Evolution and global distribution of a pre-extensively drug-resistant Mycobacterium tuberculosis clade centred in Belarus

Abstract Belarus experiences some of the highest rates of drug-resistant tuberculosis (DR-TB) worldwide, with a substantial proportion of cases attributable to the Lineage 4 SIT-266 spoligotype. These isolates have been postulated as geographically restricted to Belarus, yet, whole genome sequencing (WGS) studies assessing the international distribution of these isolates remains sparse. In this study, by utilising publicly available genomic and hierarchical clustering data, we perform an in-depth genomic characterisation of 1362 isolates and reveal a highly resistant and internationally distributed clade, EurA1. Within this, we also provide the first large-scale WGS link to the SIT-266 spoligotype, identifying a highly resistant and mostly Pre-XDR-TB subclade centred in Belarus, termed EurA1.1. Genomic variant analysis revealed widespread resistance to key first line and second line antibiotics, as well as emerging resistance to novel therapeutics such as bedaquiline and linezolid, currently used to treat MDR-TB. Mutations were additionally identified in key DNA repair genes previously linked to a hypermutable phenotype, and concerningly, evolutionary analysis revealed cross-border genomic indicators of relatedness between EurA1.1 isolates collected outside of Belarus to other Eurasian countries such as Germany, Ukraine, Moldova, Russia, and Georgia. Overall, this study provides implications for TB control in both low and high burden settings, and exemplifies how DR-TB is an interconnected global concern.