivity rates varied between 1.1% and 2.7%. The isolation rate of STEC O157:H7/H- remained stable over the years while the isolation rate of non-O157 serotypes increased, mainly since 2011. The majority of the patients were children. Uncomplicated- and bloody diarrhea were the most prevalent gastrointestinal manifestations (respectively 51.9% and 13.6%), 4.3% of the strains were related to the hemolytic uremic syndrome (HUS), and 30.2% of the patients showed none of these symptoms. The strains were very diverse; they belonged to 72 different O-serovars and all stx subtypes except stx1d and stx2g were identified. Out of the 23 stx2f-positives one was associated with HUS and one belonged to the E. albertii species. As seen in other studies, the frequency of strains of the O157:H7/H- serotype and strains carrying stx2a, eaeA and ehxA was higher in patients with HUS.

Conclusions

The characteristics and trends of STEC infection seen in our patient population are similar to those noted in other countries. STEC infections in our hospital are mainly sporadic, and a substantial portion of the patients were asymptomatic carriers. Human STEC Stx2f infection was less rare than previously assumed and we report the first Belgian STEC stx2f HUS case and stx2f positive E. albertii infection.

Pathogenic potential of Shiga toxin-producing Escherichia coli strains of caprine origin: virulence genes, Shiga toxin subtypes, phylogenetic background and clonal relatedness

BACKGROUND

All over the world, Shiga toxin-producing Escherichia coli (STEC) are considered as important zoonotic pathogens. Eight serogroups have the greatest role in the outbreaks and diseases caused by STEC which include O26, O45, O103, O111, O113, O121, O145 and O157. Ruminants, especially cattle are the main reservoirs but the role of small ruminants in the epidemiology of human infections has not been thoroughly assessed in many countries. The objective of this research was to investigate the pathogenic potential of the STEC strains isolated from slaughtered goats. In this study, a total of 57 STEC strains were recovered from 450 goats and characterized by subtyping of stx genes, O-serogrouping, phylo-typing and DNA fingerprinting.

RESULTS

Amongst 57 STEC strains isolated from goats, the prevalence of stx1 was significantly more than stx2 (98.2% vs. 24.5%; P ≤ 0.05), and 22.8% of strains harbored both stx1 and stx2 genes. Three (5.2%) isolates were characterized as EHEC, which carried both eae and stx genes. A total of five stx-subtypes were recognized namely: stx1c (94.7%), stx1a (53.7%), stx2d (21%), stx2c (17.5%), and stx2a (15.7%). In some parts of the world, these subtypes have been reported in relation with severe human infections. The stx subtypes predominantly occurred in four combinations, including stx1a/stx1c (35%), stx1c (31.5%), stx1c/stx2a/stx2c/stx2d (5.2%) and stx1c/stx2c/stx2d (%5.2%). In serogrouping, the majority of STECs from goats did not belong to the top 8 serogroups but two strains belonged to O113, which has been recognized as an important pathogenic STEC in Australia. Interestingly, none of stx + eae + isolates belonged to the tested serogroups. In phylo-typing the isolates mostly belonged to phylo-group B1 (82.4%), followed by phylo-group A (12.3%). STEC strains showed a substantial diversity in DNA fingerprinting; there were 24 unique ERIC-types (with a ≥95% similarity) among the isolates.

CONCLUSIONS

Despite the fact that the top 8 STEC serogroups were uncommon in caprine strains, the presence of highly pathogenic stx subtypes indicates that small ruminants and their products can be considered as an overlooked public health risk for humans, especially in developing countries which consume traditional products.

