Porcine methicillin resistant Staphylococcus aureus CC5/t002 from southwestern Nigeria lacks mec gene and carried PVL and IEC genes on prophages incorporate

Abstract

Despite their public health importance, data on methicillin-resistant Staphylococcus aureus lacking mec genes (MRLM) is not common in Africa. Here, we provide genome-based insights into two porcine MRLM isolates from Ogbomoso, southwestern Nigeria. Antibiotic susceptibility testing (Vitek2) and Illumina whole genome sequencing revealed closely related (ANI value of 99.997%) CC5/t002 strains showing resistance to methicillin without a corresponding mec gene, but with mutation (D105N) in gdpP associated with β-lactam resistance among MRLM isolates. Further, both isolates carried blaZ, arsBC, cadC, and the enterotoxin gene sel30 on identical mobilizable plasmids. Additional virulence genes detected in both isolates include serine proteases (splA, splB), and three copies of the staphylococcal complement inhibitor gene scn. One scn was part of the immune evasion cluster (IEC) genes on prophages which also carried PVL at the 5’ end. The prophages were incorporated in the β-hemolysin region as commonly found in human-adapted isolates, and a truncated phage autolysin was inserted between the chp and sak genes at the IEC region. Our results showed a concerning presence of animal-adapted isolates with enhanced human pathogenic potentials in the food animal production chain in the study area.