Comparative evaluation of metagenomic and targeted next-generation sequencing for pathogen detection in bronchoalveolar lavage fluid from patients with lower respiratory tract infections: a retrospective cohort study

Abstract

Rapid and precise pathogen identification is crucial for managing lower respiratory tract infections (LRTIs). While metagenomic next-generation sequencing (mNGS) and targeted next-generation sequencing (tNGS) are emerging as valuable diagnostic tools, large-scale studies directly evaluating their real-world impact on antimicrobial stewardship remain scarce. We conducted a retrospective cohort study encompassing 941 patients with suspected LRTIs who underwent bronchoalveolar lavage fluid (BALF) sequencing. Patients were evaluated in either an mNGS cohort (n = 479; DNA-only sequencing) or a tNGS cohort (n = 462; DNA and RNA sequencing). Diagnostic performance, pathogen spectrum, and clinical utility were compared against a composite final clinical diagnosis, which served as the reference standard. Both sequencing platforms demonstrated diagnostic efficacy superior to traditional laboratory tests. In the tNGS cohort, polymicrobial infections were highly prevalent (93.5%). Furthermore, tNGS demonstrated high sensitivity for fastidious pathogens, identifying 54 cases of Mycobacterium tuberculosis (a cohort in which routine smears missed 77.8% of cases) and effectively detecting Pneumocystis jirovecii. The overall diagnostic sensitivity was 90.6% (95% CI: 87.5-93.1%) for mNGS and 73.4% (95% CI:69.2%-77.3%) for tNGS. Guided by tNGS results, clinicians escalated antimicrobial therapy in 22.6% of positive cases. The clinical improvement rate following this targeted escalation was 66.2%, comparable to the 66.7% improvement rate observed in patients receiving appropriate initial empirical therapy (P = 0.946). Both tNGS and mNGS offer substantial diagnostic value for LRTIs, with tNGS showing particular utility in identifying fastidious and low-titer pathogens. Sequencing-guided diagnostics frequently informed antimicrobial adjustments and were associated with favorable clinical progress; however, future prospective paired-testing studies are required to isolate the direct impact of sequencing on patient survival outcomes.