Correlation between rrs gene mutations and amikacin resistance in Mycobacterium abscessus: implications for fitness cost and clinical prevalence

OBJECTIVES: Amikacin is crucial for treating Mycobacterium abscessus (Mab) infections, with resistance primarily attributed to rrs gene mutations. The correlation between specific mutations and amikacin susceptibility, along with the associated fitness cost, requires further investigation. METHODS: We isolated spontaneous amikacin-resistant mutants in vitro and identified their mutation sites in the rrs gene via Sanger sequencing, which were then compared with existing reports. Using CRISPR/Cas12a-assisted recombineering, we engineered Mab strains with specific rrs mutations. The growth rate and fitness costs in vitro were evaluated, in conjunction with drug susceptibility testing to determine the relationship between rrs mutations and amikacin resistance. RESULTS: The mutation frequency of Mab for amikacin resistance ranged from 4.68 × 10⁻⁷ to 9.38 × 10⁻⁹. Three rrs mutation sites (A1375G, C1376T, G1458T) were identified, with A1375G being the most prevalent. Two additional sites, T1373A and T1465A, have been reported previously but not detected in this study. The five gene-edited strains demonstrated resistance to amikacin and cross-resistance to other aminoglycosides, and all exhibited slower in vitro growth rates than the wild-type Mab. Competitive experiments revealed that T1373A and T1465A have high fitness costs, while C1376T and G1458T have weak fitness costs and A1375G shows no fitness costs. CONCLUSIONS: Our findings confirm that rrs mutations confer high-level amikacin resistance, with the limited mutation spectrum in clinical isolates possibly linked to higher spontaneous mutation frequency and lower fitness costs.