Targeted next-generation sequencing for microbial and clinical diagnosis: a prospective controlled comparison between sputum and bronchoalveolar lavage fluid in patients with community-acquired pneumonia.

BACKGROUND: Accurate identification of pathogens causing community-acquired pneumonia (CAP) in adults is a crucial step for successful diagnosis and treatment. However, some patients cannot tolerate bronchoscopy, or bronchoalveolar lavage fluid (BALF) cannot be obtained in a timely manner. Currently, targeted next-generation sequencing (tNGS) is increasingly used for detecting pathogens. As an easily accessible lower respiratory tract specimen, the diagnostic efficacy of sputum tNGS in detecting pathogens causing CAP remains unclear.

METHODS AND DESIGN: Between August 2023 and May 2025, 181 patients clinically diagnosed with CAP were enrolled from the Department of Respiratory and Critical Care Medicine, the People's Hospital of Nanbu County, Sichuan Province. Sputum and BALF samples were collected from each patient on the same day. The samples underwent tNGS to compare the diagnostic performance of sputum tNGS and BALF tNGS in laboratory microbial detection and pathogen identification.

RESULTS: In total, 181 adult patients were included in this study, comprising 98 males (54.1%) and 83 females (45.9%). Finally 175 patients were diagnosed with CAP, and 6 patients had non-infectious diseases. Concerning laboratory microbial detection, the overall microbial detection rates of sputum tNGS and BALF tNGS were 96.1% (174/181) and 95.5% (173/181), respectively. Using the results of BALF tNGS microbial detection as the reference, sputum tNGS showed high overall consistency for bacterial detection (Kappa value: 0.71). Consistency was lower for fungal and viral detection (Kappa values: 0.47, 0.44). Furthermore, using the comprehensive clinical judgment criteria for pathogenic microorganisms as the gold standard, the diagnostic accuracy of sputum tNGS and BALF tNGS for pathogens leading to CAP was evaluated. The overall concordance rates of sputum compared to BALF tNGS for diagnosing pathogenic bacteria, fungi, viruses, Mycobacterium tuberculosis, and atypical pathogens were 0.70 vs. 0.72, 0.93 vs. 0.93, 0.81 vs. 0.85, 0.97 vs. 0.98, and 0.99 vs. 0.98, respectively. Cost-effectiveness analysis indicated that the cost of sputum tNGS was significantly lower than that of BALF tNGS and the conventional method of pathogen detection (p&#x2009;<&#x2009;0.0001).

CONCLUSIONS: The diagnostic accuracy of sputum tNGS for microorganisms causing CAP is comparable to that of BALF tNGS. It is easy to implement and has lower costs, suggesting its value as an alternative to BALF tNGS or conventional microbiological tests for the early and rapid diagnosis of CAP.