Public health approach to detection of non-O157 Shiga toxin-producing Escherichia coli: summary of two outbreaks and laboratory procedures

The "Big Six": Hidden Emerging Foodborne Bacterial Pathogens

Non-O157 Shiga toxin-producing Escherichia coli (STEC) are emerging serogroups that often result in diseases ranging from diarrhea to severe hemorrhagic colitis in humans. The most common non-O157 STEC are O26, O45, O103, O111, O121, and O145. These serogroups are known by the name "big six" because they cause severe illness and death in humans and the United States Department of Agriculture declared these serogroups as food contaminants. The lack of fast and efficient diagnostic methods exacerbates the public impact of the disease caused by these serogroups. Numerous outbreaks have been reported globally and most of these outbreaks were caused by ingestion of contaminated food or water as well as direct contact with reservoirs. Livestock harbor a variety of non-O157 STEC serovars that can contaminate meat and dairy products, or water sources when used for irrigation. Hence, effective control and prevention approaches are required to safeguard the public from infections. This review addresses the disease characteristics, reservoirs, the source of infections, the transmission of the disease, and major outbreaks associated with the six serogroups ("big six") of non-O157 STEC encountered all over the globe.

Is Shiga Toxin-Producing Escherichia coli O45 No Longer a Food Safety Threat? The Danger is Still Out There

Many Shiga toxin-producing Escherichia coli (STEC) strains, including the serogroups of O157 and most of the top six non-O157 serotypes, are frequently associated with foodborne outbreaks. Therefore, they have been extensively studied using next-generation sequencing technology. However, related information regarding STEC O45 strains is scarce. In this study, three environmental E. coli O45:H16 strains (RM11911, RM13745, and RM13752) and one clinical E. coli O45:H2 strain (SJ7) were sequenced and used to characterize virulence factors using two reference E. coli O45:H2 strains of clinical origin. Subsequently, whole-genome-based phylogenetic analysis was conducted for the six STEC O45 strains and nine other reference STEC genomes, in order to evaluate their evolutionary relationship. The results show that one locus of enterocyte effacement pathogenicity island was found in all three STEC O45:H2 strains, but not in the STEC O45:H16 strains. Additionally, E. coli O45:H2 strains were evolutionarily close to E. coli O103:H2 strains, sharing high homology in terms of virulence factors, such as Stx prophages, but were distinct from E. coli O45:H16 strains. The findings show that E. coli O45:H2 may be as virulent as E. coli O103:H2, which is frequently associated with severe illness and can provide genomic evidence to facilitate STEC surveillance.

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).

Complete Genome Sequences of Three Shiga Toxin-Producing Escherichia coli O111:H8 Strains Exhibiting an Aggregation Phenotype

Non-O157 Shiga toxin-producing Escherichia coli (STEC) strains are a common source of foodborne illness. STEC O111 is among the most prevalent non-O157 STEC serogroups.

Non-O157 Shiga toxin-producing Escherichia coli (STEC) strains are a common source of foodborne illness. STEC O111 is among the most prevalent non-O157 STEC serogroups. Few completed genomes of STEC O111 strains have been reported to date. We report here the complete genomic sequences of three O111:H8 strains that display a distinct aggregation phenotype.

Multi-Year Persistence of Verotoxigenic Escherichia coli (VTEC) in a Closed Canadian Beef Herd: A Cohort Study

