This study investigated the genomic variation of *Listeria* species in natural and food-associated environments across the United States. Comparative genomics analysis of 449 soil isolates and 390 isolates from agricultural water and produce processing facilities revealed significant differences in genomic profiles between environments within each species (*L. monocytogenes*, *L. seeligeri*, *L. innocua*, and *L. welshimeri*). Environment-associated subclades, differential presence of plasmids, stress islands, and accessory genes related to cell envelope biogenesis and carbohydrate metabolism were observed. Core genomes were also strongly linked to environments and could predict isolation sources using machine learning. The genomic variation appears to be driven by soil properties, climate, land use, and co-occurring bacterial species (Actinobacteria and Proteobacteria). This suggests genetic adaptation to specific environments, potentially limiting transmission between natural and food-associated settings.

Jingqiu Liao, Xiaodong Guo, Shaoting Li, Sai Manohar Balu Anupoju, Rachel A. Cheng, Daniel L. Weller, Genevieve Sullivan, Hailong Zhang, Xiangyu Deng, Martin Wiedmann