The participants agree that sequencing offers huge advantages over the 20-year-old genetic fingerprinting technique used previously, 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 to a witness in a hit and run accident. While PFGE might identify the vehicle as a brown Toyota Corolla, whole genome sequencing provides the license number and even the vehicle identification number.
“They both help identify the culprit,” he says, but one identifies the specific bug implicated.
The CDC began experimenting with whole genome sequencing in the fall of 2013, joining the FDA and USDA in a pilot project to sequence all reported cases of listeriosis in patients and upload those sequences on the GenomeTrakr database.
For the pilot, CDC compared whole genome sequencing to PFGE, and found that sequencing reduced the number of red herrings—cases that look similar but aren’t.
In the first year of the Listeria project, whole genome sequencing identified 19 Listeria clusters and solved four outbreaks. That compared with identifying 14 dusters and solving one outbreak the year earlier.
Mixed Blessing
For the food industry, the ability to more quickly match bacteria from a patient sample with their plants is a mixed blessing.
FDA’s Dr. Musser thinks the technology will ultimately be embraced by industry, which could use sequencing to see if suppliers are bringing contamination into their plants or if bacteria has taken up residence in a corner of the plant.
“These are things industry could just never get to before,” says Dr. Musser.
Bernie Steves of Aon Risk Solutions Crisis Management Practice, who advises companies on product recalls, says sequencing is tying illnesses in people to the source “faster than we’ve seen before,” allowing companies to “nip things in the bud.”
Conversely, he says, “it gives regulators another tool to find out where a potential problem is being sourced from.”
That could mean more recalls. According to the Center for Science in the Public Interest, only about 40 percent of reported foodborne disease outbreaks from 2002 to 2011 were ever solved, letting many manufacturers off the hook.
To allay some of those concerns and still get more samples, the FDA and its partners are working on ways to allow companies to provide blind samples through a third party.
One such program called VoluntaryNet at the University of Georgia would allow companies to provide samples anonymously. For companies, the program could alert them pathogens residing in their plants. If a submitted pathogen starts making people sick, public health officials could alert companies about the problem, and possibly pull food off market shelves more quickly.
FDA statistician Errol Strain says several companies have agreed in principle to supply samples and they are working out details on how to participate anonymously.
Great job as always!