DNA testing and whole genome sequencing have become increasingly important tools in the arsenal of public health professionals. Specifically with regard to food- borne illness outbreaks, these techniques have been employed to successfully trace the sources of infection. Thus far, they have been used mostly in Salmonella outbreaks, but Jeremiah Johnson, assistant professor of microbiology, hopes to extend their capability to trace other bacteria.
“Something that’s actually starting to happen nationally, in terms of public health, is that they’re moving away from more archaic genomic analyses and actually mandating that all state public health departments start using whole genome sequencing,” he said.
This is where his team steps in. While many health departments are acquiring the equipment necessary to conduct this kind of sequencing, they are lacking the in-house expertise needed to conduct the work. Johnson’s team possesses the bioinformatics experience required to analyze the genomes of the subject bacteria—in this case, Campylobacter.
Campylobacter was recently identified by the CDC as a serious threat to public health, as it is becoming increasingly resistant to antibiotics. It also takes significantly less of the bacterium to make a person sick than other bacteria in the past.
“With Campylobacter, it only takes a few hundred bacterial cells to make a person sick,” said Johnson. Another hurdle with Campylobacter is how rapidly the bacteria mutate and evolve, making some older genomic techniques ineffective.
In the first year of support, Johnson’s team focused on acquiring Campylobacter samples from a variety of sources. The cooperative effort saw contributions from UT’s College of Veterinary Medicine and the US Food and Drug Administration. Team members also ventured out into other areas of East Tennessee to collect additional samples for sequencing.
“We’ve collected samples from area farmer’s markets and grocery stores. We’ve done local waterways, including the Tennessee River and the Hiwassee River. We’ve also done animals around here, like sheep, pigs, cows, and some birds,” said Johnson.
In the second year of the project, the team is hoping to establish proof of concept by running a transmission study with Johnson’s ORNL partner, computational biologist Dan Jacobson. The goal, based on a genomic sequencing conducted on the front end, is to see if the ORNL collaborators can identify the original strain of Campylobacter once it’s passed through this transmission study.