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

Bovine tuberculosis (bTB), caused by Mycobacterium bovis, is an important livestock disease raising public health and economic concerns around the world. In New Zealand, a number of wildlife species are implicated in the spread and persistence of bTB in cattle populations, most notably the brushtail possum (Trichosurus vulpecula). Whole Genome Sequenced (WGS) M. bovis isolates sourced from infected cattle and wildlife across New Zealand were analysed. Bayesian phylogenetic analyses were conducted to estimate the substitution rate of the sampled population and investigate the role of wildlife. In addition, the utility of WGS was examined with a view to these methods being incorporated into routine bTB surveillance. A high rate of exchange was evident between the sampled wildlife and cattle populations but directional estimates of inter-species transmission 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, acts to endorse WGS as a typing tool. In agreement with the current knowledge of bTB in New Zealand, transmission of M. bovis between cattle and wildlife was evident. Without direction, these estimates are less informative but taken in conjunction with the low prevalence of bTB in New Zealand’s cattle population it is likely that, currently, wildlife populations are acting as the main bTB reservoir. Wildlife should therefore continue to be targeted if bTB is to be eradicated from New Zealand. WGS will be a considerable aid to bTB eradication by greatly improving the discriminatory power of molecular typing data. The substitution rates estimated here will be an important part of epidemiological investigations using WGS data. The online version of this article (doi:10.1186/s12864-017-3569-x) contains supplementary material, which is available to authorized users.

牛结核病（bTB）由牛分枝杆菌引起，是一种重要的家畜疾病，在全球引发了公共卫生和经济方面的担忧。在新西兰，许多野生动物物种与牛群中牛结核病的传播和持续存在有关，其中最显著的是帚尾袋貂（Trichosurus vulpecula）。对来自新西兰各地感染的牛和野生动物的全基因组测序（WGS）牛分枝杆菌分离株进行了分析。进行了贝叶斯系统发育分析以估计抽样群体的替代率并调查野生动物的作用。此外，还检验了WGS的实用性，以期将这些方法纳入常规的牛结核病监测中。 抽样的野生动物和牛群之间存在明显的高交换率，但种间传播的定向估计对所采用的抽样策略敏感。估计出相对较高的替代率，这与强烈的空间特征以及与先前分型方法的良好一致性相结合，使得WGS成为一种分型工具得到认可。 与新西兰对牛结核病的现有认识一致，牛分枝杆菌在牛和野生动物之间的传播是明显的。没有方向的话，这些估计的信息量较小，但结合新西兰牛群中牛结核病的低患病率来看，目前野生动物种群很可能是牛结核病的主要储存宿主。因此，如果要在新西兰根除牛结核病，就应该继续以野生动物为目标。WGS将通过大大提高分子分型数据的鉴别能力，对根除牛结核病有很大帮助。这里估计的替代率将是使用WGS数据进行流行病学调查的重要部分。 本文的在线版本（doi:10.1186/s12864 - 017 - 3569 - x）包含补充材料，授权用户可获取。