Ribosome protection as a mechanism of lincosamide resistance in Mycobacterium abscessus

Mycobacterium abscessus has emerged as a successful pathogen owing to its intrinsic drug resistance. Macrolide and lincosamide antibiotics share overlapping binding sites within the ribosome and common resistance pathways. Nevertheless, while M. abscessus is initially susceptible to macrolides, they are completely resistant to the lincosamide antibiotics. Here we have used RNA sequencing to determine the changes in genes expression in M. abscessus upon exposure to the lincosamide, clindamycin (CLY). We show that Mab_1846 encoding a putative ARE-ABCF protein, was upregulated upon exposure to macrolides and lincosamides, but conferred resistance to CLY alone. An M. smegmatis homologue of Mab_1846 , Ms_5102 , was similarly found to be required for CLY resistance in M. smegmatis . We demonstrate that Ms5102 mediates CLY resistance by directly interacting with the ribosomes and protecting it from CLY inhibition. Additional biochemical characterization showed that ribosome binding is not nucleotide dependent, but ATP hydrolysis is required for dissociation of Ms5102 from the ribosome, as well as for its ability to confer CLY resistance. Finally, we show that in comparison to the macrolides, CLY is a potent inducer of Mab_1846 and the whiB7 regulon, such that exposure of M. abscessus to very low antibiotic concentrations induces a heightened expression of erm41, hflX and Mab_1846 which likely function together to result in a particularly antibiotic resistant state.