An illustration representing E.coli bacteria

The New Era of Smarter Food Safety

Whole genome sequencing is emerging as a key tool for foodborne outbreak and prevention

Andrea Tolu

The globalization of the food supply chain gave manufacturers access to international suppliers and created more food choices for consumers. But it also made foodborne outbreak prevention and response extremely complicated, with a serious impact on public health. The Centers for Disease Control and Prevention (CDC) estimates that every year, 48 million Americans get sick, 128,000 become hospitalized, and 3,000 die due to foodborne diseases.

Resolving a foodborne outbreak requires matching the pathogen to a specific food, identifying the contaminated ingredient, and tracing it back to its source, which may be located abroad. In less straightforward outbreaks, this process can require significant time and resources.

The 2011 Food Safety Modernization Act was an important step toward a safer supply chain. To continue the modernization process, in July 2020 the Food and Drug Administration (FDA) launched the New Era of Smarter Food Safety blueprint, with a 10-year goal of adapting the approach to food safety to the modern world. The FDA’s vision is a supply chain where food is traced to its source in seconds, consumers are alerted of contaminations in real time, and public health advocates, government, and the food industry work together to keep everyone safe.

A key technology for safer food

The New Era of Smarter Food Safety blueprint is based on four pillars: end-to-end traceability, prevention and outbreak response, new business models for producing and distributing food, and food safety culture. 

A key technology of the second pillar is whole genome sequencing (WGS), which Frank Yiannas, FDA deputy commissioner for Food Policy and Response defines as “the number one thing that has advanced food safety in the twenty-first century.” 

WGS is routinely used in foodborne illness outbreak response. Data from each investigation—sequenced pathogens, contaminated food, and location—is added to the GenomeTrakr network, a publicly available database run by the FDA and maintained by the National Center for Biotechnology Information (NCBI).

The main advantage of WGS is—in Yiannas’ words—that it “allowed us to make the invisible visible.” Compared to pulsed-field gel electrophoresis (PFGE), WGS provides more information about a pathogen's genetic footprint, which can be used to match infections to a specific food and connect outbreaks together in different areas.

A good example of the difference WGS can make during crisis management is the investigation of a 2019 multistate outbreak of Escherichia coli (STEC) O26:H11. 

An initial analysis of the bacteria with PFGE found a match with a 2018 outbreak associated with beef. Interviews with patients supported this hypothesis, as many of them reported eating ground beef before feeling ill.

While investigators were trying to find out where the contaminated beef came from, an analysis made with WGS found that beef couldn’t be the responsible ingredient, because the 2019 and 2018 strains were different. By following other leads, health authorities eventually connected the outbreak to all-purpose flour.  

“Back in the days when we were only using PFGE, we would have thought it was a ground beef problem and involved the USDA instead of the FDA,” says Sharon Shea, director of Food Safety Programs at the Association of Public Health Laboratories (APHL), commenting on the outcome of the 2019 outbreak. "It would have been a waste of time and public resources.”

Using WGS for foodborne outbreak prevention

Tracking pathogen source with WGS has great potential for outbreak prevention, too. Genomic information allows companies to better assess effectiveness of cleaning and sanitization and improve Good Agricultural Practices (GAPs) and Good Manufacturing Practices (GMPs).

“Regulators and public health authorities will know what isolates caused the outbreak,” says Shea. “But if you make whole genome sequencing part of preventive controls and root cause analysis, you'll know a lot more about when and where that strain came from and where to find it.”

Possibilities don’t stop there, though. As the FDA explains in this video, thanks to WGS we know that “certain Salmonella is now resistant to heavy metals and lives in tuna and other top predators in the sea, where heavy metals accumulate.”

Yet, the adoption of WGS in the food industry so far has been limited to larger companies. High cost is a major obstacle, albeit a temporary one. Data from the National Human Genome Research Institute shows that the cost of human genome sequencing has constantly decreased since 2001, and the trend has accelerated in the last six years.

A bigger challenge, says Shea, comes from companies’ legal departments: “Food safety managers understand the science behind WGS, but lawyers don't always understand it. What they see is an expensive technology that will potentially find more positives, forcing them to talk to regulators more often and exposing the business to more risks."

The road ahead for smart food safety programs

Eventually, the goal of the FDA and the rest of the public health authorities is to win this resistance over. If both WGS and the collaboration of the food industry are crucial for the “new era of smarter food safety,” then it makes perfect sense that companies start using WGS more.

“We want to use this data for the prevention piece and get the industry to make changes to their processes, so that the contamination event never happens,” says Shea. “That’s everyone’s idea; the question is, how we get there. Public health and regulatory agencies can help, but ultimately companies need to take it upon themselves to do their own in-house investigations, if they have the resources to do so, and come to their own conclusions about what keeps their products safe.”

Making genomic data part of preventive controls doesn’t necessarily mean adopting WGS right away, Shea explains. There are at least two low-cost, low-risk steps that smaller companies can take. One is to learn from early adopters that are successfully using WGS. The other is to take advantage of the GenomeTrackr to get a better idea of what’s happening in the food supply chain.

“You want to get in earlier, rather than later, and build your knowledge base,” says Shea. “When you determine that WGS is affordable for you, you'll be ready to go, and you can start making a safe product that people can enjoy.”

Top Image:
An illustration representing E.coli bacteria.