Bovine TB: reconstructing the molecular evolution of Mycobacterium bovis

Abstract

Bovine tuberculosis (bTB), caused by Mycobacterium bovis, remains a significant challenge in Ireland, affecting cattle, wildlife, and agricultural trade despite decades of control measures. 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.

Chapter 1 provides a comprehensive review of M. bovis biology, genetics, and evolution, highlighting the role of genomics in resolving epidemiological complexities.

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.

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.

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. The spread of a recently emerged variant in Northern Ireland is linked to cattle movement and historical heterogeneity in the application of control strategies.

The findings of this thesis, summarised in Chapter 5, highlight the power of genomic data to inform on epidemiological events in the present and the past, providing critical insights for future disease surveillance and intervention. By integrating these insights, tools and approaches, existing bTB control strategies can be enhanced, ultimately supporting efforts toward disease management and eradication.

Date of Award	Dec 2025
Original language	English
Awarding Institution	Queen's University Belfast
Sponsors	Department of Agriculture, Environment and Rural Affairs & Department of Agriculture, Food & the Marine
Supervisor	Rose Hynes (Supervisor), Paulo Prodohl (Supervisor), Adrian R. Allen (Supervisor) & R Skuce (Supervisor)