Microbiological diagnostic performance of metagenomic next-generation sequencing compared with conventional culture for patients with community-acquired pneumonia

Frontiers in Cellular and Infection Microbiology

Cellular and Infection Microbiology

Xueliang Tu¹  Xiaodong Dai²  Xiaoling Chen²  Ling Huang²  Tianlai Lin²  Hongling Zhang²  Shouxin Wu³  Jiangman Zhao⁴  Jingwei Lou⁴  Yaoyao Wang⁴  Yue Xu⁴  Wushuang Li⁴ 

[1] Department of Clinical Laboratory, Huanghe Sanmenxia Hospital Affiliated to Henan University of Science and Technology, Sanmenxia, China;Department of Intensive Care Unit, Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou, China;Shanghai Biotecan Pharmaceuticals Co., Ltd., Shanghai, China;Shanghai Biotecan Pharmaceuticals Co., Ltd., Shanghai, China;Shanghai Zhangjiang Institute of Medical Innovation, Shanghai, China;

关键词: metagenomic next-generation sequencing;    culture;    community-acquired pneumonia;    conventional microbiological test;    pathogen detection;   

DOI  :  10.3389/fcimb.2023.1136588

 received in 2023-01-03, accepted in 2023-02-23,  发布年份 2023

来源: Frontiers

【 摘 要 】

BackgroundCommunity-acquired pneumonia (CAP) is an extraordinarily heterogeneous illness, both in the range of responsible pathogens and the host response. Metagenomic next-generation sequencing (mNGS) is a promising technology for pathogen detection. However, the clinical application of mNGS for pathogen detection remains challenging.MethodsA total of 205 patients with CAP admitted to the intensive care unit were recruited, and broncho alveolar lavage fluids (BALFs) from 83 patients, sputum samples from 33 cases, and blood from 89 cases were collected for pathogen detection by mNGS. At the same time, multiple samples of each patient were tested by culture. The diagnostic performance was compared between mNGS and culture for pathogen detection.ResultsThe positive rate of pathogen detection by mNGS in BALF and sputum samples was 89.2% and 97.0%, which was significantly higher (P < 0.001) than that (67.4%) of blood samples. The positive rate of mNGS was significantly higher than that of culture (81.0% vs. 56.1%, P = 1.052e-07). A group of pathogens including Mycobacterium abscessus, Chlamydia psittaci, Pneumocystis jirovecii, Orientia tsutsugamushi, and all viruses were only detected by mNGS. Based on mNGS results, Escherichia coli was the most common pathogen (15/61, 24.59%) of non-severe patients with CAP, and Mycobacterium tuberculosis was the most common pathogen (21/144, 14.58%) leading to severe pneumonia. Pneumocystis jirovecii was the most common pathogen (26.09%) in severe CAP patients with an immunocompromised status, which was all detected by mNGS only.ConclusionmNGS has higher overall sensitivity for pathogen detection than culture, BALF, and sputum mNGS are more sensitive than blood mNGS. mNGS is a necessary supplement of conventional microbiological tests for the pathogen detection of pulmonary infection.

【 授权许可】

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Copyright © 2023 Lin, Tu, Zhao, Huang, Dai, Chen, Xu, Li, Wang, Lou, Wu and Zhang