Transcriptomic and genomic analysis of successful Ethiopian Mycobacterium tuberculosis sub-lineage 4.2.2.2 reveals differential expression of DosR-regulated genes

Mycobacterium tuberculosis (Mtb) sub-lineage 4.2.2.2 is the most frequently isolated strain of Mtb from Ethiopian treatment-refractory tuberculosis patients. This study investigated the underlying molecular background to Mtb sub-lineage 4.2.2.2 through transcriptomic and genomic analyses. Comparative whole genome sequencing and transcriptomics (RNAseq) was performed with other circulating clinical Ethiopian lineages and sub-lineages: lineage 7, lineage 3, lineage 4 sub-lineage 4.1.2.1, and sub-lineage 4.6.3. We identified seven genes differentially expressed in sub-lineage 4.2.2.2 compared to other Mtb lineages. Of these, six (Rv0331, Rv0720, Rv1993c, Rv2030c, Rv2034 and Rv3129) were upregulated, while Rv0997a was downregulated. These differentially expressed genes are associated with lipid metabolism, stress responses, protein synthesis and metal transport, suggesting that sub-lineage 4.2.2.2 may be better able to adapt to the complex host-pathogen interactions of infection and transmission. Interestingly, this observation is mirrored by mild induction of DosR-regulated genes in sub-lineage 4.2.2.2 compared to other lineages in vitro, suggesting that enhanced expression of the DosR regulon may influence this sub-lineage’s ability to cause disease in Ethiopia. Taken together, our findings reveal genes that might impact the pathogenicity of Mtb clinical isolates in Ethiopia and identifies single nucleotide polymorphisms that could influence their expression.