Clinical factors associated with composition of lung microbiota and important taxa predicting clinical prognosis in patients with severe community-acquired pneumonia

Abstract

Few studies have described the key features and prognostic roles of lung microbiota in patients with severe community-acquired pneumonia (SCAP). We prospectively enrolled consecutive SCAP patients admitted to ICU. Bronchoscopy was performed at bedside within 48 h of ICU admission, and 16S rRNA gene sequencing was applied to the collected bronchoalveolar lavage fluid. The primary outcome was clinical improvements defined as a decrease of 2 categories and above on a 7-category ordinal scale within 14 days following bronchoscopy. Sixty-seven patients were included. Multivariable permutational multivariate analysis of variance found that positive bacteria lab test results had the strongest independent association with lung microbiota (R²=0.033; P=0.018), followed by acute kidney injury (AKI; R²=0.032; P=0.011) and plasma MIP-1β level (R²=0.027; P=0.044). Random forest identified that the families Prevotellaceae, Moraxellaceae, and Staphylococcaceae were the biomarkers related to the positive bacteria lab test results. Multivariable Cox regression showed that the increase in α-diversity and the abundance of the families Prevotellaceae and Actinomycetaceae were associated with clinical improvements. The positive bacteria lab test results, AKI, and plasma MIP-1β level were associated with patients’ lung microbiota composition on ICU admission. The families Prevotellaceae and Actinomycetaceae on admission predicted clinical improvements.

Keywords

severe community-acquired pneumonia / lung microbiota / clinical improvements / 7-category ordinal scale / Prevotellaceae

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Acknowledgements

This study was funded by the National Key Research and Development Program of China (No. 2017YFC1309301), the CAMS Innovation Fund for Medical Sciences (CIFMS, No. 2018-I2M-1-003), the National Science Grant for Distinguished Young Scholars (No. 81425001/H0104), and the Ministry of Science and Technology of China (No. 2017ZX10103004).

Compliance with ethics guidelines

Sisi Du, Xiaojing Wu, Binbin Li, Yimin Wang, Lianhan Shang, Xu Huang, Yudi Xia, Donghao Yu, Naicong Lu, Zhibo Liu, Chunlei Wang, Xinmeng Liu, Zhujia Xiong, Xiaohui Zou, Binghuai Lu, Yingmei Liu, Qingyuan Zhan, and Bin Cao declare that they have no competing interests. Our study was conducted in China-Japan Friendship Hospital, Beijing, China, and approved by the China-Japan Friendship Hospital Ethics Committee (Approval No. 2018-20-K15). It was conducted in accordance with the he Helsinki Declaration of 1975, as revised in 2000 (5). We obtained written informed consent from all enrolled patients or their legal representative for patients who were unable to provide consent.

Electronic Supplementary Material

Supplementary material is available in the online version of this article at https://doi.org/10.1007/s11684-021-0856-3 and is accessible for authorized users.

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