Abstract
Bovine tuberculosis (bTB) is of low burden in New Zealand in comparison to many developing countries. However, the presence of an established wildlife reservoir of disease and a large farming industry makes the complete eradication of the disease incredibly difficult. The public health and economic burden of Mycobacterium bovis persistence in New Zealand has proven to be extensive. Since its divergence from the common ancestor of M. tuberculosis, M. bovis appears to have developed the ability to infect a wider host range, most likely due to acquired mutations thought to be a driving factor in its endurance within a wildlife reservoir. In many developed countries, persistence of bTB is due to its success at the human-livestock-wildlife interface. In New Zealand the livestock-wildlife interface appears to be driven by the maintenance host, the brushtail possum (Trichosurus vulpecula), and the continued transmission to domestic livestock (mainly cattle). However, the human-livestock-wildlife interface is yet to be characterised in New Zealand, the impact of which is vital towards pandemic preparedness and eventual eradication of the disease. Advancements in whole genome sequencing (WGS) takes a comprehensive look at the genome in its entirety, using single nucleotide polymorphisms (SNPs) to rapidly identify the route of transmission. In this study we incorporated the whole genome sequences of 505 animal isolates and 9 clinical isolates collected between 1948 and 2018 from throughout New Zealand. SNPs from the clinical and animal isolates were used to identify route of transmission of the disease at the human-livestock-wildlife interface of New Zealand. Through the study we identified 6 distinct clusters containing both animal and clinical isolates from both the North and South Island. This is the first study of its kind to analyse the human-livestock-wildlife interface within New Zealand by looking extensively at inter- and intra-species transmission as to decode risk factors for pandemic prevention and complete eradication of bTB in New Zealand. Resistance profiles of clinical and animal isolates were also uncovered to determine risk of the development of multi and extensively drug resistant strains within the population whilst also looking at SNPs present in clinical isolates and their effect on virulence and pathogenicity of the bacterium. This study sets a foundation leading the way for future research and implementation of preventative measures to eradicate the transmission of the disease.