Year: 2026
Type: preprint
Study design: Observational Study
Abstract: Background: Staphylococcus aureus is a leading cause of severe pneumonia in mechanically ventilated patients. Clinical cultures identify pathogen presence but may not reflect lower respiratory tract microbial ecology. Whether culture-confirmed S. aureus pneumonia encompasses compositional heterogeneity with prognostic implications remains unknown. Methods: We performed 16S rRNA gene sequencing and shotgun nanopore metagenomics on endotracheal aspirate samples from mechanically ventilated patients with culture-confirmed S. aureus pneumonia in a prospective ICU registry. We quantified Staphylococcus abundance, assessed correlations with culture characteristics and host inflammatory biomarkers, and examined associations with 60-day mortality using Kaplan-Meier and Cox hazards analyses. Results: Among 109 patients, semi-quantitative culture growth and methicillin resistance showed no associations with outcomes. 16S sequencing (n=54) revealed marked heterogeneity in Staphylococcus relative abundance (range 0-96.7%), with only 33% demonstrating dominance (>50%). Dominance was associated with worse 60-day survival (50% vs. 80%,p=0.013) and remained independently predictive after adjusting for age, sex, and methicillin resistance (adjusted HR 3.24 [95%CI 1.12-9.36],p=0.030). Patients with dominance exhibited elevated pentraxin-3 (p=0.01) and reduced fractalkine (p=0.02). Nanopore metagenomics (n=28) validated these findings, with high absolute S. aureus read counts independently predicting mortality (adjusted HR 11.23 [95%CI 2.25-55.9],p=0.003). In an exploratory analysis of virulence genes (n=19), staphylokinase detection was associated with the hyperinflammatory phenotype (p=0.003) and mortality (p=0.046). Conclusions: Metagenomic profiling reveals clinically meaningful heterogeneity within culture-confirmed S. aureus pneumonia, masked by conventional diagnostics. Staphylococcus dominance identifies a high-risk phenotype with elevated bacterial burden, dysregulated host responses, and increased mortality, challenging the assumption that culture positivity represents a uniform clinical entity.
Source: medRxiv
Language: English
Topic: Nosocomial Infections in ICU
Field: Medicine
Domain: Health Sciences
Open Access status: green
Awards: Precision Medicine Approach to Glucocortisteroids in Sepsis, G5514976981, Precision Medicine for Nutrition in EDEN, G5728561071, Immunosuppression in Acute Lung Injury, G9000189855, Improving Characterization of Individualized Treatment Effects in Critical Illness, Airspace Candida Colonization and Lung Injury (AirCCoLIN)
OpenAlex ID: W7213769627