Bovine TB: reconstructing the molecular evolution of Mycobacterium bovis

This thesis employs genomic tools to enhance our understanding of M. bovis evolution and epidemiology, with the goal of refining bTB surveillance and management strategies. By integrating whole-genome sequence (WGS) diversity and transmission dynamics, we reconstruct the evolutionary history of M. bovis in Ireland.<br><br>Chapter 1 provides a comprehensive review of M. bovis biology, genetics, and evolution, highlighting the role of genomics in resolving epidemiological complexities.<br><br>In Chapter 2, we analyse 992 WGS samples, identifying 17 genetic variants and developing a novel SNP-typing panel to overcome limitations of traditional methods.

This approach enables rapid and cost-effective genotyping, for triaging samples and thus reducing the reliance on WGS usage for accurate monitoring.<br><br>Chapter 3 applies phylodynamic models to 481 M. bovis WGS samples, uncovering and quantifying bi-directional cross-border transmission between the Republic of Ireland and Northern Ireland. Despite imbalanced livestock trade, local spread of M. bovis dominates relative to cross-border, informing the effectiveness of border control policies.<br><br>In Chapter 4, Bayesian phylogenetic analyses trace the evolutionary history of M. bovis in Ireland, dating the origin of its extant, major lineage to the 12th century and showing how its population has been shaped by disease control schemes.