The incidence and prevalence of nontuberculous mycobacterial (NTM) disease has been steadily increasing globally. Among these, rapidly growing mycobacteria (RGM), including Mycobacterium fortuitum, and Mycobacterium chelonae, have emerged as important pathogens, contributing to a growing number of pulmonary and extrapulmonary infections. Effective treatment of RGM infections relies on timely species and subspecies identification, as well as accurate detection of drug-resistant strains.

This dissertation consists of three studies aimed at enhancing the identification and antimicrobial resistance (AR) characterization of RGM. In the first study, we assess the proportions of the different M. abscessus subspecies (comprising M. abscessus subsp. abscessus, M. abscessus subsp. massiliense, and M. abscessus subsp. bolletii) among 41 extrapulmonary RGM isolates collected from four U.S. sites and determine the utility of erm(41) and partial rpoB (region V, ~ 720 bp) sequencing for subspecies differentiation. In the second study, we determine the level of concordance between genotypic resistance markers identified by whole genome sequencing and resistance detected phenotypically by broth microdilution testing of 20 extrapulmonary RGM isolates. In the third study, we comprehensively characterized a previously unidentified, RGM isolated from the bloodstream of 52 oncology clinic patients.

Collectively, these studies highlight the utility of molecular and genomic approaches in addressing current gaps in RGM diagnostics and resistance detection. The findings strengthen clinical laboratory capacity to more accurately identify and characterize RGM infections. Furthermore, the knowledge generated provides a foundation for understanding resistance mechanisms and informs future research by identifying priority areas where AR in RGM remains poorly understood.