In the 2000s, grocery stores felt like a microbial minefield: First there was Escherichia coli in bags of spinach, then Salmonella in peanut butter, and even Listeria in turkey. It seemed like no food was safe from foodborne pathogens. In 2008 alone, Salmonella and E. coli outbreaks spanning multiple states affected more than 1,500 people in the United States.1
As consumers grew frustrated, so did the federal agencies responsible for tracking down the sources of the outbreaks. Even the state-of-the-art molecular tools of the time were no match for wily, evolving microbes. In response, the Food and Drug Administration set aside more than a million dollars with a mandate to find a better solution. This laid the foundation for what would eventually become GenomeTrakr: a network of public and academic labs using high-resolution whole-genome sequencing (WGS) technologies to detect foodborne pathogens using their DNA sequences.
“With sequencing, we're solving more outbreaks. Knowing where to look is half the game.”
- Steven Musser, FDA
More than a decade later, GenomeTrakr remains the FDA’s not-so-secret weapon in fighting foodborne pathogens. By sequencing more than 1,000 bacterial samples isolated from food, environmental sources, and infected people each month, GenomeTrakr labs helped the FDA identify and investigate 225 outbreaks in 2024 alone, according to Steven Musser, associate commissioner for Human Foods Research at the FDA.
Fourteen years ago, Musser was a regulator at the FDA when they tasked him with improving the foodborne pathogen surveillance system. “Back then, most [outbreaks] weren't solved,” Musser said. “With sequencing, we're solving more outbreaks. Knowing where to look is half the game.”
New Sequencing Tools to Trace Pathogens
The idea of eating microbes might make some people squeamish, but many foodborne microbes are harmless. Take E. coli, for example. Most E. coli are harmless to humans and even live in our intestines. However, some kinds, such as Shiga toxin-producing E. coli, can cause intense gastrointestinal symptoms. Similarly, strains of Salmonella, Campylobacter, and Listeria can wreak havoc on the digestive system—and in immunocompromised individuals, these infections can be fatal.
Physicians can easily test a patient for a foodborne pathogen. It is harder, however, to figure out where the pathogen came from. If two people test positive for Salmonella, for example, they could have both been infected by the same species of bacteria, but not from the same source. Pinpointing the origin of the pathogen is critical for detecting outbreaks and preventing further illness.
Tracing the origins of an infection requires both anecdotal and molecular evidence. Epidemiologists interview patients about their recent food and travel history, while scientists analyze genetic material from bacteria collected from the patient, food products, restaurant kitchens, factories, and even the environment. If the bacterial DNA from a patient matches that of a food product, they likely stem from the same source. If the patient’s interview confirms they ate the food before falling ill, it becomes the primary suspect.
Steven Musser has been leading the FDA's GenomeTrakr since its first pilot study in 2012.
Food and Drug Administration
Before scientists developed tools to analyze bacterial DNA, the state-of-the-art method to molecularly investigate these isolates was pulse field gel electrophoresis (PFGE), a method that involved chopping up a strand of bacterial DNA at specific positions and measuring the size of the resulting pieces. Two bacteria with the same DNA sequence should end up with the same-sized pieces. However, PFGE was far from perfect: For starters, it was hard to interpret. “It's almost like interpreting barcodes by eye,” said Martin Wiedmann, a food scientist at Cornell University.
Moreover, it was possible for two different bacterial subtypes to yield fragments of similar sizes, while two isolates of the same bacteria could produce different fragments. Combined with the difficulty of conducting epidemiological investigations, this created blind spots in the FDA’s outbreak tracing efforts. In one case, a Salmonella outbreak identified through PFGE was mistakenly attributed to tomatoes rather than the real culprit, jalapeño peppers.1
Back in 2011, when GenomeTrakr was in its infancy, WGS was still an evolving technology and could cost as much as $200 per bacterial isolate. But Musser believed detailed information about each nucleotide would enable a much higher-resolution comparison of bacterial isolates—a game-changer for pathogen detection.
Following Musser’s recommendation, the FDA recruited 10 FDA laboratories and four state laboratories to participate in GenomeTrakr. In partnership, the Centers for Disease Control and Prevention (CDC) began incorporating WGS into their pathogen surveillance program, PulseNet, with a focus on sequencing bacterial isolates from patients. Musser realized that the FDA could help complete the puzzle by sequencing isolates from food products and production environments, allowing comparisons with patient-derived isolates.
