Probing the natural genomic diversity of Babesia microti

描述(申请人提供)：人类巴贝斯虫病，一种类似疟疾的发热性疾病，是由微小巴贝斯虫(BM)引起的一种新的扁虱传播疾病，它与莱姆病病原体伯氏疏螺旋体处于类似的地方性循环。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缺陷宿主中导致约20%的死亡率。这种病原体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跨地理和宿主分布的病原体全基因组序列(WGS)。获取媒介传播病原体的完整多样性谱的唯一方法是直接从肩部硬蜱中测序，因为若虫以幼虫的形式取食所有潜在的水库宿主。然而，由于病原体的基因组大小相对于寄主来说很小，而且在混合DNA样本中它们的拷贝数往往很低，病原体的基因组信号被“外源”DNA淹没，导致下一代鸟枪式测序这些模板的效率低且成本高。需要一种新的方法来为流行病学和临床界提供各种下游应用的基因组资源。我们提出了一种新的不依赖于培养的方法来获得媒介传播的和人畜共患病原体的全基因组序列，允许直接从扁虱和人类血液样本中研究病原体的基因组变异，从而能够以前所未有的分辨率进行分析。具体地说，我们将采用以前在人类基因组分析中使用的DNA靶标捕获技术，在直接从野外采集的我肩胛虫的120个菌株以及从人血中采集的20个菌株中探索微小芽孢杆菌的基因组多样性。这种方法以前从未被应用于病媒传播和人畜共患病原体。利用这些基因组资源，我们将分析微小芽孢杆菌的遗传多样性格局，并表征微小杆菌在中国的传播规律。 美国东北部。这一探索性的分析将阐明微小杆菌空间结构的程度，识别人类感染株的来源，并使我们能够重建东北地区微小杆菌的入侵历史。结合对病原体种群结构的了解，我们将确定可能导致人类疾病的寄生虫库，从而为未来的疾病监测和控制战略做出贡献。这些基线数据将使未来旨在了解人类传染性潜在机制的流行病学研究和临床调查成为可能，并为寄生虫诊断提供与传染性和疾病严重性等重要特征的特定谱系变异相关的基础。

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.