The landscape of lung microbiota predicts the outcome of severe community-acquired pneumonia by interacting with the host immune response

Abstract

Abstract Background: The lung microbiota and host immune response is thought to be a key player in the progression of pneumonia. However, the critical features of the microbiota have rarely been studied in severe community-acquired pneumonia (SCAP) patients. This study aimed to explore the correlations among the lung microbiota and the host immune defense, the disease severity, and the outcome in SCAP patients. Methods: A prospective and observational study in the intensive care unit (ICU) of four hospitals in China was performed. The lung microbiota was quantified and characterized using metagenomic next-generation sequencing (mNGS), collecting sputum and bronchoalveolar lavage fluid (BALF) in SCAP and CAP patients. Risk factors for disease progress and prognosis were investigated by logistic regression. In addition, transcriptomics was applied to explore host immune variation and the interaction between microbiota and host immune responses. Results: Our results showed that the microbiome α- and β-diversity in SCAP patients were significantly lower than those in CAP patients and lower in nonsurvivors than survivors. The Simpson index, the existence of Streptococcus pneumonia, the delta-SOFA score, the use of immunosuppressor, and activated partial thromboplastin time (APTT) were independently associated with the 28-day mortality of SCAP patients. Furthermore, the differentially expressed genes, including Opiorphin Prepropeptide (OPRPN), Histatin 1 (HTN1), Histatin 3 (HTN3), Lipocalin 1 (LCN1), Follicular Dendritic Cell Secreted Protein (FDCSP) and Statherin (STATH) in SCAP were correlated with immune response pathways. The neutrophil proportions and degranulation were suppressed in the nonsurvivors of SCAP. At the same time, interleukin-10 signaling was activated, while interferon-α, -β, and -γ responses were suppressed in the dismal outcome patients. Conclusions: Our findings confirmed that the lung microbiota played an essential role in association with the severity of pneumonia and represented a significant contributor to heterogeneity in SCAP by altering host immune responses.