Understanding the epidemiology of pathogen transmission across the human-wildlife-livestock interface using environmental surveillance and metagenomic

利用环境监测和宏基因组了解病原体在人类-野生动物-牲畜界面传播的流行病学

• 批准号: 2888376
• 金额: --
• 依托单位: University of Aberdeen
• 依托单位国家: 英国
• 项目类别: Studentship
• 财政年份: 2023
• 资助国家: 英国
• 起止时间: 2023 至 无数据
• 项目状态: 未结题
• 来源: https://gtr.ukri.org/projects?ref=studentship-2888376
• 关键词: Understanding; epidemiology; pathogen; transmission; across

Environmentally transmitted pathogens are responsible for some of the most important zoonoses and livestock diseases in the world. The epidemiology of these diseases is often complex, with environments, such as water sources, playing a crucial role as interfaces across which transmission can occur between multiple host species. There is increasing evidence that the diversity of multi-host, environmentally transmitted pathogens is underestimated, and that virulence and the importance of environmental transmission may differ between species or strains, even within the same pathogen genera. Therefore, characterising the diversity of these pathogens in the environment is crucial to improving diagnostic assays, identifying which strains are responsible for human and livestock disease and predicting and mitigating disease risk. Many environmentally transmitted pathogens are exceptionally challenging and time consuming to culture, making traditional microbiological approaches to characterising pathogen diversity difficult. However, rapid advances in whole genome and marker gene metagenomic approaches and portable DNA sequencing technologies are revolutionising our ability to isolate and sequence target DNA from complex sample matrices, such as environmental samples, or samples with low levels of target DNA, such as clinical samples. These approaches, which enable characterisation of pathogen diversity from field samples without requiring culture, are particularly useful in the developing world where the specialised facilities and capacity required for culturing pathogens may be lacking. Leptospira spp. are some of the world's most common environmentally transmitted pathogens, responsible for an estimated 60000 human deaths a year and significant livestock productivity loss, with the greatest burden of disease falling on the poorest communities in the developing world. Humans and livestock are predominantly infected through contact with environments, such as water sources, contaminated with urine from infected maintenance hosts. In Africa, recent studies have identified a wide diversity of Leptospira strains, many of which are not represented in any reference culture collections, in small mammals and livestock. Although these findings suggest that the diversity of potentially pathogenic Leptospira spp. in Africa is underestimated, sampling the broad range of potential reservoir hosts in Africa would be logistically unfeasible. Building on existing and ongoing projects in South Africa, Madagascar, Tanzania and Scotland, this project will use samples from potentially contaminated environments, data from concurrent wildlife reservoir host sampling and clinical samples from humans and livestock to i) characterise the diversity of potentially pathogenic Leptospira strains in the environment, ii) identify the strains responsible for human and livestock disease, iii) tailor existing assays to improve the diagnosis of leptospirosis and iv) explore how results could be used to inform strategies aimed at mitigating disease risk for humans and livestock.

环境传播的病原体负责世界上一些最重要的人畜共患病。这些疾病的流行病学通常很复杂，环境（例如水源）起着至关重要的作用，就像在多种宿主物种之间可能发生传播的界面。越来越多的证据表明，多宿主，环境传播病原体的多样性被低估了，即使在同一病原体属中，毒力和环境传播的重要性也可能有所不同。因此，表征这些病原体在环境中的多样性对于改善诊断测定法至关重要，确定哪些菌株导致人类和牲畜疾病以及预测和减轻疾病风险。许多环境传播的病原体对文化具有极具挑战性和耗时的作用，使传统的微生物学方法变得困难地表征了病原体多样性。然而，整个基因组和标记基因宏基因组方法和便携式DNA测序技术的快速进步正在彻底改变我们与复杂样品矩阵的分离和序列靶向DNA的能力，例如环境样品，例如环境样品，或靶DNA水平较低的样品，例如临床样品。这些方法在不需要文化的情况下能够从现场样本中表征病原体多样性，在可能缺乏培养病原体所需的专门设施和能力的发展中国家中特别有用。 Leptospira spp。是一些世界上最常见的环境传播病原体，估计每年有60000人死亡和牲畜生产率损失，疾病的最大负担落在了发展中国家最贫穷的社区上。人类和牲畜主要是通过与环境（例如水源接触）受感染的，被感染维护宿主污染的环境（例如水源）。在非洲，最近的研究发现了各种各样的钩端螺旋体菌株，其中许多菌株在任何参考培养物收集中均不代表，在小型哺乳动物和牲畜中。尽管这些发现表明潜在的致​​病性钩端螺旋体属的多样性。在非洲被低估了，在非洲，在非洲的广泛储层托管中取样将是不可行的。该项目以南非，马达加斯加，坦桑尼亚和苏格兰的现有和正在进行的项目为基础，该项目将使用潜在污染环境的样本，来自并发的野生动植物储藏宿主的数据数据，以及来自人类的临床样本，并从人类和i）临床，以表征潜在的致病性lunterain and and perive and and and perive and perive and and perive and and perive ant in the Enviment ii rivest ii rivest ii rivest inii selterains inii restains ii ii ii），II）改善钩端螺旋体病和IV的诊断的测定法探索如何使用结果来告知旨在减轻人类和牲畜疾病风险的策略。