Review: Whole-genome sequencing reveals hidden S. aureus transmission in hospitals

This review summarizes findings from an observational study conducted in two interconnected hospitals, where whole-genome sequencing was applied to 4,779 S. aureus isolates from admission screening, clinical cultures, and serial or discharge screening. The study compared this approach to standard surveillance for detecting S. aureus transmission events.

The key finding was that whole-genome sequencing identified 361 transmission events that were undetected by standard surveillance. Notably, 90% of these events were detected only at readmission, not during the index hospitalization. Clinical isolates alone were insufficient for detection. Transmission was concentrated in methicillin-resistant strains and increased when healthcare exposure aligned with hospital-associated strain lineages.

The authors note important limitations: the practical limits of prospective whole-genome sequencing are unclear, and such approaches are unlikely to scale if applied universally. The review does not report funding or conflicts of interest.

For practice, the findings suggest that surveillance must be targeted, and serial or discharge screening is likely required to capture transmission. However, the evidence is observational, and causality cannot be inferred. Clinicians should interpret these results cautiously, recognizing the potential but also the practical constraints of genomic surveillance.