Identification and drug resistance profiling of Mycobacterium orygis from an African elephant using whole-genome sequencing

Authors

• Hassan Ghayas, Aga Khan UniversityFollow
• Javaria Ashraf, Aga Khan UniversityFollow
• Noureen Saeed, Aga Khan UniversityFollow
• Sadaf Zaka, Aga Khan UniversityFollow
• Samreen Shafiq, Aga Khan UniversityFollow
• Joveria Farooqi, Aga Khan UniversityFollow
• Kauser Jabeen, Aga Khan UniversityFollow
• Abida Rais, Karachi Metropolitan Corporation
• Aamir Ismail Rizvi, Karachi Metropolitan Corporation
• Ghulam Mustafa, University of Veterinary and Animal Sciences
• Samreen Ashraf Quresh, Health Department, Government of Sindh
• Yusra Askari, Ministry of Local Government (Zoo Safari)
• Naseem Salahuddin, Indus Hospital, Karachi
• Egon A. Ozer, Northwestern University
• Rumina Hasan, Aga Khan UniversityFollow

Document Type

Article

Department

Pathology and Laboratory Medicine

Abstract

Tuberculosis (TB) caused by members of the Mycobacterium tuberculosis complex (MTBC) has been increasingly reported in wildlife and captive animals, posing zoonotic risks. Accurate diagnosis and speciation are essential to trace the infection source and to tailor therapy accordingly. Current diagnostic tools, however, have limitations in speciating MTBC strains. In this study, we investigated a lung biopsy sample of a deceased adult female elephant (Loxodonta africana) for mycobacterial infection. Mycobacterial Growth Indicator Tube culture was positive, and initial immunochromatographic testing (BD MPT64) confirmed the isolate as a member of the MTBC. To further confirm species identity and assess drug resistance, whole-genome sequencing was performed. Species was identified using Genome Detective and KmerFinder. Species identification and lineage analysis consistently classified the isolate as Mycobacterium orygis (lineage La3), a rare and often overlooked zoonotic member of the MTBC. Antimicrobial resistance profiling through TB-Profiler and PhyResSE identified resistance to isoniazid, attributed to the presence of the katG p.Ser315Thr mutation. No resistance-associated mutations were detected for rifampicin, levofloxacin, or pyrazinamide. These findings were consistent with phenotypic drug susceptibility testing. The detection of M. orygis in a captive elephant suggests that the infection was of zoonotic origin and underscores its potential for spreading disease, and thus the need for integrated surveillance in animal reservoirs.
Importance: This study reports the first case of Mycobacterium orygis infection in an African elephant in captivity. Currently, the methods for differentiation of Mycobacterium tuberculosis complex (MTBC) subspecies have limitations. This case highlights the importance of precise species identification and drug resistance profiling of MTBC organisms and the use of whole-genome sequencing in diagnosis. Additionally, our findings underline the need for surveillance of mycobacteria and other potential pathogens in captive animals and in animal caregivers to reduce the potential for zoonotic disease transmission.

Comments

Volume, issue, and pagination are not provided by the author/publisher.

Publication (Name of Journal)

Microbiology Spectrum

DOI

DOI: 10.1128/spectrum.03586-25

Recommended Citation

Ghayas, H., Ashraf, J., Saeed, N., Zaka, S., Shafiq, S., Farooqi, J., Jabeen, K., Rais, A., Rizvi, A. I., Mustafa, G., Quresh, S. A., Askari, Y., Salahuddin, N., Ozer, E. A., Hasan, R. (2026). Identification and drug resistance profiling of Mycobacterium orygis from an African elephant using whole-genome sequencing. Microbiology Spectrum.
Available at: https://ecommons.aku.edu/pakistan_fhs_mc_pathol_microbiol/1750