An ongoing Center for Produce Safety-funded study is investigating the genetic fitness traits and environmental conditions that may contribute to the persistence of Escherichia coli REPEXH02—a reoccurring, emerging, and persisting (REP) E. coli O157:H7 subtype linked to multiple leafy greens-associated foodborne illness outbreaks—with the goal of developing a tool to help growers respond to this food safety threat.

A decade ago, whole genome sequencing (WGS) revealed E. coli REPEXH02’s connection to multiple foodborne illness outbreaks caused by contaminated leafy greens. Although the strain has demonstrated persistence, it remains relatively rare in the environment.

Understanding the biological and environmental factors that enabled E. coli REPEXH02’s emergence is now the focus of a two-year, multi-disciplinary research effort led by Teresa Bergholz, Ph.D., Associate Professor in the Department of Food Science and Human Nutrition at Michigan State University (MSU).

Not only is the project exploring contributing factors to REPEXH02’s persistence, but the researchers also aim to develop a predictive, user-friendly online tool to help leafy greens growers assess field-level risks associated with REPEXH02 and similar subtypes.

Also representing MSU, joining Dr. Bergholz are co-principal investigators Shannon Manning, Ph.D., M.P.H., an expert in E. coli bioinformatics, and Jiyoon Yi, Ph.D., who specializes in artificial intelligence (AI) and machine learning (ML) for predictive modeling. Michelle Carter, Ph.D., Research Microbiologist at the U.S. Department of Agriculture’s Agricultural Research Service (USDA-ARS), is also contributing, bringing access to a robust collection of E. coli isolates for comparative genomic analysis.

In March of 2025, the team conducted baseline sampling in a leafy greens production region, collecting soil, sediment, water, and wildlife fecal samples. No E. coli O157:H7 was detected—an unsurprising result given the dry pre-irrigation conditions. Monthly sampling will resume in November, with each sample analyzed for soil texture, pH, soluble salts, organic matter, and heavy metals.

Of particular interest is arsenic tolerance, which may reside in the accessory genome of REPEXH02. This trait could be passed between subtypes and may confer broader stress tolerance. The U.S. Centers for Disease Control and Prevention (CDC) has previously identified REPEXH02 strains with a specific WGS variation that may be linked to arsenic resistance.

In parallel, Drs. Bergholz and Carter are sequencing both new and historical isolates to trace REPEXH02’s evolutionary origins. AI and ML tools will be used to identify environmental and crop-associated traits that distinguish REPEXH02 from other subtypes.

The ultimate goal is a validated online model that allows growers to input field data—such as soil test results or wildlife observations—and receive a risk assessment indicating the likelihood of REPEXH02 presence. Before public release, the tool will be tested against known positive and negative samples to ensure accuracy and reliability.

In the April/May 2025 issue of Food Safety Magazine, Dr. Bergholz and co-authors Dr. Joshua Owade and Dr. Jade Mitchell published an article investigating whether the cold storage time of leafy greens influences E. coli entry into dormant states and the corresponding risk of illness. Read the article here.