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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

Year: 2026

Type: article

Abstract: Background: 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. Methods: 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. Results: 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). Conclusion: 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.

Source: Frontiers in Cellular and Infection Microbiology

DOI: 10.3389/fcimb.2026.1877320