Frequency, characterization and genotypic analysis of Shiga toxin-producing Escherichia coli in beef slaughterhouses of Argentina

Study of the transfer of Shiga toxin-producing Escherichia coli during the slaughter of cattle using molecular typing combined with epidemiologic data

Investigation on the distribution and biological characteristics of Shiga-toxin producing Escherichia coli (STEC) during beef processing is essential for in-plant critical control points and food safety risk assessment. Serogroups and subtypes of stx genes of STEC strains isolated from beef processing lines were first investigated. Identification to cross-contamination among different sampling sites was further conducted by combining multilocus sequence typing (MLST) with the previous distribution and characterization data. The PCR-positive rate for STEC in 435 samples from two slaughter plants in China was 14.3% and the isolation rate for the 62 PCR positive and the entire set of 435 samples were 26% and 3.68% respectively. The existence of serotype O157:H7 (33%) and serogroups O121 (42%) and O26 (21%) as well as the high detection rate of high pathogenic gene stx2a (68%) in these serogroups indicated potential risk to the safety of beef. Traceability analysis showed that hide plays a critical role in cross-contamination between feces, lairage pens and post-washing carcasses from a molecular perspective. Intervening measures revolves around de-hiding should be involved in the in-plant safety control policy according to the tracing analysis.

Transforming Shiga toxin-producing Escherichia coli surveillance through whole genome sequencing in food safety practices

Introduction

Shiga toxin-producing Escherichia coli (STEC) is a gastrointestinal pathogen causing foodborne outbreaks. Whole Genome Sequencing (WGS) in STEC surveillance holds promise in outbreak prevention and confinement, in broadening STEC epidemiology and in contributing to risk assessment and source attribution. However, despite international recommendations, WGS is often restricted to assist outbreak investigation and is not yet fully implemented in food safety surveillance across all European countries, in contrast to for example in the United States.

Methods

In this study, WGS was retrospectively applied to isolates collected within the context of Belgian food safety surveillance and combined with data from clinical isolates to evaluate its benefits. A cross-sector WGS-based collection of 754 strains from 1998 to 2020 was analyzed.

Results

We confirmed that WGS in food safety surveillance allows accurate detection of genomic relationships between human cases and strains isolated from food samples, including those dispersed over time and geographical locations. Identifying these links can reveal new insights into outbreaks and direct epidemiological investigations to facilitate outbreak management. Complete WGS-based isolate characterization enabled expanding epidemiological insights related to circulating serotypes, virulence genes and antimicrobial resistance across different reservoirs. Moreover, associations between virulence genes and severe disease were determined by incorporating human metadata into the data analysis. Gaps in the surveillance system were identified and suggestions for optimization related to sample centralization, harmonizing isolation methods, and expanding sampling strategies were formulated.

Discussion

This study contributes to developing a representative WGS-based collection of circulating STEC strains and by illustrating its benefits, it aims to incite policymakers to support WGS uptake in food safety surveillance.

The Importance of Shiga Toxin-Producing Escherichia coli O145:NM[H28]/H28 Infections in Argentina, 1998–2020

Shiga toxin-producing Escherichia coli (STEC) is known as a pathogen associated with food-borne diseases. The STEC O145 serogroup has been related with acute watery diarrhea, bloody diarrhea, hemorrhagic colitis, and hemolytic uremic syndrome (HUS). Argentina has the highest rate of HUS worldwide with 70% of the cases associated with STEC infections. We aimed to describe the epidemiology and genetic diversity of STEC O145 strains isolated across Argentina between 1998–2020. The strains isolated from 543 cases of human disease and four cattle, were pheno-genotipically characterized. Sequencing of five strains was performed. The strains were serotyped as O145:NM[H28]/H28, O145:H25, and O145:HNT, and mainly characterized as O145:NM[H28]/stx_2a/eae/ehxA (98.1%). The results obtained by sequencing were consistent with those obtained by traditional methods and additional genes involved in different mechanisms of the pathogen were observed. In this study, we confirmed that STEC O145 strains are the second serogroup after O157 and represent 20.3% of HUS cases in Argentina. The frequency of STEC O145 and other significant serogroups is of utmost importance for public health in the country. This study encourages the improvement of the surveillance system to prevent severe cases of human disease.

