Genomics brings new precision to identifying, characterizing, and tracking threats to food and water safety

June 2016

Genomics is an information-generating science for many applications. Among many benefits realized through this relatively new science is the capacity it provides to make a positive identification of virtually any organism, living or dead.

DNA evidence has become a valuable tool for law enforcement. And now, federal government scientists are applying “microbial forensics” to enhance food and water safety in Canada.

The Food and Water Safety (FWS) project

Through its Genomics Research and Development Initiative (GRDI), the Government of Canada funded the FWS project—a unique, multi-year research collaboration that leveraged 53 scientific experts from six different federal departments, supported by their numerous technical personnel. Through complementary research efforts, new knowledge and tools emerged to address some of the most serious bacterial threats to the safety of our food and water supply. Their names—E. coli and Salmonella Enteritidis—are familiar to most Canadians.

While their names may be familiar, Dr. Morag Graham, Chief of Genomics at the Public Health Agency of Canada's National Microbiology Lab, points out that identifying these threats can be difficult.

Correct identification is critical

"There are many varieties of E. coli, for example," explains Dr. Graham, "Most are harmless, but several strains, known as Shiga toxin-producing E. coli or just STEC—E. coli 0157:H7 is one of them—are very toxic to humans and can cause serious illness, even death. Using traditional methods, it can be very challenging to quickly tell ordinary E. coli and STEC apart."

Misidentification could have significant impact. "If STEC in a sample of food or water is mistakenly identified as a harmless strain, the consequences for public health could be substantial," says Dr. Graham. "Similarly, mistaking a harmless strain for STEC could set off unnecessary investigations, unnecessary food recalls or costly interruption of food exports."

There are also variations within individual strains of STEC. "An 0157:H7 isolate found in uncooked ground beef at a retail store, for example, may be only slightly different from another isolate found at a supplier’s cattle farm," explains Dr. Graham. "So the more accurate we can be in characterizing each bacterium, the more accurate we can be in identifying the true source of a contamination incident."

Greater precision, better response

To reduce the risk of misidentification, Dr. Graham and her team have used the newest, highest-resolution genomics technologies to comprehensively sequence the DNA for hundreds of isolates of STEC as well as Salmonella Enteritidis bacteria collected from across Canada.

"With these detailed genetic blueprints," says Dr. Graham. "We can now tell one strain of the bacterium from another with high confidence."

The team sequenced more than 95 percent of the genome for each isolate. "Importantly, we also completely finished 20 genomes," says Dr. Graham. "These reference genomes provided details of these bacteria right down to each individual nucleotide. When you consider the STEC genome has nearly 5.5 million nucleotides, you get an idea how precise we can be when it comes to identification."

Putting the pieces together

Dr. Graham’s team was not only involved in sequencing; they also comprehensively catalogued the genomes and other characteristics of the bacteria. "We noted important information about each isolate we studied," says Dr. Graham, "from their level of toxin expression and whether any item in their genome might account for when they are found in certain locations, such as feedlots or watersheds, or certain sample types, to how they grow under different conditions."

Dr. Graham says the multidisciplinary approach and collaboration across departments enabled by the GRDI allowed for accelerated progress across the FWS project. "For example, Dr. Franco Pagotto at Health Canada applied our findings to advance his team’s efforts to enhance isolation of STEC via the use of different lab growth techniques," says Dr Graham. "In turn, Dr. Pagotto's work contributed to the development of new STEC testing methods."

Together, these advancements have cut several days from the time required to confirm the presence of these dangerous contaminants in a sample of water. "The knowledge and understanding we gained from the genomes permitted the development of approaches that enable the isolation of all strains of STEC within a given sample simultaneously, even when there may be miniscule amounts of STEC in the sample," says Dr. Pagotto.

Protecting Canadians

The genomic information for these hundreds of bacterial strains was catalogued with other relevant information—so-called “metadata”—such as where and under what circumstances they were found. This extensive library of genomes and metadata has been fed into new analytical capacity—the bioinformatics platform developed by another FWS project team—enabling rapid analysis of the data.

"Through the FWS project, public health authorities and other investigators will have access to these knowledge resources and new sets of efficient and accurate tools to rapidly identify and forensically characterize these bacterial contaminants," says Dr. Graham, "This is important to act or respond in order to protect Canadians from illness."

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