Comparative genomics ofMycobacterium africanumLineage 5 and Lineage 6 from Ghana suggests different ecological niches

AbstractMycobacterium africanum(Maf) causes up to half of human tuberculosis in West Africa, but little is known on this pathogen. We compared the genomes of 253Mafclinical isolates from Ghana, including both L5 and L6. We found that the genomic diversity of L6 was higher than in L5, and the selection pressures differed between both groups. Regulatory proteins appeared to evolve neutrally in L5 but under purifying selection in L6. Conversely, human T cell epitopes were under purifying selection in L5, but under positive selection in L6. Although only 10% of the T cell epitopes were variable, mutations were mostly lineage-specific. Our findings indicate thatMafL5 and L6 are genomically distinct, possibly reflecting different ecological niches.