DISSERTATION RESEARCH: Pathogen transmission in wild and domestic ungulates: Quantifying risk and identifying transmission routes among cattle and wildlife in central Kenya

野生动物疾病是一个公认的保护威胁和公共卫生问题，但关于疾病如何在野生动物种群中传播的信息却非常少。在这项研究中，微生物遗传学和网络分析相结合，以评估肯尼亚(I)网状长颈鹿种内病原体传播途径，以及（II）野生和家养食草动物（黑犀牛、格雷维斑马、长颈鹿、黑斑羚、水牛和牛）种间传播途径。我们对病原体传播动力学的了解是有限的，因为很难评估谁向谁传播。本项目使用大肠杆菌作为病原体传播的代理。如果两个人拥有基因相似的大肠杆菌亚型，就可以推断他们之间的传播。推断传播将用于在肯尼亚建立一个野生动物和牲畜传播网络。该项目的第一个组成部分调查了长颈鹿种群的空间和社会组织如何影响传播动态。第二个组成部分量化种间传播的程度和方向性，并确定对病原体传播有不成比例贡献的物种，称为“超级传播者”。在这项研究中包括的两个物种，格雷维？S斑马和黑犀牛是濒危物种，易受疾病相关种群数量下降的影响，这使得这项研究具有直接的保护意义。更广泛的影响。虽然通常不具有致病性，但大肠杆菌的传播途径表明接触足以发生传播。对这些途径的了解可以纳入疾病控制战略。理论上，对超级传播者进行有针对性的疫苗接种在限制疾病方面比传统的疫苗接种策略更有效，但是目前还没有在野生种群中识别超级传播者的方法。该项目的一个主要成果将是开发用于识别超级传播者和追踪野生动物传播途径的新工具。这是一种新颖的方法，将广泛应用于提高我们预测疾病影响的能力。

Wildlife diseases are a recognized conservation threat and public health concern, yet there is remarkably little information on how diseases spread through wildlife populations. In this study, microbial genetics and network analysis are integrated to assess routes of (I) intraspecific pathogen transmission in reticulated giraffe, and (II) interspecific transmission between wild and domestic herbivores (black rhinoceros, Grevy's zebra, giraffe, impala, buffalo, and cattle) in Kenya. Our understanding of the dynamics of pathogen transmission is limited because it is difficult to assess who transmitted to whom. This project uses Escherichia coli as a proxy for pathogen transmission. Transmission between two individuals can be inferred if they share genetically similar subtypes of E. coli. Inferred transmission will be used to construct a transmission network for wildlife and livestock in Kenya. The first component of this project investigates how the spatial and social organization of the giraffe population influences transmission dynamics. The second component quantifies the extent and directionality of interspecific transmission and identifies species that contribute disproportionately to pathogen spread, termed "super-spreaders." Two of the species included in this study, the Grevy?s zebra and black rhinoceros, are endangered and vulnerable to disease-related population declines, which gives this study immediate conservation relevance. Broader impacts. Although not usually pathogenic, E. coli transmission routes demonstrate where contact is sufficient for transmission to occur. Knowledge of these routes can be incorporated into disease control strategies. Targeted vaccination of super-spreaders is theoretically more effective at limiting disease than conventional vaccination strategies, but there are no existing methods to identify super-spreaders in wild populations. A major outcome of this project will be to develop new tools for identifying super-spreaders and tracing transmission routes in wildlife. This is a novel approach and will be broadly applicable in improving our ability to predict the impacts of disease.