Lay Summary

Salmonella is an important cause of foodborne illness in Canada. Each year, approximately 88,000 people become sick from consuming food that is contaminated with Salmonella. While foods such as poultry have long been recognized as causes of Salmonella food poisoning, fresh fruits and vegetables have recently emerged as important sources of Salmonella. This is because fruits and vegetables are grown in soil, where contamination due to animals and non-potable water can occur. As a result, most foodborne illnesses now occur due to consumption of contaminated fresh produce, and a majority of the illnesses caused by these commodities are due to Salmonella.

During this project, the problems associated with Salmonella contamination of fresh produce will be addressed through the development of natural solutions to control the presence of Salmonella on fruits and vegetables as they are growing in the field. New tests will also be developed so that fresh produce can be quickly and efficiently tested for the presence of Salmonella before being sold to consumers. Finally, new tools will be developed to allow public health officials to better determine the source of Salmonella illnesses when they occur, which will allow for contaminated food to be removed from grocery stores, before purchase by consumers.

This project will lead to social and economic benefits for Canadians.  For example, the development of faster tests and better tools for public health officials will lead to a reduction in the number of people who become ill from eating contaminated fresh fruits and vegetables.  The cost of foodborne diseases caused by Salmonella is estimated to be as high as $1 billion annually in Canada, due to costs associated with medical care, work absenteeism and economic loss to food companies and restaurants.  The results of this project will decrease the amount of people who become ill from Salmonella, thereby increasing the health and well-being of Canadians.

Executive Summary


Non-typhoidal Salmonella is a foodborne bacterial pathogen of global public health importance with an estimated annual Canadian economic burden of $1 billion. The presence of Salmonella on fresh produce – leafy greens, tomatoes, peppers, cantaloupes, most of which is consumed raw – is the first step along a continuum that leads to an increasing number of salmonellosis outbreaks. As no method currently exists to reduce the growth of Salmonella on fresh produce, better control strategies are urgently needed to inhibit its contamination. Also needed are more specific rapid methods to accurately test foods for the presence of Salmonella. During foodborne outbreaks of salmonellosis, there is an immediate need for better tools to determine the epidemiological links between Salmonella isolated from foods and patients. Previous research has demonstrated differences in the virulence potential of different Salmonella serovars. To better understand the relationship between environmental Salmonella – isolates from water, soil, food, etc. (the majority of which are not commonly linked to human illness) – and clinical isolates of Salmonella that cause human disease, this project will use comparative whole-genome next-generation sequencing techniques. The genomic knowledge will be applied to develop new biological control methods to reduce the presence and growth of Salmonella on fresh produce, as well as better rapid diagnostic assays and strain typing methods for Salmonella spp. Collectively, the proposed systems approach to reducing salmonellosis will improve detection in foods and surveillance during outbreak investigations, resulting in less recalled food, ultimately decreasing the occurrence, duration and magnitude of salmonellosis outbreaks.

GE3LS. We will assess the viability and implementability of a novel genomic test for Salmonella that can determine the pathogenic status of a given isolate, and assess the need to shift to a risk-based approach to food safety that classifies foodborne microbial adulterants on the basis of their pathogenicity, in contrast to the current regulatory practice of classifying a microbial adulterant based on species determination alone. We will also evaluate the economic impacts of this novel genomic test as compared to existing technology. We will use an anticipatory governance approach that will include a regulatory assessment integrating a careful consideration of: the evidentiary requirements; the economic, legal, ethical, regulatory and global policy constraints; and the trade implications of supporting such a paradigm shift.

Deliverables. At conclusion of this project, 3 deliverables will be available to end users; D1 – A biocontrol method to control Salmonella contamination of fresh produce in the field and reduce its presence on fresh produce during harvest and processing; D2 – More specific and rapid diagnostic assays to test fresh produce for Salmonella; D3 – Whole-genome based typing tools to enable more precise differentiation of Salmonella isolates during foodborne outbreak investigations. Data and results from this project will also be used by risk assessors to set regulations that would distinguish between foods contaminated with pathogenic Salmonella, and those foods that contain less or non-pathogenic Salmonella.

Socio-economic benefits. Reducing the presence of salmonellosis by the use of a biocontrol method is expected to result in an economic benefit of $50–$60 million. The development of more specific assays will save the fresh produce industry approximately $1.4-$2.8 million annually. Finally, reducing the duration of foodborne outbreaks will decrease the magnitude of the outbreaks by 35%, resulting in less illness and an annual cost savings of approximately $36 million. The social benefits to Canadians include improvements in food security, as less food would be destroyed due to contamination, as well as health benefits. For example, the development of WGS methods to link Salmonella isolates during outbreaks will reduce the duration of the outbreaks by at least 4 days, reducing the number of people who become ill.

Organisation structure

Organisation structure2