Diagnostic value and clinical performance of targeted next-generation sequencing for lower respiratory tract infections: A real-world prospective study

Abstract Objectives Systematic evaluations of targeted next-generation sequencing (tNGS) for lower respiratory tract infections (LRTIs) remain limited. This study assesses tNGS diagnostic performance and clinical utility. Methods We prospectively analyzed bronchoalveolar lavage fluid (BALF) from 1,251 patients with LRTIs, comparing tNGS results against conventional culture and galactomannan (GM) testing. Results tNGS achieved a significantly higher pathogen positivity rate than culture (95.6% vs 25.7%, p < 0.0001), with an agreement of 25.2%; stratified agreement was 50.9% for bacteria and 63.5% for fungi. For bacterial targets, tNGS showed 92% positive percent agreement (PPA) and 92% negative percent agreement (NPA); fungal targets showed 74% PPA and 95% NPA. For AMR determinants, the PPA and NPA relative to phenotypic resistance were 72% and 79%, respectively; PPA was 71% for carbapenem resistance and 100% for mecA/C. Higher semiquantitative tNGS levels were significantly associated with culture positivity overall and for bacterial and fungal targets. Clinically adjudicated PPV was 80.3% for tNGS-positive findings, with higher PPV for bacterial than fungal targets (77.3% vs 18.2%). Overall concordance between tNGS and GM for Aspergillus was 84.2%. tNGS positively influenced clinical outcomes in 69.6% of patients and prompted antibiotic adjustments in 42.7%. Conclusions In LRTIs, tNGS is significantly more sensitive than culture with high qualitative accuracy. Although it effectively guides clinical decision-making, caution is warranted when using tNGS to predict carbapenem resistance or to initiate antifungal therapy.