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

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

Estimates of the burden of illness for eight enteric pathogens associated with animal contact in Canada

Enteric pathogens are commonly known to be transmitted through food or water; however, contact with animals is another important transmission route. This study estimated the annual burden of illness attributable to animal contact for eight enteric pathogens in Canada. Using data from a Canadian expert elicitation on transmission routes, the proportion of enteric illnesses attributable to animal contact was estimated for each pathogen to estimate the annual number of illnesses, hospitalizations and deaths in Canada. For each estimate, a mean and probability intervals were generated. Of all illnesses caused by these eight pathogens, 16% were estimated attributable to animal contact. This estimate translates to 86 000 (31 000–166 000) illnesses, 488 (186–890) hospitalizations and 12 (2–28) deaths annually for the eight pathogens combined. Campylobacter spp. is the leading cause of illnesses annually, with an estimated 38 000 (14 000–71 000) illnesses occurring each year, followed by non-typhoidal Salmonella spp. (17 000, 6000–32 000). The majority of hospitalizations were attributable to non-typhoidal Salmonella spp. (36%) and Campylobacter spp. (31%). Non-typhoidal Salmonella spp. (28%) and Listeria monocytogenes (31%) were responsible for the majority of the estimated deaths. These results identify farm animal and pet/pet food exposure as key pathways of transmission for several pathogens. The estimated burden of illness associated with animal contact is substantial.

Characterization and zoonotic impact of Shiga toxin producing Escherichia coli in some wild bird species

Aim:

Wild birds are considered silent vectors of some zoonotic water and food borne pathogens of public health significance. Owing to the importance of Shiga toxin producing Escherichia coli (STEC) as the most pathogenic among the emerging diarrheagenic E. coli groups that can infect man; the present study was designed to detect the occurrence of STEC among wild birds in Egypt.

Materials and Methods:

A total of 177 intestinal content swab samples originating from five wild bird species were investigated for the presence of E. coli and STEC by standard culture methods. Suspect STEC isolates were further characterized by serotyping, random amplified polymorphic DNA polymerase chain reaction (RAPD PCR), antimicrobial resistance pattern and PCR detection of stx₁, stx₂, and eae genes.

Results:

A total of 30 suspect STEC isolates from 30 positive birds’ samples were detected and identified on STEC CHROMagar (semi-captive pigeons, 15; house crows, 8; cattle egrets, 3; moorhens, 2; and house teals, 2). 25 isolates were grouped into 13 serogroups (O:20, O:25, O:26, O:27, O:63, O:78, O:111, O:114, O:125, O:128, O:142, O:153, and O:158), while five were rough strains. The distribution of STEC virulence genes among wild birds was as follows: 16 birds carried stx₁ gene only (nine pigeons [28.1%], six crows [7.1%], and one cattle egret [5.6%]). Stx₁ and stx₂ genes together were detected in four birds (one cattle egret [5.6%], two moorhens [6.1%], and one house teal, [10%]). Only one pigeon (3.1%) possessed the three alleles. Disk diffusion test results showed that cefixime was the most effective against STEC serotypes with (93.3%) sensitivity, followed by gentamycin (56.7%), and amoxicillin (50%). On the other hand, all the recovered STEC isolates were resistant to cefotaxime, doxycycline, cephalothin, and sulfisoxazole. RAPD fingerprinting using primers OPA-2 and OPA-9 showed that STEC isolates were heterogeneous; they yielded 30 and 27 different clusters, respectively.

Conclusions:

Wild birds carry STEC and may add to the contamination of the surrounding environment.

The Mobilome; A Major Contributor to Escherichia coli stx2-Positive O26:H11 Strains Intra-Serotype Diversity

Shiga toxin-producing Escherichia coli of serotype O26:H11/H- constitute a diverse group of strains and several clones with distinct genetic characteristics have been identified and characterized. Whole genome sequencing was performed using Illumina and PacBio technologies on eight stx2-positive O26:H11 strains circulating in France. Comparative analyses of the whole genome of the stx2-positive O26:H11 strains indicate that several clones of EHEC O26:H11 are co-circulating in France. Phylogenetic analysis of the French strains together with stx2-positive and stx-negative E. coli O26:H11 genomes obtained from Genbank indicates the existence of four clonal complexes (SNP-CCs) separated in two distinct lineages, one of which comprises the "new French clone" (SNP-CC1) that appears genetically closely related to stx-negative attaching and effacing E. coli (AEEC) strains. Interestingly, the whole genome SNP (wgSNP) phylogeny is summarized in the cas gene phylogeny, and a simple qPCR assay targeting the CRISPR array specific to SNP-CC1 (SP_O26-E) can distinguish between the two main lineages. The PacBio sequencing allowed a detailed analysis of the mobile genetic elements (MGEs) of the strains. Numerous MGEs were identified in each strain, including a large number of prophages and up to four large plasmids, representing overall 8.7-19.8% of the total genome size. Analysis of the prophage pool of the strains shows a considerable diversity with a complex history of recombination. Each clonal complex (SNP-CC) is characterized by a unique set of plasmids and phages, including stx-prophages, suggesting evolution through separate acquisition events. Overall, the MGEs appear to play a major role in O26:H11 intra-serotype clonal diversification.

