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Whether it’s Listeria in food or West Nile virus in people, outbreaks of infectious disease require quick action. A Winnipeg lab is using advanced surveillance systems and the power of genomics to track outbreaks in as close to real time as possible.
People don’t expect to die from eating cantaloupes. Yet that’s just what happened in the fall of 2011 when at least 29 Americans died after consuming the sweet but Listeria-tainted fruit. More fell ill in 28 U.S. states. Through its DNA fingerprint, the virulent strain of Listeria was found to originate in Rocky Ford-brand melons grown by Jensen Farms in Colorado.
The high cost of contaminated food
A Public Health Agency of Canada report estimates there are 11 million episodes of food-borne disease in Canada each year — although most would not be reported to public authorities. Based on one study, the estimated annual cost of these illnesses is C$3.7 billion in health care and lost productivity.
Each day, sophisticated distribution systems result in food crossing borders — state, provincial and national. And disease-causing bacteria, such as Salmonella, Listeria and Escherichia coli (E. coli), sometimes catch a lift.
The widespread transportation of food is the reason that countries need national systems to monitor and respond quickly to food-borne illnesses, says Canadian microbiologist Dr. Matthew Gilmour of the National Microbiology Laboratory (NML) in Winnipeg.
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Spotting dangerous bacteria in a crowd
An NRC device can identify dangerous bacteria using hundreds of tiny sensors that fit on a silicon chip the size of a fingernail. The National Microbiology Laboratory in Winnipeg developed the antibodies that NRC is using to test the device.
Learn more about the sensor on a chip.
The NML, which is part of the Public Health Agency of Canada, uses advanced surveillance systems to track food and water-borne diseases across the country. Each week, its National Enteric Surveillance Program (NESP) collects and analyzes data about incidences of food-borne illnesses from provincial laboratories. Weekly reports identify emerging trends, such as sudden surges in E. coli-caused illnesses, which might indicate disease clusters or outbreaks linked to a common source.
Tracking a pathogen’s DNA fingerprint
In 2000, the federal laboratory added PulseNet Canada, a network that provides technical expertise to help labs across Canada generate DNA fingerprints of pathogens quickly. The lab also includes a virtual electronic network dedicated to sharing and tracking these same DNA fingerprints.
PulseNet gives provincial microbiology labs, Health Canada and the Canadian Food Inspection Agency access to the “PulseNet Discussion Board,” where they can post DNA-fingerprint information about cases of enteric diseases and contaminated foods. The information is shared immediately.
We report on a real-time or as close to real-time basis as we possibly can. If there is a contaminated food product on the shelf, responding in six months is pointless.
Dr. Matthew Gilmour, National Microbiology Laboratory, Winnipeg
“PulseNet enables minute-by-minute surveillance and response,” Dr. Gilmour says. “You could consider it the arms and eyes of the public health system across the country.”
Importantly, PulseNet connects Canadian public health laboratories with the Canadian Food Inspection Agency, which can help to pinpoint the cause of outbreaks when they occur. An E. coli outbreak in Alberta, for example, could be immediately linked to the eating of contaminated raw walnuts that the Canadian Food Inspection Agency has identified.
PulseNet allows scientists to identify outbreaks and their causes even when individual cases of intestinal illness are geographically distant from each other. The system also allows for sharing of information with American labs, including the prestigious Centers for Disease Control and Prevention in Atlanta.
Advances in genomics make it easier to identify bacteria
Massive technological improvements in whole genome sequencing could soon make it possible to track outbreaks with unprecedented precision, according to Dr. Gilmour.
Whole genome sequencing, pioneered by the Human Genome Project in 2000, determines the complete DNA sequence of an organism. Historically, this type of detailed genetic information was extremely difficult to acquire, so other methods were used to fingerprint bacteria.
But with sequencing innovations such as better software tools and increased computer capacity to process huge data sets, public health investigators around the globe are preparing for revolutionary changes to laboratory investigations, says Dr. Gilmour.
“The weight of evidence provided by whole genome sequencing is vastly improved over traditional methods. It is almost indisputable in regards to determining the cause and scope of human illness and outbreaks.”
Not only can whole genome sequencing provide inarguable pieces of evidence about the sources of food or water-borne pathogens, it may ultimately have a role to play in treatment, since it can reveal traits in pathogens such as antibiotic resistance.
Whole genome sequencing versus DNA fingerprinting
According to Dr. Gilmour, DNA fingerprinting is akin to looking at the table of contents of a novel by Charles Dickens. “You can tell that it’s The Tale of Two Cities and not The Christmas Carol,” he says. “But unless you’ve read the book, you don’t have the points of the plot. Whole genome sequencing is like getting a full book on the pathogen.”
An example of the value of genome sequencing was shown in the summer of 2011, when a new strain of E. coli was identified in a serious and controversial outbreak of food-borne illness — ultimately attributed to bean sprouts grown by an organic farm in Germany. This outbreak resulted in 50 deaths, with more than 4000 confirmed cases in Europe and North America, including Canada and the U.S.
During the outbreak, several countries performed whole genome sequencing and shared that information for analyses. A global community of researchers jointly (and rapidly) analyzed the genomic sequences to reveal important details about this unknown strain of E. coli, including why it was particularly tenacious.
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Disease outbreaks that travel
Although many of the worst food and water-borne pathogens are not endemic to Canada, Canadians are still exposed to them when they travel.
Learn how Haiti’s cholera epidemic highlighted the risk posed by outbreaks in other countries.
“This particular pathogen had never been seen before, and it was through genomics that public health investigators got the clearest picture on the pathogen’s specific identity and its arsenal of traits that cause human disease,” says Dr. Gilmour.
The scope of information emerging from enormous genome datasets like this one is so detailed that the value of the analysis is correspondingly high.
“Genome sequencing will soon substantially contribute to the diagnosis, surveillance and control of disease by providing tremendously detailed lab evidence on the food-borne pathogens causing illness,” says Dr. Gilmour. “We are piloting technology that will be a bona fide part of our future public lab systems.” 
ISSN 1927-0275 = Dimensions (Ottawa. Online)