Quantitative risk assessment of haemolytic uremic syndrome associated with beef consumption in Argentina

We developed a quantitative microbiological risk assessment (QMRA) of haemolytic uremic syndrome (HUS) associated with Shiga toxin-producing Escherichia coli (STEC)-contaminated beef (intact beef cuts, ground beef and commercial hamburgers) in children under 15 years of age from Argentina. The QMRA was used to characterize STEC prevalence and concentration levels in each product through the Argentinean beef supply chain, including cattle primary production, cattle transport, processing and storage in the abattoir, retail and home preparation, and consumption. Median HUS probability from beef cut, ground beef and commercial hamburger consumption was <10-15, 5.4x10-8 and 3.5x10-8, respectively. The expected average annual number of HUS cases was 0, 28 and 4, respectively. Risk of infection and HUS probability were sensitive to the type of abattoir, the application or not of Hazard Analysis and Critical Control Points (HACCP) for STEC (HACCP-STEC), stx prevalence in carcasses and trimmings, storage conditions from the abattoir to retailers and home, the joint consumption of salads and beef products, and cooking preference. The QMRA results showed that the probability of HUS was higher if beef cuts (1.7x) and ground beef (1.2x) were from carcasses provided by abattoirs not applying HACCP-STEC. Thus, the use of a single sanitary standard that included the application of HACCP-STEC in all Argentinean abattoirs would greatly reduce HUS incidence. The average number of annual HUS cases estimated by the QMRA (n = 32) would explain about 10.0% of cases in children under 15 years per year in Argentina. Since other routes of contamination can be involved, including those not related to food, further research on the beef production chain, other food chains, person-to-person transmission and outbreak studies should be conducted to reduce the impact of HUS on the child population of Argentina.

Identification and molecular characteristics of verotoxin-producing Escherichia coli (VTEC) from bovine and pig carcasses isolated in Poland during 2014-2018

The presence of verotoxin-producing Escherichia coli (VTEC) on bovine (n = 330) and pig (n = 120) carcasses in Poland was investigated using the ISO/TS 13136 standard. A total of 115 (34.8%) and 37 (30.8%) cattle and pig samples were positive in real-time PCR, respectively. Isolation of the bacteria revealed that from bovine carcasses 37 (32.2%) VTEC were obtained whereas only 5 (13.5%) pig carcasses were positive for the stx gene. The VTEC were characterized using whole genome sequencing (WGS) and bovine isolates were classified into 25 serotypes with the most prevalent O113:H21 (5 strains) whereas pig strains belonged to 5 different serotypes which were not identified among cattle strains. The majority of bovine VTEC (35; 94.6% isolates) were positive for the stx2 gene, either alone or together with the stx1 gene. All strains isolated from pig carcasses resulted positive for the stx2 gene only. Only two isolates of bovine origin contained the eaeA intimin gene, together with the ehxA and lpfA markers. VTEC were highly molecularly diverse as shown by classification into 29 different MLST STs. The obtained results suggest that further studies related to cattle and pig carcasses are needed to assess the role of these sources for human VTEC infections.

Occurrence and characterization of Shiga toxin-producing Escherichia coli (STEC) isolated from Chinese beef processing plants

In order to investigate the prevalence, O serogroup, virulence genes and antibiotic resistance of Shiga toxin-producing Escherichia coli (STEC) in two beef plants in China, a total of 600 samples collected from 6 sites (feces, hide, pre-evisceration carcasses, post-washing carcasses, chilled carcasses and meat, 50 samples per site in each plant) were screened for the existence of Shiga toxin-encoding genes by PCR. STEC strains in positives were isolated and characterized for serogroup and antibiotic sensitivity. The PCR prevalence rate in each site was 45.0%, 31.0%, 14.0%, 13.0%, 9.0% and 18.0%, respectively. Sixteen O serogroups including O157, O146 and O76 which are associated with disease were identified. The existence of both stx₁ and stx₂ genes was the most common among the isolated strains (42.3%). Among the overall 26 isolates, seven and three were resistant to at least three and ten antibiotics, indicating a high antibiotic resistance in STEC strains isolated from the study.

Recent Advances in Shiga Toxin-Producing Escherichia coli Research in Latin America

Pathogenic Escherichia coli are known to be a common cause of diarrheal disease and a frequently occurring bacterial infection in children and adults in Latin America. Despite the effort to combat diarrheal infections, the south of the American continent remains a hot spot for infections and sequelae associated with the acquisition of one category of pathogenic E. coli, the Shiga toxin-producing E. coli (STEC). This review will focus on an overview of the prevalence of different STEC serotypes in human, animals and food products, focusing on recent reports from Latin America outlining the recent research progress achieved in this region to combat disease and endemicity in affected countries and to improve understanding on emerging serotypes and their virulence factors. Furthermore, this review will highlight the progress done in vaccine development and treatment and will also discuss the effort of the Latin American investigators to respond to the thread of STEC infections by establishing a multidisciplinary network of experts that are addressing STEC-associated animal, human and environmental health issues, while trying to reduce human disease. Regardless of the significant scientific contributions to understand and combat STEC infections worldwide, many significant challenges still exist and this review has focus in the Latin American efforts as an example of what can be accomplished when multiple groups have a common goal.