Whole Genome Sequencing based Identification of Human Tuberculosis caused by Animal-lineageMycobacterium orygis

Abstract

ABSTRACTA recently described member of theMycobacterium tuberculosiscomplex (MTBC) isMycobacterium orygis,which can cause disease primarily in animals but also in humans. AlthoughM. orygishas been reported from different geographic regions around the world, due to a lack of proper identification techniques, the contribution of this emerging pathogen to the global burden of zoonotic tuberculosis is not fully understood. In the present work, we report single nucleotide polymorphisms (SNPs) analysis using whole genome sequencing (WGS) that can accurately identifyM. orygisand differentiate it from other members of MTBC species. WGS-based SNPs analysis was performed for 61 isolates from different Provinces in Canada that were identified asM. orygis. A total of 56M. orygissequences from the public databases were also included in the analysis. Several unique SNPs ingyrB, PPE55, Rv2042c, leuS, mmpL6,andmmpS6genes were used to determine their effectiveness as genetic markers for the identification ofM. orygis. To the best of our knowledge, five of these SNPs,viz., gyrB277(A→G),gyrB1478(T→C),leuS1064(A→T),mmpL6486(T→C), andmmpS6334(C→G) are reported for the first time in this study. Our results also revealed several SNPs specific to other species within MTBC. The phylogenetic analysis shows that studied genomes were genetically diverse and clustered withM. orygissequences of human and animal origin reported from different geographic locations. Therefore, the present study provides a new insight into the high confidence identification ofM. orygisfrom MTBC species based on WGS data, which can be useful for reference and diagnostic laboratories.