Microenvironment shapes Staphylococcus aureus phenotypes in children with cystic fibrosis over time

Staphylococcus aureus is a common pathogen in children with cystic fibrosis (CF), frequently preceding or coexisting with Pseudomonas aeruginosa. The impact of transient P. aeruginosa infection and therapeutic intervention on S. aureus phenotypic shaping remains poorly understood. We characterized 546 isolates from a longitudinal cohort of sixteen pediatric patients in CF follow-up, either monoinfected or coinfected, over eighteen months. Isolates were grouped into three phenotypic clusters. Monoinfected patients were enriched in a cluster with high pigment and biofilm, whereas transient P. aeruginosa detection was associated with a shift toward reduced pigment and biofilm, while coinfected patients maintained stable phenotypes. Phenotypes were determined by the airway microenvironment rather than by clonal background. In two monoinfected patients, this shift coincided with transient infection and ciprofloxacin treatment with increased MRSA; in vitro, MRSA predominated over MSSA when both P. aeruginosa and ciprofloxacin were present, underscoring the need to monitor S. aureus phenotypic transitions.