In the past, it was very difficult to compare what's happening in your lab with, say, a lab in some other part of the world. GenomeTrakr has really helped to break those silos and cross those bridges.
– Sid Thakur, North Carolina State University
To demonstrate the utility of this new surveillance system, the FDA and CDC partnered in 2013 to take on a formidable foodborne foe: Listeria monocytogenes. Listeria was the perfect target, Wiedmann said, because it was relatively rare but had a high fatality rate. “Detecting outbreaks earlier offered a high return-on-investment,” he said. “It was a no-brainer.”
And it worked. Using WGS, the agencies solved 14 Listeria outbreaks over two years, compared to just two outbreaks per year prior to WGS.2 The average number of cases per outbreak also dropped because of quicker detection.
“The whole idea of a GenomeTrakr is to make an active surveillance program and to really act while something is ongoing so that we can prevent more people from falling sick,” said Sid Thakur, a molecular epidemiologist at North Carolina State University who is part of the GenomeTrakr network and receives GenomeTrakr funding. “This is better than a passive surveillance program, where the outbreak has already ended and we are picking up the bits and pieces to try to make a story.”
DNA Detectives Prevent Food Outbreaks From Milkshakes and More
Since its inception, GenomeTrakr has expanded to include more than 60 labs across the United States—spanning federal, state, academic, and hospital institutions—as well as 24 international labs. “Pathogens don't know or respect borders,” Musser said. By working with international partners, the FDA is able to trace pathogens that may have come from imported foods, such as a multicountry 2016-2020 Listeria outbreak due to contaminated mushrooms from South Korea.3
Consistency and quality are two key tenets of GenomeTrakr’s work. To ensure this, participating labs follow a meticulous protocol to process, sequence, and analyze bacterial isolates. Thakur’s lab uses GenomeTrakr protocols to sequence more than 400 isolates each year ranging from bacteria found in retail meat or seafood in North Carolina to samples sent from international collaborators. “The stringency conditions are very conservative and for the right reasons,” Thakur said.
As part of GenomeTrakr, Thakur’s lab publicly shares their bacterial sequences through the National Center for Biotechnology Information’s (NCBI) Pathogen Detection platform. This platform has been integral to GenomeTrakr’s mission since the beginning. Musser realized that sequencing thousands of bacterial isolates would produce large amounts of data, potentially benefiting state public health agencies, the FDA, and researchers alike. He worked with David Lipman, then the NCBI director, to design an online platform to store, share, and analyze pathogen genome sequences. The website automatically groups sequences based on their similarity to identify potential clusters of related infections and checks sequences for antimicrobial resistance genes.
Wiedmann, like many other researchers outside of the GenomeTrakr network, uses the data to help companies or state health labs identify the source of outbreaks. “In the past, it was very difficult to compare what's happening in your lab with, say, a lab in some other part of the world,” Thakur said. “GenomeTrakr has really helped to break those silos and cross those bridges.”
Researchers use whole-genome sequencing to identify microbes in samples from patients, food, and food production environments.
CDC/Courtney Wheeler
Scientists at the Washington State Department of Health’s Public Health Laboratories (PHL), part of the GenomeTrakr network, know this firsthand. This interdisciplinary team works on the ground and in the lab to investigate outbreaks in local communities. In 2012, they received a sequencer from the FDA, along with a request to help the FDA with an initial pilot project to test the effectiveness of sequencing for pathogen surveillance.
Philip Dykema, a microbiologist at the PHL, noted how this technology has transformed the way the team investigates outbreaks. “The information is much denser than with PFGE…You can see all the differences in the genome, and you can [ask], ‘is this related to the disease that is in the neighboring county?’” he said. “You have much more assurance that you're looking at transmission or you're looking at separate events.”
The lab in Shoreline, just outside Seattle, receives between 20 to 50 bacterial isolates per week from people who reported foodborne infections across the state. While local health officials interview patients, scientists in the lab extract DNA from the bacteria, sequence it, and put the data through the CDC’s analysis pipeline. Epidemiologists then try to identify clusters of cases with bacteria that have highly similar genome sequences and compare the foods the patients ate to figure out what might be the cause.
Genomic data can be the critical piece linking cases together. In 2023, Washington State experienced a Listeria outbreak with six cases and three deaths. Listeria outbreaks are especially difficult to trace because the bacteria can remain dormant in a person for over a month, making it difficult for infected individuals to remember everything they ate. As more and more cases emerged, the Washington State Public Health Laboratories sequenced bacterial isolates from patients and saw that the sequences were very similar.
