In a new study, Cornell food scientists have created a national atlas for Listeria monocytogenes. They hope the new genomic and geological mapping tool will make it easier to track down Listeria in food recalls and other investigations.

The study, “Nationwide genomic atlas of soil-dwelling Listeria reveals effects of selection and population ecology on pangenome evolution,” published o July in Nature Microbiology, developed a nationwide atlas of 1,854 Listeria isolates, collected systematically from soils across the United States.

“As we’re trying to figure out the risk of getting listeria from soil and different locations, our group created a more systematic way of assessing how frequently different listeria are found in different locations,” said senior author Martin Wiedmann, Ph.D, the Gellert Family professor in Food Safety and Food Science in the College of Agriculture and Life Sciences.

“We’ve studied listeria in places as diverse as New York, Colorado and California, but before this atlas, (it) was difficult to make comparisons and assess listeria diversity in different locations.”

Lead author Jingqiu Liao, Ph.D, stated that the goal of the study was to systematically collect soil samples across the United States, and to capture the true large-scale spatial distribution, genomic diversity and population structure of listeria species in the natural environment.

“With whole genome sequencing and comprehensive population genomics analyses,” Liao said, “we provided answers to the ecological and evolutionary drivers of bacterial genome flexibility – an important open question in the field of microbiology.”

Liao thinks that this work can serve as a reference for future population genomics studies and will likely benefit the food industry by locating listeria contaminants that may have a natural origin.

Weidmann provided an example of its potential use if listeria is found in a processing facility in the western U.S. find that facility had used ingredients from a distant state, knowing the genomic information of listeria isolates and their possible locations across the U.S., they can better narrow the origins to a specific region.

“You can use this information almost like a traceback. It’s not always proof, but it leads you to evidence,” Weidmann said.

The study
The researchers found that Listeria was present across a wide range of environmental parameters. The presence of Listeria was affected by soil moisture, molybdenum and salinity concentrations.

Whole genome data from 594 representative strains allowed the Cornell scientists to break down Listeria diversity into 12 phylogroups, each with differences in habitat breadth and endemism.

“Cosmopolitan.” also called wide-ranging, phylogroups, prevalent across many different habitats, had more open pangenomes and displayed weaker linkage disequilibrium, reflecting higher rates of gene gain and loss, and allele exchange than phylogroups with narrow habitat ranges. Cosmopolitan phylogroups also had a large fraction of genes affected by positive selection.

According to the study, the effect of positive selection was more pronounced in the phylogroup-specific core genome, suggesting that lineage-specific core genes are important drivers of adaptation. 

Researchers concluded that these results indicate that genome flexibility and recombination are the consequence of selection to survive in variable environments.

The full study can be viewed here.

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