Comparative Analysis of Virulence Genes in Non-Tuberculosis Mycobacteria (NTM) Isolated from Kenyan Camel Milk Suggests Potential Pathogenicity.

Mycobacteria are a concern in camel milk due to their potential pathogenicity. This study explored the genetic characteristics of thirteen Mycobacteria isolates from camel milk collected in Isiolo County, Kenya, focusing on the identification and comparison of virulence genes. Using whole-genome sequencing (WGS) and the PATRIC annotation platform, we analyzed subsystems and specialty genes to uncover functional capability and potential pathogenic mechanisms. There were significant variations observed in the number of genes assigned to key subsystems such as metabolism, protein processing, stress response, and energy, suggesting diverse metabolic and survival strategies among the strains. Notably, strains such as Mycobacterium vaccae (JACC_055) and Mycobacterium pulveris (EL_188) exhibited a higher number of genes in the metabolism and stress response subsystems, respectively, indicating enhanced metabolic potential and adaptation to harsh environments. Virulence genes were identified across the isolates with Mycobacterium heidelburgense (EL_135), Mycobacterium colombiense (EL_158), and Mycolicibacterium pulveris (EL_188) showing the highest counts (22, 22, and 16, respectively), suggesting their increased pathogenic potential. The key virulence genes including ideR, relA, mbtH, esxR, phoP, and icl, were frequently present, highlighting their essential role in Mycobacterium virulence. Unique genes in certain isolates such as fbpC and esxN in EL_135 and EL_158 isolates indicate specific adaptations for nutrient acquisition and host interaction. A comparative analysis with Mycobacterium tuberculosis and M. avium revealed shared virulence genes (fbpA, fbpB, icl, ideR, relA, esxH, phoP) and unique ecc genes, highlighting similarities in pathogenic mechanisms and potential for host immune manipulation. Phylogenetic analysis demonstrated the genetic closeness of M. colombiense and M. heidelbergense to M. tuberculosis and M. avium, implying similar virulence capabilities. These findings enhance our understanding of the genetic diversity and pathogenic potential of Mycobacterium species in camel milk, emphasizing the importance of strain-specific analysis for disease management, therapeutic development, and public health awareness.