mGem: Population genomics of Staphylococcus aureus bacteremia and the impact of the COVID-19 pandemic.

The pressure of the coronavirus disease 2019 (COVID-19) pandemic on global healthcare systems and societies was unprecedented in the modern era. Social restrictions, containment measures, and disruptions in antimicrobial prescriptions and consumption during the pandemic have been reported to alter the epidemiology of bacterial diseases, although these effects likely differed markedly between locations. Here, we compare the clinical, clonal distribution, and genomic features of Staphylococcus aureus bloodstream isolates before, during, and after COVID-19 in two hospitals on different continents: Parc Taulí University Hospital (Spain) and Dartmouth-Hitchcock Medical Center (USA). We hypothesize that pandemic-related environmental perturbations, such as those due to infection control practices and antimicrobial exposure, may have contributed to shifts in the diversity of circulating bacterial lineages and genomic elements. Our findings revealed changes in the distribution of low-frequency clones, antimicrobial resistance genes, and virulence factors, potentially reflecting changes in selective pressures in clinical environments.