Using whole genome sequencing to investigate transmission in a multi-host system: bovine Tuberculosis in New Zealand

Elucidating the role of different hosts in multi-host systems is paramount to efficient and effective control. The role of reservoirs in the maintenance of bTB in domestic livestock populations has been investigated around the world. Despite being a focus of current research, the extent and direction of exchange of Mycobacterium bovis between livestock and wildlife populations has been largely unquantified. In New Zealand, a number of wildlife species are implicated in the spread and persistence of bovine Tuberculosis (bTB) in cattle populations, most notably the brushtail possum (Trichosurus vulpecula). Whole Genome Sequenced (WGS) isolates taken from infected cattle and wildlife across New Zealand were analysed. Bayesian phylogenetic analyses were conducted using the program BEAST to investigate the mutation rate in this bovine TB cycle and characterise the role wildlife populations in the maintenance of M. bovis infection in the cattle population. In addition, the utility of WGS techniques was examined with a view to these methods being incorporated in routine bTB surveillance. A high rate of exchange was evident between the sampled wildlife and cattle populations. Directional estimates of exchange were sensitive to the sampling strategy employed. A relatively high substitution rate was estimated, this, in combination with a strong spatial signature and a good agreement to previous typing methods, act to endorse WGS as a typing tool.