E. coli: Canadian genomics research continues to deliver food safety, economic benefits


- Ottawa, Ontario

Infections of the O157:H7 strain of E. coli are usually associated with contaminated food or water. The illness it causes is often referred to as "hamburger disease" because a number of early outbreaks of infection were traced to undercooked ground beef.Footnote 3

Verotoxigenic Escherichia coli O157:H7—better-known to Canadians as just E. coli—is one of the most common causes of food-borne illness around the world. While most infected individuals will recover within two weeks, so-called "hamburger disease" can lead to serious, permanent kidney damage. In some cases, young children and the elderly especially, E. coli can be fatal.

The incidence of E. coli infection in Canada has fallen significantly since the beginning of the century,Footnote 1 but outbreaks continue—an average of some 800 Canadians are infected each yearFootnote 2—and the bacteria remains a key public health priority.

Genomics investments making important contribution

Along with enhanced food safety practices and regulations, research funded through the Government of Canada's Genomics Research and Development Initiative (GRDI) has played, and continues to play, a prominent role in advancing Canada's capacity to manage the risk of E. coli.

Until relatively recently, for example, it could take as long as 3 weeks just to identify the particular type of E. coli involved in an incident of contamination—information crucial to tracking the source of an outbreak. Today, thanks to a series of GRDI-funded research projects involving scientists from a number of federal departments, new genomics-based test methods can provide this and other key information in a matter of hours enabling faster and more directed action to limit the impacts of an incident.

At the Canadian Food Inspection Agency (CFIA), new research supported by the GRDI is creating new opportunities to further limit the health and economic impacts of an outbreak.

Understanding E. coli

As CFIA Research Scientist Dr. Burton Blais explains, these new advances will enable food safety investigations to benefit from the growing understanding of E. coli.

"Most of the hundreds of types of E. coli out there are harmless," says. Dr. Blais. "The problem is verotoxin-producing E. coli, known as VTEC. These are the ones, like O157:H7, that can cause illness. Since O157:H7 was identified in the early 1980s, a number of other VTEC have been discovered."

"While all VTEC produce verotoxins, only a small proportion of them can make people sick, and some make people sicker than others," adds Dr. Blais. "A lot of research in Canada and elsewhere has gone into identifying the genetic markers that differentiate VTEC that cause illness from those that don't, as well as markers that can be used to predict the severity of illness likely to be caused by a type of VTEC detected in food."

Applying the knowledge

To give that knowledge a practical application, Dr. Blais and his colleagues at CFIA have developed a new tool for VTEC investigation they call GeneSeekR.

"We're combining next generation sequencing technology with bioinformatics," says Dr. Blais. "Once genomic DNA isolated from VTEC colonies recovered from food samples has been sequenced, we feed the raw genomic data into GeneSeekR for analysis.

"In a few hours, including the time it takes to complete the initial sequencing, GeneSeekR gives us a detailed picture of what we're dealing with. The algorithms we've written seek out the genetic markers that will confirm whether the E. coli is a VTEC, whether it is a VTEC that can cause illness, and if so, also give an indication of the severity of the illness it can cause."

Speed, precision, flexibility

"As well as speed, the kind of genetic detail about the bacteria we get from GeneSeekR enables a new degree of precision in responding to an incident of E. coli contamination in food," says Dr. Blais. "For example, rather than a precautionary recall of all the lettuce grown across a wide area, contamination can be traced to an individual farm—limiting both the health risk and the economic impact of an incident."

GeneSeekR is also adaptable. "As new markers for other characteristics of VTEC are identified, we can load those into the program," says Dr. Blais. "For example, as part of the Federal Action Plan on Antimicrobial Resistance and Use in Canada, we are using GeneSeekR to analyse VTEC samples for markers that indicate resistance to antibiotics."

Increasing food safety

At global food corporation Cargill, Inc., Dr. Angie Siemens Vice President, Food Safety, Quality and Regulatory says the GRDI-funded research led by Dr. Blais is making an important contribution.

"Anything we can do to understand the ability of not just the type, but of individual strains of E. coli to cause illness is going to help the food industry and public health," says Dr. Siemens. "The research being done at CFIA in compiling this detailed biometric data complements work being done by others in the US, Canada and elsewhere that, combined, will help to inform the actions we can take in the future to continue reducing the potential of someone becoming ill from these organisms."