Littlefair, J. C. | Search bioRxiv

bioRxiv2026

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

Effective treatment of infections is a global challenge, complicated by bacterias 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.

microbiology↗

bioRxiv2026

Insertion sequence elements associated with Staphylococcus epidermidis evolution in persistent orthopaedic device-related infections

BackgroundStaphylococcus epidermidis is a major cause of orthopaedic device-related infections (ODRIs), which are often challenging to treat due to their extensive antimicrobial resistance (AMR) and biofilm formation. It has been hypothesised that S. epidermidis may rapidly adapt to the medical device niche, enhancing persistence, but direct evidence of within-host pathoadaptive evolution remains limited. ResultsTo investigate within-host evolution during chronic infection by S. epidermidis, we analysed isolates from patients with confirmed ODRIs and used a rat infection model to examine the evolution of strains from two distinct epidemic lineages (ST2 and ST23). Our analysis revealed that the replicative transposition of insertion sequence (IS) elements within the accessory genome was the predominant mechanism of genetic diversification. This was largely driven by the IS256 family, which accounted for approximately 25% of all mutational events. However, other than SCCmec deletions resulting in the loss of mecA, no mutations, including those which exhibited parallel evolution, were predicted or observed to influence AMR or biofilm formation. These findings suggest that the strains investigated in this study, which already exhibited high-level multidrug resistance and biofilm-forming ability, were likely pre-adapted epidemic S. epidermidis clones well suited to establishing persistent ODRIs. ConclusionsOur findings highlight the prominent role of IS elements in driving genetic diversification in S. epidermidis, underscoring the need for closer examination of their contribution to pathoadaptation during persistent infection.

genomics↗