Nanopore Targeted Sequencing in Lower Respiratory Infections: A Retrospective Study on Diagnostic Applications, Clinical Characterization, and Antimicrobial Guidance

Qian Chen¹Yifan Qiu¹Jintao Zhang²Shilong Chen²Xinjun Han¹Qingshi Zeng²Guanghai Wang²Xiang Ji²Dong Liang^2*

• ¹Shandong University, Jinan, China
• ²Shandong Provincial Qianfoshan Hospital, Jinan, China

Objective This 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. Methods A 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. Results This 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, This is a provisional file, not the final typeset article 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. Conclusion NTS 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.