Analytical Track 4: Whole Genome Sequencing

分析专题 4：全基因组测序

• 批准号: 10175629
• 负责人: Siddhartha Thakur
• 金额: $ 15.18万
• 依托单位: NORTH CAROLINA STATE UNIVERSITY RALEIGH
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-09-01 至 2025-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10175629
• 关键词: Analytical; Track; Whole; Genome; Sequencing

Summary: Project Since 2016, North Carolina State University (NCSU) has participated in the Food and Drug Administration (FDA) GenomeTrakr program and helped expand the program on a global scale. There is an urgent need for national and international surveillance of foodborne pathogens because despite major advances in hygiene, food and water quality and pathogen detection, foodborne illnesses remain a tremendous burden for public health. Bacterial pathogens such as Salmonella, Listeria and Shiga toxin-producing Escherichia coli (STEC) are among the leading causes of foodborne illnesses worldwide and importantly, do not respect international boundaries. The environment and food products such as retail meats and fresh produce have been implicated as sources of foodborne bacterial pathogens, and establishing standardized surveillance of these sources can help monitor key pathogens and trace contamination routes to prevent and control outbreaks. The overarching aim of this project is to enhance WGS-based surveillance of bacterial pathogens associated with foodborne illness at the national and global level using a One Health approach. This will improve and protect public health by strengthening the surveillance of drug-resistant bacterial pathogens in human, animal and environmental sectors in the US and worldwide. The investigators have an extensive global network comprised of organizations in 13 countries spanning three continents. This includes the Institut Pasteur de Dakar (IPD) in Senegal, a major biomedical research center for West Africa. Altogether, this global network has enabled NCSU laboratories to sequence 1,127 bacterial isolates from international locations over the last three years. To achieve the overarching goal of the project, the investigators will pursue the following specific aims. Aim 1: Expand the existing surveillance system of Salmonella, Listeria, STEC and other bacterial pathogens related to foodborne illness that have been isolated from food and environmental sources in the US and international locations. The investigators will generate WGS profiles of 400 isolates, including 300 from the US and 100 from outside the US. Through collaborations with global partners, they will continue to expand the GenomeTrakr database of WGS profiles for specific bacterial pathogens on a global scale. Aim 2: Compare WGS profiles of Salmonella, Listeria and STEC isolated from national and international samples to advance outbreak investigations and track emerging strains of public health importance. The investigators will continue to conduct bioinformatics-based analysis of WGS profiles and corresponding metadata to identify new emerging bacterial strains in the US and globally. Findings will be shared via the NCBI platform and with public health agencies to inform control and intervention strategies. Expected outcomes: By characterizing 400 new isolates from national and international sources, this work will provide the food safety community with information to facilitate the identification of new, clinically relevant emerging bacterial strains, and safeguard US and global public health.

摘要：项目 自2016年以来，北卡罗来纳州州立大学（NCSU）参与了美国食品药品监督管理局（FDA） GenomeTrakr计划，并帮助在全球范围内扩大该计划。迫切需要国家 和国际监测食源性病原体，因为尽管在卫生，食品和 除了水质和病原体检测外，食源性疾病仍然是公共卫生的巨大负担。 细菌病原体如沙门氏菌、李斯特菌和产滋贺毒素的大肠杆菌（STEC）是 全球食源性疾病的主要原因，重要的是，不尊重国际边界。 环境和食品，如零售肉类和新鲜农产品已被牵连的来源， 食源性细菌病原体，并建立这些来源的标准化监测，可以帮助监测 关键病原体和追踪污染途径，以预防和控制疫情。这项工作的首要目标是， 该项目旨在加强基于WGS的食源性疾病相关细菌病原体监测 在国家和全球一级使用一个健康方法。这将改善和保护公众健康， 加强对人类、动物和环境部门耐药细菌病原体的监测 在美国和世界各地。调查人员拥有广泛的全球网络，由13个国家的组织组成。 横跨三大洲的国家。这包括塞内加尔的达喀尔巴斯德研究所， 西非生物医学研究中心总而言之，这个全球网络使NCSU实验室能够 在过去三年中，对来自世界各地的1，127个细菌分离株进行了测序。实现 为了实现该项目的总体目标，调查人员将努力实现以下具体目标。目标1：扩大 现有的沙门氏菌、李斯特菌、STEC和其他与食源性相关的细菌性病原体的监测系统 在美国和国际地区从食品和环境来源中分离出来的疾病。的 研究人员将生成400个分离株的WGS图谱，其中300个来自美国，100个来自美国以外。 通过与全球合作伙伴的合作，他们将继续扩大WGS的GenomeTrakr数据库 在全球范围内对特定细菌病原体进行分析。目的2：比较沙门氏菌、李斯特菌的WGS图谱 和从国家和国际样本中分离出的STEC，以推进疫情调查和跟踪 新出现的对公共卫生具有重要意义的菌株。研究人员将继续进行基于生物信息学的 分析WGS概况和相应的元数据，以识别美国新出现的细菌菌株， 在全球调查结果将通过NCBI平台与公共卫生机构共享，以告知控制和 干预策略。预期结果：通过表征来自国家和国际的400株新分离株 这项工作将为食品安全界提供信息，以促进识别新的， 临床相关的新出现的细菌菌株，并保护美国和全球公众健康。