Probing the natural genomic diversity of Babesia microti

描述（由申请人提供）：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）引起的一种新出现的蜱传疾病，它与莱姆病病原体伯氏疏螺旋体保持相似的地方性循环。Bm是美国最常见的输血传播病原体，在输血接受者和其他免疫功能低下的宿主中导致约20%的死亡率。这种病媒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分布在其地理和宿主分布的病原体的足够数量的全基因组序列（WGS）。捕获媒介传播病原体完整多样性谱的唯一方法是直接从肩胛骨硬蜱的蜱虫幼虫中进行测序，因为蜱虫幼虫以所有潜在宿主为食。然而，由于病原体相对于宿主的基因组大小较小，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，使得这些模板的下一代霰弹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社区提供各种下游应用的基因组资源。我们提出了一种新的非培养方法，用于获得媒介传播和人畜共患病原体的全基因组序列，允许直接从蜱虫和人类血液样本中研究病原体基因组变异，从而实现前所未有的分辨率分析。具体而言，我们将采用先前用于人类基因组分析的DNA靶点捕获技术，对120株直接从野外采集的镰形蜱和20株从人类血液中采集的蜱虫进行基因组多样性探测。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，我们将分析现存小蠊的遗传多样性模式，并表征小蠊的传播模式

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.