Diagnostic performance of pathogen-targeted next-generation sequencing for pulmonary infections: a retrospective observational study

Abstract Background This study addresses diagnostic limitations of conventional etiological tests (CETs) in pulmonary infections by evaluating clinical utility of pathogen-targeted next-generation sequencing (ptNGS). Methods A retrospective observational study was conducted using clinical records from 108 patients with suspected pulmonary infections who underwent bronchoalveolar lavage fluid pathogen-targeted next-generation sequencing (BALF-ptNGS) during routine clinical care at a tertiary hospital in Northern China between November 2022 and August 2023. ptNGS findings were evaluated alongside conventional etiological tests (CETs). Demographic, laboratory, imaging, microbiological, and treatment-related data were retrospectively extracted from the available medical records. Diagnostic performance, pathogen concordance, and antimicrobial management were comparatively analyzed, with clinically significant pathogens defined as meeting American Thoracic Society/Infectious Diseases Society of America (ATS/IDSA) diagnostic criteria. Results ptNGS significantly outperformed CETs in sensitivity for pathogens overall (68.7% vs. 44.8%; p = 0.003), bacteria (66.1% vs. 23.8%; p = 0.001), and viruses (81.8% vs. 51.7%; p = 0.04), with superior negative predictive value ( p < 0.05). Concordance analysis revealed significant agreement (kappa = 0.50–0.86) for 18 pathogen species, predominantly bacteria (50% concordance rate). In pneumonia cases ( n = 86), ptNGS detected pathogens in 95.3%, distinguishing monomicrobial (70.9%) and polymicrobial infections (29.1%). Critically, ptNGS informed antibiotic adjustments in 74.1% of cases: therapy escalation (44.4%), discontinuation (23.2%; avoiding unnecessary antimicrobial exposure), and empirical regimen (10.2%). Pathogen sequence loads were significantly elevated in pneumonia patients versus controls (bacterial: p < 0.05; viral: p < 0.01). Conclusions In this retrospective cohort, ptNGS showed higher sensitivity than conventional etiological tests for bacterial and viral pathogen detection and provided rapid information that was frequently associated with antimicrobial treatment modifications. However, ptNGS findings require careful interpretation within the clinical context, and further prospective multicenter studies are needed to validate their impact on patient-centered outcomes.