New technology tracks Listeria through DNA sequencing

ListeriaBlue_blackbkgrd_blogGenetic epidemiology is changing the detection of foodborne illnesses, according to a new study performed by the U.S. Centers for Disease Control and Prevention (CDC) in which researchers have sequenced the DNA of every Listeria sample tied to an illness in the United States—about 800 per year.

The new detection method can identify gaps in the food safety system, especially when used alongside similar efforts by the Food and Drug Administration (FDA) to sequence samples from food and from places where food is prepared, Brendan Jackson, a medical epidemiologist with CDC, said in a recent article.

“Now that we’re turning whole-genome sequencing on, we’re identifying outbreak after outbreak and finding smaller outbreaks that we were able to find before. They’re also finding them originating in previously unsuspected foods, from caramel apples to ice cream.”

DNA sequencing is what finally cracked the recent Listeria outbreak, in which three people died and many others were hospitalized over a time period longer than a year. As stated in the article, Infection Prevention and Control Coordinator Kären Bally at Via Christi Health had been searching for anything to tie together the infections, which started with a single illness in January 2014. Traditional epidemiological tools showed nothing. Diet records were inconclusive, and Listeria samples from the first four patients seemed unrelated using the standard technique for DNA analysis.

Then, when the fifth patient fell ill in early 2015, standard DNA analysis finally showed a link to a previous case. The state of Kansas sent a sample to CDC for confirmation and whole-genome sequencing revealed that the two samples of Listeria were a near-perfect match. “That was like the ‘aha’ moment,” Bally said in the article.

The FDA was then contacted, who had just sequenced tainted ice cream samples from a facility where inspectors had discovered Listeria. When they compared those results to the CDC samples, they found another match. The CDC then looked into other unsolved Listeria cases and by sequencing samples still in storage, they confirmed five additional cases, dating back to 2010.

“It’s not something that we’ve seen before—being able to look at cases so far back,” Jackson said in the article. “Although it took many tools to track the current outbreak, whole-genome sequencing made all the difference.”

Before this, investigators used diet interviews and DNA analysis known as genetic fingerprinting as their two main tools for tracking foodborne illness cases. According to the article, fingerprinting shows the degree to which two different samples of DNA are related but it is not 100% accurate. In some cases, different bacterial strains can appear related and similar strains can appear to be unrelated.

Whole-genome sequencing, in contrast, allows scientists to accurately compare every single DNA base pair in samples, giving them “a much sharper look at the differences and similarities in the strains,” Jackson said. The process takes 72 hours for testing, which is about 24 hours longer than fingerprinting and costs more as well.

However, the CDC’s goal is to create a national DNA database for foodborne pathogens from clinical samples that could be integrated with an already-existing FDA database of foodborne pathogens from food and environmental samples. The agency plans to add other foodborne illnesses, including Salmonella and the most common disease-causing strain of Escherichia coli (E.coli), to the project within the next three years.

“Whole-genome sequencing shines a new light in this area that helps us find unsuspected gaps in the food safety system,” Robert Tauxe, deputy director of CDC’s Division of Foodborne, Waterborne, and Environmental Diseases, said in the article.

Ice cream, for example, was rarely tested for Listeria prior to this outbreak but in the weeks since, several states have said that Listeria testing in ice cream will now be part of their regimen.

“Finding these outbreaks related to foods we never suspected before is a very surprising thing,” Tauxe added. “This is a wake-up call to the ice cream industry in general and to the regulators.”

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