Metagenomic next-generation sequencing of bronchoalveolar lavage fluid in non-severe and severe pneumonia patients

Hongqin Zhao; Yanhong Zhao; Nana Yan; Yu Wang; Wushuang Li; Jiangman Zhao; Yue Xu; Hui Tang; Xunchao Liu

doi:10.1016/j.mimet.2023.106848

Metagenomic next-generation sequencing of bronchoalveolar lavage fluid in non-severe and severe pneumonia patients

J Microbiol Methods. 2023 Dec:215:106848. doi: 10.1016/j.mimet.2023.106848. Epub 2023 Oct 21.

Authors

Hongqin Zhao¹, Yanhong Zhao¹, Nana Yan¹, Yu Wang¹, Wushuang Li², Jiangman Zhao², Yue Xu², Hui Tang³, Xunchao Liu⁴

Affiliations

¹ Department of Pulmonary and Critical Care Medicine, Heze Municipal Hospital, Heze 274000, Shandong Province, China.
² Shanghai Biotecan Pharmaceuticals Co., Ltd., 180 Zhangheng Road, Shanghai 201204, China; Shanghai Zhangjiang Institute of Medical Innovation, Shanghai 201204, China.
³ Shanghai Biotecan Pharmaceuticals Co., Ltd., 180 Zhangheng Road, Shanghai 201204, China; Shanghai Zhangjiang Institute of Medical Innovation, Shanghai 201204, China; Department of Interventional and Vascular Surgery, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai 200092, China. Electronic address: tang11_23@126.com.
⁴ Department of Pulmonary and Critical Care Medicine, Heze Municipal Hospital, Heze 274000, Shandong Province, China. Electronic address: lxunchao@163.com.

PMID: 37871727
DOI: 10.1016/j.mimet.2023.106848

Abstract

Metagenomic next-generation sequencing (mNGS) is widely used as a more promising technology than conventional tests. However, its clinical utility in the context of bronchoalveolar lavage fluid (BALF) samples for discriminating between non-severe and severe pneumonia is not well established. Thus, this study aimed to investigate the diagnostic performance of mNGS on BALF samples from 100 individuals suspected of pneumonia, and compared it with conventional microbiological tests (CMT) of BALF samples and the final clinical diagnosis. Twenty-seven cases of non-severe pneumonia and 73 cases of severe pneumonia patients were finally clinically diagnosed. Among 100 cases, diagnostic performance of mNGS and culture showed a significant difference; 65 cases had the same sample types, of which 25 cases were diagnosed as positive by mNGS only (38.46%) and 1 was diagnosed as positive by culture only (1.54%). Moreover, 24 cases were diagnosed positive in both mNGS and culture (36.92%) and 15 cases tested negative in both mNGS and culture (23.08%). Among 35 cases, 28 out of 35 cases were diagnosed as positive by mNGS, while only 4 out of 35 cases were diagnosed as positive by the indirect immunofluorescence method (IIFT). In addition, the positive rate of mNGS was higher than that of culture in cases regardless of prior antibiotic exposure. Mixed pathogens were found to be significantly more prevalent in severe pneumonia patients than in non-severe pneumonia patients. Importantly, among 38 cases who were diagnosed solely by mNGS, 25 patients experienced an improved outcome after physicians changed the therapy according to the mNGS results. In conclusion, the results showed that mNGS of BALF represents a potentially effective tool for detection of mixed pathogens in severe pneumonia.

Keywords: Conventional microbiological tests; Metagenomic sequencing; Mixed pathogens; Non-severe pneumonia; Severe pneumonia.

Publication types

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

MeSH terms

Anti-Bacterial Agents
Bronchoalveolar Lavage Fluid
High-Throughput Nucleotide Sequencing*
Humans
Metagenome
Metagenomics
Pneumonia* / diagnosis
Sensitivity and Specificity

Substances

Anti-Bacterial Agents