Microbiome Profiling Reveals Prognostic Heterogeneity in Staphylococcus aureus Pneumonia
- 1University of Pittsburgh
Abstract
BackgroundStaphylococcus 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.
MethodsWe 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.
ResultsAmong 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).
ConclusionsMetagenomic 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.
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BibTeX
@misc{kitsios2026microbiome,
title = {{Microbiome Profiling Reveals Prognostic Heterogeneity in Staphylococcus aureus Pneumonia}},
author = {G. Kitsios and M. A. Sy and W. G. Bain and M. Hensley and S. Qin and X. Wang and K. W. Inman and C. Dela Cruz and K. Robinson and S. M. Nouraie and F. A. Shah and P. Benos and B. J. McVerry and A. Morris},
howpublished = {medRxiv},
year = {2026},
month = sep,
doi = {10.64898/2026.09.17.26363347},
url = {https://www.medrxiv.org/content/10.64898/2026.09.17.26363347v1},
note = {CC BY-NC-ND},
}
RIS
TY - UNPB
TI - Microbiome Profiling Reveals Prognostic Heterogeneity in Staphylococcus aureus Pneumonia
AU - G. Kitsios
AU - M. A. Sy
AU - W. G. Bain
AU - M. Hensley
AU - S. Qin
AU - X. Wang
AU - K. W. Inman
AU - C. Dela Cruz
AU - K. Robinson
AU - S. M. Nouraie
AU - F. A. Shah
AU - P. Benos
AU - B. J. McVerry
AU - A. Morris
PY - 2026
DA - 2026/09/17
PB - medRxiv
DO - 10.64898/2026.09.17.26363347
UR - https://www.medrxiv.org/content/10.64898/2026.09.17.26363347v1
AB - BackgroundStaphylococcus 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. MethodsWe 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. ResultsAmong 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). ConclusionsMetagenomic 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.
ER -