Combined host depletion and metagenomics sequencing significantly improves the diagnosis of pulmonary tuberculosis.

Abstract Rapid and accurate detection of MTB (Mycobacterium tuberculosis) is key to eliminating tuberculosis. Metagenomic sequencing combining host depletion can significantly improve the diagnostic performance for tuberculosis. Here we compared the performance for diagnosis of 98 suspected pulmonary tuberculosis (PTB) among mycobacterial culture, Xpert, metagenomic next-generation sequencing (mNGS), mNGS of depletion human DNA (mNGS-DH), and nanopore sequencing of depletion human DNA (Nanopore-DH). In the 82 cases of PTB, the PPA (Positive percentage agreement) of mNGS-DH was 71.95% (95%CI, 60.77–81.04%,59/82). In the definite PTB groups(n = 50), the sensitivity of mNGS-DH was up to 86.00%, which was superior to the other four methods. Removing host DNA enhanced the sequencing depth and coverage of the MTB and improved tuberculosis detection, increasing the mean coverage of MTB by 16-fold. Our data demonstrated that mNGS-DH significantly improved the sensitivity of tuberculosis detection in the BALF (bronchoalveolar lavage fluid). Thus, it could be used as a promising alternative to assist the diagnosis of pulmonary TB patients.