Comparative Analysis of Metagenomic Next-Generation Sequencing, Sanger Sequencing, and Conventional Culture for Detecting Common Pathogens Causing Lower Respiratory Tract Infections in Clinical Samples

Metagenomic next-generation sequencing (mNGS) has emerged as a revolutionary tool for infectious disease diagnostics. The necessity of mNGS in real-world clinical practice for common Lower Respiratory Tract Infections (LRTI) needs further evaluation. A total of 184 bronchoalveolar lavage fluid (BALF) samples and 322 sputa associated with LRTI were fully examined. The detection performance was compared between mNGS and standard microbiology culture, using Sanger sequencing as the reference method. 52.05% (165/317) of sputa showed identical results for all three methods. Compared to Sanger sequencing, the same results obtained by mNGS were 88.20% (284/322). In 2.80% (9/322) of cases, Sanger sequencing detected more microorganisms, while mNGS detected more in 9% (29/322) of cases. For BALF, 49.41% (85/172) of cases showed identical results for all three methods. In 91.30% (168/184) of cases, identical results were produced by both mNGS and Sanger sequencing. mNGS detected more species in 7.61% (14/184) of cases, whereas in 2.80% (2/184) instances, the Sanger sequencing detected more microorganisms than mNGS. In the 184 BALF samples, 66 samples were identified as having co-infections by mNGS, Sanger sequencing identified 64 samples, and cultures identified 22 samples. Our study demonstrates that mNGS offers a significant advantage over conventional culture methods in detecting co-infections. For common bacterial pathogens, conventional culture methods are sufficient for detection. However, mNGS provides comprehensive pathogen detection and is particularly useful for identifying rare and difficult-to-culture pathogens.