Technology Transfer—Transforming Food Safety with the GenomeTrakr Collaboration

By: Alice Welch

In my last blog post I discussed how FDA’s Technology Transfer program helps drive innovation by building collaborations that can solve today’s public health challenges using leading-edge science. This blog post describes one of those FDA collaborations—a pathogen detection network that is transforming food safety.

Alice WelchAccording to the Centers for Disease Control and Prevention (CDC), foodborne disease outbreaks are responsible for about 48 million illnesses, 325,000 hospitalizations, and 3,000 deaths every year in the United States. The annual toll for Salmonella poisoning alone in this country is 1 million illnesses, 19,000 hospitalizations, and nearly 400 deaths. As the world becomes even more interconnected, FDA has recognized the urgency of creating new approaches and better tools to detect food contamination and stop outbreaks in their tracks.

The FDA-established GenomeTrakr is an innovative response to this global public health challenge. Using a cutting-edge technology called Whole Genome Sequencing (WGS), FDA’s Center for Food Safety and Applied Nutrition (CFSAN) and Office of Regulatory Affairs (ORA) are collaborating with federal and state public health laboratories to build a publicly accessible genomic database called GenomeTrakr. GenomeTrakr enables us to compare some of the bacterial pathogens that cause foodborne diseases and trace them back to their sources faster and more precisely than traditional methods.

WGS is a laboratory process that identifies the complete DNA sequence of an organism’s genetic material at a single time. The process is being used together with GenomeTrakr to identify pathogens isolated from food or environmental samples and compare them to pathogens isolated from sick patients. If the isolates from food or environmental samples match the pathogens taken from the sick patients, scientists can establish a reliable link that helps characterize the size and location of the foodborne disease outbreak. It can even help public health officials determine which ingredient in a multi-ingredient food is causing the outbreak—so that we can get contaminated food out of the food supply. Used by epidemiologists in combination with traditional methods, WGS is advancing our understanding of contaminations in the food supply.

Pathogens evolve very quickly and have thousands of genetic variations. After spending time in a particular geographic location, a pathogen like Salmonella begins to acquire unique genetic signatures that identify it as coming from that location. Until recently, some strains of Salmonella have looked much the same to us, no matter where we found them, because some of the older methods of testing have been unable to distinguish between certain strains of pathogens. But WGS can detect unique signatures within and between species with far greater precision than previous methods, which makes it one of our biggest secret weapons in tackling foodborne illness outbreaks.

FDA scientists and our collaborators in federal and state public health laboratories are using WGS and the GenomeTrakr database to identify those unique signatures. The signatures can often tell us, for example, if a Salmonella that has contaminated a certain part of the food supply is from the U.S. West Coast, New England, or even Germany. FDA and state lab scientists upload the entire genome sequence for a pathogen into the GenomeTrakr database at the National Center for Biotechnology Information, where it’s available for further use. As the database continues to grow, it’s becoming an increasingly powerful tool to help investigations home in faster on the root causes of outbreaks and track their location.

The potential of technologies like WGS to enhance food safety could not be realized without the development of a powerful database like GenomeTrakr. But to build that kind of database FDA needed to form a web of collaborations. Enter FDA’s Technology Transfer team. It plays a critical role in working with our researchers to create the successful relationships that make huge databases like GenomeTrakr work.

To achieve CFSAN’s vision, FDA’s Technology Transfer team worked with CFSAN researchers to create agreements tailored to the project’s needs. The team drafted collaboration agreements that included provisions for establishing relationships between FDA and state laboratories to perform WGS and upload genome sequences into GenomeTrakr. Once CFSAN’s project concept and goals were established, Technology Transfer experts negotiated and put agreements in place so FDA could begin linking federal and state partners to advance the use of WGS across public health.

Since the first state public health lab collaboration was established in February 2012, FDA, along with other international, federal, and state laboratories have added genome sequences for more than 11,000 isolates to the GenomeTrakr database, and we are already seeing impressive results! In early 2014, through a partnership with CDC, FDA and state department of health laboratories used GenomeTrakr to match environmental and food samples with human biological samples, which helped FDA confirm the source of Listeria in an outbreak.

This collaboration is just one of many that our Technology Transfer team has helped create to support FDA efforts to speed innovation in public health. Stay tuned for my next post, where I’ll discuss an FDA invention that is preventing hundreds of thousands of Africans from contracting the debilitating disease of Meningitis.

Learn more:  Whole Genome Sequencing: The Future of Food Safety

HHS Innovates Award Paves Way for the Future of Food Safety and PulseNet

Alice Welch, Ph.D., is Director of FDA’s Technology Transfer Program

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