Q&A: How does technology help track foodborne pathogens and outbreaks?

After a cyclospora outbreak and recalls of imported beef over the summer, a recent Gallup poll found that Americans’ confidence in food safety has fallen to a record low, and consumers may be wondering how foodborne illness outbreaks can be tracked and mitigated.

In this Q&A, experts Jasna Kovac, Dorothy Foehr Huck and J. Lloyd Huck Chair in Microbiomes in Food Safety, and Edward Dudley, director of the E. coli Reference Center and professor of food science, both from Penn State’s College of Agricultural Sciences, discussed how technology can be used to track outbreaks and pathogens, as well as the work happening at Penn State to help keep the food supply safe.

What types of foodborne pathogens can be tracked?

Kovac: The pathogens that are routinely tracked are bacteria that can be cultured from clinical, food and environmental samples, such as salmonella, Listeria monocytogenes, Shiga toxin-producing E. coli and campylobacter. Viruses such as norovirus and hepatitis A may cause a large share of foodborne illness, but they are harder to track the same way because they cannot be easily cultured.

Tracking pathogens enables identification of the major sources and reservoirs, and that information can then inform the design of more targeted and effective interventions to prevent spread from those sources to food and to humans.

What types of technologies can track these pathogens?

Dudley: Whole genome sequencing—a process that determines the complete DNA sequence of an organism’s genetic material—can identify bacteria down to the strain level.

For example, if you have a salmonella sample from a food product and one from a patient, you can look at the DNA of those two samples and determine whether they’re the same strain or not. If they are, it’s possible the patient may have gotten sick from that product. If they’re distinct, investigators may need to keep looking for what else the individual ate that made them ill.

Additionally, there’s growing interest in eventually applying this method to parasites. Cyclospora, for example, was a problem with lettuce this past summer. But the genomes of cyclospora are much bigger than they are with bacteria, so it’s more expensive and the analysis pipelines aren’t as established as they are with bacteria.

What kind of work are researchers at Penn State doing in this field?

Kovac: My lab uses whole-genome sequencing along with other methods to predict how foodborne pathogens survive and grow in food, as well as how risky they are in terms of causing illness and resisting antimicrobials.

We also are studying the relationship between pathogen contamination in food processing facilities and the composition of microbial communities, which are all the microorganisms in an environment that we sample. We are exploring this to see whether community composition can serve as an early warning of increased risk for pathogen persistence in those environments.

Dudley: Another one that my lab has been leading is Pennsylvania’s effort in a federal program called GenomeTrackr for about the last 10 years. We’ve sequenced species of some of the common foodborne bacterial pathogens—salmonella, E. coli, listeria, campylobacter—and provided this genomic data along with metadata, such as the date it was collected and where it came from. And we make all this data publicly available, so it’s there for public health labs around the world.

We’re asking whether wastewater is an appropriate way to track foodborne outbreaks. Right now, researchers rely on bacteria isolates from tests doctors run on sick patients and sequence those isolates to start tracking outbreaks.

But just as was done with the SARS-CoV-2 virus that causes COVID-19, we’re asking whether we can monitor wastewater to get an idea of whether organisms such as salmonella are circulating within a community. Or whether this technology can determine when an outbreak is over.

What technologies may be used in the future to track foodborne illnesses?

Kovac: Sequencing already gives us very high resolution for distinguishing among pathogen subtypes, which is what makes it so valuable in outbreak investigations that depend on source tracking. One new direction could be moving sequencing out of centralized laboratories and into smaller labs and potentially, into food companies themselves. This would shorten the gap between detecting a problem in a facility and acting on it.

A second is sequencing directly from food samples without first isolating the microorganism. That would help with pathogens that are difficult to culture and with clinical cases where no isolate is available.

Dudley: Other technologies we could potentially leverage are social media and artificial intelligence (AI). It’s been shown that social media and self-reporting sites can play a role in identifying an outbreak, not by relying on people going to their doctor, but by following social media—people get sick, and they start using social media or using Google to research symptoms. And if you get enough of those similar questions in the same area, it can lead to the assumption that there’s a problem with that pathogen.

As we expand on AI, I think we may see it being used to watch for problems such as foodborne outbreaks by following people’s interactions with social media or keywords from search engines.

What should consumers know about the current safety of the food system?

Kovac: It’s important for the public to know that when detection improves, it can look like the food supply is getting less safe. However, smaller outbreaks identified and more recalls issued often mean the surveillance system is working better, not that more contamination is occurring.

Dudley: Many of the outbreaks that we see are associated with fresh produce, and that is something that consumers need to be aware of since, by definition, we’re not providing heat treatment to fresh fruits and vegetables. With that, consumers should remember some rules of thumb, such as keeping meats and fresh produce separated in the kitchen and washing produce whenever possible to lessen the risk. Understanding where these risks lie—and how to mitigate them—is essential for protecting yourself and your family.

Who’s behind this story?

Lisa Lock

BA art history, MA material culture. Former museum editor, paramedic, and transplant coordinator. Editing for Science X since 2021.

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Andrew Zinin

Master’s in physics with research experience. Long-time science news enthusiast. Plays key role in Science X’s editorial success.

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