Integrated tNGS profiling reveals co-detection, drug resistance, and host pharmacogenetics of mycobacterial detections in Jiangxi, China

Tuberculosis (TB) and non-tuberculous mycobacterial (NTM) detections pose overlapping diagnostic and therapeutic challenges, particularly in high-burden regions. Detailed molecular epidemiological data from tertiary care settings in Jiangxi Province, southern China, remain limited, hindering tailored control strategies. This single-center study retrospectively analyzed 83 respiratory specimens positive for Mycobacterium tuberculosis complex (MTC) by Xpert MTB/RIF. Targeted next-generation sequencing (tNGS) was performed to detect MTC and NTM, profile drug resistance-associated mutations, and assess host NAT2 acetylator genotypes. MTC/NTM co-detection occurred in 26.7% of bronchoalveolar lavage fluid (BALF) samples (20/75; 24.1% of the total cohort [20/83]). Among these 20 co-detected patients, 3 harbored two distinct NTM species simultaneously alongside MTC, resulting in 23 total NTM species detections ( M. chelonae , n = 12; M. abscessus , n = 9; M. intracellulare , n = 1; M. gordonae , n = 1). Genotypically predicted fluoroquinolone resistance was identified in 10.8% of MTC detectionss (9/83 patients), with a total of 14 distinct gyrA mutation occurrences detected across these detections, suggestive of potential subclonal heteroresistance rather than confirmed phenotypic heteroresistance. Mutations potentially conferring resistance to newer agents (e.g., bedaquiline/clofazimine) were also observed as unconfirmed candidate variants. Two pre-extensively drug-resistant TB cases were identified, both displaying multi-drug resistance with additional resistance to fluoroquinolones. NAT2 acetylator phenotypes distributed across slow, intermediate, and fast metabolizers, with no gender disparity. The study highlights a significant rate of MTC/NTM co-detection and substantial fluoroquinolone resistance in Jiangxi. Integrating tNGS-based resistance profiling and host pharmacogenetics provides an exploratory framework that, subject to future clinical validation, may inform hypotheses regarding personalized therapy and underscore the need for sustained molecular surveillance in DR-TB management within a specialized referral context. Not applicable.