Comparison of the fate of the top six non-O157 shiga-toxin producing Escherichia coli (STEC) and E. coli O157:H7 during the manufacture of dry fermented sausages

The study examined the relative fate of the top six non-O157 shiga-toxin producing Escherichia coli (STEC) and E. coli O157:H7 during the manufacture of dry fermented sausages (DFS). Three separate batches of sausages containing a five-strain cocktail for each serogroup and uninoculated control were manufactured and subjected to identical fermentation, maturation and dry curing conditions. Changes in physicochemical properties and inoculated STEC numbers were enumerated during the DFS production stages and log reduction and log reduction rates were calculated. Inoculation of very high concentrations (8logCFUg^-1) of STEC in the sausage batter did not significantly (P>0.05) affect the changes in the pH, a_w, moisture, protein, fat content compared to the uninoculated DFS. There was a significant (P<0.05) reduction in counts within the 48h fermentation for all STEC serogroups inoculated by about 0.97- to 1.42-log units. However, during the sausage maturation stage, all serogroups except O121 and O45 showed a significant reduction in numbers. During the extended 34day drying stage, all STEC serogroups showed a significant reduction in counts reaching a 5-log reduction within 20 to 27days of drying. ANOVA of the log reduction rates revealed significant differences in the reduction rates among the STEC serogroups examined. During the fermentation stage, serogroup O45 had the highest reduction rate at 0.98-logCFUg^-1day^-1 which was significantly higher compared to all other STEC serogroups (P<0.05), while O26 was the most tolerant to the conditions encountered during the fermentation stage with a reduction rate of 0.49-logCFUg^-1day^-1. However, during the extended 34days drying stage all STEC serogroups showed a steady reduction in population with a reduction rate ranging from 0.11- to 0.18-logCFUg^-1day^-1. The log reduction rate of E. coli O157:H7 was similar to that of serogroups O111 and O103, but was significantly lower (P<0.05) than all other STEC serogroups examined in the study. The log reduction rates of serogroups O121, O45, O145 and O26 during drying were not significantly different (P>0.05) from each other. These results indicate that the lethality of DFS production processes observed against E. coli O157:H7 would result in a similar inactivation of the top six non-O157 STEC.

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

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

Virulence factors of Shiga toxin-producing Escherichia coli and the risk of developing haemolytic uraemic syndrome in Norway, 1992-2013

Shiga toxin-producing Escherichia coli (STEC) may cause haemolytic uraemic syndrome (HUS). Age ≤5 years and presence of stx2a and eae are risk factors for the development of HUS. In this study, we investigated STEC isolates for the presence of adhesins, toxins and molecular risk assessment (MRA) factors to identify virulence genes associated with HUS development. We included non-duplicate isolates from all STEC infections (n = 340, HUS = 32) reported to the Norwegian National Reference Laboratory (NRL) for Enteropathogenic Bacteria from 1992 to 2013. The most common STEC were O157:H7/H^- (34%) and O103:H2 (14%). We retrospectively screened the isolates by three multiplex polymerase chain reactions (PCRs) for adhesins (n = 11), toxins (n = 5) and MRA (n = 15). We calculated odds ratios (ORs) and adjusted odds ratios (aORs) for associations with HUS development. On average, isolates were positive for 15 virulence genes (range: 1-24); two toxins (range: 0-4), five adhesins (range: 0-8) and eight MRA genes (range: 0-13). The gene combinations were clustered within serotypes. Isolates from HUS cases were positive for eae and IpfA _O26, and negative for saa, eibG, astA, cnf, subA and pic. We identified 11 virulence genes with a significant association to HUS development. Multivariable analyses adjusted for age group and Shiga toxin identified nleH1-2 [aOR 8.4, 95% confidence interval (CI); 2.18-32.3] as an independent risk factor for the development of HUS from an STEC infection. This study demonstrated that the non-LEE effector protein nleH1-2 may be an important predictor for elevated risk of developing HUS from STEC infections. We recommend the NRL for Enteropathogenic Bacteria to consider including nleH1-2 screening as part of routine STEC surveillance.

