Whole genome sequencing and comparative genomics of Mycobacterium orygis isolated from different animal hosts to identify specific diagnostic markers

• Published in: Frontiers in cellular and infection microbiology Vol. 13; p. 1302393
• Main Authors: Karthik, Kumaragurubaran, Subramanian, Saraswathi, Vinoli Priyadharshini, Michael, Jawahar, Ayyaru, Anbazhagan, Subbaiyan, Kathiravan, Ramaiyan Selvaraju, Thomas, Prasad, Babu, Ramasamy Parthiban Aravindh, Gopalan Tirumurugaan, Krishnaswamy, Raj, Gopal Dhinakar
• Format: Journal Article
• Language: English
• Published: Switzerland Frontiers Media S.A 2023
• Subjects: Animals; buffalo; Buffaloes; Cattle; comparative genomics; Deer; Genomics; India; Mycobacterium orygis; region of difference; sambar deer; Whole Genome Sequencing; region of difference; SNP; Mycobacterium orygis; buffalo; sambar deer; comparative genomics; India
• ISSN: 2235-2988; 2235-2988
• DOI: 10.3389/fcimb.2023.1302393

, a member of MTBC has been identified in higher numbers in the recent years from animals of South Asia. Comparative genomics of this important zoonotic pathogen is not available which can provide data on the molecular difference between other MTBC members. Hence, the present study was carried out to isolate, whole genome sequence from different animal species (cattle, buffalo and deer) and to identify molecular marker for the differentiation of from other MTBC members. Isolation and whole genome sequencing of was carried out for 9 samples (4 cattle, 4 deer and 1 buffalo) died due to tuberculosis. Comparative genomics employing 53 genomes (44 from database and 9 newly sequenced) was performed to identify SNPs, spoligotype, pangenome structure, and region of difference. was isolated from water buffalo and sambar deer which is the first of its kind report worldwide. Comparative pangenomics of all strains worldwide (n= 53) showed a closed pangenome structure which is also reported for the first time. Pairwise SNP between TANUVAS_2, TANUVAS_4, TANUVAS_5, TANUVAS_7 and NIRTAH144 was less than 15 indicating that the same strain may be the cause for infection. Region of difference prediction showed absence of RD7, RD8, RD9, RD10, RD12, RD301, RD315 in all the analyzed. SNPs in virulence gene, PE35 was found to be unique to which can be used as marker for identification. The present study is yet another supportive evidence that is more prevalent among animals in South Asia and the zoonotic potential of this organism needs to be evaluated.