Investigations into foodborne illness are being radically transformed by whole genome sequencing, which federal officials say is enabling them to identify the source of an outbreak far more quickly and prevent additional cases.
Previously, samples from sick patients were sent to state and federal labs, where disease detectives ran tests to see if the infections were caused by the same bug. When enough matches emerged, typically a dozen or so, epidemiologists interviewed sick people, looking for a common food that was causing the outbreak.
But the testing wasn’t definitive, and linking one case to another took time. “While all of this was going on, more contaminated product was getting out into the public,” says Dr. Steven Musser, deputy director for scientific operations at the U.S. FDA’s Center for Food Safety and Applied Nutrition.
Now, the FDA is building a network of state and federal 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 technology does not only differentiate a pathogen from multiple related species, but can also show slight mutations within the same strain.
At the same time, the FDA has begun sequencing pathogens found during routine plant inspections and adding those to the database. One benefit of that, they say, is being able to quickly connect patients within an outbreak. Another is the potential to identify the source of an outbreak after just a few patients fall ill, shortening the time it takes to get tainted food off store shelves.
To increase the odds of a match, the FDA wants manufacturers to contribute samples of pathogens found during their own plant inspections. Some contamination is common in food plants. When it is found in the manufacturing facility, but not in food products, companies generally are required only to clean it up without recalling products.
But eliminating pathogens is tough, and convincing companies to offer up potentially incriminating evidence has been a hard sell, according to interviews with public health officials, food manufacturers, and experts on recalls.
“That is not something that we’ve solved yet,” says Ruth Timme, an FDA microbiologist who has talked to 10 to 15 companies over the past year about the benefits of sequencing.
‘Bam! You’ve Got Em’
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 of Oregon.
The FDA had just activated a network of state, federal, and academic laboratories to do whole genome sequencing, and the agency had also begun sequencing pathogens it collected from swabbing surfaces 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, looking for matches with inspection samples. They found the DNA of bugs taken from two sick patients were “almost indistinguishable” from Salmonella the FDA had found at nSpired Foods, says 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.
“You catch things far earlier” with sequencing, says Dr. David Lipman, director of the National Center for Biotechnology Information. “It can be two cases. If you see a match, Bam! You’ve got em.”
A More Precise Tool
Since the start of GenomeTrakr in 2012, 25,000 genomes from a variety of pathogens have been added to the database, and several state and federal partners, including the USDA and the CDC, have signed on.