Analytical Track 4: Whole Genome Sequencing

摘要：项目 自2016年以来，北卡罗来纳州立大学(NCSU)一直参与食品和药物管理局(FDA) GenomeTrakr计划，并帮助在全球范围内扩展该计划。迫切需要国家 和食源性病原体的国际监测，因为尽管在卫生方面取得了重大进展，但食品和 在水质和病原体检测方面，食源性疾病仍然是公共卫生的巨大负担。 沙门氏菌、李斯特氏菌和产志贺毒素的大肠杆菌(STEC)等细菌病原体 食源性疾病是全球食源性疾病的主要原因，而且重要的是，不尊重国际边界。 环境和食品，如零售肉类和新鲜农产品，被认为是 食源性致病菌，建立对这些来源的标准化监测有助于监测 关键病原体和追踪污染途径，以预防和控制疫情。这样做的首要目标是 项目是加强以WGS为基础的与食源性疾病有关的细菌病原体的监测 在国家和全球一级使用“一个健康”的办法。这将通过以下方式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 在美国和世界范围内。调查人员拥有广泛的全球网络，由13个组织组成 横跨三大洲的国家。这包括塞内加尔的巴斯德·达喀尔研究所(IPD)，一个主要的 西非生物医学研究中心。总而言之，这一全球网络使NCSU实验室能够 对过去三年来自国际地点的1,127个细菌分离物进行了测序。要实现 为了实现该项目的总体目标，调查人员将追求以下具体目标。目标1：扩大 现有的沙门氏菌、李斯特氏菌、STEC和其他与食源性有关的细菌病原体的监测系统 已从美国和国际各地的食品和环境来源分离出来的疾病。这个 调查人员将生成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 全球范围内特定细菌病原体的概况。目的2：比较沙门氏菌、李斯特菌的WGS图谱 从国家和国际样本中分离出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。调查人员将继续进行基于生物信息学的 分析WGS图谱和相应的元数据以识别美国和美国新出现的细菌菌株 全球范围内。调查结果将通过NCBI平台共享，并与公共卫生机构共享，以告知控制和 干预策略。预期结果：通过鉴定来自国内和国际的400个新分离株 消息来源，这项工作将为食品安全界提供信息，以方便识别新的， 临床相关新出现的细菌菌株，并保障美国和全球公共健康。

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.