D17-06 “Staph Is Not Shy”: Microbiota Profiles Identify a High-risk, Dominant Phenotype in S. Aureus Pneumonia

Abstract Background Staphylococcus aureus is the most common pathogen in severe pneumonia in mechanically ventilated patients and mandates specific antimicrobial therapy distinct from empiric regimens targeting community-acquired or resistant gram-negative pathogens. However, the clinical dictum that "Staph is not shy"—referring to the robust growth of S. aureus on routine cultures—raises concerns that S. aureus may overgrow other organisms, potentially masking the true microbial complexity of lower respiratory tract (LRT) infections. Methods To characterize microbiota heterogeneity in S. aureus pneumonia, we analyzed 16S rRNA gene Illumina MiSeq profiles from endotracheal aspirates (ETA) of 67 mechanically ventilated patients with microbiologic confirmation of S. aureus pneumonia within 3 days of intubation. A subset underwent validation with Nanopore metagenomic sequencing analyzed via the BugSeq platform, confirming species-level S. aureus abundance beyond 16S genera. We defined Staphylococcus dominance as relative abundance 50% in 16S sequencing profiles and correlated microbiota profiles with culture results, LRT inflammatory biomarkers, and clinical outcomes. Results Staphylococcus dominance was present in only 33% of patients despite all having culture-confirmed S. aureus pneumonia, with relative abundance ranging from 1% to 100% (Figure 1A). Patients with Staphylococcus dominance demonstrated significantly higher ETA pentraxin-3 levels (p = 0.002, Figure 1B), indicating more severe LRT inflammation. S. aureus clinical bacteremia (n = 7) was associated with higher Staphylococcus relative abundance in ETA (p = 0.007). Among LRT clinical culture patterns, S. aureus isolated alone showed higher relative abundance of Staphylococcus in corresponding ETA samples, compared to co-detection with other gram-positive or negative pathogens or commensal normal respiratory flora by culture (p = 0.003), though with substantial variability. Critically, Staphylococcus dominance in the ETA microbiota was associated with significantly worse 60-day survival (p = 0.02), with only 50% survival in the dominance group versus 75% in the non-dominance group. Conclusions These findings reveal unappreciated compositional heterogeneity within culture-confirmed S. aureus pneumonia. Microbiota dominance—not merely presence—of Staphylococcus identifies a distinct phenotype with heightened LRT inflammation and worse survival. These results highlight the importance of microbiota profiling for prognostication and biological phenotyping, even in infections presumed to be caused by a single major pathogen and challenge the assumption that all S. aureus pneumonias are biologically equivalent. This abstract is funded by: NIH (R01HL176668). American Lung Association COVID-19 Respiratory Virus Research