Every year, approximately 48 million people in the United States are sickened by foodborne diseases like salmonella, listeria and E. coli. Of those,128,000 are hospitalized and 3,000 die.
Where it used to take public health authorities weeks or months to track the cause of an outbreak, the source of a foodborne pathogen can now be pinpointed more quickly, shared immediately and the tainted products removed from the food chain thanks to the use of whole genome sequencing and a data platform developed under the leadership of Steven Musser.
“Steve was an early adopter and a true champion of this concept of genomic epidemiology,” said Marc Allard, a Food and Drug Administration research microbiologist. Applying whole genome sequencing technology to food safety “has been a game-changer for public health,” Allard added. “It is transforming how foodborne illness outbreaks are investigated, preventing thousands of foodborne illnesses and averting disruptions to the food supply.”
The whole genome sequencing approach implemented by Musser “is the most powerful tool in our toolbox of food microbiology today,” said Mark Moorman, the director of FDA’s Office of Food Safety. He likened this innovation to “the difference between binoculars and the Hubble telescope.”
While the medical community had been using data from whole genome sequencing to make advances in human genomic analysis, Musser pioneered the use of this technology with food pathogens to speed up the identification of the source of a foodborne infection, remove the tainted products from the marketplace and cleanup sites that produced the infected food.
Whole genome sequencing allows for the rapid identification and characterization of the unique fingerprints of pathogens found in produce, eggs, poultry, meat, seafood and other food products as well as in food production facilities. The process can also link those microorganisms discovered in sick individuals, helping officials trace the source of outbreaks.
Musser, as the official in charge of overseeing FDA research and development, persuaded the agency’s leadership to adopt this approach and secured support to integrate the technology across all FDA offices and eventually with many partner federal agencies.
He also helped set up an infrastructure to use genome sequencing to address other emergent public health issues beyond foodborne illnesses by working with state and academic labs across the country and internationally. As an example, Allard pointed to New York State’s use of the technology to sequence two dozen pathogens that included West Nile virus in birds and tuberculosis in homeless populations. The technique is also has been used to trace COVID-19 in wastewater.
In addition, Musser oversaw the formation and establishment of the GenomeTrakr database at the National Center for Biotechnology Information in collaboration with other public health agencies and universities. The open-access GenomeTrakr collects and shares genomic and geographic data from foodborne pathogens, helping find contamination sources and deal with environmental conditions associated with the infection from agricultural products.
Musser said the use of genome sequencing was “a quantum improvement in our approach to solving foodborne outbreak investigations.” He said that building the GenomeTrakr network was “a eureka moment’’ because it allowed so much genomic data to be analyzed, stored and shared, providing instant additional information.
“When we first started working to store and analyze the data, there were less than 1,000 sequences of all bacteria in the public database and fewer than 50 sequences from foodborne pathogens,” Musser said. “Today, the GenomeTrakr database contains over one million sequences from 48 organism groups, of which more than 750,000 are foodborne pathogens.”
Musser said the data used to analyze foodborne illnesses requires specialized analysis. “The GenomeTrakr made it all simple and put the information in everyone’s hands,” he said. “This publicly available database is a true national treasure.”
The GenomeTrakr also has allowed authorities to detect and stop the low-level leakage of pathogens into food that had often been causing sporadic illnesses over several years. And because it is a global network, it has enabled authorities to identify and stop foodborne outbreaks involving the same contaminated food in multiple countries.
Initially, there was resistance to Musser’s transformative approach. Federal partners were wary of changing the public health infrastructure, the food industry was worried it would cause disruptions and other countries did not want to be implicated in pathogen outbreaks.
Musser collaborated with each stakeholder to point out the benefits of whole genome sequencing and allay their concerns. Importantly, he created protocols so that food companies could remove foodborne pathogens in their facilities before there was a major outbreak.
In 2014, for example, the FDA performed a routine inspection of a nut butter facility which identified a strain of salmonella in one of the facility’s drains that matched the whole genome sequencing data of a recent human illness. This discovery enabled the FDA to halt production and have the facility sanitized. At the end of this investigation, there were only six illnesses in five states.
Five years earlier, an investigation of contaminated peanut butter without use of the whole genome sequencing and the GenomeTrakr took many months. By the end of the investigation, the contaminated products had sickened over 700 people in 46 states, led to the recall of thousands of products and cost the peanut industry more than one billion dollars.
“Steve Musser saw a public health problem that needed scientific solutions, and by using creative out of the box thinking, he came up with a new way to link contaminated food to people who were affected by foodborne illness outbreaks,” said Susan Mayne, the director of FDA’s Center for Food Safety and Applied Nutrition. “This is the most paradigm-changing development in food safety that we’ve ever seen.”