A Genomic Signature for Genotyping Mycobacterium tuberculosis

Mycobacterium tuberculosis (MTB), the causative agent of tuberculosis (TB), has a vast diversity of genotypes including Beijing, CAS, EAI, Haarlem, LAM, X, Ural, T, AFRI1 and AFRI2. However, genotyping can be expensive, time consuming and in some cases, results may vary depending on methodology used. Here, we proposed a new set of 10 SNPs using a total of 249 MTB genomes, and selected by first the inclusion/ exclusion (IE) criteria using spoligotyping and phylogenies, followed by the selection of the nonsynonymous SNPs present in the most conserved cluster of orthologous groups (COG) of each genotype of MTB. Genotype assignment of the new set of 10 SNPs was validated using an additional of 34 MTB genomes and results showed 100% correlation with their known genotypes. Our set of 10 SNPs have not been previously reported and cover the MTB genotypes that are prevalent worldwide. This set of SNPs could be used for molecular epidemiology with drug resistant markers.