Petri dish, food safety
Data from positive samples taken at food manufacturing companies and from foodborne illness victims are cross referenced using a global database of what is the equivalent of a fingerprint for every pathogen.

Culture collection

Regardless of the W.G.S. technique, the goal is to both detect and traceback pathogens.

“Right now, I’d say it’s largely used in public health for identifying outbreaks and being able to not just identify the outbreak, but even trace it back to its source," Mr. Doyle said.

Listeria was the initial model used by the F.D.A., C.D.C. and U.S.D.A. to determine if W.G.S. could be used to identify clusters of cases of foodborne illnesses that could be categorized as outbreaks. The technology facilitated faster detection of outbreaks while reducing the number of cases required to confirm the occurance of a foodborne illness outbreak.

Mr. Doyle said it is not sufficient to conclude that isolates from a patient that match the isolates in a food product or in a food plant establish the source of the illness outbreak.

“You have to have epidemiology to connect the two," he said.

There can be, for example, a strain of Listeria that was detected in food and there might be some cases in the PulseNet database that match it, but if the ill patients didn’t ingest the food in question, the food or food company cannot and should not be implicated.

This aspect has proven to be a point of contention.

“If you don’t have a direct connection showing that they ate that food or were exposed to the source, whether it’s the food processing plant or whatever, you can’t say that person became ill from exposure to that food,” Mr. Doyle said.

Today, the F.D.A. officials routinely go to food processing plants and conduct what Mr. Doyle says are known as “swab-a-thons” and take swab samples throughout the processing plant environment. If any of the swabs test positive a whole genome sequence is conducted, and that information is put into the growing cloud-based database. If there are cases or outbreaks in the future, that database is queried to find out if there is a match. If a match is found, further testing of the processing plant and testing of the food manufactured there can be done to determine if there is an epidemiologic link.

“Their database is now able to guide them in terms of where they should start looking if there is an outbreak or several clusters of a certain fingerprint of a Listeria or a Salmonella, Campylobacter or an E. coli associated with human cases,” Mr. Doyle said.

In the public health realm, there are outbreak cases of foodborne illness and sporadic cases. Sporadic cases are those that cannot be connected or linked to an outbreak. Thanks to W.G.S. technology and the F.D.A. and F.S.I.S. maintaining and adding to the database of all cases, C.D.C. officials have begun tracing sporadic cases and linking them to specific food plants. Solving the puzzle of sporadic cases also includes querying the people who became ill to find out if they were exposed to food from that processing plant. This facilitates connecting the outbreak and shortening the time needed to positively identify the source and take the appropriate action, which can include shutting down the plant.