Lung Microbiota is Associated with Bacterial Detection and with Clinical Improvements in Severe Community-Acquired Pneumonia Patients

Abstract Background: Few studies have described the key features of the lung microbiota in patients with severe community-acquired pneumonia (SCAP). We conducted the study to identify the association between the lung microbiota on admission and the clinical prognosis in SCAP patients. Methods: The consecutive SCAP patients admitted from intensive care unit (ICU) were enrolled prospectively. 16S rRNA gene sequencing was applied to bronchoalveolar lavage fluid (BALF) collected within 48 hours. The clinical information was recorded during the stay of hospitalization. The primary endpoint was the rate of clinical improvements defined as a decrease of 2 categories and above on a 7-category ordinal scale within 14 days following bronchoscopy.Results: Sixty-seven patients were included. Multivariable Permutational multivariate analysis of variance (PERMANOVA) found that bacterial detection had the strongest independent relationship with the lung microbiota (R2=0.033; p=0.018), followed by acute kidney injury (AKI R2=0.032; p=0.011) and plasma MIP-1beta level (R2=0.027; p=0.044). Random forest identified that families Prevotellaceae, Moraxellaceae, Staphylococcaceae were the biomarkers related to bacterial detection. In the patients with positive bacteriology results, the mean relative abundance of families Prevotellaceae and Actinomycetaceae decreased while families Moraxellaceae, Staphylococcaceae and Streptococcaceae increased. Multivariable Cox regression showed that the increase in alpha-diversity and the abundance of families Prevotellaceae and Actinomycetaceae were associated with clinical improvements.Conclusions: The bacterial detection and patients’ intrinsic factors were associated with the lung microbiota. The increased alpha diversity and the enrichment of families Prevotellaceae and Actinomycetaceae in the lung microbiota were associated with clinical improvements.