Mycobacterium tuberculosis complex lineage 5 exhibits high levels of within lineage genomic diversity

Pathogens of the Mycobacterium tuberculosis complex (MTBC) are considered monomorphic, with little gene content variation between strains when compared with other bacteria. Nevertheless, several genotypic and phenotypic factors separate the different MTBC lineages (L), especially L5 and L6 (traditionally termed Mycobacterium africanum), from each other. However, genome variability and gene content especially of L5 and L6 strains have not been fully explored, but may be potentially important for pathobiology and current approaches for next generation sequencing (NGS) analysis of MBTC genomes. Through genomic comparison of 208 L5 clinical isolates genomes (including 3 completed genomes and 205 Illumina NGS datasets) and H37Rv, we identified multiple genes differentially present or absent between H37Rv and L5 strains. Additionally, considerable gene content variability was found between L5 strains. Several of the unique L5 genes contain significant diversity in pairwise L5 strains comparison, thus, providing additional discriminatory power e.g. for genome-based transmission analysis that would be missed in the current H37Rv-centric mapping approach. In conclusion, our data show that using H37Rv as reference genome results in missing SNPs in genes unique for L5 strains. This potentially leads to an underestimation of the diversity present in the genome of L5 strains. As such, a full capture of the gene diversity e.g. for high resolution outbreak analysis requires a variation of the single reference genome mapping approach currently used in most NGS data analysis pipelines. Moreover, the high within-lineage gene …