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

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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.