Genome co-adaptation and the evolution of methicillin resistant Staphylococcus aureus (MRSA)

Background Antimicrobial resistance (AMR) in bacterial pathogens is a major threat to global health, rendering standard treatments ineffective and increasing the risk of severe infection or death. Resistance is often conferred by genes that are transferred horizontally among species and strains. However, for many bacteria, little is known about the genetic variation that potentiates resistance gene acquisition and accommodates acquired genes in the coadapted recipient genome. Results Here we introduce a new bioinformatics genome-wide association study approach with Guided Omission of Linkage Disequilibrium (GOLD-GWAS) that masks covarying alleles explained by coinheritance and genome proximity to reveal genes where covarying sequence likely represents functional linkage between loci, consistent with epistasis. Analysing 806 Staphylococcus aureus isolate genomes, including methicillin-resistant (MRSA) and methicillin-susceptible (MSSA) strains, we identify genes that covary with the presence of the acquired staphylococcal cassette chromosome mec (SCC mec ) that houses the mecA resistance gene. Conclusions Uncovering known and new gene-gene associations, we demonstrate how resistance can involve genetic coalitions beyond the well-known AMR genes. Understanding how genome change, here extrinsic resistance cassettes, are integrated within coadapted bacterial genomes is an important step towards mitigating AMR evolution by identifying novel genetic targets for risk prediction, diagnosis and therapy.