Atypical genomic features among Listeria monocytogenes strains isolated from the pig manure management chain

Listeria monocytogenes is a major foodborne pathogen found in outdoors, wild and domesticated animals, food-processing environments and food products. Genomic studies have mainly focused on strains from clinical or food-associated sources, but other reservoirs have been mostly underexplored. We performed in-depth phylogenetic and pangenome analyses of 371 L. monocytogenes strains isolated along the pig manure management chain, from living pigs to treated manure. Chromosome and plasmid-related virulence and resistance markers were thoroughly examined. Genomic islands along with mobile genetic elements were characterized. Anaerobic digestion and nitrification-denitrification treatments did not significantly impact the clonal diversity. We identified a novel Listeria Genomic Island 3 (LGI3) variant carrying a new internalin gene in 46 strains of Clonal Complex CC77. Chromosomal resistance to tetracycline was found in 7% of strains, linked to one Tn5801 and four distinct Tn916 acquisition events. In total, 100 plasmids were identified and characterized, including several multi-heavy metal resistance plasmids and one associated with multidrug antibiotic resistance. We characterized a large diversity of 932 prophages integrated across 10 chromosomal sites. This study provides innovative genomic insights into L. monocytogenes populations within the pig manure value chain and highlights potential routes of transmission between pig, farm environment and humans.