Nationwide Genomic Atlas of Soil-Dwelling Listeria created in the US


Cornell food scientists have created a new genomic and geological mapping tool to better identify Listeria monocytogenes in food recalls and similar investigations. 

The national atlas will tell scientists where listeria and other related species are within the US, which could help to trace and pinpoint sources of listeria found in ingredients, food processing facilities and finished products, according to research published July 15 in Nature Microbiology. 

“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,” College of Agriculture and Life Sciences Gellert Family Professor in Food Safety and Food Science, senior author Martin Wiedmann said. 

“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.” 

Listeria mononcytogenes in foods can make people extremely sick. The Centres for Disease Control and Prevention (CDC) estimate that each year 1,600 people in the US get listeriosis – of those, about 260 die. 

Knowing that listeria occurs naturally in soil, the Cornell group asked other US scientists to find soil samples from generally undisturbed places in the natural world, such as the off-trail areas of state and national parks. 

From these samples, the group developed a nationwide atlas of 1,854 listeria isolates, representing 594 strains and 12 families of the bacteria called phylogroups. 

Lead author Jingqiu Liao, who worked in Wiedmann’s laboratory as a graduate student, is now a post-doctoral researcher at Columbia University. She had supplemented the research by acquiring soil samples in her own travels and found listeria present across a wide range of environmental circumstances. This bacterium is controlled mainly by soil moisture, salinity concentrations and molybdenum – a trace mineral found in milk, cheese, grains, legumes, leafy vegetables and organ meats. 

“The goal of this work was to systematically collect soil samples across the United States,” Liao said. 

“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, we provided answers to the ecological and evolutionary drivers of bacterial genome flexibility – an important open question in the field of microbiology.” 

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

If listeria is found in a processing facility in the western US, for example, and that facility had used ingredients from a distant state, Wiedmann said, “knowing the genomic information of listeria isolates and their possible locations across the US, we 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.” 

In addition to Wiedmann and Liao, the other authors on “Nationwide Genomic Atlas of Soil-Dwelling Listeria Reveals Effects of Selection and Population Ecology on Pangenome Evolution,” include School of Integrative Plant Science Soil and Crop Sciences Section professor of microbial ecology Daniel Buckley; Massachusetts Institute of Technology (MIT) associate professor of civil and environmental engineering Otto Cordero; MIT postdoctoral researcher Shaul Pollak; CDC researcher Daniel Weller; and Cornell research technician Sean (Xiaodong) Guo. 

The research was funded by the Centre for Produce Safety in Woodland, California. 

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