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

Kumaragurubaran Karthik; Saraswathi Subramanian; Michael Vinoli Priyadharshini; Ayyaru Jawahar; Subbaiyan Anbazhagan; Ramaiyan Selvaraju Kathiravan; Prasad Thomas; Ramasamy Parthiban Aravindh Babu; Krishnaswamy Gopalan Tirumurugaan; Gopal Dhinakar Raj

doi:10.3389/fcimb.2023.1302393

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

Front Cell Infect Microbiol. 2023 Dec 22:13:1302393. doi: 10.3389/fcimb.2023.1302393. eCollection 2023.

Affiliations

¹ Department of Veterinary Microbiology, Veterinary College and Research Institute, Tamil Nadu Veterinary and Animal Sciences University, Udumalpet, India.
² Translational Research Platform for Veterinary Biologicals, Tamil Nadu Veterinary and Animal Sciences University (TANUVAS), Chennai, India.
³ Indian Council of Medical Research (ICMR)-National Animal Resource Facility for Biomedical Research, Hyderabad, Telangana, India.
⁴ Division of Bacteriology and Mycology, Indian Council of Agricultural Research (ICAR)- India Veterinary Research Institute, Bareilly, Uttar Pradesh, India.
⁵ Department of Animal Biotechnology, Madras Veterinary College, Tamil Nadu Veterinary and Animal Sciences University (TANUVAS), Chennai, India.

Abstract

Introduction: Mycobacterium orygis, 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 M. orygis from different animal species (cattle, buffalo and deer) and to identify molecular marker for the differentiation of M. orygis from other MTBC members.

Methods: Isolation and whole genome sequencing of M. orygis 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.

Results: M. orygis was isolated from water buffalo and sambar deer which is the first of its kind report worldwide. Comparative pangenomics of all M. orygis 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 M. orygis strain may be the cause for infection. Region of difference prediction showed absence of RD7, RD8, RD9, RD10, RD12, RD301, RD315 in all the M. orygis analyzed. SNPs in virulence gene, PE35 was found to be unique to M. orygis which can be used as marker for identification.

Conclusion: The present study is yet another supportive evidence that M. orygis is more prevalent among animals in South Asia and the zoonotic potential of this organism needs to be evaluated.

Keywords: India; Mycobacterium orygis; SNP; buffalo; comparative genomics; region of difference; sambar deer.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Buffaloes*
Cattle
Deer*
Genomics
Whole Genome Sequencing

Supplementary concepts

Mycobacterium orygis

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This research project has been implemented with financial contributions from the Department of Biotechnology, Government of India under the DBT Network Program on Bovine Tuberculosis Control: Mycobacterial Diseases in Animals Network (MyDAN) Program (Scheme Code No.22270) and Department of Biotechnology, Government of India under the Translational Research Platform for Veterinary Biologicals- Phase III (BT/TRPVB/TANUVAS/2011- Phase III).