Clinical utility of metagenomic next-generation sequencing in pathogen detection for lower respiratory tract infections and impact on clinical outcomes in southernmost China

作者：Jinxiang Hao, Weili Li, Yaoyao Wang, Jiangman Zhao, Yu Chen · 发表于：Frontiers in Cellular and Infection Microbiology · 年份：2023 · DOI：10.3389/fcimb.2023.1271952 · 被引用次数：25 · 研究领域：Gut microbiota and health、Antibiotic Resistance in Bacteria、Pneumocystis jirovecii pneumonia detection and treatment

Background Today, metagenomic next-generation sequencing (mNGS) has emerged as a diagnostic tool for infections. However, since Hainan has a complicated pathogen spectrum, the diagnostic value and impact on patient outcomes of mNGS in Hainan are to be explored. Methods From April 2020 to October 2021, 266 suspected lower respiratory tract infections (LRTIs) patients in Hainan were enrolled, and specimens were collected before antibiotic treatment. Bronchoalveolar lavage fluid (BALF) samples were subjected to mNGS and culture to compare the diagnostic performance. Other conventional microbiological tests (CMT) were also performed. Patients’ treatments and clinical outcomes were recorded, and the antibiotic resistance genes (ARGs) were detected via mNGS workflow. Results The positive rate of mNGS outperformed that of culture (87.55% vs. 39.30%, p <0.001) and CMT (87.12% vs. 52.65%, p <0.001). Specifically, mNGS detected more P. aeruginosa (12.03% vs 9.02%, p <0.05), H. influenzae (9.77% vs 2.26%, p <0.001), Aspergillus fumigatus (3.00% vs 0.75%, p <0.05), Candida albicans (26.32% vs 7.52%, p <0.001) and uncommon pathogens. It also demonstrated great diagnostic advantages in Mycobacterium tuberculosis with 80% sensitivity and 97.4% specificity. Over half of the patients (147, 55.26%) had modified empirical treatment according to mNGS results and 89.12% of them responded well. For three deaths with modified treatment, multiple drug resist...