Identification of efflux pump mutants and genetic variants conferring cross-resistance between bedaquiline and clofazimine in Mycobacterium tuberculosis clinical strains

TB is a contagious, endemic infectious disease with polymorphic clinical and radiological features. The prognosis of this disease is usually favorable under well-conducted treatment. The treatment is based on anti-tuberculosis drugs whose success requires compliance with treatment; Bedaquiline and Clofazimine are included in the use of drugs in WHO category 5 antibiotics. That's why the genetic bibliography on resistance mechanisms for the two antibiotics is lacking. This study is the first in Turkey, using 100 local MDR-TB strains to show the mechanisms of resistance in relation to MIC values. Our work is based genetically on the isolation of spontaneous mutants in the genes PepQ, RV0678, and Rv1666 through sanger sequencing and the effect on the expression of the efflux pump, phenotypically on the determination of MIC values, and, in the end, epidemiologically on the building of a table that will improve the bibliography of resistance by using spoligotype methods. MIC values of bedaquiline and clofazimine for our TB strains were determined as 0.25 g/mL:>6.4 g/mL and 0.016 g/mL:>3 g/mL, respectively. The mutations responsible for cross-resistance to bedaquiline and clofazimine in our Turkish strains were not detected by Sanger sequencing, but we did find the mutation C415A in the PepQ gene. Among the clinical samples of Turkish patients, according to the result obtained by the Spoligotyping method, Ghana families with 45.9% members and LAM families with 28.6% members were determined. In conclusion, the mutations we observed reduce the antituberculous effect but do not create a complete resistance for cross-resistance; It has been determined that the high MIC values have a significant bactericidal activity, especially when combined with two antibiotics.