How the CFIA Uses DNA to Fight Food-borne Illness

Learn more about how whole genome sequencing is improving the safety and well-being of Canadians.
How the CFIA Uses DNA to Fight Food-borne Illness
October 14, 2019

The ability to respond to or prevent food-borne illness outbreaks and other food safety hazards is a critical component to safeguarding the health and well-being of people, the environment and the economy.

The Canadian Food Inspection Agency (CFIA) works to protect Canadians from unsafe food by tracking down the source of harmful organisms (e.g. bacterial pathogens) in the country's food supply and removing contaminated food items from the market.

A world-leader in food safety analysis, the CFIA can now prevent outbreaks faster than ever with the help of whole genome sequencing (WGS), a process of decoding the genetic information of disease-causing bacteria like Salmonella, Listeria and E. coli.

What is whole genome sequencing?

Whole genome sequencing (WGS) is a laboratory procedure that determines the entire genetic structure of an organism in one process. Unlike biochemical techniques of the past, which could reveal little more than the presence of a bacterial pathogen in a contaminated food sample, whole genome sequencing unlocks the organism’s DNA, revealing genetic markers, such as:

  • the exact species or strain of the bacteria
  • how harmful it is to humans
  • whether or not it is resistant to antibiotics

Whole genome sequencing provides CFIA investigators with far more information than previous technologies and can be done much faster — in some cases, twice as fast.

Where biochemical techniques took days or even weeks, whole genome sequencing can identify the genomic blueprint of an organism in as little as 24 hours — which makes a big difference when it comes to minimizing the impact of food-borne illness outbreaks.

How does whole genome sequencing help to prevent food-borne illness?

Once an organism’s entire genome is known, a short piece of it can be used to identify the species. That short piece of the genome acts as a fingerprint, which makes it possible for food safety investigators to identify the organism in samples taken from food, people or specific food processing facilities.

With the organism’s fingerprint, CFIA investigators can:

  • detect food-borne illness outbreaks faster
  • confirm the presence of a particular food-borne pathogen in food, people or facilities
  • link cases of illness or food contamination to one another
  • identify sources of contamination in the food manufacturing environment or processes

When a potential health risk is identified, the CFIA facilitates a health risk assessment and determines the most appropriate action, like whether or not to recall the product.


If a recall is necessary, the CFIA works quickly to inform the public, initiate voluntary removal of the product(s) from the market and verify that the recalled product(s) have been removed from store shelves.

CIFS Members get access to food recalls, allowing them to stay on top of the latest food safety updates that could affect their business.

CIFS Membership is free for 12 months with registration in the CIFS Food Handler Certificate Course.

Note: It is the responsibility of the industry to remove the product from sale or distribution.


After a recalled product is removed from the market, the CFIA continues to work with the processor, manufacturer or importer to ensure that any food safety issues that led to the recall are resolved.

CFIA inspectors will conduct an immediate site visit to inspect equipment, hygiene and production practices, collect food samples for laboratory testing and identify corrective actions the company should take.

Later, inspectors will return for a follow-up inspection. If new samples taken during the follow-up inspection match the DNA fingerprint of the sample taken the first time, they know the original problem was not properly addressed or corrected.


While whole genome sequencing is still a relatively new technology, it has already changed the landscape in terms of how food is processed in Canada.

In May 2017, CFIA scientists started using whole genome sequencing to investigate food-borne illness outbreaks linked to frozen breaded chicken products.

Following 17 national outbreaks of Salmonella infection and 566 laboratory-confirmed cases, the CFIA implemented new regulations requiring all manufacturers of frozen breaded chicken products to reduce Salmonella levels to below detectable levels, thus improving the safety of the Canadian food supply.

To learn more about food safety in Canada, visit our food safety blog.