Profiling of omadacycline resistance in clinical MRSA: A nationwide genomic survey and in vitro evolutionary analysis

Objective

We aimed to evaluate the susceptibility of various clinical methicillin-resistant Staphylococcus aureus (MRSA) lineages to omadacycline and investigate the mechanisms underlying omadacycline resistance.

Methods

Omadacycline MICs for all MRSA isolates were determined via broth dilution. Representative clinical MRSA isolates of ST59, ST5 and ST9 were exposed to increasing concentrations of omadacycline. Mutants developing omadacycline resistance were isolated, sequenced, and compared using breseq. Molecular cloning was employed to elucidate the mechanisms of omadacycline resistance.

Results

Omadacycline MICs against MRSA ranged from 0.06 to 8 mg/L, with MIC₅₀ and MIC₉₀ values at 0.25 and 4 mg/L, respectively, and an overall resistance rate of 13%. All CC59 isolates were susceptible to omadacycline. Resistant isolates were mainly concentrated in HA-MRSA clones CC5. All 47 isolates with MICs ≥4 mg/L harbored tet(M) and the rpsJ K57M mutation. Cloning experiments demonstrated that both tet(M) and mutated rpsJ reduced susceptibility to omadacycline. The rpsJ gene was a common target in different MRSA lineages for decreased omadacycline susceptibility. Continuous exposure to omadacycline induced novel mutations in rpsJ (H56Y in ST9; H56R, K57M in ST59; and K57M, H56Y in ST5), which cloning experiments confirmed could variably reduce omadacycline susceptibility. Furthermore, mutated mepA also contributed to reduced omadacycline susceptibility.

Conclusion

Susceptibility to omadacycline varied among different MRSA lineages, while some CC5 isolates exhibiting the resistance phenotype. The rpsJ gene serves as a general target for the evolution of omadacycline resistance and plays an important role in the refinement of future tetracycline derivatives.