FDA Requests Food Company Pathogen Samples for Database for Identifying Sources of Foodborne Illnesses

The Food and Drug Administration (FDA) is asking food companies to submit pathogen samples for genome sequencing, to facilitate faster identification of sources of foodborne illnesses and quicker action to prevent additional cases.

Before whole genome sequencing was developed, samples from sick patients were sent to state and federal labs for testing to determine if the same bug had caused the infections. When enough matches—about a dozen—emerged, epidemiologists then interviewed sick people to see if they could find the food in common that was causing the outbreak, Reuters reports.

This testing took time, though, and during that time, “more contaminated product was getting out into the public,” according to Dr. Steven Musser, the FDA’s deputy director for scientific operations at the Center for Food Safety and Applied Nutrition. The FDA is building a network of labs able to map the exact DNA sequence of strains of Listeria, Salmonella and other foodborne pathogens. These sequences form 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 as well, creating the potential to identify the source of an outbreak after just a few patients fall ill and shortening the time it takes remove tainted food from store shelves. In a 2014 salmonella outbreak, Genome Trackr allowed the FDA to quickly identify the source of the illness: peanut butter from nSpired Natural Foods in Oregon. Only six people became 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 it has been difficult to convince companies to give the FDA what could potentially be incriminating evidence, Reuters says. If a food company find contamination in its manufacturing facility but not in the food products, the company is usually not required to report the contamination but must clean it up. Sometimes, though, eliminating pathogens can be difficult and the bugs may eventually contaminate the food.

Some 25,000 pathogen genomes have been added to GenomeTrakr since it was established in 2012. 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 significant advantages over the genetic fingerprinting technique, PFGE, previously used. David Acheson, a former official at both the USDA and the FDA, now advises companies on food safety. He likens the difference in the two technologies to different methods for identifying a vehicle in a hit and run accident. PFGE might identify the vehicle make and model, but whole genome sequencing provides the license plate number and even the vehicle identification number, Acheson said, according to Reuters. Both methods “help identify the culprit,” but one identifies the specific bug involved.

Food companies are hesitant about supplying pathogen samples because they are concerned that pathogen sequencing could lead to more recalls. To allay these 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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