Challenges and advances in mycobacterial molecular typing

Mycobacterium tuberculosis (MTB) and nontuberculous mycobacteria (NTM) present distinct clinical and epidemiological challenges and thus require tailored genotyping approaches. MTB is a globally transmissible pathogen for which diagnostic and surveillance infrastructures are well defined, whereas NTM infections are environmentally acquired, taxonomically diverse, and increasingly prevalent among vulnerable populations. Molecular genotyping is indispensable for both pathogen groups, supporting outbreak investigation and drug resistance prediction for MTB and species-level identification and relapse-versusreinfection distinction for NTM. In this review, the evolution of strategies for genotyping mycobacteria are outlined, and traditional techniques (e.g., spoligotyping and mycobacterial interspersed repetitive unit–variable number tandem repeat genotyping) and advanced methods (multilocus sequence typing and whole-genome sequencing) are compared. We highlight the divergent drivers of genotyping between MTB and NTM, examine key technical and interpretive challenges, and discuss how cross-learning between these two fields can accelerate innovation. Emerging technologies such as portable sequencing platforms, artificial intelligence-assisted analysis, and curated genomic databases are expanding access to high-resolution genotyping. However, significant gaps remain, particularly in standardizing NTM genomic analyses and integrating genotypic data into global surveillance systems. By exploring the intersections between MTB and NTM molecular epidemiology, a synergistic pathway for more precise, accessible, and effective mycobacterial genotyping is highlighted.