Something you ate? Episode 3: Tales from the lab

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Laboratory Investigation
Transcript - Laboratory Investigation

The Government of Canada and food industry maintain high standards for food safety practices. However, no system is perfect and outbreaks of enteric illness happen from time to time.

Identifying outbreaks involves investigations conducted by epidemiologists and laboratories.

Lab and surveillance experts identify outbreaks through various surveillance networks.

Matthew Gilmour, PhD, Director, Bacteriology and Enteric Diseases Program, Public Health Agency of Canada
PulseNet Canada is a national system that's used to quickly identify and respond to food-borne disease outbreaks. It's a virtual network that ties the public health labs of all provinces together by linking their computers and a central database of genetic fingerprints of bacteria. This is how outbreaks can be detected and tracked across the country.

Lab experts also have access to the Canadian Network for Public Health Intelligence. This network is a system that helps with the sharing of information and the coordination of the public health response.

Just as people are genetically different from each other, bacteria have genetic differences. The National Microbiology Laboratory uses leading-edge technology, called PFGE, to get a "genetic fingerprint" for bacteria specimens from the people who got sick.

Matthew Gilmour, PhD, Director, Bacteriology and Enteric Diseases Program, Public Health Agency of Canada
To fingerprint a bacterial pathogen, first we cut its DNA into several pieces. The segments of DNA are placed in a gel that's made of seaweed or algae, it's actually quite similar to really stiff gelatin.

Matthew Gilmour, PhD, Director, Bacteriology and Enteric Diseases Program, Public Health Agency of Canada
Then we run electricity through the gel, which causes the DNA fragments to separate based upon their lengths. So this arrangement of the DNA fragments by size actually looks like a bar code and represents the PFGE fingerprint.

The Lab compares PFGE fingerprinting results to help figure out if cases of illness could be related to each other.

Matthew Gilmour, PhD, Director, Bacteriology and Enteric Diseases Program, Public Health Agency of Canada
If different samples have identical fingerprints then the infections MAY have been caused by the same food. If we then run the same test on bacterial pathogens that have been isolated from a suspect food sample, and we get the same fingerprint, we may very well have found the source of the outbreak.

PFGE fingerprint testing is completed across the country at provincial and federal labs that are a part of the PulseNet Canada network.

By sharing these results from human and food samples in real time into the PulseNet Canada database for analysis and comparison, outbreaks in any part of the country can be rapidly detected.

To identify and respond to outbreaks, labs and epidemiologists across the country monitor the findings and identify trends that are shared on the PulseNet Canada online discussion board.

For more information and updates, please visit our website at

A message from the Government of Canada.

White coats; cool work.

The Public Health Agency of Canada’s National Microbiology Laboratory (NML) is Canada's main infectious disease public health laboratory. The NML is home to a reference library of pathogens. When other labs are seeking information about a certain pathogen they’ve detected, the NML can tell those labs when and where the pathogen has been detected before and other important information that can help in an illness investigation.

Did You Know

Pathogen: a microorganism that’s capable of producing a disease. Bacteria that can cause foodborne illnesses such as Salmonella or Listeria are examples of pathogens.

What is PulseNet Canada?

The NML also coordinates PulseNet Canada, which is an electronic network that ties together the public health laboratories of all provinces (plus some federal laboratories) by linking their computers and databases. This national network is dedicated to tracking the DNA fingerprints of all cases of E. coli and most cases of Salmonella.

Why are the PulseNet Canada national databases important?

A critical component in the investigation of human foodborne outbreaks is the DNA “fingerprinting” of the pathogens suspected of being involved. These fingerprints are obtained through a process called pulsed-field gel electrophoresis (PFGE). To learn more about this process, watch the video, above.

Once these DNA fingerprints are generated, they are entered into an electronic database at the NML that is available on line to participants. This way, fingerprints can be compared rapidly and outbreaks of disease can be detected faster than using traditional laboratory surveillance. Detecting disease faster means we can respond more quickly and reduce the outbreak’s impact on public health.

PulseNet Canada fingerprints all cases of E. coli and most cases of Salmonella as part of its work and, when needed, can fingerprint Listeria monocytogenes, Shigella, Campylobacter and Vibrio.

How PulseNet Canada makes a difference

  • detects clusters of cases with matching DNA “fingerprints”
  • aids early identification and investigation of foodborne disease outbreaks
  • assists in investigations to differentiate an outbreak from sporadic cases and to identify the source of outbreaks
  • provides a rapid communications platform and links public health laboratories across the nation

For more information about PulseNet Canada, go to PulseNet - Overview.

More food safety information

Visit the Government of Canada food safety portal to stay on top of food safety.

Health Canada has food safety information aimed at specific groups that are at greater risk for serious illness, including a chart that lists foods to avoid and safer alternatives to those foods.

Canadian Partnership for Consumer Food Safety Education provides information about food safety in the home.

Action on Weatherill Report Recommendations to Strengthen the Food Safety System: Final Report to Canadians describes changes made to the food safety system since 2008.

These links provide more detailed information about the tools we use to help us in our food safety work.

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