The Deputy Heads of the Canadian federal food safety partner agencies (Public Health Agency of Canada, Health Canada and Canadian Food Inspection Agency) have identified the application of emerging science to support the management of food safety issues as a key priority for the modernization of regulatory food safety. One example of an emerging science is whole genome sequencing (WGS), a technology that provides detailed characterization of the genetic content of organisms, such as foodborne pathogenic bacteria. WGS supplements traditional approaches based on phenotypic properties and has the potential to provide more information than is currently being exploited. There is potential to mine genomic data, to go beyond established uses for surveillance and outbreak response in order to inform future food safety decision making, policy and program development, and early interventions to respond to or prevent illnesses and outbreaks. The application of WGS technology in the analysis of verotoxigenic Escherichia coli (VTEC) was deemed a good fit because of the importance of this pathogen to public health and the need for clear guidance in determining which characteristics of foodborne VTEC must be considered in identifying isolates most likely to cause serious human illness. This treatise examines the current state of knowledge with respect to the salient characteristics of VTEC of public health concern, the relevant activities of the federal health portfolio food safety partners, and how WGS technology might best be leveraged in identifying the key genomic markers of foodborne isolates to support regulatory food safety objectives

Executive Summary

Verotoxigenic Escherichia coli (VTEC) are recognized as a significant foodborne hazard, and consequently, have been the subject of regulatory food safety inspection programs aimed at reducing the burden of foodborne illness in Canada. Current food testing protocols use a decade's old definition of VTEC of public health significance predicated on inclusion of a small number of O serogroups, carriage of verotoxin types 1 and 2, and the eae gene coding for intimin, a protein involved in host colonisation. Recent worldwide food safety trends and public health data indicate that there is a need to revise this outdated definition to include other VTEC, which have emerged as food safety hazards. The Emerging Science Whole Genome Sequencing Working group reporting to the Federal Committees on Food Safety has undertaken an extensive review of Canadian public health data and the scientific literature to investigate whether a better definition of VTEC of public health significance can be achieved in order to meet contemporary public health trends. To support understanding of the context in which genomic data is applied to food safety decision making this review also addresses the topics of the foods associated with VTEC exposure, existing monitoring programs for VTEC illness and food contamination, analytical methods for VTEC and risk mitigation efforts in Canada.

It was determined that VTEC are a complex family of pathogens with significant variability in the presence of specific virulence factors, and that the scope of analysis and decision-making should not be limited to specific serogroups, since Canadian public health data show that infections with diverse serotypes may occur. Next generation sequencing technologies are well suited for the analysis of food and clinical isolates of VTEC to identify genetic characteristics, which can inform hazard characterisation. A number of knowledge gaps have been identified which if addressed through focused research have the potential to improve understanding of the factors determining VTEC virulence.