SISTR born in Canada being adopted around the world
Researchers at the Public Health Agency of Canada (PHAC) have developed a genomics-based tool that is changing the way authorities have investigated incidents of salmonellosis for close to 100 years. The Salmonella In Silico Typing Resource—SISTR—also promises to support more informed strategies to prevent the spread of the Salmonella bacteria that causes the illness, one of the most common forms of so-called food poisoning in Canada and around the world.
Is it an outbreak?
As PHAC Research Scientist Dr. Ed Taboada explains, the incidence of salmonellosis is carefully monitored by agencies in public health and food safety, watching for potential outbreaks that may require a response, such as a food recall, to limit the spread of the infection.
"Part of tracking the source involves finding out whether the people who've become ill have been infected by the same strain or type of the bacteria," says Dr. Taboada. "For Salmonella, we do a test called serotyping, and it's been done the same way for decades—a lab test that can take four or five days. And, since most infections are caused by one type of the Salmonella bacteria—S. enteritidis—investigators may need additional subtyping information, which takes more days in the lab."
DNA - the power of genomics
With support from the Government of Canada's Genomics Research and Development Initiative (GRDI), Canadian researchers are making those long days in the lab a thing of the past. "My colleagues here at PHAC—people like Dr. John Nash, biologist Catherine Yoshida and Dr. Roger Johnson—have developed DNA-based tests that can do typing and then subtyping in under one day," says Dr. Taboada. "These methods also give more accurate results, and they cost less to run."
In developing the new test methods, the PHAC researchers used 'next-generation' sequencing (NGS) to sequence the entire genomes of hundreds of types and subtypes of Salmonella. Along with genome sequences completed by researchers in other countries, these were analyzed to identify the specific sections of DNA that would enable them to predict type and subtype.
NGS - the superpower of genomics
It used to take many months and millions of dollars to sequence an entire genome. With NGS, a bacterial genome can be sequenced in a day or two for less than a thousand dollars.
"This has changed everything," says Dr. Taboada. "We started out using the genomics data generated with NGS to develop faster and more accurate lab tests, but we've come to realize that with the information we can get with NGS, we can virtually eliminate the lab."
With funding from GRDI, Dr. Taboada and his collaborators assembled computer algorithms that use the data generated in the earlier research to simulate the results of the genomics-based lab tests for Salmonella typing and subtyping.
The SISTR database enables the identification of Salmonella genomes through in silico typing, comparative genomics, and epidemiologic analysis.
"In essence, with SISTR, the computer has become the lab—that's the 'in silico' part of its name," says Dr. Taboada. "Now, researchers anywhere in the world can just upload the genomes of the Salmonella they want to identify to our website, and SISTR does the rest—giving them the type and subtype in one shot."
While the immediate benefit of SISTR will be seen in faster and more effective investigations into salmonellosis infections, its full value may not be realized for some time. "SISTR provides fast and accurate typing and subtyping, but it also performs more advanced forms of analysis," says Dr. Taboada. "As users become more familiar with the information SISTR can provide, we're going to see a revolution in how we investigate these types of events and prevent and control the incidence of salmonellosis."
SISTR already making a mark for Canada
Dr. Taboada notes that researchers in other countries have been working on similar platforms but, in benchmarking conducted by a consortium of European Union genomics research institutions, SISTR was rated significantly higher than other systems tested.
SISTR is now in use at the Canadian Food Inspection Agency and Canada's National Microbiology Laboratory as their standard protocol for Salmonella investigation. The U.S. Food and Drug Administration is also expected to adopt SISTR and it is being used by EnteroBase, an international centre for web-based bacterial genomic analysis at the University of Warwick in England.
"SISTR represents a significant contribution to reducing the public health risk posed by Salmonella not only in Canada, but around the world," says Dr. Taboada. "That's something I think all Canadians can be proud of."
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