GenomeTrakr Transforming Outbreak Investigations

September 5, 2019

The use of Whole Genome Sequencing (WGS) has rapidly changed the way outbreaks are investigated across the world and was the focus of the Food Safety presentation during the UEP area briefings.  Frank Yiannas, former VP of Food Safety at Walmart, addressed the 2018 Chicken Marketing Summit and made a profound statement:  “Each and every one of you in the room today are in this race, and that race is between your ability and your company's ability to prevent poultry-related illnesses and our ability as a society to detect them. ... I believe that public health detection is outpacing industry prevention."  Yiannas emphasized that the industry has a duty to accelerate the prevention of food safety issues related to poultry products.

Now serving as FDA Deputy Commissioner of Food Policy and Response, Yiannas’ statement is even more relevant.  During the 2018 egg recall associated with Salmonella Braenderup, CDC utilized a tool called Whole Genome Sequencing (WGS) along with traditional epidemiology tools to traceback and link the outbreak. This was one of the egg industry’s first exposures to WGS during an investigation. There were many more industry questions than answers, leading to confusion about the science and how the public health and regulatory communities were utilizing the tool.

After the recall, UEP staff began researching WGS, consulting with experts, academia, and food safety attorneys. Joe Levitt and Brian Eyink with Hogan Lovells provided an excellent overview at UEP’s Legislative meeting in May and in a follow-up meeting with staff and consultants in July in Washington DC. This led UEP staff to begin exploring the in-depth impact of WGS on the entire food system.

The development of GenomeTrakr is a game-changer.  Trakr is the first distributed network of labs to utilize WGS for pathogen identification and has sequenced over 343,000 isolates and continues to add approximately 9,000 more per month. This has created a vast database of genomes that can be compared to clinical isolates of patients, environmental sample isolates, and food isolates. This comparison provides real-time clues to potential sources and the geographical origin of foodborne illness outbreaks.

WGS and GenomeTrakr  will be a major topic for discussion at the UEP Annual Meeting October 14 – 17 at the Greenbrier. For more information, watch GenomeTrakr: Transforming Food Safety, that was shown at the UEP area meetings and share with those in your organization that many not have had the chance to attend.