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

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.