Diagnostic value of metagenomic next-generation sequencing in the etiological diagnosis of lower respiratory tract infection

Metagenomic next-generation sequencing (mNGS) has been widely used in infectious diseases. However, reports on mNGS for lower respiratory tract infection (LRTI) diagnosis remain limited, potentially offering significant value for improving pathogen identification. This study evaluates the diagnostic performance and clinical value of mNGS compared to traditional methods in LRTI. We analyzed traditional and mNGS detection results from 165 patients with suspected LRTI using different specimens including bronchoalveolar lavage fluid (BALF), blood, tissue samples, and pleural effusion. We compared diagnostic differences and characteristics between mNGS and traditional methods, and evaluated the effect of mNGS results on antibiotic treatment.Among 165 cases, 146 (88.48%) patients with LRTI had microbial etiology finally identified. Compared with traditional diagnostic methods, mNGS showed significantly higher positive rate (143/165, 86.7% vs 69/165, 41.8%, P < 0.05). The diagnostic performance of mNGS was not affected by sample types. mNGS demonstrated significant advantage in detecting poly-microbial infections and rare pathogens. Twenty-nine kinds of pathogens were detected only by mNGS, including non-tuberculous mycobacteria (NTM), Prevotella, anaerobic bacteria, Legionella gresilensis, Orientia tsugamushi, and viruses. The pathogen spectrum differed between immunocompetent and immunocompromised individuals. mNGS resulted in treatment changes in 119 patients (72.13%), with 54 patients (32.73%) having reduced antibiotics. mNGS has obvious advantages over traditional detection methods with results unaffected by sample types. mNGS demonstrates significant value for pathogen detection and may provide guidance in clinical practice.