Drug resistance in tuberculosis (TB) poses a major ongoing challenge to public health. The recent
inclusion of bedaquiline into TB drug regimens has improved treatment outcomes, but this advance is
threatened by the emergence of strains of Mycobacterium tuberculosis (Mtb) resistant to bedaquiline.
Clinical bedaquiline resistance is most frequently conferred by resistance-associated variants (RAVs)
in the Rv0678 gene which can also confer cross-resistance to clofazimine, another TB drug. We
compiled a dataset of 3,682 Mtb genomes, including 223 carrying Rv0678 bedaquiline RAVs. We
identified at least 15 cases where RAVs were present in the genomes of strains collected prior to the
use of bedaquiline in TB treatment regimes. Phylogenetic analyses point to multiple emergence events
and circulation of RAVs in Rv0678, often prior to the introduction of bedaquiline or clofazimine. We
also identify one case where the RAV Ile67fs is estimated to have emerged prior to the antibiotic era.
The presence of a pre-existing reservoir of bedaquiline-resistant Mtb strains augments the need for rapid
drug susceptibility testing and individualised regimen selection to safeguard the use of bedaquiline in
TB care and control
