Evaluation of the deeplex Myc-TB-targeted next-generation sequencing assay for mycobacterial identification and drug resistance detection

Abstract

Rapid and accurate identification of mycobacteria and detection of drug resistance are essential for timely patient management and public health control of tuberculosis and nontuberculous mycobacterial infections. However, routine diagnostics often rely on multiple sequential assays, which can delay comprehensive results. In this study, we demonstrate that targeted next-generation sequencing using Deeplex Myc-TB can provide high-resolution species identification and clinically meaningful drug-resistance information in a single workflow within a U.S. clinical laboratory setting. The assay showed complete concordance with GeneXpert MTB/RIF for identification of the Mycobacterium tuberculosis complex and produced genotypic resistance predictions consistent with phenotypic drug susceptibility testing, where interpretive criteria were available. For nontuberculous mycobacteria, the assay confirmed MALDI-TOF MS identifications and enabled subspecies-level discrimination within clinically important groups, including the Mycobacterium avium complex and Mycobacterium abscessus . These findings support the integration of targeted sequencing into routine mycobacterial diagnostics to streamline laboratory workflows, improve the timeliness and clinical relevance of reporting, and enhance molecular surveillance efforts.