Molecular Characterization and Antibiotic Profiling of Mycobacterium tuberculosis Complex Isolates from Slaughtered Cattle at Yola Modern Abattoir, Adamawa State, Nigeria

Bovine tuberculosis (bTB), caused predominantly by members of the Mycobacterium tuberculosis complex (MTBC), particularly Mycobacterium bovis, remains a major zoonotic and economic challenge in Nigeria. Abattoir-based surveillance provides a critical opportunity to detect and characterize circulating MTBC strains at the livestock–human interface. This study aimed to molecularly characterize MTBC isolates recovered from slaughtered cattle at Yola Modern Abattoir, Adamawa State, Nigeria, using targeted next-generation sequencing (tNGS). Fifteen MTBC isolates previously confirmed by SD Bioline MPT64 antigen testing were subjected to targeted sequencing using the Deeplex® Myc-TB assay. The assay enabled simultaneous species identification, phylogenetic lineage assignment, spoligotyping, and detection of mutations associated with resistance to first- and second-line anti-tuberculosis drugs. Sequencing was performed on the Illumina MiSeq platform, and data were analyzed using the Deeplex automated bioinformatics pipeline. All fifteen isolates were identified as members of the MTBC and were classified as Mycobacterium bovis based on hsp65 sequence analysis, SNP-based phylogenetic lineage assignment, and spoligotyping. Composite target coverage breadth ranged from 93.9% to 100%, with high sequencing depth across target regions. Drug-resistance profiling revealed that all isolates harbored mutations in the pncA gene conferring resistance to pyrazinamide. Two isolates additionally carried mutations associated with ethionamide resistance. Variants of uncertain or uncharacterized significance were detected in genes associated with fluoroquinolones, linezolid, aminoglycosides, and isoniazid. The exclusive detection of M. bovis highlights its dominant role in bovine tuberculosis in northeastern Nigeria. The universal pyrazinamide resistance observed underscores important public health implications for zoonotic tuberculosis management. These findings demonstrate the utility of targeted next-generation sequencing for high-resolution characterization of MTBC in cattle and provide essential data to inform bTB surveillance, control strategies, and One Health interventions in Nigeria. Keywords: Mycobacterium tuberculosis complec (MTBC), Deeplex Myc-TB, Bovine tuberculosis (BTB), Mycobacterium tuberculosis Growth Indication Tube