Emerging science fostering regulatory policy development

June 2020 | Ottawa Laboratory Carling, Canadian Food Inspection Agency | by Burton Blais

The Canadian Food Inspection Agency (CFIA) safeguards the health of Canadians by using science to figure out what poses the greatest risk to the food supply, and conducts inspections accordingly. This allows the CFIA to focus on interventions that maximize the public health impacts. An example of how CFIA combines inspection and science, is the detection of microbial hazards in foods through routine inspection activities designed to check if food manufacturers are complying with food safety regulations. Key to successful detections is to use food testing laboratory methods capable of rapidly generating informative test results.

With progress in science and technology, it is important for government policies and/or procedures to keep up to best ensure protection of the interests of Canadians. This is particularly important where new technologies make improvements on “gold standard” methodologies currently in place, pushing the boundaries of what is possible. Moving beyond or replacing the gold standard requires scientific research and validation, and offers new possibilities for more refined policies and guidelines to guide regulatory decisions.

An example of technological progress from the past decade or so is the shift in regulatory food microbiology testing. Harmful microbes are routinely identified on the basis of their genes using rapid methods such as polymerase chain reaction (PCR) technology, enabling delivery of test results days sooner than traditional techniques. However, PCR technology is limited by its rather fragmentary nature, that is, the fact that only a relatively small number of different DNA markers can be assessed in a single procedure.

Whole Genome Sequencing (WGS) is an example of a new technology that can provide exquisitely detailed analyses of microbes on the basis of their entire genetic blueprint, as opposed to mere fragments. WGS technology can be used in support of regulatory food inspection as it allows for detection, identification and detailed characterization of harmful microbes of high priority such as vero-toxigenic Escherichia coli (VTEC), Salmonella enterica and Listeria monocytogenes. WGS has the potential to go beyond established uses for surveillance and outbreak response to inform future food safety risk assessment, policy and program development, and early interventions to respond to or prevent illnesses and outbreaks.

Finding a fit for emerging science in the federal food safety regulatory framework

Regulatory food safety in Canada is a shared responsibility between the Public Health Agency of Canada, Health Canada, and the Canadian Food Inspection Agency. All three organizations have been working on the use of WGS technology and are modernizing laboratories to incorporate WGS testing. Together, the three organizations developed a pilot for using WGS to enhance regulatory food safety investigative issues, with a focus on VTEC. Using WGS technology to analyze VTEC is a good fit because of the importance of this harmful microbe to public health and the need for clear guidance in finding out which components of VTEC are most likely to cause serious human illness.

How we worked together

The first task of the inter-departmental team was to do a scan of the current science by reviewing scientific literature, consulting with experts, looking at Canadian public health trends, and how the broader regulatory community approaches the problem. At the same time, the technological capability of each partner agency was mapped to find out how best to coordinate the use of WGS technology and to align with any new policy or guidance that might emerge from the exercise.

Based on this work, a document was created to serve as an authoritative reference to provide guidance on (1) updating the definition of actionable VTEC found in foods to reflect current science; (2) clarifying current knowledge on the most important components of food-borne VTEC to consider for regulatory actions; and (3) finding gaps in knowledge that can be addressed by future research. The document also clearly establishes the role and processes undertaken by each federal food safety partner in food safety investigations. The resulting report, titled "Review of the State of Knowledge on Verotoxigenic Escherichia coli and the Role of Whole Genome Sequencing as an Emerging Technology Supporting Regulatory Food Safety in Canada", outlines the Canadian approach to defining VTEC of public health concern for regulatory purposes. It was deemed necessary that the document should be published, in keeping with the intent of the GoC Open Science policy, and the best avenue for making it widely accessible is its publication on Science.gc.ca.

This document represents a consensus of opinion achieved by the inter-departmental team and is intended to serve as a reference in support of policy development with regard to how VTEC in foods are assessed for regulatory action. It will also inform the team’s future work on determining the risk profile, guidance and risk assessment of VTEC.


Modern food microbiology research has improved our understanding of the dangers posed by harmful food microbes. The combination of new scientific knowledge and sophisticated technological capability creates exciting new opportunities for refining food microbiology testing programs to meet the needs of CFIA’s risk-based inspection approach. Advances in WGS technology mark a new chapter in food microbiology in which harmful microbes will be characterized on the basis of their genetic profile rather than traditional approaches relying on their shapes or how they use nutrients for growth. This will play a critical role in informing regulatory decisions and tracing sources of food contamination.