In this study, fecal samples were collected from a closed beef herd in Alberta, Canada from 2012 to 2015. To limit serotype bias, which was observed in enrichment broth cultures, Verotoxigenic Escherichia coli (VTEC) were isolated directly from samples using a hydrophobic grid-membrane filter verotoxin immunoblot assay. Overall VTEC isolation rates were similar for three different cohorts of yearling heifers on both an annual (68.5 to 71.8%) and seasonal basis (67.3 to 76.0%). Across all three cohorts, O139:H19 (37.1% of VTEC-positive samples), O22:H8 (15.8%) and O?(O108):H8 (15.4%) were among the most prevalent serotypes. However, isolation rates for serotypes O139:H19, O130:H38, O6:H34, O91:H21, and O113:H21 differed significantly between cohort-years, as did isolation rates for some serotypes within a single heifer cohort. There was a high level of VTEC serotype diversity with an average of 4.3 serotypes isolated per heifer and 65.8% of the heifers classified as "persistent shedders" of VTEC based on the criteria of >50% of samples positive and ≥4 consecutive samples positive. Only 26.8% (90/336) of the VTEC isolates from yearling heifers belonged to the human disease-associated seropathotypes A (O157:H7), B (O26:H11, O111:NM), and C (O22:H8, O91:H21, O113:H21, O137:H41, O2:H6). Conversely, seropathotypes B (O26:NM, O111:NM) and C (O91:H21, O2:H29) strains were dominant (76.0%, 19/25) among VTEC isolates from month-old calves from this herd. Among VTEC from heifers, carriage rates of vt1, vt2, vt1+vt2, eae, and hlyA were 10.7, 20.8, 68.5, 3.9, and 88.7%, respectively. The adhesin gene saa was present in 82.7% of heifer strains but absent from all of 13 eae+ve strains (from serotypes/intimin types O157:H7/γ1, O26:H11/β1, O111:NM/θ, O84:H2/ζ, and O182:H25/ζ). Phylogenetic relationships inferred from wgMLST and pan genome-derived core SNP analysis showed that strains clustered by phylotype and serotype. Further, VTEC strains of the same serotype usually shared the same suite of antibiotic resistance and virulence genes, suggesting the circulation of dominant clones within this distinct herd. This study provides insight into the diverse and dynamic nature of VTEC populations within groups of cattle and points to a broad spectrum of human health risks associated with these E. coli strains.

Promising Nucleic Acid Lateral Flow Assay Plus PCR for Shiga Toxin-Producing Escherichia coli

Shiga toxin (Stx)-producing Escherichia coli (STEC) is a frequent cause of foodborne infections, and methods for rapid and reliable detection of STEC are needed. A nucleic acid lateral flow assay (NALFA) plus PCR was evaluated for detecting STEC after enrichment. When cell suspensions of 45 STEC strains, 14 non-STEC strains, and 13 non-E. coli strains were tested with the NALFA plus PCR, all of the STEC strains yielded positive results, and all of the non-STEC and non-E. coli strains yielded negative results. The lower detection limit for the STEC strains ranged from 0.1 to 1 pg of genomic DNA (about 20 to 200 CFU) per test, and the NALFA plus PCR was able to detect Stx1- and Stx2-producing E. coli strains with similar sensitivities. The ability of the NALFA plus PCR to detect STEC in enrichment cultures of radish sprouts, tomato, raw ground beef, and beef liver inoculated with 10-fold serially diluted STEC cultures was comparable to that of a real-time PCR assay (at a level of 100 to 100,000 CFU/ml in enrichment culture). The bacterial inoculation test in raw ground beef revealed that the lower detection limit of the NALFA plus PCR was also comparable to that obtained with a real-time PCR assay that followed the U.S. Department of Agriculture guidelines. Although further evaluation is required, these results suggest that the NALFA plus PCR is a specific and sensitive method for detecting STEC in a food manufacturing plant.

High genotypic and phenotypic similarity among Shiga toxin-producing Escherichia coli O111 environmental and outbreak strains

Escherichia coli serogroup O111 is among the six most commonly reported non-O157:H7 Shiga toxin-producing E. coli (STEC), which are emerging as important foodborne pathogens. We have assembled a collection of environmental and clinical strains of E. coli O111 from diverse sources and investigated various genotypic and phenotypic characteristics of these strains to gain a better understanding of the epidemiology and biology of this serogroup. Sixty-three percent of the strains (24/38) were of H-type 8, which dominated the environmental- and outbreak-strains group, whereas the sporadic-case strains were more heterogeneous in H-type. All of the environmental and outbreak strains harbored the Shiga toxin 1 gene (stx1), eae, and ehx, and a subset of these also carried the Shiga toxin 2 gene (stx2). Only 9 of 16 sporadic-case strains produced stx1 and/or stx2, and these were mostly of H-type 8 and 10. Pulsed-field gel electrophoresis analysis revealed a cluster of environmental, outbreak, and sporadic illness strains with high phylogenetic similarity. Strains in this pulsogroup were all of the H8 type and STEC pathotype, and carried eae and ehx. Smaller clusters of highly similar STEC O111 strains included outbreak and sporadic illness strains isolated during different time periods or from different geographical locations. A distinct aggregative behavior was observed in the cultures of all environmental and outbreak STEC O111 strains, but not in those of sporadic-case strains. Among environmental and outbreaks strains, aggregation was positively correlated with production of curli fimbriae and RpoS function, and negatively with cellulose synthesis, while the nonaggregative behavior of sporadic-case strains correlated (positively) only with cellulose production. Our results indicate that STEC O111 strains sharing high genotypic similarity and important phenotypic traits with STEC O111 outbreak strains are present in the agricultural environment and may contribute to the burden of foodborne disease.

