Comparison of the diagnostic value of targeted next-generation sequencing, metagenomic next-generation sequencing, and Xpert MTB/RIF in adult pulmonary tuberculosis.

UNLABELLED: Tuberculosis (TB) has high morbidity and mortality rates, and drug-resistant strains pose an increasing challenge. Traditional methods for detecting thecomplex (MTBC) are insufficient for rapid clinical diagnosis. This prospective study compared the diagnostic efficacy of targeted next-generation sequencing (tNGS), metagenomic next-generation sequencing (mNGS), and Xpert MTB/RIF using bronchoalveolar lavage fluid (BALF) samples from 121 patients with suspected pulmonary TB. Against the reference standard of mycobacterial culture, tNGS demonstrated the highest sensitivity (97.44%), followed by Xpert MTB/RIF (92.31%) and mNGS (84.62%), specificities were 69.51%, 69.51%, and 75.61%, respectively. To address the limitations of culture as an imperfect reference standard and the potential bias from clinical diagnosis, Bayesian Latent Class Analysis (BLCA) was employed. BLCA, which does not assume a perfect gold standard, estimated sensitivities of 98.7%, 99.8%, and 91.0% for tNGS, Xpert MTB/RIF, and mNGS, with corresponding specificities of 89.3%, 93.3%, and 97.8%, respectively. Both tNGS and Xpert MTB/RIF consistently detected rifampicin resistance mutations () ( = 0.219, Kappa = 0.730). In conclusion, tNGS offers comparable specificity and sensitivity to Xpert MTB/RIF for TB diagnosis, with the advantage of distinguishing between MTBC,(NTM), and other microorganisms. Simultaneously, it provides insights into anti-TB drug resistance. Thus, tNGS is a valuable tool for diagnosing TB in various clinical settings. Clinical trial number, Not applicable.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12879-026-12673-4.