South Africa-Pittsburgh Public Health Genomic Epidemiology Research Training Program (SAPPHGenE)

摘要 公共卫生基因组学是一个新兴的领域，涉及利用病原体基因组， 全面表征人类病原体。这包括监测抗菌素耐药性， 确定疫苗可预防的负担，监测免疫接种计划的影响，以及检测 控制与医疗保健和社区相关的疫情，并研究传播动力学。 然而，尽管这一领域的重要性日益增加，但非洲公共卫生基因组学的科学能力 是有限的。为了解决这个问题，我们建议建立南非-匹兹堡公共卫生基因组 流行病学研究培训计划（SAPPHGenE）在匹兹堡大学（皮特），领先的 美国国家传染病研究所（NICD）， 南非约翰内斯堡的主要国家公共卫生参考和研究机构。整体 SAPPHGenE的使命是为南非年轻的公共卫生和学术研究人员提供来自 历史上处于不利地位的背景，需要多学科的工具来进行尖端的 公共卫生基因组学研究。主要重点是流行病学和基因组流行病学的研究 肺炎、其他呼吸道疾病以及侵袭性细菌和真菌疾病的细菌原因， 包括抗微生物剂抗性病原体。该计划主任是李哈里森博士，教授 他是皮特大学流行病学和医学研究所微生物基因组流行病学实验室的负责人。 安妮·冯·戈特伯格，呼吸系统疾病和脑膜炎中心实验室主任， NICD。该计划包括一个多学科小组的经验丰富的导师在三个培训地点：皮特， 亚特兰大疾病控制和预防中心，以及NICD。我们将提供非学位的组合 和研究生（硕士和博士）学位培训。学位将由该大学提供。 威特沃特斯兰德，位于15公里的NICD，和学位研究使用南非的数据和 在亚特兰大和匹兹堡的训练基地进行的标本。学员将有机会获得 培训地点提供的大量研究培训机会和资源。重点将 包括基因组流行病学和生物信息学方面的培训，重点是使用这些学科 在公共卫生方面。该方案的最终目标是提供当地监测、预防和控制能力 我们的目标是细菌和真菌疾病，其中一些是疫苗可预防的或抗微生物药物耐药的， 所有这些都是南非、非洲其他地区和全球发病率和死亡率的主要原因。的 本申请中描述的培训机会将大大提高研究能力， 在南非培养一代公共卫生基因组研究导师。最终我们 预计NICD将作为非洲的区域培训中心，用于公共卫生研究和实践， 非洲的健康基因组学。

ABSTRACT Public health genomics is a burgeoning field that involves the exploitation of the pathogen genome to comprehensively characterize human pathogens. This includes the monitoring of antimicrobial resistance, determining vaccine-preventable burden, monitoring the impact of immunization programs, as well as detecting and controlling healthcare- and community-associated outbreaks and studying transmission dynamics. However, despite the increasing importance of this field, scientific capacity in public health genomics in Africa is limited. To address this problem, we propose to establish the South Africa-Pittsburgh Public Health Genomic Epidemiology Research Training Program (SAPPHGenE) at the University of Pittsburgh (Pitt), a leading research institution in the United States and the National Institute for Communicable Diseases (NICD), a premier national public health reference and research institution in Johannesburg, South Africa. The overall mission of SAPPHGenE is to provide young South African public health and academic investigators from historically-disadvantaged backgrounds with the multidisciplinary tools needed to conduct cutting-edge research on public health genomics. The main focus is research on epidemiology and genomic epidemiology of bacterial causes of pneumonia, other respiratory diseases, and invasive bacterial and fungal diseases, including antimicrobial-resistant pathogens. The Program Directors are Dr. Lee Harrison, Professor of Epidemiology and Medicine and the head of the Microbial Genomic Epidemiology Laboratory at Pitt and Dr. Anne von Gottberg, Section Lead of the laboratory of the Centre for Respiratory Diseases and Meningitis at the NICD. The program includes a multidisciplinary group of experienced mentors at three training sites: Pitt, the Centers for Disease Control and Prevention in Atlanta, and NICD. We will provide a combination of non-degree and post-graduate (masters and PhD) degree training. Degrees will be provided by the University of the Witwatersrand, located 15 kilometers from NICD, and the degree research using South African data and specimens being conducted at the training sites in Atlanta and Pittsburgh. Trainees will have access to substantial research training opportunities and resources that are available at the training sites. The focus will encompass training in genomic epidemiology and bioinformatics, with emphasis on the use of these disciplines in public health. The ultimate goal of the program is to provide local capacity to monitor, prevent, and control our target bacterial and fungal diseases, some of which are vaccine preventable or antimicrobial resistant and all which are major causes of morbidity and mortality in South Africa, the rest of Africa, and globally. The training opportunities described in this application will substantially increase research capacity and foster the development of a generation of public health genomic research mentors in South Africa. Ultimately, we anticipate that NICD will serve as regional training center within Africa for research in and practice of public health genomics in Africa.