When culture-based whole-genome sequencing can change management in severe ocular bacterial infections

ABSTRACT Nationwide multicenter surveillance demonstrates a substantial burden of antimicrobial resistance among ocular bacterial pathogens. In the 2009–2018 ARMOR collection, methicillin-resistant Staphylococcus aureus (MRSA) accounted for 34.9% of S. aureus ocular isolates, and methicillin resistance was strongly associated with fluoroquinolone resistance. Ocular infections can destroy tissue within hours; timely microbiologic diagnosis and treatment adjustment are essential; however, culture is constrained by small specimen volumes, low inoculum, and prior antimicrobial exposure. To tackle multidrug-resistant (MDR) infections, we propose that phenotypic testing could be complemented with targeted whole-genome sequencing in cases of severe or persistent eye infections, to provide lineage characterization, resistance and virulence determinants, and critical features of pathogenic MDR bacteria that are clinically relevant to predict patient outcomes. A genome-informed workflow, sequencing from pure culture, and integration with phenotypic data could refine empiric therapy, enable earlier de-escalation, and strengthen surveillance of high-risk lineages to reduce vision-threatening treatment failures and save patients’ vision.