Longitudinal two-year comparative genomic analysis of respiratory Staphylococcus aureus isolates from intensive care unit mechanically ventilated patients

Ventilator-associated pneumonia (VAP) is the main healthcare-associated infection in intensive care units with Staphylococcus aureus as the first pathogen in early VAP. To compare, using whole-genome sequencing (WGS), consecutive S. aureus isolates from lower respiratory samples of mechanically ventilated patients for identification of potential cross-transmissions; and to determine a potential link between S. aureus WGS data and patients with S. aureus early VAP. All mechanically ventilated patients with a documentation of respiratory S. aureus isolates were included over a two-year period. WGS allowed typing, comparative genomic and phylogenic analyses, as well as analyses of antibiotic resistance genes and virulence genes. Virulence genes were compared between patients who developed respiratory infectious event and those who did not. A total of 172 S. aureus isolates from 167 patients were sequenced. WGS revealed that the S. aureus population was polyclonal with only two potential healthcare cross-transmissions, each involving two isolates (2.3%). A very low resistance rate was observed with a strong genotypic/phenotypic association, and with a virulence profile highly dependent on the sequence type. No significant correlation was observed between VAP and virulence profile. This study on consecutive respiratory S. aureus isolates of mechanically ventilated patients revealed a very low level of cross-transmission. No association was observed between S. aureus WGS data and VAP occurrence.