Key resistance-associated mutations in multidrug-resistant tuberculosis: a genomic study from Shanghai, China, with a focus on aminoglycosides

The aminoglycosides are essential drugs in the treatment of multidrug-resistant tuberculosis. Antibiotic resistance of Mycobacterium tuberculosis is a major public health concern worldwide. Therefore, it is of great significance to characterize the mutations by which susceptible M. tuberculosis evolves into drug resistance. A total of 110 clinical isolates of MDR-TB were used for Whole-genome sequencing (WGS) and phenotypic drug susceptibility testing to aminoglycosides, including amikacin, kanamycin, and streptomycin. Among 110 clinical MDR-TB strains, 7 (6.36%) were cross-resistant to amikacin and kanamycin, and 81 (73.64%) were resistant to streptomycin. The resistance rates to rifabutin, streptomycin, moxifloxacin, ofloxacin, and ethambutol were observed in 79.09%, 73.64%,35.45%, 34.55%, and 30.91%, respectively. Among the 81 MDR-TB strains resistant to streptomycin, the MIC values of streptomycin against MDR-TB showed the following distribution: 61 strains (75.31%) demonstrated resistance with MICs ≥ 32 µg/ml. The rrs gene mutations were detected in 6 (85.71%; 6/7) of the amikacin/kanamycin-resistant isolates, with the most frequent mutation being A1401G. Mutations in the eis promoter were identified at two positions in 3 amikacin/kanamycin-susceptible and streptomycin-resistant isolates (-10G > A and - 37G > T). In 80.25% (65 out of 81) of streptomycin-resistant MDR-TB isolates, two types of amino acid substitutions associated with rpsL mutations were identified. K43R was observed in 86.15% of isolates with mutations in rpsL, followed by K88R at 13.85%. In conclusion, current critical concentration methods and the design of molecular diagnostics need to be revisited to provide more accurate assessments of streptomycin resistance for rspL mutation-bearing isolates.