A frameshift mutation in the methyltransferase rlmN is associated with increased linezolid resistance in Mycobacterium tuberculosis

Linezolid is a key component of treatment regimens for multidrug-resistant and extensively drug-resistant tuberculosis, which is caused by the pathogen Mycobacterium tuberculosis (MTB). Resistance to linezolid in MTB has traditionally been attributed to mutations in the 23S rRNA ( rrl ) and ribosomal protein L3 ( rplC ), but only a fraction of clinically observed linezolid resistance is explained by mutations in these two genes. We report that an analysis of strains with paired whole-genome sequencing and linezolid minimum inhibitory concentration (MIC) phenotyping from the Bacterial and Viral Bioinformatics Resource Center (BV-BRC) reveals that a relatively common frameshift mutation in MTB methyltransferase rlmN (5.3% of assessed isolates) is significantly associated with increased linezolid MIC. In additional to statistical associations, we provide evolutionary evidence of homology to an established linezolid resistance mechanism in Staphylococcus aureus , and structural evidence that the frameshift mutation likely ablates rlmN methyltransferase functionality.