Multi-scale ecological drivers shape the genome flexibility of soil-dwelling Listeria monocytogenes

Understanding bacterial genome flexibility is key to predicting evolutionary trajectories and ecological interactions. Genome flexibility has been attributed to adaptive evolution, yet the underlying ecological drivers for bacterial pathogens persisting in natural environments remain poorly understood. Listeria monocytogenes (Lm), a foodborne pathogen prevalent in the environment, serves as an ideal model in this context. Through pangenome analysis of 177 Lm isolates representing three evolutionary lineages (I, II, and III) that we isolated from soils across the USA, we detected substantial genomic variation strongly associated with climatic factors, soil properties, and bacterial community composition, particularly the relative abundance of Nitrospirae, Planctomycetes, Acidobacteria, and Cyanobacteria. These factors were linked to many gene functions, particularly those involved in cell envelope synthesis, defense mechanisms, and replication, recombination, and repair. Among Lm lineages, distinct pangenome structure were observed. Lineage III exhibited a highly open pangenome, which was attributed to local adaptation to nutrient-limited conditions and strong dispersal limitation. In contrast, lineage I maintained a more conserved pangenome, likely due to frequent homogenizing dispersal across locations. Consistent with the dispersal patterns, lineage I showed an elevated risk for transmission along environmental-human pathways, evidenced by epidemiological links between three soil-derived and 17 clinical isolates. Collectively, this study suggests the pivotal roles of abiotic factors and bacterial communities in shaping genomic diversity of Lm and potentially other bacterial pathogens in soil. It also highlights significant differences in genome flexibility and transmission dynamics across lineages of the same pathogen species, underscoring the need for tailored source tracking strategies.