May 23, 2019
Joe Levitt, the former director of FDA’s Center for Food Safety and Applied Nutrition, provided attendees at the UEP Legislative Meetings with an in-depth look at whole genome sequencing (WGS). Levitt, along with his colleague Brian Eyink, both from the law firm Hogan Lovells US LLP, spoke about the implications for the egg industry, understanding the WGS testing process and proactive measures to prevent additional outbreaks once a pathogen is identified.
WGS is used by both FDA and the Center for Disease Control (CDC) to rapidly identify foodborne illness outbreaks and the potential source. Even though there are hundreds of types of Salmonella, each individual Salmonella strain has its own unique gene sequence, similar to a “super fingerprint.”
The FDA and its sister agency the Centers for Disease Control and Prevention (CDC) are compiling huge databases that contain these unique identifiers for all types of Salmonella, as well as for other pathogens, primarily Listeria monocytogenes and E. Coli O157:H7.
For the past several years, every time FDA tests food products or takes environmental samples from a food facility and finds a pathogen, the agency determines the specific WGS and puts it on file in its database. Similarly, whenever doctors or hospitals make a medical diagnosis of foodborne illness based on human testing, they are required to report that to state health authorities, which in turn report to the CDC database. Any confirmation of human illness is also linked to a unique WGS.
Those two databases have now been linked. If FDA has pathogen data from a food product and a food facility with the same WGS, FDA will conclude that the contamination came from that food facility. Similarly, if the CDC has data on a particular person getting sick and that person has bacteria with the same WGS as from the FDA databank, then that link is made. See “Using Science to Find the Sources of Foodborne Illness Outbreaks,” published by FDA.
If there is an epidemiological link, FDA will determine that the company needs to recall the product and will have to demonstrate the facility is pathogen-free before resuming operations.
WGS is not all bad from a producer perspective. Levitt encourages companies that encounter Salmonella environmental positives to immediately perform a root cause analysis to determine the potential source and take the proper corrective action. If another positive is found soon after the first, WGS can determine if the two are identical and likely from the same source. This will help determine whether there is a recurring problem or a completely new introduction onto a farm. Either way, it will assist in being proactive to prevent additional events.
United Egg Producers will continue to engage with experts in the field of WGS, regulatory agencies, and others to bring the necessary resources to its members so informed decisions can be made on what to test, how to test, and how producers can use WGS and other resources more effectively.
For video, photos and other resources, view Resources.