AUTHOR=Chen Qian , Qiu Yifan , Zhang Jintao , Chen Shilong , Han Xinjun , Zeng Qingshi , Wang Guanghai , Ji Xiang , Dong Liang 

TITLE=Nanopore targeted sequencing in lower respiratory infections: a retrospective study on diagnostic applications, clinical characterization, and antimicrobial guidance

JOURNAL=Frontiers in Cellular and Infection Microbiology

VOLUME=Volume 15 - 2025

YEAR=2025

URL=https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2025.1660347

DOI=10.3389/fcimb.2025.1660347

ISSN=2235-2988

ABSTRACT=ObjectiveThis study aims to evaluate the pathogen detection and diagnostic performance of Nanopore targeted sequencing (NTS) versus conventional microbiological tests (CMTs) in patients with suspected lower respiratory infections (LRIs). It also explores the clinical characteristics of patients with discrepant detection results and analyzes the clinical significance of antimicrobial resistance (AMR) gene detection using NTS.MethodsA retrospective analysis was performed on patients with suspected LRIs admitted to the Department of Respiratory and Critical Care Medicine at Shandong Provincial Qianfoshan Hospital from January 2023 to January 2024. Bronchoalveolar lavage fluid (BALF) and sputum samples were collected from enrolled patients and subjected to both CMTs and NTS.ResultsThis retrospective study included 70 suspected LRIs patients (66 BALF, 4 sputum samples), with 56 diagnosed as LRIs, 12 as non-infectious diseases, and 2 undetermined. CMTs detected 14 pathogens, while NTS identified 76. NTS showed higher complete (73.21% vs. 16.07%) and partial (23.21% vs. 35.71%) diagnostic rates than CMTs. Diagnostic metrics favored NTS: sensitivity (96.43% vs. 69.64%), NPV (75.00% vs. 32.00%), Youden index (0.464 vs. 0.363), and AUC (0.732 vs. 0.682), though CMTs had higher specificity (66.67% vs. 50.00%) and PPV (90.70% vs. 90.00%). Patients with concordant positive results (CMTs+NTS+) exhibited more severe clinical features and inflammatory markers than NTS-single positive cases, and had higher exposure to invasive procedures—an confirmed independent risk factor. NTS detected 16 resistance genes in 15 patients, with high ESKAPE pathogen coverage.ConclusionNTS overcomes the technical limitations of traditional methods for fastidious pathogens (e.g., intracellular bacteria, mycobacteria) and mixed infections, providing robust technical support for precision anti-infective therapy and complex infection pathogen tracing. Notably, NTS is particularly suitable for early diagnosis in patients with mild symptoms or intact immune function. Compared with CMTs, NTS’s highly efficient and sensitive detection capabilities hold significant practical implications for early infection source isolation, nosocomial outbreak prevention, and optimization of antibacterial drug management strategies.