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

Stéphanie Nouws; Bavo Verhaegen; Sarah Denayer; Florence Crombé; Denis Piérard; Bert Bogaerts; Kevin Vanneste; Kathleen Marchal; Nancy H C Roosens; Sigrid C J De Keersmaecker

doi:10.3389/fmicb.2023.1204630

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

Front Microbiol. 2023 Jul 13:14:1204630. doi: 10.3389/fmicb.2023.1204630. eCollection 2023.

Authors

Affiliations

¹ Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium.
² IDlab, Department of Information Technology, Ghent University-IMEC, Ghent, Belgium.
³ National Reference Laboratory for Shiga Toxin-Producing Escherichia coli (NRL STEC) and for Foodborne Outbreaks (NRL FBO), Foodborne Pathogens, Sciensano, Brussels, Belgium.
⁴ National Reference Centre for Shiga Toxin-Producing Escherichia coli (NRC STEC), Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel, Brussels, Belgium.
⁵ Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.

Abstract

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.

Keywords: Shiga toxin-producing Escherichia coli; food safety; implementation; surveillance; whole genome sequencing.