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（由申请方提供）：人类巴贝西虫病是一种疟疾样发热性疾病，是一种新出现的蜱传疾病，由小Babalyprotimicroti（Bm）引起，与莱姆病病原体伯氏疏螺旋体（Borrelia burgdorferi）保持相似的地方性流行周期。BM是美国最常见的输血传播病原体，在输血受者和其他免疫功能低下的宿主中导致约20%的死亡率。这种和其他媒介传播的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的病原体的全基因组序列（WGS）。捕获病媒传播病原体的完整多样性谱的唯一方法是直接从肩突硬蜱若虫蜱中测序，因为蜱虫作为幼虫在所有潜在的储存宿主上进食。然而，由于病原体相对于宿主的小基因组大小，以及它们在混合DNA样品中的通常低拷贝数，病原体的基因组信号被“外源性”DNA淹没，使得这些模板的下一代鸟枪测序效率低且成本高。需要一种新的方法来为流行病学和临床社区提供用于各种下游应用的基因组资源。我们提出了一种新的文化独立的方法来获得全基因组序列的媒介传播和人畜共患病原体，允许病原体基因组变异直接从蜱和人类血液样本进行研究，从而使分析在一个前所未有的分辨率。具体来说，我们将采用以前用于人类基因组分析的DNA靶捕获技术来探测B的基因组多样性。从田间直接采集的120个菌株中，I.肩胛蜱以及20种来自人类血液的菌株。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，我们将分析站立B的模式。B的遗传多样性和特征模式。显微镜检查 美国东北部。该探索性分析将阐明B的程度。microti空间种群结构，确定人类感染菌株的起源，使我们能够重建B。东北地区的田鼠入侵史结合对病原体种群结构的了解，我们将确定可能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，旨在了解潜在的人类感染性的机制，并提供基础的寄生虫诊断相对于谱系特异性变异的重要特征，如感染性和疾病的严重程度。