Genomic characterization of Listeria monocytogenes isolated from small ruminants in integrated crop-livestock systems

Listeria monocytogenes (L. monocytogenes), a foodborne pathogen shed by asymptomatic ruminants, poses a contamination risks in integrated crop-livestock systems (ICLS), where ruminants are introduced to graze cover crops prior to replanting fresh produce in a field. As a follow-up study, we conducted whole genome sequencing of 30 L. monocytogenes isolates obtained from sheep and goat fecal and soil samples collected during our previously published ICLS field trial studies (2019-2022) at organic farms in California and Minnesota. One goat fecal isolate was genetically identical to one soil isolate collected at seven days post-grazing. Most isolates (28/30, 93.3%) belonged to lineage I, specifically to serogroup IVb or IVb-v1, and were classified as CC1 or CC554, both clonal complexes previously associated with human listeriosis outbreaks. The majority of isolates harbored virulence associated genes, including LIPI-1 or LIPI-3 genes, and agrA, associated with biofilm formation and survival in agricultural soils. In antimicrobial susceptibility testing, all isolates were susceptible to antibiotics commonly used to treat ruminant and human listeriosis, including ampicillin and penicillin. These findings suggest that asymptomatic small ruminants in ICLS may introduce pathogenic L. monocytogenes strains into the agricultural environment, posing a potential contamination risk to fresh produce despite the low overall prevalence observed.