Hemolytic uremic syndrome following infection with O111 Shiga toxin-producing Escherichia coli revealed through molecular diagnostics

We report a case of hemolytic uremic syndrome in a 69-year-old woman due to Shiga toxin-producing Escherichia coli, possibly serotype O111, to illustrate the potentially deleterious implications of a Campylobacter enzyme immunoassay (EIA) result and the increasing importance of molecular testing when conventional methods are limited.

A sensitive multiplex, real-time PCR assay for prospective detection of Shiga toxin-producing Escherichia coli from stool samples reveals similar incidences but variable severities of non-O157 and O157 infections in northern California

Rapid and accurate detection of Shiga toxin-producing Escherichia coli (STEC) of all serotypes from patients with diarrhea is critical for medical management and for the prevention of ongoing transmission. In this prospective study, we assessed the performance of a multiplex, real-time PCR assay targeting stx1 and stx2 for the detection of O157 and non-O157 STEC in diarrheal stool samples enriched in Gram-negative broth. We show that the assay is 100% sensitive (95% confidence interval [CI], 89.1% to 100%) and 98.5% specific (95% CI, 90.6% to 99.9%) based on a panel of 40 known STEC-positive specimens and 65 known negative specimens. During a 2-year postvalidation period, the assay detected more positive samples from patients in northern California than did culture and PCR testing performed at a public health reference laboratory, with a positive predictive value of 95.6% (95% CI, 87.6% to 99.1%). Serotyping data showed an incidence rate of 51.2% for non-O157 STEC strains, with 5.8% of patients (1/17) with non-O157 strains and 42.9% (6/14) with O157 strains (P = 0.03) developing hemolytic-uremic syndrome. The findings from this study underscore the recommendations of the CDC for laboratories to test all diarrheal stool samples from patients with acute community-acquired diarrhea for non-O157 STEC in addition to the O157 serotype by using a sensitive assay. Additionally, a survey of 17 clinical laboratories in northern California demonstrated that nearly 50% did not screen all stool specimens for the presence of Shiga toxins, indicating that many clinical microbiology laboratories still do not routinely screen all stool specimens for the presence of Shiga toxins as recommended in the 2009 CDC guidelines.

Detection of Shiga toxin-producing Escherichia coli in ground beef using the GeneDisc real-time PCR system

Escherichia coli O157:H7 and certain non-O157 Shiga toxin-producing Escherichia coli (STEC) serogroups have emerged as important public health threats. The development of methods for rapid and reliable detection of this heterogeneous group of pathogens has been challenging. GeneDisc real-time PCR assays were evaluated for detection of the stx(1), stx(2), eae, and ehxA genes and a gene that identifies the O157 serogroup followed by a second GeneDisc assay targeting serogroup-specific genes of STEC O26, O45, O91, O103, O111, O113, O121, O145, and O157. The ability to detect the STEC serogroups in ground beef samples artificially inoculated at a level of ca. 2-20 CFU/25 g and subjected to enrichment in mTSB or buffered peptone water (BPW) was similar. Following enrichment, all inoculated ground beef samples showed amplification of the correct set of target genes carried by each strain. Samples inoculated with STEC serogroups O26, O45, O103, O111, O121, O145, and O157 were subjected to immunomagnetic separation (IMS), and isolation was achieved by plating onto Rainbow agar O157. Colonies were confirmed by PCR assays targeting stx(1), stx(2), eae, and serogroup-specific genes. Thus, this work demonstrated that GeneDisc assays are rapid, sensitive, and reliable and can be used for screening ground beef and potentially other foods for STEC serogroups that are important food-borne pathogens worldwide.

