PE/PPE proteins contribute to Mycobacterium tuberculosis drug resistance

The mycobacterial outer membrane (OM) creates a formidable permeability barrier, and whether drugs traverse it by mechanisms other than passive diffusion remains unclear. The proline-glutamic acid (PE) and proline-proline-glutamic acid (PPE) proteins of pathogenic mycobacteria include several OM transporters. Because bacterial transporters are also major contributors to drug resistance, we tested the role of PE/PPE proteins in Mycobacterium tuberculosis (Mtb) drug susceptibility. We identified mutations in multiple pe/ppe genes that were strongly associated with drug resistance in a genetic association study. A mutation in ppe42 linked to clinical amikacin resistance also conferred higher amikacin resistance in vitro. Deletion of ppe51 led to in vitro resistance to multiple drugs and was accompanied by upregulation of inner membrane efflux pumps. Deletion of a pe/ppe pair that responded transcriptionally to drug exposure, pe25/ppe41, led to increased resistance to isoniazid (INH) in strains across all major Mtb lineages and accelerated the emergence of INH resistance in vitro. These data show a role of several Mtb PE/PPE proteins in drug resistance consistent with the PE/PPE transporter paradigm and suggest a wider role of the PE/PPE family in Mtb drug susceptibility and clinical drug resistance.