Genetic context drives evolution of divergent antibiotic survival phenotypes in Staphylococcus epidermidis

Effective treatment of infections is a global challenge, complicated by bacteria’s capacity to endure antibiotics. Survival under drug pressure is often driven by interactions between genetic factors rather than single genes. To investigate the genomics underlying antibiotic survival, we analysed Staphylococcus epidermidis isolates from clinical infections and carriage using high-throughput phenotyping, population genomics, and directed evolution. We observed widespread multidrug resistance, with strong links between specific genomic elements and resistance. All isolates harbouring mecA were resistant to oxacillin, though minimum inhibitory concentrations varied significantly, suggesting modulation by additional genetic factors. Directed evolution revealed potentiating mutations that enhanced oxacillin resistance in mecA ⁺ strains. In mecA ^- isolates, however, evolution of mutations in the same genes conferred increased survival to oxacillin through antibiotic tolerance. These findings show that antibiotic resistance and tolerance can be genetically connected yet phenotypically distinct, and suggest a complex epistatic genetic landscape that shapes antibiotic survival phenotypes in S. epidermidis .