Genomic characterisation and antimicrobial resistance profiles of Listeria monocytogenes isolated from pig farms

Abstract

Listeria monocytogenes is a zoonotic foodborne pathogen, transmissible from the natural agricultural environment to animals and humans. In recent years, the pig production industry has experienced a series of monetary losses as a result of the L. monocytogenes outbreak which threatened the economy of South Africa. This outbreak also had a detrimental effect on the health system of the country. In South Africa however, there is limited information regarding the genomic diversity of L. monocytogenes. Therefore, an overview of the genomic diversity of L. monocytogenes strains circulating at different levels of the pork production chain needs to be determined so as to be able to identify routes of contamination of the pathogen and thus improve meat safety. This study was aimed to determine the antimicrobial resistance patterns and population structure of L. monocytogenes isolated from pig farms in South Africa. Based on wholegenome sequence analysis, 77 isolates of L. monocytogenes were differentiated into four molecular serogroups with IIa (45.5%) being the most prevalent followed by IIc (26.0%), IVb (22.1%) and IIb (6.5%). Overall, 11 clonal complexes (CCs) were identified in this study, with the predominance being observed from; CC204 (23.4%), CC1 (19.5%) and CC2 (16.9%). Genetic elements associated with biocide, antimicrobial and heavy metal resistance were noted in 24.7 %, 48% and 11.7% of the isolates, respectively. Listeria pathogenicity island 1 and 3 that harbored clusters of virulence genes were present in 38.8% of the isolates. Five different plasmids were found in 68.9% of the isolates. This study has given baseline data on the genomic diversity of L. monocytogenes strains that are associated with biocides, heavy metal and antibiotics resistance genes. The data again demonstrated the genotypes of L. monocytogenes that are prone to contaminate the farm environment and possibly cause diseases in animals and humans.