Diverse mobile genetic elements support the persistence of listeria monocytogenes on dairy farms

Abstract Listeria monocytogenes is a food-borne pathogen and a resilient environmental saprophyte. Dairy farms are a reservoir of L. monocytogenes and strains can persist on farms for years. Here, we sequenced the genomes of 250 L. monocytogenes isolates to investigate the persistence and mobile genetic elements of Listeria inhabiting dairy farms. We found that prophages and other mobile elements were significantly more numerous among persistent than sporadically occurring strains. We identified a remarkable diversity of mobile elements among farm isolates, including a novel group of plasmids infecting hypervirulent subtypes of L. monocytogenes and occasionally carrying biocide resistance determinants bcrABC or qacH. Resistance genes against bacitracin, arsenic and cadmium were significantly more prevalent among persistent than sporadic strains. Several of the mobile elements in Listeria were identical to the mobile elements of Enterococci, indicative of recent transfer between these genera. Finally, we demonstrated that the CRISPR-cas IIa system and a type II restriction-modification system were negatively associated with persistence on farms. Our findings suggest that mobile elements support the persistence of L. monocytogenes on dairy farms and that L. monocytogenes inhabiting the agroecosystem is a potential reservoir of mobile elements harbouring resistance genes against antimicrobials, biocides, and heavy metals.