The diagnostic value of metagenomic next-generation sequencing in suspected pulmonary tuberculosis patients with scarce sputum or negative sputum etiological test results

•mNGS has higher diagnostic value for PTB compared with some conventional tests.•T-SPOT in series with mNGS cannot diagnose PTB more precisely than mNGS alone.•mNGS in parallel with conventional tests can diagnose PTB patients more accurately. To compare the diagnostic value between mNGS and conventional tests in suspected pulmonary tuberculosis (PTB) patients with scarce sputum or with negative sputum etiological test results. We enrolled eligible patients admitted to our department from 2018 to 2021. Their bronchoalveolar lavage fluid (BALF) and lung biopsy tissue samples were sent for mNGS and conventional tests. The diagnostic value of mNGS was compared respectively with that of conventional tests. 94 of 226 enrolled patients were diagnosed PTB. The diagnostic concordance rate of mNGS was significantly higher than that of acid-fast staining in all samples (p < 0.001), as well as that of culture in BALF samples (p = 0.011). mNGS in parallel with conventional tests had significantly higher AUC than mNGS alone (p = 0.013). mNGS has higher diagnostic value than some conventional tests. mNGS in parallel with conventional tests is more reliable to accurately diagnose these suspected PTB patients.