A recent USDA study’s goal is to improve the ability of regulatory agencies to trace E. coli back to its source during a foodborne outbreak investigation. The study is researching how the DNA of a specific population gradually evolves within its natural environment.
The bacteria is found in the intestines of cattle. Scientists at the U.S. Meat Animal Research Center (USMARC) found information on specific elements of the bacterium’s DNA to narrow down where to look for the outbreak source, USDA said.
Scientists analyzed samples from USMARC’s closed cattle feedlot from 1997-2019 to study the subtypes of E. coli O157:H7 found in the samples.
“The samples used in this research gave us a unique opportunity to study the genomes of a specific population of E. coli O157:H7 in their natural environment,” said Maggie Weinroth, a computational biologist with the Poultry Microbiological Safety and Processing Research Unit (working at USMARC at the time of the research).
Since the USMARC feedlot has been closed to any introduction of cattle except for those raised in the feedlot, the E. coli strains have not been influenced by cattle from other locations for 23 years. This allowed the scientist to focus on changes in the bacteria genomes as they evolved over the years, Weinroth said.
The scientists found four unique groups of organisms that shared specific characteristics, called clades, within the specific bacteria population they studied. The clades all shared a portion of their genetic composition, but they also contained unique elements that can be shared, called mobile elements.
“We noticed that bacteria were able to exchange mobile elements in their genome over time,” said Jim Bono, a USMARC research microbiologist. “Some of these elements stayed in all strains and became part of the core sequence of that specific bacterium’s DNA.”
Interpreting the mobile elements’ roles during an outbreak investigation can help identify relatedness between human and environmental isolates of the bacteria, Bono said.
Scientists will continue to study the DNA of the specific populations of E. coli O157:H7 found in the closed feedlot and record additional variations. Results from the latest study and future studies will build information for rapid, more accurate traceback responses during outbreak investigations, USDA said.
The study was published in the scientific journal GMC Genomics and was funded by the Agricultural Research Service and a grant from the Beef Checkoff administered by the Foundation for Meat and Poultry Research and Education. — Anna Miller, WLJ managing editor