“Having the whole genome sequencing that tied these cases together was super important,” said Laurie Stewart, an epidemiologist at the PHL. “If we hadn't known these cases were all the same, we wouldn't have known to push so hard to try to find the common denominator among them.” After careful investigation, officials discovered that all infected individuals had purchased milkshakes from the same fast-food restaurant. Investigators collected bacterial samples from the milkshake machine and sequenced them—it was a perfect match to the patient isolates.
The Future of Food Safety
The overall impact of GenomeTrakr is hard to quantify, but it is substantial. Since 2017, Musser said that WGS has helped the FDA investigate 1,300 incidents. Sequencing each isolate costs just $35 to $50, but according to a 2019 report by the FDA, preventing outbreaks saves nearly $500 million per year in health expenses.4 Outbreaks are also getting caught earlier, reducing their impact, Musser said.
Wiedmann estimates that prior to the use of WGS, it could take 50 cases to detect an outbreak, but WGS has cut that down to four or five cases—and sometimes, even just one case is enough.
Reaching zero outbreaks may not be a feasible outcome, though, Wiedmann said. “A lot of people expect food to be 100 percent safe, but that's like saying you want automobile travel to be 100 percent safe,” he said. In particular, he points to efforts to reduce Salmonella in chicken: Even when Salmonella incidence decreased, cases of illness did not. This is likely because interventions shifted the overall balance of Salmonella subtypes, decreasing those that don’t release disease-causing toxins while sparing those that do, he said. WGS, however, can help tease apart these differences to identify the best subtypes to target.
“We’re trying to apply the principle of precision medicine to food safety by not saying all Salmonella are the same, but saying, hey, they're different,” he said. “Their differences provide important information to consider when we're trying to control Salmonella.”
This distinction could be especially important right now. Illnesses and deaths due to foodborne pathogens may be ticking upwards in the United States, although researchers are unsure whether this reflects an actual increase in unsafe foods or simply increased reporting and detection.5,6 However, studies have predicted that climate change could drive further increases in foodborne pathogens as humidity promotes bacterial growth.7
Musser hopes to expand GenomeTrakr into a more robust network of labs for comprehensive foodborne pathogen surveillance, similar to the CDC’s pathogen surveillance efforts. Currently, the FDA funds 22 states through GenomeTrakr to sequence foodborne pathogen isolates, but securing sufficient funding is an obstacle. “We don't have enough money to fund all the states to do this,” he said. He also thinks that new tools such as long-read sequencing and antimicrobial resistance detection will make pathogen detection even more effective.
Thakur appreciates GenomeTrakr’s broad focus, which includes the bacteria found in humans, but also those on microbes in the food and environment around us, which have serious implications for human health. Proponents of the idea of “One Health” have long emphasized interconnectedness of human health with the health of all living things, and Thakur believes microbes are a key part of it.
“When you start comparing some of the [WGS] data across different food commodities, the human sector, the animal sector, the environmental sector,” Thakur said, “you can see in many of the spaces the genomic fingerprints are pretty similar.”
- Behravesh CB, et al. 2008 Outbreak of Salmonella Saintpaul infections associated with raw produce. N Engl J Med. 2011;364(10):918-27.
- Jackson BR, et al. Implementation of nationwide real-time whole-genome sequencing to enhance listeriosis outbreak detection and investigation. Clin Infect Dis. 2016;63(3):380-386.
- Pereira E, et al. Multinational outbreak of Listeria monocytogenes infections linked to enoki mushrooms imported from the Republic of Korea 2016-2020. J Food Prot. 2023;86(7):100101.
- Brown B, et al. An economic evaluation of the whole genome sequencing source tracking program in the U.S. PLoS One. 2021;16(10):e0258262.
- Murray T, Cope S. Food for thought 2025. U.S. PIRG Education Fund. 2025.
- Shah HJ, et al. Reported incidence of infections caused by pathogens transmitted commonly through food: Impact of increased use of culture-independent diagnostic tests — Foodborne Diseases Active Surveillance Network, 1996–2023. MMWR Morb Mortal Wkly Rep. 2024;73(26):584-593.
- Dixon MH, et al. Time of arrival during plant disease progression and humidity additively influence Salmonella enterica colonization of lettuce. Appl Environ Microbiol. 2024;90(9):e0131124.
