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 病原体的壁虱和啮齿动物监视需要实质性的技术专业知识和实验室基础设施。 大多数监视活动侧重于检测矢量或储层中的一种或两种潜在病原体 人口和非目标病原体仍未发现。克服与 传统的壁虱监视方法，我们提出了一种新颖的双重元基因组和元文字组。 使用尖端纳米孔自适应采样（NAS）方案进行测序解决方案。 NAS方法利用 牛津纳米孔技术测序技术（便携式奴才序列）和最近开发的 生物信息学的管道促进单个核苷酸分子的立即映射（DNA，cDNA， 当每个分子测序时，或RNA）至给定参考。用户定义的阈值然后指定保留 或拒绝特定分子，以实时参考映射结果告知，因为它们在物理上是 通过给定的测序纳米孔。数百至成千上万个单独的测序毛孔是 使用功能强大的图形处理单元（GPU）和带有保留/拒绝的NAS软件实时控制 每个毛孔的决定不到一秒钟。这允许对非常宽的敏感检测 靶向病原体和宿主物种条形码序列的范围，而不会淹没在非 - 靶宿主和共生细菌核酸。该系统可以进行现场部署，需要最小 基础设施。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，特异性和 检测阈值），检测多种体外生长DNA和基于RNA的病原体的测试， 区分密切相关的病原体物种和菌株，开发和地面真相方案，用于现场测试 来自特征良好的地区（明尼苏达州）的野生tick虫和啮齿动物，并全面测试方法 和预测具有最高密度的啮齿动物相关的区域之一 在美国（堪萨斯州中部）的人畜共患病。我们希望NAS成为重要且负担得起的工具 各种监视应用。