Genomic insights into Mycobacterium orygis in wild ungulates in Chennai, India.

Bovine tuberculosis (bTB) represents a significant global threat to livestock, wildlife, and human health, yet wildlife tuberculosis (wTB) remains underreported in India. This study aimed to investigate the presence of Mycobacterium tuberculosis complex (MTBC) species in wild ungulates at Guindy National Park, Chennai. Postmortem tissue samples and fecal pellets were collected from spotted deer, sambar deer, and blackbuck, and analyzed using culture, molecular diagnostics, histopathology, and whole genome sequencing (WGS). Mycobacterium orygis was isolated from tissue samples of four animals, while molecular assays detected MTBC DNA in nine fecal samples. Drug resistance was identified in three fecal samples. Histopathology revealed characteristic granulomatous lesions, and WGS confirmed M. orygis in all tissue-derived isolates. Pangenome analysis identified 4222 genes with an estimated γ value of 0.0086, suggesting an open pangenome with novel genes accumulating at a slow rate. Comparative genomic analysis, including insertion sequence (IS) profiling and SNP analysis, revealed limited overall diversity but unique SNPs in Chennai isolates, suggesting local genomic differentiation. These findings highlight the dynamic nature of M. orygis within MTBC and highlight the importance of functional studies to understand host specificity and adaptability and the urgent need for systematic wTB surveillance and One Health-based interventions in India.