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Investigations into foodborne illness are being transformed by whole genome sequencing, which federal officials say is enabling them to identify the source of an outbreak more quickly and prevent additional cases.
Previously, samples from sick patients were tested to see if the infections were caused by the same bug. When enough matches emerged, epidemiologists interviewed sick people, looking for a common food that was causing the outbreak. But the testing wasn’t definitive and took time.
Now, the FDA is building a network of labs equipped to map out the exact DNA sequence of strains of Listeria, Salmonella and other foodborne pathogens found in sick patients. These sequences are then uploaded to a public database housed at the National Institutes of Health.
The FDA became convinced of the superiority of the new approach during a 2014 outbreak of salmonella affecting peanut butter made by nSpired Natural Foods.
The FDA had just activated a network of laboratories to do whole genome sequencing, and begun sequencing pathogens it collected during factory inspections. All of these codes were uploaded to the database, known as GenomeTrakr.
When people started getting sick, FDA scientists and partners searched GenomeTrakr. They found the DNA of bugs taken from two sick patients were “almost indistinguishable” from salmonella the FDA had found at nSpired Foods, said Dr. Eric Brown, director of FDA’s Division of Microbiology.
The match allowed officials to quickly recall tainted peanut butter. Only six people got sick.
Since the start of GenomeTrakr in 2012, 25,000 pathogen genomes have been added to the database, and several state and federal partners, including the USDA and the U.S. Centers for Disease Control and Prevention, have signed on.
The participants agree that sequencing offers huge advantages over the genetic fingerprinting technique used previously.
Read full, original post: FDA Wants Food Makers to Hand over Their Contaminated Samples