Characterization of non-O157 shiga toxin-producing Escherichia coli isolates from healthy fat-tailed sheep in southeastern of Iran

The objectives of this study were to determine the presence and prevalence of non-O157 shiga toxin-producing Escherichia coli (STEC) isolates from faeces of healthy fat-tailed sheep and detection of phylogenetic background and antibiotic resistance profile of isolates. One hundred ninety-two E. coli isolates were recovered from obtained rectal swabs and were confirmed by biochemical tests. Antibiotic resistance profiles of isolates were detected and phylogenetic background of isolates was determined according to the presence of the chuA, yjaA and TspE4.C2 genetic markers. The isolates were examined to determine stx (1), stx (2) and eae genes. Non-O157 STEC isolates were identified by using O157 specific antiserum. Forty-three isolates (22.40 %) were positive for one of the stx (1), stx (2) and eae genes, whereas 10.42 % were positive for stx (1), 19.38 % for eae and 2.60 % for stx (2) gene. None of the positive isolates belonged to O157 serogroup. Twenty isolates possessed stx ( 1 ) were distributed in A (six isolates), B1 (13) and D (one) phylogroups, whereas stx (2) positive isolates fell into A (three isolates) and B1 (two) phylogenetic groups. Eighteen isolates contained eae gene belonged to A (five isolates), B1 (seven) and D (six) phylogroups. The maximum and minimum resistance rates were recorded against to penicillin and co-trimoxazole respectively. The positive isolates for stx (1), stx (2) and eae genes showed several antibiotic resistance patterns, whereas belonged to A, B1 and D phylogroups. In conclusion, faeces of healthy sheep could be considered as the important sources of non-O157 STEC and also multidrug-resistant E. coli isolates.

Enhanced identification and characterization of non-O157 Shiga toxin-producing Escherichia coli: a six-year study

Non-O157 Shiga toxin-producing Escherichia coli (STEC) are emerging pathogens with the potential to cause serious illness and impact public health due to diagnostic challenges. Between 2005 and 2010, the Wadsworth Center (WC), the public health laboratory of the New York State (NYS) Department of Health, requested that Shiga toxin enzyme immunoassay (EIA)-positive stool enrichment broths and/or stool specimens be submitted by clinical and commercial reference laboratories testing NYS patient specimens. A total of 798 EIA-positive specimens were received for confirmation and serotyping, and additionally a subset of STEC was assessed for the presence of six virulence genes (stx1, stx2, eaeA, hlyA, nleA, and nleB) by real-time polymerase chain reaction. We confirmed 591 specimens as STEC, 164 (28%) as O157 STEC, and 427 (72%) as non-O157 STEC. Of the non-O157 STEC serogroups identified, over 70% were O103, O26, O111, O45, O121, or O145. During this time period, WC identified and characterized a total of 1282 STEC received as E. coli isolates, stool specimens, or EIA broths. Overall, the STEC testing identified 59% as O157 STEC and 41% as non-O157 STEC; however, out of 600 isolates submitted to the WC as E. coli cultures, 543 (90%) were identified as O157 STEC. This report summarizes a 6-year study utilizing enhanced STEC testing that resulted in increased identification and characterization of non-O157 STEC in NYS. Continued utilization of enhanced STEC testing may lead to effective and timely outbreak response and improve monitoring of trends in STEC disease epidemiology.

Identification of shiga toxin and intimin coding genes in Escherichia coli isolates from pigeons (Columba livia) in relation to phylotypes and antibiotic resistance patterns

Shiga toxin-producing Escherichia coli (STEC) strains are responsible for outbreaks of human intestinal diseases worldwide. Pigeons are distributed in public areas and are potential reservoirs for pathogenic bacteria. One hundred fifty-four fresh fecal samples were obtained from trapped pigeons in southeast of Iran and were cultured for isolation of E. coli. The isolates were examined to determine the prevalence of stx1, stx2, and eae genes, antimicrobial resistance, and their phylotypes. The confirmed E. coli isolates (138) belong to four phylogenetic groups: A (54.34%), B1 (34.05%), B2 (3.62%), and D (7.79%). Thirteen (9.42%) isolates were positive for one of the examined genes. Eight isolates (5.79%) were positive for eae, four (2.89%) for stx2, and one isolate (1.44%) for stx1 gene. Phylotyping assays showed that eight eae-positive isolates fall into three phylogroups; A (three isolates), B1 (three isolates), and D (two isolates), whereas four stx2-positive isolates belonged to the A (three isolates) and D (one isolate) groups. The stx1-positive isolate belonged to phylogroup A. One hundred six isolates (76.81%) showed resistance to at least one of the selected antibacterial agents. The maximum resistance rate was against oxytetracycline (73.91%), and the minimum was against flumequine (2.17%). Twenty different patterns of drug resistance were observed. According to the results, pigeons could be considered as carriers of STEC strains. However, E. coli isolates of pigeon feces increase the potential of these birds to act as a reservoir of multiple antibiotic resistant bacteria.