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Gene Sequencing Could Limit Foodborne Illness

In 2010, over the course of seven months, an outbreak of Salmonella caused an estimated 1,939 cases of food poisoning across 11 states, including Tennessee. The US Centers for Disease Control (CDC) launched an investigation to trace the source of the infections, which was ultimately attributed to eggs from two distributors in Iowa.

The CDC investigation was successful due to DNA testing of the specific strains of Salmonella causing the epidemic. This testing allowed the CDC to locate the source of the infection and prevent further spread of the epidemic by encouraging a recall of the contaminated eggs. Such effective techniques, however, are not widely available for another source of foodborne illness, Campylobacter. Jeremiah Johnson, assistant professor of microbiology, and his JDRD team plan to change that.

Jeremiah Johnson, assistant professor of microbiologyCampylobacter recently became the most common cause of foodborne bacterial infection in the United States,” said Johnson. “It is thought that most people get it from eating contaminated undercooked chicken, because birds carry it within their digestive tract—Campylobacter is to chickens what E. coli is to cattle. Unfortunately, there’s not a lot of data that chickens are the primary cause of Campylobacter infection in humans, and it remains mostly circumstantial.”

According to Johnson, this information gap for Campylobacter results from the use of older techniques, such as pulse-field gel electrophoresis, which can look only at coarse differences in the genomes of bacterial strains. This has been effective for studying E. coli and Salmonella transmission, but Campylobacter is unique in that its genome changes very rapidly, making it difficult to trace back to a source. To combat this challenge, state public health departments have received directives to start using whole-genome sequencing in an attempt to locate the sources of the infections.

“Unfortunately, a lot of the public health departments don’t have that know-how yet. They’re acquiring the sequencing machines, but they don’t have the bioinformatics expertise needed to analyze those genomes. That’s where we come in,” said Johnson.

Jeremiah Johnson and graduate student Brittni KelleyJohnson’s JDRD team is working with Campylobacter strains isolated across East Tennessee, including those collected by the US Food and Drug Administration and the Tennessee Department of Health, to conduct an in-depth analysis of the bacterium’s genome. Once the analysis is complete, Johnson hopes it will lead to a better understanding of the bacterium, as well as discovering why East Tennessee has the highest rate of Campylobacter infection in the state.

“The Department of Health suspects that it’s not entirely linked to chicken consumption. They don’t really know where it’s coming from. Because of our experience with whole-genome sequencing, they’re thinking that we can take our expertise, the expertise at ORNL, and try to find out where some of these infections are coming from,” said Johnson.

Dan Jacobson, Johnson’s ORNL partner and a computational biologist, will use the information generated by the JDRD team to conduct a broad analysis of the Campylobacter genome. Given the rate at which Campylobacter’s genome changes, this evolutionary view should aid in tracing strains back to their origination point.