Pan-genome analysis of Mycobacterium tuberculosis identifies accessory genome sequences deleted in modern Beijing lineage

Beijing sub-lineage of Mycobacterium tuberculosis has been reported to have increased transmissibility and drug resistance. This led us to get insights of the genomic landscape of modern Beijing sub-lineages in comparison with other lineages of M. tuberculosis utilizing pan-genomics approach. Pangenome analysis was performed using software Spine (v0.2.3), AGEnt (v0.2.3) and ClustAGE (v0.7.6). The average pangenome size was 45,40,849 bp with 4,391 coding sequences (CDS), with a GC content of 65.4%. The size of the core genome was 36,83,161 bp, contained 3,698 CDS and had an average GC content of 65.1%. The average accessory genome size was 6,96,320.9 bp, with 539.4 CDS and GC content of 67.9%. Among the accessory elements complete deletion of CRISPR-associated endoribonuclease cas1 (Rv2817c), cas2 (Rv2816c), CRISPR type III-a/mtube-associated protein csm6 (Rv2818c), CRISPR type III-a/mtube-associated ramp protein csm5 (Rv2819c) and partial deletion (61.5%) CRISPR type III-a/mtube-associated ramp protein csm4 (Rv2820c) sequences was found specifically in modern Beijing lineages taken in assortment. The sequences were validated using the conventional PCR method, which precisely amplified the corresponding targets of sequence elements with 100% sensitivity and specificity. Deletion of accessory CRISPR sequence elements amongst the modern Beijing sub-lineage of M. tuberculosis suggests more defective DNA-repair in these strains which may enhance the virulence of the strains. Further, the developed conventional PCR approach for the detection of virulent modern Beijing lineage may be of interest to public health and outbreak control organizations for rapid detection of modern Beijing lineage.