The South Africa – Pittsburgh Public Health Genomic Epidemiology (SAPPHGenE) Training Program was established as a collaborative effort between the University of Pittsburgh (Pitt) in the United States, and the National Institute for Communicable Diseases (NICD), Johannesburg, South Africa. The programme involves the multidisciplinary training of young South African health and academic researchers from historically-disadvantaged backgrounds, focusing on the genomic epidemiology of respiratory disease-causing bacterial and fungal pathogens of importance in South Africa and globally. The overall aim is to improve the public health genomics scientific capacity in South Africa and ultimately in Africa, by implementing genomics characterization to improve the swift detection and control of healthcare and community outbreaks, understanding transmission dynamics, monitoring of antimicrobial resistance and impact of immunization programs. The programme directors are Professor Lee Harrison, head of the Epidemiology and Medicine as well as the Microbial Genomic Epidemiology Laboratory at Pitt, and Professor Anne von Gottberg, section lead of the Centre for Respiratory Diseases and Meningitis (CRDM) at the NICD. The programme involves a multidisciplinary group of experienced mentors at three training sites: Pitt, the Centres for Disease Control and Prevention (CDC) in Atlanta, and the NICD. Trainees are a combination of full-time and part-time post-graduate (MSc and PhD) degree candidates, of which degrees will be provided by the University of the Witwatersrand, South Africa.
South Africa has a major research capacity gap in the area of public health genomic epidemiology, including bioinformatics expertise as well as the integration of genomic and epidemiology data into public health. The SAPPHGenE program will have an extensive and long-lasting impact in the elevation of scientific capacity in the public health genomics field in South Africa.