Researchers at Michigan State University (MSU) are leading a two-year study to better understand the persistence of Escherichia coli REPEXH02, a subtype of E. coli O157:H7 linked to multiple leafy greens-related foodborne illness outbreaks. The project, funded by the Center for Produce Safety, aims to identify genetic and environmental factors contributing to the strain's survival and to develop a predictive tool to help growers assess field-level risks.
Whole genome sequencing (WGS) first linked REPEXH02 to several outbreaks a decade ago. Despite its recurring detection, the strain remains relatively uncommon in the environment. The ongoing research seeks to determine why REPEXH02 has persisted and how environmental conditions may support its presence in leafy green production regions.
The project is led by Teresa Bergholz, Ph.D., Associate Professor in MSU's Department of Food Science and Human Nutrition, with co-principal investigators Shannon Manning, Ph.D., M.P.H., and Jiyoon Yi, Ph.D. Dr. Manning specializes in E. coli bioinformatics, while Dr. Yi applies artificial intelligence (AI) and machine learning (ML) tools for predictive modeling. Michelle Carter, Ph.D., Research Microbiologist at the U.S. Department of Agriculture's Agricultural Research Service (USDA-ARS), is contributing isolates for comparative genomic analysis.
In March 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 found, which researchers attributed to dry pre-irrigation conditions. Monthly sampling will continue from November, with analyses focusing on soil texture, pH, soluble salts, organic matter, and heavy metals.
Researchers are particularly examining arsenic tolerance, which may exist in REPEXH02's accessory genome and could contribute to broader stress resistance. The U.S. Centers for Disease Control and Prevention (CDC) has previously identified REPEXH02 strains showing a genome variation associated with arsenic resistance.
Drs. Bergholz and Carter are sequencing both new and archived isolates to trace the evolutionary development of the strain. Using AI and ML, the team will identify environmental and crop-related traits that distinguish REPEXH02 from other E. coli subtypes.
The outcome of the project will be an online risk assessment model. The tool will allow growers to enter field data, such as soil test results or wildlife activity, to evaluate the potential risk of REPEXH02 presence. Before release, the tool will undergo validation against known positive and negative samples.
In related research published in the April/May 2025 issue of Food Safety Magazine, Dr. Bergholz and co-authors Dr. Joshua Owade and Dr. Jade Mitchell examined whether cold storage duration affects E. coli dormancy in leafy greens and its associated food safety risks.
Source: FoodSafety Magazine
