Diagnostic strategy of metagenomic next-generation sequencing for gram negative bacteria in respiratory infections

Wenyan Liang; Qun Zhang; Qian Qian; Mingyue Wang; Yuchen Ding; Ji Zhou; Yi Zhu; Yu Jin; Xuesong Chen; Hui Kong; Wei Song; Xin Lu; Xiaodong Wu; Xiaoyong Xu; Shanling Dai; Wenkui Sun

doi:10.1186/s12941-024-00670-x

Diagnostic strategy of metagenomic next-generation sequencing for gram negative bacteria in respiratory infections

Ann Clin Microbiol Antimicrob. 2024 Feb 1;23(1):10. doi: 10.1186/s12941-024-00670-x.

Authors

Wenyan Liang¹, Qun Zhang¹, Qian Qian², Mingyue Wang¹, Yuchen Ding¹, Ji Zhou¹, Yi Zhu¹, Yu Jin¹, Xuesong Chen¹, Hui Kong¹, Wei Song¹, Xin Lu³, Xiaodong Wu⁴, Xiaoyong Xu⁵, Shanling Dai¹, Wenkui Sun⁶

Affiliations

¹ Department of Respirology and Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China.
² Jiangsu Health Vocational College, Nanjing, 211800, China.
³ Department of Respiratory and Critical Care Medicine, The Affiliated Jiangning Hospital of Nanjing Medical University, Nanjing, China.
⁴ Department of Respiratory and Critical Care Medicine, Shanghai East Hospital, Tongji University, Shanghai, China.
⁵ Department of respiratory and critical care medicine, The Second Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, Jiangsu, 210000, China.
⁶ Department of Respirology and Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China. sunwenkui@njmu.edu.cn.

Abstract

Objective: This study aims to identify the most effective diagnostic method for distinguishing pathogenic and non-pathogenic Gram-negative bacteria (GNB) in suspected pneumonia cases using metagenomic next-generation sequencing (mNGS) on bronchoalveolar lavage fluid (BALF) samples.

Methods: The effectiveness of mNGS was assessed on BALF samples collected from 583 patients, and the results were compared with those from microbiological culture and final clinical diagnosis. Three interpretational approaches were evaluated for diagnostic accuracy.

Results: mNGS outperformed culture significantly. Among the interpretational approaches, Clinical Interpretation (CI) demonstrated the best diagnostic performance with a sensitivity of 87.3%, specificity of 100%, positive predictive value of 100%, and negative predictive value of 98.3%. CI's specificity was significantly higher than Simple Interpretation (SI) at 37.9%. Additionally, CI excluded some microorganisms identified as putative pathogens by SI, including Haemophilus parainfluenzae, Haemophilus parahaemolyticus, and Klebsiella aerogenes.

Conclusion: Proper interpretation of mNGS data is crucial for accurately diagnosing respiratory infections caused by GNB. CI is recommended for this purpose.

Keywords: Diagnostic accuracy; Gram-negative bacteria; Interpretational approaches; Metagenomic next-generation sequencing.

MeSH terms

Bronchoalveolar Lavage Fluid
Gram-Negative Bacteria / genetics
High-Throughput Nucleotide Sequencing
Humans
Metagenomics
Respiratory Tract Infections* / diagnosis
Sensitivity and Specificity