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.