Phylogeographic dynamics of tick-borne pathogens

蜱传病原体的系统发育地理学动态

• 批准号: 10630808
• 负责人: Dustin Brisson
• 金额: $ 46.7万
• 依托单位: UNIVERSITY OF PENNSYLVANIA
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-06-01 至 2024-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10630808
• 关键词: Affect; Anaplasma phagocytophilum; Babesia microti; Biological; Black-legged Tick; Borrelia burgdorferi; Data Set; Demography; Diffusion; Disease; Disease Vectors; Ecology; Emerging Communicable Diseases; Environment; Environmental Risk Factor; Evolution; Future; Genome; Genomic DNA; Geography; Growth; Knowledge; Modeling; Nature; New England; Pattern; Population; Population Dynamics; Population Growth; Process; Public Health; Research; Sampling; Site; Structure; System; Techniques; Technology; Ticks; Time; Vector-transmitted infectious disease; base; climatic factors; disorder control; disorder risk; emerging human pathogen; emerging pathogen; insight; microbial; microbial genome; microbial genomics; migration; next generation sequencing; novel; pathogen; prospective; tick-borne pathogen; vector-borne pathogen; whole genome

Vector-borne diseases are one of the most prevalent types of emerging infectious diseases worldwide and are a major threat to public health. Our collaborative team has used our extraordinary set of samples - which were collected during the time and space of a rapid range expansion of Ixodes scapularis ticks - to elucidate the environmental and climatic factors that facilitated the emergence of this disease vector in the Northeastern United States. The proposed research aims are to identify the patterns of, and processes affecting, the population dynamics of three important emerging human pathogens - Borrelia burgdorferi, Anaplasma phagocytophilum, and Babesia microti -by analyzing genome sequences in coalescent-based, phylodynamic analytical frameworks. The biological, environmental, and technical knowledge we have acquired, along with our ever-expanding sample set (75,887 tick samples from 515 sites over 14 years), provides a powerful system to identify environmental factors affecting the demography of these pathogens. We propose to use this dataset to (a) determine the current and historical dynamic patterns of 3 tick-borne pathogens; (b) identify and quantify the influence of environmental features on the demography of each microbial species; and (c) use prospective sampling to validate demographic models and the influence of environmental factors on migration and population growth. Characterizing the environmental factors that affect the demography of emerging pathogens at very fine scales is achievable through the application of sophisticated analyses to populations of genomes. To this end, we developed the selective whole genome amplification (SWGA) technique to generate sufficient quantities of microbial genomic DNA for next generation sequencing. Using this enabling technology, we can sequence hundreds of microbial genomes in order to develop mechanistic models describing how environmental factors impact migration and population growth; few examples are known of the functional bases determining the rates and directions of dispersal of pathogens in nature. The proposed phylogeographic diffusion modeling framework is ideally suited to assess how each species is geographically structured and to identify the environmental features associated with migration and growth. We will utilize the results of our proposed studies to develop and experimentally validate models that estimate future disease spread into novel environments. Uncovering common biotic and abiotic factors that influence the distribution and abundance of, and thus disease risk from, all of these vector-borne pathogens is immediately applicable to disease control strategies.

媒介传播疾病是全球最普遍的新兴传染病类型之一，是对公共卫生的主要威胁。我们的协作团队使用了我们的非凡样本，这些样本是在ixodes capapularis tick虫快速扩张的时间和空间中收集的 - 阐明了促进美国东北部该疾病载体出现的环境和气候因素。拟议的研究目的是确定三种重要的新出现的人类病原体的种群动态的模式和过程 - 伯氏伯氏菌，纳帕氏菌吞噬细胞噬菌体和Babesia microti -by -by分析基于煤层的基因组，天然动力学分析框架的基因组序列。我们获得的生物学，环境和技术知识以及我们不断扩展的样本集（从14年内的515个地点的75,887个壁虱样本）提供了一个强大的系统来识别影响这些病原体人口统计学的环境因素。我们建议将此数据集用于（a）确定3个tick传播病原体的当前和历史动态模式； （b）识别和量化环境特征对每种微生物物种人口统计学的影响； （c）使用前瞻性抽样来验证人口模型以及环境因素对迁移和人口增长的影响。通过将复杂的分析应用于基因组种群，可以实现影响非常细大病原体人口统计学的环境因素。为此，我们开发了选择性的全基因组扩增（SWGA）技术，以生成足够数量的微生物基因组DNA来进行下一代测序。使用这种启用技术，我们可以对数百个微生物基因组进行测序，以开发描述环境因素如何影响迁移和人口增长的机械模型。很少有人知道确定自然病原体分散率和方向的功能库。所提出的植物地理扩散建模框架非常适合评估每个物种在地理结构上的结构，并确定与迁移和生长相关的环境特征。我们将利用我们提出的研究的结果来开发和实验验证估计未来疾病扩散到新环境中的模型。探索影响所有这些载体传播病原体的常见生物和非生物因素，从而影响疾病的分布和丰度，从而影响疾病的风险，这立即适用于疾病控制策略。

项目成果

Epidemiology and Spatial Emergence of Anaplasmosis, New York, USA, 2010‒2018.

• DOI: 10.3201/eid2708.210133
• 发表时间: 2021-08
• 期刊: Emerging infectious diseases
• 影响因子: 11.8
• 作者: Russell A;Prusinski M;Sommer J;O'Connor C;White J;Falco R;Kokas J;Vinci V;Gall W;Tober K;Haight J;Oliver J;Meehan L;Sporn LA;Brisson D;Backenson PB
• 通讯作者: Backenson PB

Heartland Virus Transmission, Suffolk County, New York, USA.

• DOI: 10.3201/eid2712.211426
• 发表时间: 2021-12
• 期刊: Emerging infectious diseases
• 影响因子: 11.8
• 作者: Dupuis AP 2nd;Prusinski MA;O'Connor C;Maffei JG;Ngo KA;Koetzner CA;Santoriello MP;Romano CL;Xu G;Ribbe F;Campbell SR;Rich SM;Backenson PB;Kramer LD;Ciota AT
• 通讯作者: Ciota AT

Identification and characterization of novel lineage 1 Powassan virus strains in New York State.

• DOI: 10.1080/22221751.2022.2155585
• 发表时间: 2023-12
• 期刊: EMERGING MICROBES & INFECTIONS
• 影响因子: 13.2
• 作者: Lange, Rachel E.;Dupuis II, Alan P.;Prusinski, Melissa A.;Maffei, Joseph G.;Koetzner, Cheri A.;Ngo, Kiet;Backenson, Bryon;Oliver, JoAnne;Vogels, Chantal B. F.;Grubaugh, Nathan D.;Kramer, Laura D.;Ciota, Alexander T.
• 通讯作者: Ciota, Alexander T.

Host phenology can drive the evolution of intermediate virulence strategies in some obligate-killer parasites.

• DOI: 10.1111/evo.14507
• 发表时间: 2022-06
• 期刊: Evolution; international journal of organic evolution

A fast machine-learning-guided primer design pipeline for selective whole genome amplification.

• DOI: 10.1371/journal.pcbi.1010137
• 发表时间: 2023-04
• 期刊: PLoS computational biology
• 影响因子: 4.3