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

Tianlai Lin; Xueliang Tu; Jiangman Zhao; Ling Huang; Xiaodong Dai; Xiaoling Chen; Yue Xu; Wushuang Li; Yaoyao Wang; Jingwei Lou; Shouxin Wu; Hongling Zhang

doi:10.3389/fcimb.2023.1136588

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

Front Cell Infect Microbiol. 2023 Mar 16:13:1136588. doi: 10.3389/fcimb.2023.1136588. eCollection 2023.

Authors

Tianlai Lin¹, Xueliang Tu², Jiangman Zhao^{3

4}, Ling Huang¹, Xiaodong Dai¹, Xiaoling Chen¹, Yue Xu^{3

4}, Wushuang Li^{3

4}, Yaoyao Wang^{3

4}, Jingwei Lou^{3

4}, Shouxin Wu³, Hongling Zhang¹

Affiliations

¹ Department of Intensive Care Unit, Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou, China.
² Department of Clinical Laboratory, Huanghe Sanmenxia Hospital Affiliated to Henan University of Science and Technology, Sanmenxia, China.
³ Shanghai Biotecan Pharmaceuticals Co., Ltd., Shanghai, China.
⁴ Shanghai Zhangjiang Institute of Medical Innovation, Shanghai, China.

Abstract

Background: Community-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.

Methods: A 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.

Results: The 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.

Conclusion: mNGS 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.

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

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Bronchoalveolar Lavage Fluid
Community-Acquired Infections* / diagnosis
Dietary Supplements
Escherichia coli
High-Throughput Nucleotide Sequencing
Humans
Metagenomics
Pneumonia* / diagnosis
Sensitivity and Specificity

Grants and funding

This work was supported by National key Research & Development plan (2018YFE0102400), Shanghai Special Project for Artificial Intelligence Innovation and Development (2020-RGZN-02039), and Quanzhou Guiding Science and Technology Project in Medical and Health Field (2021N062S).