SAPPHGenE

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.

Objectives

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

Impact

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.

Results

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.

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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.

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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.

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Students

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)

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)

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)

Fahima Moosa

PhD Student

Prevalence and molecular epidemiology of Bordetella pertussis infection in South Africa

M210676 (Wits Human Research Ethics Committee - Medical)

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)

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),

Buhle Ntozini

MSc Student

Molecular characterization of Group B Streptococcus in South Africa, 2019-2020

M210476 (Wits Human Research Ethics Committee - Medical)

Nosihle Msomi

MSc Student

Development of Advanced Molecular Diagnostics for Meningitis

M210478 (Wits Human Research Ethics Committee - Medical)

Dikeledi Kekana

MSc Student

Molecular Characterization of Candida auris Clinical Isolates at a Large Tertiary Academic Hospital

M210298 (Wits Human Research Ethics Committee - Medical)

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)