Functional genomics reveals the mechanism of hypoxic adaptation in nontuberculous mycobacteria

Mycobacterium intracellulareis a major etiological agent of the recently expandingMycobacterium avium–intracellularecomplex pulmonary disease (MAC-PD). Therapeutic regimens that include a combination of macrolides and antituberculous drugs have been implemented with limited success. To identify novel targets for drug development that accommodate the genomic diversity ofM. avium–intracellulare, we subjected eight clinical MAC-PD isolates and the type strain ATCC13950 to genome-wide profiling to comprehensively identify universally essential functions. Among these strains, we identified 131 shared essential or growth-defect-associated genes. Unlike the type strain, the clinical strains showed an increased requirement for genes involved in gluconeogenesis and the type VII secretion system under standard growth conditions, the same genes required for hypoxic pellicle-type biofilm formation in ATCC13950. Consistent with the central role of hypoxia in the evolution ofM. intracellulare, the clinical MAC-PD strains showed more rapid adaptation to hypoxic growth than the type strain. Importantly, the increased essentiality of hypoxic fitness genes was confirmed in a mouse lung infection model. These findings confirm the concordant gene essentiality under hypoxic conditionsin vitroand hypoxia-related conditionsin vivo, and highlight the importance of using clinical strains and host-relevant growth conditions to identify high-value targets for drug development.