About this project

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.

  1. Improvement of public health genomic epidemiology in Africa, which is a rapidly expanding field for the transformation of the global public health.
  2. Establish a dynamic training programme that focuses on bacterial and fungal genomics.
  3. Promote and anchor existing collaborations between investigators at NICD, CDC, and University of Pittsburgh, with expertise in epidemiology, genomics and metagenomics, and bioinformatics.
  4. Align South African research capacity with global activities in public health genomic epidemiology, including the CDC’s advanced molecular detection program.
  5. Provide a model for the introduction of public health genomic epidemiology into other parts of Africa and the developing world.

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.


Genotype, Antifungal Susceptibility, and Virulence of Clinical South African Cryptococcus neoformans Strains from National Surveillance, 2005–2009.
Naicker, SD, Magobo, RE, Maphanga, TG, Firacative, C, van Schalkwyk, E, Monroy-Nieto, J, Bowers, J, Engelthaler, DM, Shuping, L, Meyer, W and Govender, NP (2021). Journal of Fungi 7(5): 338. DOI: 10.3390/jof7050338.
Molecular characterization of invasive Group B Streptococcus in South Africa.
Ntozini, B, Von Gottberg, A, De Gouveia, L, Meiring, S, Quan, V, Walaza, S and Wolter, J (2021). The International Conference on Group B Streptococcus (ICGBS). Presentation. Virtual, 20 - 21 July 2021.
Genomic epidemiology of invasive pneumococcal serotype 8 in the pre- and post-PCV13 eras in South Africa, 2005 – 2014.
Cebile Lekhuleni, Kedibone Ndlangisa, Stephanie Lo, Linda de Gouveia, Jackie Kleynhans, Vanessa Quan, Paulina Hawkins, Lesley McGee, Stephen D. Bentley, Cheryl Cohen, Anne von Gottberg, Mignon du Plessis. 12th International Symposium on Pneumococci and Pneumococcal Diseases (ISPPD-12). Poster presentation with spotlight talk.Toronto, Canada. 19 – 23 June 2022.


1 Cebile new
Cebile Lekhuleni
PhD Student
Molecular Characterization and Population Structure Determination of Streptococcus pneumoniae in South Africa using Whole-Genome Analysis
M210749 (Wits Human Research Ethics Committee - Medical)
2 Rito
Rito Mikhari
PhD Student
Whole genome sequence characterization of Neisseria meningitidis among carriage and invasive strains in South Africa
M210689 (Wits Human Research Ethics Committee - Medical)
3 Rutendo
Rutendo Mapengo
PhD Student
Investigating diagnostic methods for histoplasmosis and the ecological niche and comprehensive population structure genomic analysis of African Histoplasma capsulatum
M210109 (Wits Human Research Ethics Committee - Medical)
4 Fahima
Fahima Moosa
PhD Student
Prevalence and molecular epidemiology of Bordetella pertussis infection in South Africa
M210676 (Wits Human Research Ethics Committee - Medical)
5 Maimuna
Maimuna Carrim
PhD Student
Understanding carriage and transmission of Streptococcus pneumoniae through a community cohort study in South Africa, 2016-2018
M210367 (Wits Human Research Ethics Committee - Medical)
7 Wilhelmina
Wilhelmina Strasheim
PhD Student
The human and porcine resistome on a commercial farm in South Africa – A descriptive study
M190244 (Wits Human Research Ethics Committee - Medical),
8 Buhle
Buhle Ntozini
MSc Student
Molecular characterization of Group B Streptococcus in South Africa, 2019-2020
M210476 (Wits Human Research Ethics Committee - Medical)
9 Nosihle
Nosihle Msomi
MSc Student
Development of Advanced Molecular Diagnostics for Meningitis
M210478 (Wits Human Research Ethics Committee - Medical)
10 Dikeledi
Dikeledi Kekana
MSc Student
Molecular Characterization of Candida auris Clinical Isolates at a Large Tertiary Academic Hospital
M210298 (Wits Human Research Ethics Committee - Medical)
11 Sibusiswe
Sibusisiwe Zulu
MSc Student
Whole genome sequence-based characterization of Group A streptococci (GAS; Streptococcus pyogenes) isolates causing invasive disease in South Africa, 2019-2020
M210750 (Wits Human Research Ethics Committee - Medical)

Supervisors & Mentors

3 Anne Pic
Prof Anne von Gottberg
2 Nelesh
Prof Nelesh Govender
3 Mignon
Dr Mignon du Plessis
4 Nicole
Dr Nicole Wolter
5 Kedibone
Dr Kedibone Ndlangisa
6 Sibongile
Dr Sibongile Walaza
7 Susan
Dr Susan Meiring
8 Tsidiso
Dr Tsidiso Maphanga
9 Serisha
Dr Serisha Naicker


Funders and Collaborators

National Institutes of Health
2 University of Pittsburgh
University of Pittsburgh
National Institute for Communicable Diseases
4 Wits
University of the Witwatersrand
United States Centers for Disease Control and Prevention
6 Fogarty
Fogarty International Center