Comparative study of targeted next-generation sequencing and traditional pathogen detection methods in lower...

Lower respiratory tract infections (LRTIs) are major health problem worldwide. Accurate pathogen identification using conventional microbiological tests (CMTs) is challenging. Targeted next-generation sequencing (tNGS) is a promising diagnostic approach; however, its performance compared with that of CMTs, and its impact on patient outcomes require further investigation.

This retrospective study enrolled 562 patients with suspected lower respiratory infections from 29 departments during 2023-2025. Bronchoalveolar lavage fluid samples from all patients underwent parallel testing with both tNGS and CMTs. The primary outcomes were pathogen detection rates (tNGS vs. CMTs), turnaround time, and clinical outcomes. Secondary outcomes comprised antibiotic modification rates, length of hospital stay, 28-day mortality, and intensive care unit admission rates. Multivariable logistic regression and propensity score adjustment were used to assess the independent impact of tNGS-guided therapy on patient outcomes.

The pathogen detection rate was significantly higher with tNGS than with CMTs (89.5% vs. 62.1%, p < 0.001; McNemar test). tNGS was more sensitive than CMTs for detecting special pathogens (36.8% vs. 8.9%, p < 0.001), viruses (83.5% vs. 18.3%, p < 0.001), and fungi (73.5% vs. 31.7%, p < 0.001). Among 314 patients with tNGS-adopted management, 68.8% received antibiotic modifications. In the adjusted analysis, tNGS-guided therapy was associated with a reduced length of hospital stay (adjusted β = -2.3 days, p = 0.003) and lower 28-day mortality (adjusted odds ratio: 0.42, p = 0.032).

tNGS is more sensitive than CMTs at detecting all categories of pathogens and when results are used to guide clinical management, tNGS is associated with improved clinical outcomes including reduced mortality and shorter hospital stays.