The evaluation of cross-resistance to rifabutin and accompanying mutations by DNA sequence analysis in rifampicin-resistant mycobacterium tuberculosis complex strains

The aim of this study is to phenotypically investigate rifabutin susceptibility in rifampicin-resistant strains and to identify the specific mutations associated with rifabutin susceptibility in the rpoB RRDR gene region through DNA sequence analysis. In this study, 43 rifampicin-resistant strains and 23 rifampicin-susceptible control strains of Mycobacterium tuberculosis complex, isolated from various clinical samples between 2000 and 2020 at the Microbiology Laboratories of the Departments of Medical Microbiology at Manisa Celal Bayar University Faculty of Medicine and Ege University Faculty of Medicine, were included. Phenotypic susceptibility testing was performed using the MGIT 960 culture system in accordance with CLSI recommendations. Mutations were investigated by sequencing the 81-base pair RRDR region of the rpoB gene using the Sanger DNA sequencing method. Among the 43 rifampicin-resistant strains, 39 (91%) were also resistant to rifabutin, while four (9%) were susceptible to rifabutin. All of the 23 rifampicin-susceptible strains were also susceptible to rifabutin. A total of 44 non-synonymous mutations were identified in the strains. No mutations were found in the rifampicin-susceptible control strains. The identified mutations resulted in seven different genetic variants, and one variant exhibited a double mutation. The most common mutations found in rifampicin-resistant cases were S531L (76%), H526Y (12%), D516Y (4%), H526D (2%), L511P (2%), M515I (2%), and L533P (2%). Among these, the D516Y, L511P, M515I, and L533P mutations were associated with rifabutin susceptibility. In conclusion, identifying strains with mutations associated with rifabutin susceptibility early through rapid diagnostic tests and initiating rifabutin-containing treatment regimens instead of rifampicin could increase the chances of treatment success and help prevent the rapid development of resistance to second-line drugs.