New tools for tick-borne pathogen surveillance

蜱传病原体监测新工具

• 批准号: 10585613
• 负责人: Peter A Larsen
• 金额: $ 68.99万
• 依托单位: UNIVERSITY OF MINNESOTA
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-12-08 至 2027-11-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10585613
• 关键词: Anaplasma phagocytophilum; Arthropod Vectors; Arthropods; Bacteria; Bar Codes; Biological; Black-legged Tick; Borrelia; Borrelia burgdorferi; Borrelia mayonii; Collection; Communities; Complementary DNA; Computer software; Coupled; DNA; Data; Decision Making; Detection; Diagnostic; Disease; Disease Outbreaks; Disease Surveillance; Early Diagnosis; Eukaryota; Future; Genome; Geography; Goals; In Vitro; Incidence; Individual; Infrastructure; Internet; Kansas; Laboratories; Location; Lyme Disease; Maintenance; Maps; Measures; Metagenomics; Methods; Minnesota; Molecular; Monitor; Morphology; Nucleic Acids; Nucleotides; Organism; Pathogen detection; Pathogenicity; Peromyscus; Phylogenetic Analysis; Play; Population; Protocols documentation; Protozoa; Provider; Public Health; RNA; RNA Viruses; Research; Research Personnel; Reverse Transcriptase Polymerase Chain Reaction; Rodent; Role; Sampling; Sea; Source; Specific qualifier value; Specificity; Surveillance Methods; System; Technical Expertise; Techniques; Technology; Testing; Tick-Borne Diseases; Ticks; Time; Training; Uncertainty; United States; Variant; Vector-transmitted infectious disease; Virus; Virus Diseases; Zoonoses; bioinformatics pipeline; cost effective; detection test; diagnostic accuracy; disease transmission; effective intervention; emerging pathogen; experience; exposed human population; field study; metatranscriptomics; microorganism; mitochondrial genome; multidisciplinary; nanopore; next generation; next generation sequencing; novel; pathogen; portability; predictive modeling; skills; tick transmission; tick-borne; tick-borne pathogen; time use; tool; vector; vector tick; vector-borne pathogen

Project Summary Tick and rodent surveillance for pathogens requires substantial technical expertise and laboratory infrastructure. Most surveillance activities focus on detection of one or two potential pathogens in the vector or reservoir population and non-target pathogens remain undetected. To overcome the current limitations associated with traditional tick surveillance methods, we are proposing a novel dual metagenomic and metatranscriptomic sequencing solution using cutting-edge nanopore adaptive sampling (NAS) protocols. The NAS method leverages Oxford Nanopore Technologies sequencing technology (a portable MinION sequencer) and a recently developed bioinformatic pipeline that facilitates the immediate mapping of individual nucleotide molecules (DNA, cDNA, or RNA) to a given reference as each molecule is sequenced. User-defined thresholds then specify the retention or rejection of specific molecules, informed by the real-time reference mapping results as they are physically passing through a given sequencing nanopore. Hundreds to thousands of individual sequencing pores are controlled in real-time using a powerful Graphics Processing Unit (GPU) and the NAS software with retain/reject decisions made in less than a second for each individual pore. This allows for sensitive detection of a very wide range of targeted pathogen and host species barcoding sequences without becoming swamped in the sea of non- target host and symbiotic bacterial nucleic acids. The system can be field deployed and requires minimal infrastructure. An internet connection is not required. In the course of this proposed study, we will test NAS for diagnostic accuracy (sensitivity, specificity, and threshold of detection), test for detection of a variety of in vitro grown DNA and RNA-based pathogens, differentiate closely related pathogen species and strains, develop and ground truth protocols for field testing on wild ticks and rodents from a well-characterized region (Minnesota), and comprehensively field test the methods and protocols in a region predicted to have the one of the highest densities of emerging rodent-associated zoonoses in the US (central Kansas). We expect NAS to become an important and affordable tool with a wide variety of surveillance applications.

项目摘要 蜱虫和啮齿动物病原体监测需要大量的技术专门知识和实验室基础设施。 大多数监测活动侧重于检测病媒或宿主中的一种或两种潜在病原体 人群和非目标病原体仍未被发现。为了克服目前的局限性， 传统的蜱监测方法，我们提出了一种新的双重宏基因组和元转录组学 使用尖端的纳米孔自适应采样（NAS）协议的测序解决方案。NAS方法利用 Oxford Nanopore Technologies测序技术（便携式MinION测序仪）和最近开发的 生物信息学管道，其促进单个核苷酸分子（DNA，cDNA， 或RNA）与给定参照的比对。然后，用户定义的阈值指定保留时间 或排斥特定的分子，由实时参考映射结果告知，因为它们是物理上的 通过给定的测序纳米孔。数百到数千个单独的测序孔被 使用强大的图形处理单元（GPU）和支持保留/拒绝功能的NAS软件进行实时控制 在不到一秒的时间内为每个毛孔做出决定。这允许灵敏地检测非常宽的 目标病原体和宿主物种条形码序列的范围，而不会淹没在非 靶向宿主和共生细菌核酸。该系统可以现场部署， 基础设施演进不需要互联网连接。 在这项拟议的研究过程中，我们将测试NAS的诊断准确性（敏感性，特异性， 检测阈值），用于检测多种体外生长的基于DNA和RNA的病原体的测试， 区分密切相关的病原体物种和菌株，制定实地测试方案， 野生蜱和啮齿类动物从一个良好的特点地区（明尼苏达州），并全面实地测试的方法 和协议在一个地区预测有一个最高密度的新兴啮齿动物相关的 美国（堪萨斯中部）的人畜共患病。我们希望NAS成为一种重要且经济实惠的工具， 各种监控应用。