Paediatric HUS Cases Related to the Consumption of Raw Milk Sold by Vending Machines in Italy: Quantitative Risk Assessment Based on Escherichia coli O157 Official Controls over 7 years

A quantitative risk assessment (RA) was developed to estimate haemolytic-uremic syndrome (HUS) cases in paediatric population associated with the consumption of raw milk sold in vending machines in Italy. The historical national evolution of raw milk consumption phenomenon since 2008, when consumer interest started to grow, and after 7 years of marketing adjustment, is outlined. Exposure assessment was based on the official Shiga toxin-producing Escherichia coli O157:H7 (STEC) microbiological records of raw milk samples from vending machines monitored by the regional Veterinary Authorities from 2008 to 2014, microbial growth during storage, consumption frequency of raw milk, serving size, consumption preference and age of consumers. The differential risk considered milk handled under regulation conditions (4°C throughout all phases) and the worst time-temperature field handling conditions detected. In case of boiling milk before consumption, we assumed that the risk of HUS is fixed at zero. The model estimates clearly show that the public health significance of HUS cases due to raw milk STEC contamination depends on the current variability surrounding the risk profile of the food and the consumer behaviour has more impact than milk storage scenario. The estimated HUS cases predicted by our model are roughly in line with the effective STEC O157-associated HUS cases notified in Italy only when the proportion of consumers not boiling milk before consumption is assumed to be 1%. Raw milk consumption remains a source of E. coli O157:H7 for humans, but its overall relevance is likely to have subsided and significant caution should be exerted for temporal, geographical and consumers behaviour analysis. Health education programmes and regulatory actions are required to educate people, primarily children, on other STEC sources.

Whole genome sequencing improved case ascertainment in an outbreak of Shiga toxin-producing Escherichia coli O157 associated with raw drinking milk

Five cases of STEC O157 phage type (PT) 21/28 reported consumption of raw cows' drinking milk (RDM) produced at a dairy farm in the South West of England. STEC O157 PT21/28 was isolated from faecal specimens from milking cows on the implicated farm. Whole genome sequencing (WGS) showed that human and cattle isolates were the same strain. Further analysis of WGS data confirmed that sequences of isolates from an additional four cases (who did not report consumption of RDM when first questioned) fell within the same five single nucleotide polymorphism cluster as the initial five cases epidemiologically linked to the consumption of RDM. These four additional cases identified by WGS were investigated further and were, ultimately, associated with the implicated farm. The RDM outbreak strain encoded stx2a, which is associated with increased pathogenicity and severity of symptoms. Further epidemiological analysis showed that 70% of isolates within a wider cluster containing the outbreak strain were from cases residing in, or linked to, the same geographical region of England. During this RDM outbreak, use of WGS improved case ascertainment and provided insights into the evolution of a highly pathogenic clade of STEC O157 PT21/28 stx2a associated with the South West of England.

Antimicrobial resistance in Shiga toxin-producing Escherichia coli serogroups O157 and O26 isolated from human cases of diarrhoeal disease in England, 2015

OBJECTIVES

Shiga toxin-producing Escherichia coli (STEC) are zoonotic and transmission to humans occurs via contaminated food or contact with infected animals. In this study, WGS data were used to predict antimicrobial resistance (AMR) in STEC from symptomatic human cases to assess the extent of transmission of antibiotic-resistant E. coli from animals to humans.

