Genomic epidemiology study of Mycobacterium bovis derived from cattle and deer

Mycobacterium bovis, the causative agent of animal tuberculosis, exhibits a broad host range - infecting, inducing pathology and transmitting from both bovine and wildlife hosts. Considerable effort has been extended to understanding the role wildlife may or may not play in persistence and spread of infection in the landscape. Infected cervids can spread infection to conspecifics and sympatric livestock as observed in the white-tailed deer (Odocoileus virginanus) population of Michigan, USA. However, in other territories, there is debate about whether cervids act as maintenance or spillover hosts, with ecological contexts such as deer density and proximity to livestock likely to be key determinants. In Ireland, sika deer (Cervus nippon) populations in County Wicklow have been proposed to act as maintenance hosts, an observation at odds with the view that elsewhere on the island they are primarily spillover hosts. In Northern Ireland, in response to stakeholder concern, policy makers concerned about the role cervids may be playing in the epidemiology of animal TB, a province wide cull of 522 deer was undertaken from 2019-2023. This yielded 13 lab confirmed M. bovis isolates (animal prevalence 2.5%). These isolates were subjected to whole genome sequencing, alongside a further four archived isolates from deer and 190 from cattle to undertake a genome epidemiology study. Bayesian phylogenetic methods of birth death skyline and structured coalescent analyses were applied to track epidemic progression and estimate raw counts and rates of M. bovis transmission withing and between cattle and deer. Findings were consistent with the main driver of disease transmission detected being infected cattle, with deer playing a smaller role.