Disease management at the wildlife‐livestock interface: Using whole‐genome sequencing to study the role of elk in Mycobacterium bovis transmission in Michigan, USA

Abstract

The role of wildlife in the persistence and spread of livestock diseases is difficult to quantify and control. These difficulties are exacerbated when several wildlife species are potentially involved. Bovine tuberculosis (bTB), caused by Mycobacterium bovis, has experienced an ecological shift in Michigan, with spillover from cattle leading to an endemically infected white-tailed deer (deer) population. It has potentially substantial implications for the health and well-being of both wildlife and livestock and incurs a significant economic cost to industry and government. Deer are known to act as a reservoir of infection, with evidence of M. bovis transmission to sympatric elk and cattle populations. However, the role of elk in the circulation of M. bovis is uncertain; they are few in number, but range further than deer, so may enable long distance spread. Combining Whole Genome Sequences (WGS) for M. bovis isolates from exceptionally well-observed populations of elk, deer and cattle with spatiotemporal locations, we use spatial and Bayesian phylogenetic analyses to show strong spatiotemporal admixture of M. bovis isolates. Clustering of bTB in elk and cattle suggests either intraspecies transmission within the two populations, or exposure to a common source. However, there is no support for significant pathogen transfer amongst elk and cattle, and our data are in accordance with existing evidence that interspecies transmission in Michigan is likely only maintained by deer. This study demonstrates | 2193 SALVADOR et AL.

Identifying likely transmission pairs with pathogen sequence data using Kolmogorov Forward Equations; an application to M.bovis in cattle and badgers

“…The distribution for the substitution rate ( μ ) was a beta-PERT, with mode, minimum and maximum respectively set to 0.31, 0.1 and 0.94 base pair × genome × year. These values corresponded to the average, minimum, and maximum of literature estimates from other systems 27,59–61 . We assigned a similar prior to the latency period ( 1/σ ), based on the published literature for data relevant to the geographical area (south-east England).…”

Mycobacterium bovis genomics reveals transmission of infection between cattle and deer in Ireland

“…Whole-genome sequencing of M. bovis has been used to track transmission within and between cattle and wildlife populations [21,[33][34][35][36][37]. These studies have demonstrated that genomics adds unprecedented resolution, in comparison to previous molecular-typing technologies, in many cases distinguishing infection between individual animals.…”

Animal tuberculosis: impact of disease heterogeneity in transmission, diagnosis, and control

“…Many aspects of animal TB epidemiology are yet to be elucidated, which limits the estimation of transmission model parameters. Disease modelling approaches could be helpful in decision‐making, by evaluating potential alternative diagnostic and control measures in high prevalence scenarios (Guta et al, 2014); and to improve surveillance and streamline the eradication strategies in low prevalence scenarios, when a disease outbreak occurs (Salvador et al, 2019), never losing the heterogeneity parameter from the equation. The way these knowledge gaps are considered within the mathematical models, and the different considered assumptions, may have a critical impact on the model outcomes and robustness, so extrapolation of results to a certain scenario and the underlying definition for interventions should be done with caution (Álvarez et al, 2014; Conlan et al, 2012).…”