Genomics research to better manage risk of Listeria
Experts consider Canada's food safety system to be one of, if not the best in the world, Footnote 1 so it is a measure of the challenge involved in assuring the safety of the food we eat that as many as four million people in Canada are affected by a foodborne illness every year. Footnote 2
Fortunately, for the vast majority of these people, these illnesses are not serious—but for a sizable minority, the consequences of a foodborne illness can be very serious. There is also a significant economic impact—billions of dollars a year in health care costs and lost productivity. Footnote 3
Rare, but dangerous
The Listeria bacteria is a special concern. Eating food contaminated with Listeria can cause a serious illness called listeriosis. Although it is rare in Canada, listeriosis is very dangerous to pregnant women, older adults and people with weakened immune systems. Serious cases can lead to miscarriage, brain infection, blood poisoning and even death—in 2008, 24 people in Canada died as a result of a major outbreak of listeriosis.
As with any foodborne illness, the earlier the source of listeriosis infection can be identified, the sooner authorities can take steps to limit the spread of the bacteria. At Health Canada's Bureau of Microbial Hazards, Dr. Franco Pagotto and his colleagues have recorded a number of significant advances that promise to reduce the risk posed by Listeria.
Supported by funding from the Government of Canada's Genomics Research and Development Initiative (GRDI), Dr. Pagotto and his fellow researchers have completed whole genome sequencing of hundreds of different strains of Listeria. Combining their own work with the sequencing done by other researchers around the world, they have built a databank of some 1,000 Listeria genomes, as well as the bioinformatics capacity needed to enable analysis of all the genetic data they've collected.
Through the analysis done so far, the researchers have identified a number of areas on the Listeria genome where the DNA sequences of different strains differ from one another. Dr. Pagotto—Co-Director, Listeriosis Reference Service at Health Canada—says that taking advantage of the unique differences can help food safety investigations in the future. "From here, it's a relatively simple matter to develop an automated test to see whether Listeria collected in one place is the same strain as Listeria collected somewhere else," says Dr. Pagotto. "That's a key part of determining the source of an infection and with the existing method, it can take as long as five days to make that genetic comparison. The method we're developing will do it in a single day."
Reducing the risk
Another finding may help to reduce the likelihood of Listeria entering the food supply in the first place.
In identifying the unique regions in the DNA of different strains of Listeria, Dr. Pagotto and his colleagues found that these same sections of DNA can provide a greater understanding of the biology of the bacteria. "Using our bioinformatics capacity to analyse the genetic data of the different strains of the bacteria, we found that these same genetic markers can tell us whether a particular strain of Listeria is more likely to cause disease in humans," says Dr. Pagotto. "Some of the markers we use to differentiate one strain from another are also associated with persistence—that is, a genetic trait that makes the strain more resistant, for example, to certain sanitizers. This is information that would be extremely useful to food processors, for example, who want to make sure their sanitation procedures are as effective as possible."
The bioinformatics methodology—the algorithm—developed for Listeria analysis by Dr. Pagotto's team is now contributing to food safety research outside Canada's borders.
"One of the post-doctoral fellows who worked with us on this project is now with the United States Food and Drug Administration," says Dr. Pagotto. "They've adopted our algorithm for their own work with Listeria, and they're also looking at how it can be adapted to analyse the genomes of other pathogens. We are hoping the algorithm will become a standard for how genomes are analysed for source attribution."
- Footnote 1
Conference Board of Canada, 2014 World Ranking: Food Safety Performance, accessed athttp://www.conferenceboard.ca/cfic/research/2014/foodsafety.aspx
- Footnote 2
healthycanadians.gc.ca, Yearly food-borne illness estimates for Canada,http://healthycanadians.gc.ca/eating-nutrition/risks-recalls-rappels-risques/surveillance/illness-estimates-estimations-maladies/yearly-annuel-eng.php
- Footnote 3
PHAC, Canada Communicable Disease Report, Volume 40-14, http://www.phac-aspc.gc.ca/publicat/ccdr-rmtc/14vol40/dr-rm40-14/dr-rm40-14-guid-2-eng.php
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