METHODS

WGS data from 430 isolates of STEC were mapped to genes known to be associated with phenotypic AMR. Susceptibility testing was performed by a breakpoint method on all viable isolates exhibiting resistance to at least one antimicrobial.

RESULTS

327/396 (82.6%) of STEC O157 and 22/34 (64.7%) of STEC O26 lacked identifiable resistance genes and were predicted to be fully susceptible to 11 diverse classes of antimicrobials. For the remaining 81 isolates, 74 were phenotypically tested and there was concordance between WGS-predicted resistance and expression of phenotypic resistance. The most common resistance profile was ampicillin, streptomycin, trimethoprim/sulphonamide and tetracycline occurring in 25 (5.8%) isolates. Resistance to other antimicrobials, including resistance to chloramphenicol (2.1%), resistance to azithromycin (0.2%) and reduced susceptibility to ciprofloxacin (2.6%), was less frequent. Three isolates were identified as ESBL producers.

CONCLUSIONS

β-Lactams, trimethoprim/sulphonamides and tetracyclines account for the majority of therapeutic antimicrobials sold for veterinary use and this may be a risk factor for the presence of AMR in domestically acquired human clinical isolates of STEC. Isolates that were resistant to ampicillin, streptomycin, sulphonamide, tetracycline and azithromycin and had reduced susceptibility to ciprofloxacin were associated with cases who reported recent travel abroad.

Epidemiological and Microbiological Investigation of an Outbreak of Severe Disease from Shiga Toxin-Producing Escherichia coli O157 Infection Associated with Consumption of a Slaw Garnish

Investigating outbreaks of Shiga toxin-producing Escherichia coli (STEC) in England is a priority due to the potential severity of disease. However, there are often challenges in investigating outbreaks due to the small numbers of cases, poor patient recall, and low levels of bacteria that are challenging to detect in food samples using traditional laboratory culture techniques, and frequently a source is not identified. In September 2014, we investigated an STEC O157 outbreak associated with consuming a slaw garnish, and we report our findings here. Twenty confirmed cases were identified. Outbreak cases were interviewed, and menus reviewed to identify dishes consumed outside the home. Cases shared a history of eating meals at different chain restaurants. Analysis of menu items indicated shared consumption of slaw garnishes by 85.6% cases, although just 35.7% reported consuming them during interviews. Whole-genome sequencing linked cases where interpretation of the multilocus variable number tandem repeat analysis profile was obscured and indicated that the strain originated from a domestic (i.e., United Kingdom) source. Traceback identified that carrots and cabbages grown in the United Kingdom were the likely source of infection. Samples of products were examined, but STEC was not recovered. Epidemiological investigations linked the outbreak to consumption of a slaw garnish, which was poorly recalled by cases, and likely comprised of domestically produced raw vegetables. The causative organism was not isolated from food samples, and we conclude that future investigations should include sampling of animals and wildlife in the vicinity of farms where implicated produce is grown.

Postinfectious Hemolytic Uremic Syndrome

Post-infectious hemolytic uremic syndrome (HUS) is caused by specific pathogens in patients with no identifiable HUS-associated genetic mutation or autoantibody. The majority of episodes is due to infections by Shiga toxin (Stx) producing Escherichia coli (STEC). This chapter reviews the epidemiology and pathogenesis of STEC-HUS, including bacterial-derived factors and host responses. STEC disease is characterized by hematological (microangiopathic hemolytic anemia), renal (acute kidney injury) and extrarenal organ involvement. Clinicians should always strive for an etiological diagnosis through the microbiological or molecular identification of Stx-producing bacteria and Stx or, if negative, serological assays. Treatment of STEC-HUS is supportive; more investigations are needed to evaluate the efficacy of putative preventive and therapeutic measures, such as non-phage-inducing antibiotics, volume expansion and anti-complement agents. The outcome of STEC-HUS is generally favorable, but chronic kidney disease, permanent extrarenal, mainly cerebral complication and death (in less than 5 %) occur and long-term follow-up is recommended. The remainder of this chapter highlights rarer forms of (post-infectious) HUS due to S. dysenteriae, S. pneumoniae, influenza A and HIV and discusses potential interactions between these pathogens and the complement system.