Evolutionary Processes Driving the Rise and Fall of Staphylococcus aureus ST239, a Dominant Hybrid Pathogen

Selection plays a key role in the spread of antibiotic resistance, but the evolutionary drivers of clinically important resistant strains remain poorly understood. Here, we use genomic analyses and competition experiments to study Staphylococcus aureus ST239, a prominent MRSA strain that is thought to have been formed by large-scale recombination between ST8 and ST30. Genomic analyses allowed us to refine the hybrid model for the origin of ST239 and to date the origin of ST239 to 1920 to 1945, which predates the clinical introduction of methicillin in 1959. Although purifying selection has dominated the evolution of ST239, parallel evolution has occurred in genes involved in antibiotic resistance and virulence, suggesting that ST239 has evolved toward an increasingly pathogenic lifestyle. Crucially, ST239 isolates have low competitive fitness relative to both ST8 and ST30 isolates, supporting the idea that fitness costs have driven the demise of this once-dominant pathogen strain. IMPORTANCE The rise of antibiotic resistance in most pathogenic bacteria has been driven by the spread of a small number of epidemically successful resistant strains. However, the processes that drive the rise and fall of these "superbugs" remain poorly understood. In our study, we investigated Staphylococcus aureus ST239, an important MRSA strain that has been a leading cause of serious hospital-acquired infections. We show here that ST239 was formed by the exchange of a very large fragment of DNA carrying resistance genes between strains of S. aureus sometime before 1945. The introduction of the antibiotic methicillin in 1959 provided a key advantage for Methicillin-Resistant Staphylococcus aureus (MRSA) strains. Interestingly, we found that ST239 has low competitive ability compared to other strains of S. aureus, and this evolutionary hindrance may explain why the prevalence of ST239 has declined precipitously at a global scale.