Banking Bacteria

The Department of Food Science leads Pennsylvania's efforts with the GenomeTrakr network to trace foodborne illnesses to their sources.

Ed Dudley
Ed Dudley, associate professor of food science

Was it the lettuce in the salad, the meat on the sandwich, or the fresh fruit cup that caused 25 people from a local diner to become violently ill? Did a virus or bacterium sneak in on the hands of a sick employee or hitchhike on food all the way from the farm?

Tracking the source of an outbreak historically has taken months to unravel. But time is imperative when people are falling sick and even dying.

Penn State recently became one of the first academic institutions to take the lead for its state in the U.S. Food and Drug Administration's GenomeTrakr network. Started in 2012, GenomeTrakr is a nationwide system of laboratories that utilize whole-genome sequencing--which identifies the entire genetic blueprint for particular species--to rapidly and conclusively identify pathogens involved in outbreaks of foodborne illness. According to Eric Brown, director of the Division of Microbiology within the FDA's Center for Food Safety and Applied Nutrition, whole-genome sequencing does for species identification what the Hubble Telescope did for the study of deep space; it enables researchers to look deep into foodborne outbreaks, he says, and track them back to their sources.

Why Penn State?

The laboratory of Ed Dudley, associate professor of food science, is spearheading Pennsylvania's work with GenomeTrakr. Dudley 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," says Dudley. "This is a technology that is new for most people who work for state labs, but is second nature for many of us in academia. Starting in 2019, the Centers for Disease Control will expect all state public health laboratories to actively use whole-genome sequencing. Part of our goal is to help the Pennsylvania Department of Health to use this technology."

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. Easy access to that information will speed foodborne illness outbreak investigations and reduce illnesses and deaths.

The GenomeTrakr network has sequenced more than 113,000 bacterial strains, or isolates, and completed more than 175 whole genomes, Dudley explains. The network regularly sequences more than 3,500 isolates each month, to which Penn State makes a surprising contribution.

Dudley adds that the Department of Food Science is the first academic department in the country to take the lead and train its 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 says.

According to Dudley, one reason the University was selected is because it is home to the E. coli Reference Center in the College of Agricultural Sciences. "It's the world's largest E. coli collection, with 90 million isolates from food and animals collected over 50 years, that provides us with a rich source of bacteria to sequence," he says. By analyzing the whole genomes of these bacteria, Dudley and his team will add significantly to the FDA's databases, which, in turn, will help the organization to track the sources of even more outbreaks.

A Boon for Students

For students, assisting with the GenomeTrakr effort is a valuable opportunity to learn unique skills that will set them apart in the job market.

"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 says. "It is a unique situation--this is something that few, if any, other students in food science departments across the country can get access to. It is a considerable selling point for a Penn State education."

Rebecca Abelman, a graduate student in food science, is already at work on the project. Her research focuses on whole-genome sequencing of isolates of Shigella sonnei, a species of bacteria that is partly responsible for shigellosis, which results in abdominal upset and sometimes even fever. Abelman acquired the isolates from the Pennsylvania Department of Health.

"The Shigella are all from Pennsylvania patients, but some were acquired from international locations when patients got sick on vacation or during travel," she explains. "Using whole-genome sequencing, I want to compare these isolates to one another and see if I can find a way to predict the bacteria's geographic origin. Additionally, I want to look at the genetic environment of these Shigella to see what patterns of antibiotic resistance they carry and whether they match what the Pennsylvania Department of Health saw clinically."

Abelman will upload all of the Shigella whole genomes she sequences to the GenomeTrackr database, adding to the multitude of data available through the GenomeTrackr program.

"The project is providing me with a lot of connections and allowing me to meet professionals in my field that I may not have gotten the chance to meet without being part of GenomeTrackr," says Abelman. "Whole-genome sequencing also is an excellent skill to have, so after graduating from Penn State with my master's degree, I'll likely be able to find a job that allows me to continue using this skill."

Andrea Keefer is also a food science graduate student who is working on the GenomeTrakr project. She is partnering with the Pennsylvania Department of Health to demonstrate the usefulness and research potential of whole-genome sequencing and to eventually assist the department in implementing the technology.

Specifically, she is using whole-genome sequencing to resolve the genetic relatedness of a unique collection of multi-drug-resistant Salmonella found on retail meats. "We will use whole-genome sequencing to explain each isolate's genetic antimicrobial resistance profile in an effort to advance the understanding of the frequency and complexity of resistance in the context of foodborne pathogens," says Keefer. "My project overlaps with the greater GenomeTrakr program because all of the isolates I have whole-genome sequenced will be uploaded to the GenomeTrakr data-base and, accordingly, will become publicaly available."

She adds, "My involvement in the GenomeTrakr program has allowed me to network with government scientists and gain exposure to many possible career avenues."

Dudley doesn't see the GenomeTrakr collaboration ending anytime soon. As the state Department of Health lab becomes more proficient in using the whole-genome sequencing equipment, he expects their workload to "increase exponentially" in coming years.

"We believe that when the state health lab gets up and running and starts utilizing this technology on a day-to-day basis, we'll act as their overflow facility," he says. "There will be a lot of work for our students to handle and learn from."

-- Jeff Mulhollem