Lung microbiome community state types are associated with ventilator-associated pneumonia risk: a secondary analysis of the MicroNAV cohort

ABSTRACT In the publicly available MicroNAV cohort, baseline diversity analyses did not distinguish patients who developed ventilator-associated pneumonia (VAP) from non-VAP patients, leaving it unresolved whether community-state structure contains risk information. In an independent secondary analysis, we reprocessed raw 16S rRNA gene sequencing data from bronchoalveolar lavage samples using DADA2 exact amplicon sequence variant inference and decontam quality control, and analyzed 75 at-risk mechanically ventilated patients with paired longitudinal sampling (40 VAP and 35 non-VAP). No baseline genus distinguished future VAP from non-VAP by DESeq2 or MaAsLin3 after adjustment for sex and Glasgow Coma Scale (all adjusted P > 0.05). Dirichlet multinomial mixture modeling identified three community state types (CSTs) with distinct ecological profiles. In cause-specific Cox regression, CST1, a high-burden, oral-associated state, was associated with higher VAP hazard than CST2, a low-burden, diverse state (hazard ratio, 2.85; 95% CI, 1.15–7.02, P = 0.023; Gray’s test, P = 0.042). Adding CST to a burden-only model improved fit (likelihood-ratio test, P = 0.041), whereas pathogen species cultured at VAP onset did not differ by baseline CST (simulated Fisher’s exact test, P = 0.98). During ventilation, 12 oral-associated genera declined while total bacterial burden remained stable (linear mixed model, P = 0.66), but the association between commensal loss and subsequent VAP was not consistent across abundance scales. Baseline IL-1β and TNF-α concentrations were explained primarily by bacterial burden rather than community composition. These findings suggest that baseline lower-airway ecological states capture VAP susceptibility information not resolved by single-taxon, diversity, or burden-only analyses. IMPORTANCE In mechanically ventilated ICU patients without pulmonary infection at baseline, the early lower-airway ecosystem may contain information about subsequent ventilator-associated pneumonia (VAP) susceptibility. In this independent reanalysis of the public MicroNAV cohort, baseline lower-airway communities classified by Dirichlet multinomial mixture modeling resolved into ecological states with different subsequent VAP risk, while individual genera, bacterial burden alone, and the eventual cultured pathogen did not explain the signal. Mechanical ventilation produced shared community restructuring: oral-associated genera declined and other taxa expanded, yet total bacterial burden remained stable, indicating ecological replacement rather than bacterial clearance. This restructuring was not consistently VAP-specific, and apparent community state type-dependent differences in declining-genus loss partly reflected different starting proportions. Together, these findings extend the original cohort by separating starting state heterogeneity from ventilation-associated restructuring. They suggest that initially noninfected ventilated airways represent distinct host-microbial terrains that may differ in vulnerability to pneumonia.