A diagnostic performance study of multiplex polymerase chain reaction-based targeted next-generation sequencing for the accurate identification of Mycobacterium tuberculosis in bronchoalveolar lavage fluid.

OBJECTIVE

To evaluate the diagnostic performance of multiplex PCR-based targeted next-generation sequencing (mp-tNGS) for detecting Mycobacterium tuberculosis (MTB) in bronchoalveolar lavage fluid (BALF) from patients with suspected pulmonary tuberculosis (PTB).

METHODS

This prospective study enrolled 188 patients. BALF samples were tested in parallel by AFB smear, culture, Xpert MTB/RIF, and mp-tNGS. Diagnostic performance was assessed against a composite clinical reference standard; phenotypic drug susceptibility testing (pDST) was additionally compared in a subset of 35 patients.

RESULTS

Among the cohort, 116 patients were diagnosed with PTB. The sensitivities of AFB smear, culture, Xpert MTB/RIF, and mp-tNGS were 19.8%, 33.6%, 73.3%, and 83.6%, respectively; specificities were 91.7%, 100%, 98.6%, and 97.2%. mp-tNGS demonstrated the highest diagnostic accuracy (88.8%) and the strongest agreement with the reference standard (κ = 0.868, p < 0.001); Subgroup analysis using microbiological reference standard confirmed comparable performance (sensitivity 83.8%, specificity 97.2%). The area under the ROC curve for mp-tNGS was 0.88, significantly outperforming AFB smear (0.56), culture (0.67), and Xpert MTB/RIF (0.81). In the resistance subset, mp-tNGS showed 100% sensitivity and specificity for rifampicin resistance (all rpoB S450L mutations) and 75% sensitivity with 100% specificity for isoniazid resistance (katG S315T mutations), identifying five probable multidrug-resistant cases. Xpert MTB/RIF detected rifampicin resistance with 75.0% sensitivity and 96.3% specificity.

CONCLUSION

The mp-tNGS assay provides a superior combination of rapid turnaround time (~12 hours) and high diagnostic accuracy for MTB detection in BALF. Beyond pathogen identification, it offers rapid and preliminary genotypic resistance screening, supporting early suspicion of multidrug resistance, while phenotypic confirmation remains essential. This makes mp-tNGS a highly effective tool for the rapid, accurate diagnosis and preliminary resistance screening of PTB.