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FDA Seeks Food Companies' Cooperation in Genome Sequencing to Identify Sources of Foodborne Illnesses

Aug 31, 2015

The Food and Drug Administration (FDA) is seeking food company cooperation in whole genome sequencing of pathogens, which will permit FDA officials to more quickly identify the sources of foodborne illnesses and act to prevent additional cases.

Previously, samples from sick patients were sent to state and federal labs for testing to determine if the same bug caused the infections. When enough matches emerged—about a dozen—epidemiologists then interviewed sick people, looking for a common food that was causing the outbreak, Reuters reports.

But such testing took time to link cases and during that time, “more contaminated product was getting out into the public," according to Dr. Steven Musser, deputy director for scientific operations at the FDA's Center for Food Safety and Applied Nutrition. The FDA is now building a network of labs equipped to map the exact DNA sequence of strains of Listeria, Salmonella and other foodborne pathogens. These sequences are added to the Genome Trackr database housed at the National Institutes of Health. The FDA has also begun sequencing pathogens found during routine food plant inspections and adding those to Genome Trackr, creating the potential to identify the source of an outbreak after just a few patients fall ill and shortening the time it takes to pull tainted food from store shelves. Genome Trackr allowed the FDA to act quickly in a 2014 salmonella outbreak linked to peanut butter from nSpired Natural Foods in Oregon. As a result, only six people got sick before the tainted peanut butter was recalled, Reuters reports.

The FDA has asked manufacturers to contribute samples of pathogens found during their own plant inspections. But convincing companies to offer up potentially incriminating evidence has been hard, Reuters reports. When a company finds contamination in a food manufacturing facility, but not in the food products, the company is generally not required to report the contamination but only has to clean it up, though eliminating pathogens can be difficult.

Since the start of GenomeTrakr in 2012, 25,000 pathogen genomes have been added to the database, and the Department of Agriculture and the Centers for Disease Control and Prevention have both agreed to participate in the database. The participants agree that sequencing offers great advantages over the previously used genetic fingerprinting technique, known as PFGE. David Acheson, a former official at both the USDA and the FDA, who now advises companies on food safety, likens the difference in the two technologies to differences in identifying a vehicle in a hit and run accident. PFGE might identify the vehicle make and model, while whole genome sequencing provides the license plate number and even the vehicle identification number. "They both help identify the culprit," he said, but one identifies the specific bug involved, Reuters reports.

Food companies are concerned that pathogen sequencing could lead to more recalls. To allay such concerns, the FDA is working on ways to allow companies to provide samples anonymously. FDA statistician Errol Strain said several companies have agreed in principle to supply samples and the FDA is working out details of anonymous participation.

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