Diagnostic Value of Targeted Next-Generation Sequencing in Pulmonary Infection

Abstract

Background: Rapid and accurate etiological diagnosis is essential for the management of pulmonary infections; however, conventional microbiological methods may be limited by prolonged turnaround time and incomplete pathogen coverage. Objectives: This study aimed to evaluate the diagnostic value of targeted next-generation sequencing (tNGS) for pulmonary infections. Methods: Respiratory samples, including bronchoalveolar lavage fluid and sputum, were collected from 122 patients with pulmonary infection at a tertiary care hospital in China between August and December 2025. All samples were tested using both tNGS and conventional microbiological methods. Detection time, positive detection rate, mixed-pathogen detection rate, pathogen distribution, antimicrobial resistance gene detection, and intermethod agreement were compared. Results: tNGS had a significantly shorter detection time than conventional microbiological methods: 24.00 (22.54, 25.53) hours versus 78.28 (74.58, 82.02) hours (Wilcoxon signed-rank test, Z = -9.585; P < 0.001). The positive detection rate was higher with tNGS (93.44%, 114/122) than with conventional microbiological methods (66.39%, 81/122; P < 0.001). Mixed-pathogen detection was observed in 76 patients by tNGS and in 32 patients by conventional microbiological methods; paired analysis showed a significant difference between the two methods (McNemar χ2 = 33.02; P < 0.001). tNGS detected greater numbers of bacterial, fungal, viral, and uncommon or opportunistic pathogens and identified 7 antimicrobial resistance genes. The overall concordance rate between the two methods was 64.75% (79/122), with a Kappa value of 0.014. Conclusions: Compared with conventional microbiological methods, tNGS enabled faster detection, a higher positive detection rate, and broader pathogen coverage in pulmonary infections. Therefore, tNGS may serve as a useful adjunctive tool for etiological diagnosis in clinical practice.