Abstract
Wildlife health monitoring and outbreak investigations are essential for understanding effects of disease on population dynamics. Furthermore, they are important for determining the distribution and diversity of pathogens that could influence conservation efforts or livestock or human health, and they provide baseline information for evaluating the impacts of anthropogenic changes on ecosystem health. Molecular and genomic tools can greatly enhance detection and genetic characterization of pathogens in wildlife populations. This thesis comprises three parts that explore the use of molecular tools of varying complexity for addressing particular monitoring objectives, using bacterial pathogens of wild ungulates as examples. In Part 1, polymerase chain reaction was used to determine the herd-level infection status of Mycobacterium avium subspecies paratuberculosis (MAP) in Canadian wood bison (Bison bison athabascae) in the absence of successful bacterial culture, thereby providing important data for translocation decisions. In Part 2, pathogen transmission at the wildlife-livestock interface was examined using genotyping. The detection of multiple MAP genotypes in a Rocky Mountain bighorn sheep (Ovis canadensis canadensis) population in an area of southwestern Alberta where beef cattle are grazed was an impetus to investigate whether strain sharing of MAP was occurring between these sympatric species. Finally, in Part 3, whole-genome sequencing was used to examine the diversity of the poorly characterized multi-host pathogen Erysipelothrix rhusiopathiae. Initially prompted by an investigation into large-scale muskox (Ovibos moschatus wardi) mortalities in the Canadian Arctic Archipelago associated with E. rhusiopathiae, the population structure and genomic variability of this bacterium were determined, while accounting for homologous recombination. This provided a framework within which to investigate the diversity of E. rhusiopathiae in muskoxen, caribou (Rangifer tarandus caribou) and moose (Alces alces), yielding important insights for delineating outbreaks and inferring transmission. In conclusion, this thesis clearly demonstrated the value of integrating molecular and genomic tools into wildlife health monitoring, including heightened pathogen detection, understanding multi-host diseases, and determining microbial diversity for interpreting outbreaks. Ultimately, as part of a multidisciplinary approach to studying wildlife health, these tools will greatly enhance our understanding of microbial diversity and epidemiology, and provide critical new knowledge to promote evidence-based wildlife conservation and management.
