Probing the natural genomic diversity of Babesia microti

探究田鼠巴贝虫的自然基因组多样性

• 批准号: 9064063
• 负责人: CHOUKRI BEN MAMOUN
• 金额: $ 24.98万
• 依托单位: YALE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-05-07 至 2019-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9064063
• 关键词: Babesia microti; Babesiosis; Black-legged Tick; Blood; Blood specimen; Borrelia burgdorferi; Borrelia microti; Cataloging; Catalogs; Clinical; Collection; Communities; Comparative Genomic Analysis; DNA; Data; Diagnostic; Disease; Epidemiologic Studies; Epidemiology; Fever; Future; Genetic; Genetic Structures; Genetic Variation; Genomic approach; Genomics; Geographic Locations; Goals; Health; Human; Human Characteristics; Immunocompromised Host; Incidence; Invaded; Investigation; Larva; Lyme Disease; Malaria; Methods; Molecular; Molecular Analysis; Monitor; Nature; New England; Nymph; Outcome; Parasites; Pathogenesis; Pathogenicity; Patients; Pattern; Phylogenetic Analysis; Pilot Projects; Polymorphic Microsatellite Marker; Population; Recording of previous events; Research; Resolution; Resources; Sampling; Severity of illness; Shotgun Sequencing; Signal Transduction; Stream; Structure; System; Techniques; Tick-Borne Diseases; Ticks; Time; Transfusion; United States; Variant; Virulence; Work; base; clinical investigation; comparative; design; disorder control; enzootic; feeding; genome sequencing; genome wide association study; genome-wide; genomic data; genomic variation; human disease; insight; mortality; next generation; next generation sequencing; novel; novel strategies; pathogen; pathogen genome; trait; transmission process; vector; whole genome

DESCRIPTION (provided by applicant): Human babesiosis, a malaria-like febrile illness is an emerging tick-borne disease caused by Babesia microti (Bm), which is maintained in a similar enzootic cycle as Borrelia burgdorferi, the Lyme disease agent. Bm is the most common transfusion-transmitted pathogen in the United States and results in a ~20% mortality rate in transfusion recipients and other immunocompromised hosts. A critical bottleneck for epidemiological and evolutionary studies of this and other vector-borne pathogens has been the difficulty in obtaining sufficient numbers of whole genome sequences (WGS) of pathogens distributed across their geographic and host distribution. The only means to capture the complete diversity spectrum of vector-borne pathogens is to sequence directly from Ixodes scapularis nymphal ticks, because nymphs feed as larvae on all potential reservoir hosts. However, because of the small genomic size of the pathogen relative to the host, and their often low copy number in mixed DNA samples, the pathogen's genome signal is swamped by "exogenous" DNA, rendering next generation shotgun sequencing for these templates inefficient and costly. A novel approach is required to provide the epidemiological and clinical communities with genomic resources for a variety of downstream applications. We propose a novel culture-independent method for deriving whole genome sequences for vector-borne and zoonotic pathogens, allowing pathogen genomic variation to be studied directly from tick and human blood samples and thus enabling analyses at an unprecedented resolution. Specifically, we will adapt DNA target capture techniques, previously used in human genomic analyses, to probe the genomic diversity of B. microti in 120 strains sampled directly from field collected I. scapularis ticks, as well as 20 strains from human blood. This approach has never before been applied to vector-borne and zoonotic pathogens. Using these genomic resources, we will analyze the patterns of standing B. microti genetic diversity and characterize patterns of B. microti spread in the northeastern United States. This exploratory analysis will elucidate the degree of B. microti spatial population structure, identify the origin of human infective strains, and enable us to reconstruct B. microti invasion history across the Northeast. Together with understanding of the pathogen population structure, we will define the pool of parasites that can give rise to human disease, thereby contributing to future disease surveillance and control strategies. These baseline data will enable future epidemiological studies and clinical investigations aimed at understanding the mechanisms underlying human infectivity and provide the basis for parasite diagnostics relative to lineage-specific variation in important traits such as infectivity and disease severity.

描述（由申请人提供）：人类巴贝斯虫病是一种类似疟疾的发热性疾病，是一种由微小巴贝斯虫 (Bm) 引起的新出现的蜱传疾病，其与莱姆病病原体伯氏疏螺旋体保持相似的地方性动物流行周期。 Bm 是美国最常见的输血传播病原体，导致输血受者和其他免疫功能低下宿主的死亡率约为 20%。这种和其他媒介传播病原体的流行病学和进化研究的一个关键瓶颈是难以获得足够数量的分布在其地理和宿主分布范围内的病原体的全基因组序列（WGS）。捕获媒介传播病原体完整多样性谱的唯一方法是直接对肩突硬蜱若虫蜱进行测序，因为若虫以幼虫的形式捕食所有潜在的储存宿主。然而，由于病原体相对于宿主的基因组较小，并且它们在混合 DNA 样本中的拷贝数通常较低，病原体的基因组信号被“外源”DNA 淹没，导致这些模板的下一代鸟枪测序效率低下且成本高昂。需要一种新的方法来为流行病学和临床界提供用于各种下游应用的基因组资源。我们提出了一种新颖的独立于培养物的方法，用于获取媒介传播和人畜共患病原体的全基因组序列，允许直接从蜱和人类血液样本中研究病原体基因组变异，从而能够以前所未有的分辨率进行分析。具体来说，我们将采用以前用于人类基因组分析的 DNA 目标捕获技术来探测直接从现场收集的肩胛蜱蜱中取样的 120 株田鼠小蜱以及来自人类血液的 20 株菌株的基因组多样性。这种方法以前从未应用于媒介传播和人畜共患病原体。利用这些基因组资源，我们将分析田鼠小虱的遗传多样性模式，并描述田鼠小虱在以下地区的传播模式： 美国东北部。这项探索性分析将阐明田鼠巴氏杆菌空间种群结构的程度，确定人类感染菌株的起源，并使我们能够重建田鼠伯克虫在东北地区的入侵历史。结合对病原体种群结构的了解，我们将定义可引起人类疾病的寄生虫库，从而为未来的疾病监测和控制策略做出贡献。这些基线数据将使未来的流行病学研究和临床调查成为可能，旨在了解人类感染性的机制，并为与感染性和疾病严重程度等重要特征的谱系特异性变异相关的寄生虫诊断提供基础。