Figure 5.

Patients with pneumonia in the high diversity cluster in either oropharyngeal swab (OPS) samples or endotracheal aspirates (ETA) had improved 60-day survival compared to patients into low or intermediate-diversity clusters of bacterial composition

(A and B): Shannon index comparisons between survivors and non-survivors showed significantly higher alpha diversity in ETA samples of survivors.

(C and D): Principal coordinates analyses of beta diversity (Manhattan distances) showed significant differences (by permutational analysis of variance) in ETA samples between survivors and non-survivors.

(E and F): Kaplan-Meier curves of 60-day survival between Dirichlet Multinomial Mixture model clusters in OPS and ETA samples demonstrate improved survival for patients in the high diversity cluster in both OPS and ETA samples. Adjusted hazard ratios (with 95% confidence intervals) for membership in the high diversity cluster are shown, as derived from Cox proportional hazards models adjusted for age, sex, history of COPD, chronic oxygen use, and antibiotic exposure by the day of sampling. Data in boxplots are represented as individual values with median values and interquartile range depicted by the boxplots.