Genomic analysis of new pre-XDR/XDR cluster of Mycobacterium tuberculosis Beijing genotype emerging in Russia

The Mycobacterium tuberculosis Mlva cluster 1071-32 belongs to the early ancient sublineage of the Beijing genotype. We have recently demonstrated its association with pre-XDR/XDR, increase in prevalence in parts of Russia (Northwest, Center, Siberia) and sporadic isolation in eastern Europe (Lithuania, Albania). Here, we analyzed whole genome sequencing (WGS) data in order to gain insight into genomic background of the pathogenetic properties and dissemination pattern of this cluster. The initial WGS collection (this study, GenBank, Broad Institute, GMTV) included 3089 samples, in particular, 521 from East/Southeast Asia and 1067 from Russia. Of these, 117 genomes were assigned to the Beijing early ancient sublineage. The WGS-based phylogenetic analysis subdivided samples into several clades. A large stabnd-alone branch included Russian strains of the VNTR cluster 1071-32; all were pre-XDR or XDR. Cluster-specific SNPs were determined: 15 in intergenic regions, 10 in PE_PGRS and PPE genes, 96 in other genes. Mutations leading to significant amino acid changes were found in genes of the following categories: intermediate metabolism and respiration (n=6), cell wall and cell processes (n=4), conserved hypotheticals (n=2), lipid metabolism (n=1). Three SNPs were selected for development of the real-time PCR method of detection of this resistant cluster. To conclude, the emerging highly drug-resistant Russian cluster of the M. tuberculosis Beijing genotype is characterized by a combination of potentially significant SNPs in the genes coding for intermediate metabolism and respiration and cell and cell wall processes. Supported by Russian Science Foundation (grant 19-14-00013).