Identification of novel mutations associated with clofazimine resistance in Mycobacterium abscessus

Mycobacterium abscessus ( Mab ) is a major non-tuberculous mycobacterial (NTM) pathogen responsible for about 80% of all pulmonary infections caused by rapidly growing mycobacteria. Clofazimine is an effective drug active against Mab and shows synergistic activity when given with amikacin, but the mechanism of resistance to clofazimine in Mab is unknown. Objective To investigate the molecular basis of clofazimine resistance in Mab. Methods We isolated 29 Mab mutants resistant to clofazimine, and subjected them to whole genome sequencing and Sanger sequencing to identify possible mutations associated with clofazimine resistance. Results Mutations in MAB\_2299c gene which encodes possible transcriptional regulatory protein were identified in 23 of the 29 clofazimine-resistant mutants. In addition, 6 mutations in MAB\_1483 were found in 21 of the 29 mutants, and one mutation in MAB\_0540 was found in 16 of the 29 mutants. Mutations in MAB\_0416c, MAB\_4099c, MAB\_2613, MAB\_0409, MAB\_1426 were also associated with clofazimine resistance in less frequency. Two identical mutations which are likely to be polymorphisms unrelated to clofazimine resistance were found in MAB\_4605c and MAB\_4323 in 13 mutants. Conclusion Mutations in MAB\_2299c, MAB\_1483, and MAB_0540 are the major mechanisms of clofazimine resistance in Mab . Future studies are needed to address the role of the identified mutations in clofazimine resistance in Mab , and our findings have implications for developing a rapid molecular test for detecting clofazimine resistance in this organism.