UNIVERSITY PARK, Pa. — The Department of Food Science in Penn State’s College of Agricultural Sciences recently became the first such department in the country — and the University became one of just a few academic institutions — to take the lead for their state in the U.S. Food and Drug Administration’s GenomeTrakr network.
Started in 2012, GenomeTrakr is a nationwide system of laboratories that utilizes whole-genome sequencing for pathogen identification in response to outbreaks of foodborne illness. Penn State’s involvement is a collaboration with the Pennsylvania Department of Health, with the goal of the Commonwealth benefiting from advances in genomic sciences.
The laboratory of Ed Dudley, associate professor of food science, is spearheading the work with GenomeTrakr. He and his students for years have conducted research using molecular biology and biochemistry to better understand the physiology, behavior and evolution of foodborne pathogens and to develop improved methods of tracking the spread of the organisms “from farm to fork.”
“Our goal is to help populate the whole-genome-sequence databases with foodborne isolates, particularly E. coli and Salmonella, from food and environmental sources, and to help organizations, such as our state Department of Health and the food industry, to gain the knowledge needed to enter this field or to gain the knowledge necessary to benefit from advances in genomic sciences,” he said.
Penn State’s involvement in the GenomeTrakr Network is a great development for students, according to Dudley.
“This is a prestigious thing — we are the first food science department in the country to be taking the lead and training our state’s lab in the technology. Most other states with an academic partner run everything out of the state lab, with the academic lab just playing a consulting role,” he said.
Dudley noted that whole-genome sequencing is inexpensive, easy to use, and the most accurate and high-resolution subtyping technique. In addition, it has identical sample preparation for all pathogens, and a single test yields information about resistance, serotype and virulence factors. Modern food-safety professionals need to be trained to perform cutting-edge techniques on modern equipment.
“The students in our food science department are able to work directly with the technology that many of them are going to see when they go out to work for a food-safety company,” Dudley said. “It is a unique situation — this is something that no other student at a food science department across the country can get access to. It is a considerable selling point for a Penn State education.”
The GenomeTrakr network currently consists of 15 federal labs, 25 state health and university labs, one U.S. hospital lab, two other labs located in the U.S., and 20 labs outside of the U.S. They collect and share genomic and geographic data from foodborne pathogens.
The data, which are housed in public databases at the National Center for Biotechnology Information at the National Institutes of Health, can be accessed by researchers and public-health officials for real-time comparison and analysis. Widely distributing that volume of information promises to speed foodborne illness outbreak investigations and reduce foodborne illnesses and deaths.
The GenomeTrakr network has sequenced more than 113,000 isolates and closed more than 175 genomes, Dudley explained. The network regularly sequences more than 3,500 isolates each month, to which Penn State makes a surprising contribution.
Many of the potential isolates the Dudley lab sequences are coming out of the E. coli Reference Center in the College of Agricultural Sciences. “It’s the world’s largest E. coli collection, and the fact that we have a 50-year-old collection of isolates that have come from food and animals provides us with a rich source of bacteria to sequence,” Dudley said. “And the FDA finds that really important.”
Dudley doesn’t see the GenomeTrakr collaboration ending anytime soon. As the state Department of Health lab staff becomes more proficient in using the whole genome sequencing equipment, he expects their workload “to go up exponentially” in coming years. He sees that growing burden as an opportunity for students in the Department of Food Science.
“We believe that when the state health lab gets up and running and starts utilizing this technology on a day-to-day basis, we will act sort of as their overflow facility,” he said. “There will be a lot of work for our students to handle and learn from.”