
To determine the relation between lung microbiota and clinical outcomes of COVID-19-related ARDS, enrolled mechanically ventilated patients with COVID-19. All patients had ARDS and underwent bronchoscopy with BAL. Lung microbiota was profiled using 16S rRNA gene sequencing and quantitative PCR targeting the 16S and 18S rRNA genes. Critical features of lung microbiota (bacterial and fungal burden, α-diversity, and community composition) served as predictors. Our primary outcome was successful extubation adjudicated 60 days after intubation, analyzed using a competing risk regression model with mortality as competing risk. Patients with increased lung bacterial and fungal burden were less likely to be extubated and had higher mortality. Lung microbiota composition was associated with successful extubation. Proinflammatory cytokines were associated with microbial burdens. Bacterial and fungal lung microbiota are related to non-resolving ARDS in COVID-19.
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