Summary

Our data document that pre-XDR is highly prevalent among MDR Mtbc strains in Mozambique and so is bedaquiline resistance, which quadrupled in frequency over time and was found even in Mtbc strains without fluoroquinolone resistance. Such high levels of resistance to fluoroquinolone and bedaquiline, in combination with resistance to all first line antibiotics, are likely to threaten the national roll-out of the new WHO approved 6 months regimens of bedaquiline, pretomanid, linezolid, and moxifloxacin or bedaquiline, pretomanid, and linezolid. Importantly, bedaquiline resistance in Mozambique was not limited to fluoroquinolone-resistant strains, suggesting that current treatment regimens are unable to prevent development of resistance on a population level, which has serious implications for current MDR tuberculosis therapy on a global level. An equally worrisome finding is the high proportion of Mtbc strains with the Ile491Phe mutation among MDR plus bedaquiline resistant and XDR Mtbc strains, which remains undetected by Expert MTB/RIF and commericially available line probe assays. Comparison with strains from South Africa and Eswatini supports cross border spread.