TB Genomics
Welcome to Stellenbosch University

Division of Molecular Biology and Human Genetics

​TB Genomics​

​Group Members

 

Rob Warren

rob.pngRob obtained a PhD degree in Biochemistry from the University of Cape Town in 1995 and subsequently joined the Department of Medical Biochemistry, Stellenbosch University (SU). He was appointed as Professor in the Division of Molecular Biology in 2015 and subsequently a distinguished Professor. Under his guidance the study of the molecular epidemiology of Mycobacterium tuberculosis in a high incidence setting (Cape Town, South Africa) was brought to the forefront of international tuberculosis research. This study now represents the largest molecular epidemiological data set in the developing world and has been referred to as a national heritage. Much of this work has provided new understanding, which has allowed long standing dogmas to be challenged. He has published more than 230 papers in international peer reviewed journals in the fields of molecular epidemiology, drug resistance and bacterial evolution since 1996. These studies have given me excellent experience in managing grant-related outputs and established infrastructure for conduct of ongoing research. In January 2017, He was appointed at the Unit director for the South African Medical Research flagship Centre for Tuberculosis which is housed within the Division. His current research focuses on: 1) the disease dynamics of drug sensitive and M(X)DR-TB in the Western Cape, 2) the development of novel diagnostics which are applicable to the developing world, 3) discovery of the mechanisms whereby drug resistance develops, 4) speciation of mycobacteria causing disease in humans and animals, 5) application of novel methods to improve the speed of diagnosing smear positive disease, 5) host-pathogen compatibility, 6) identification of highly pathogenic strains of M. tuberculosis, 7) pathogen evolution and 8) mycobacterial epigenetics. He co-developed a whole genome sequence analysis group with the aim to enhance the resolution of molecular epidemiological interpretation to impact on treatment and policy.

 

Lizma Streicher

lizma.pngElizabeth joined the department of Medical Biochemistry in 2001 as a B.Sc. Hons student and continued with her postgraduate studies, post-doctoral fellowship and is currently a research scientist in the Division of Molecular Biology and Human Genetics. As part of her postgraduate studies, she established and standardized a rapid tuberculosis genotyping technique, spoligotyping, in their laboratory, the first laboratory on the African continent to implement it.

During her studies, she also established a culture bank with a concomitant database of drug resistant M. tuberculosis isolates from patients from the Western Cape Province. Elizabeth continues to manage this resource, which currently has more than 45000 TB cultures (which includes drug resistant and drug susceptible strains). This is a very valuable resource in the department and forms the basis for various different student research studies and national and international collaboration. This database and sample bank contributed significantly to our current understanding and interpretation of molecular epidemiology data and was central to a paradigm shift in our understanding of exogenous reinfection, dual infections, host genetics, and mechanisms and spread of drug resistance. 

A special area of interest of Elizabeth's research has been acquisition of drug resistance and specifically the influence of hetero resistance on the molecular based drug resistance diagnostics.

 

Marisa Klopper

marisa.pngMarisa started at the Department of Biomedical Sciences at Stellenbosch University as a research assistant in 2009. She subsequently decided to pursue an academic career, starting with a Master's degree, which was upgraded to PhD. She obtained her PhD degree in Molecular Biology in 2015, with the study entitled “Molecular epidemiology of drug-resistant tuberculosis in the Eastern Cape, South Africa". During these studies, she gained experience in whole genome- and transcriptome analysis. Using these technologies, she showed that a strain of tuberculosis which is endemic to the area has acquired resistance to all standard first- and second line drugs on multiple occasions, and is spreading in such highly resistant forms.

Marisa is currently a junior researcher in Prof Rob Warren's lab. She is running a prospective clinical study investigating the prevalence and outcomes of isoniazid mono resistance in the Eastern Cape. She is also interested in the biology of compensatory mechanisms that ameliorate drug-resistance associated fitness costs.

 

 

Margaretha de Vos

Margaretha.pngMargaretha joined the Department of Biomedical Sciences at Stellenbosch University in 2007 to pursue a BSc Honours degree, where she also completed her MSc degree in 2009 and graduated with a PhD in Molecular Biology in 2013. Her PhD research focused on the analysis of the whole genomes of closely related M. tuberculosis isolates to identify mechanisms regulating the intra cellular concentration of rifampicin in M. tuberculosis. Margaretha is currently a post-doctoral fellow based at Stellenbosch University and a member of the Centre for Whole Genome Sequencing of MTB. Her research focuses on the use of whole genome sequencing to study the genomic evolution of M. tuberculosis during treatment and the acquisition of drug resistance with the aim to identify molecular markers and other risk factors for the prediction of treatment failure. Her other research interests include the development and validation of novel diagnostics for the identification of drug resistant TB..

 

 

 

 

Anzaan Dippenaar

Anzaan.pngAnzaan joined the Department of Biomedical Sciences at Stellenbosch University in 2011 when she started her PhD in Molecular Biology with a special focus on biological characteristics of the Latin-American Mediterranean strains of M. tuberculosis. Before moving to Cape Town, she studied at North-West University in Potchefstroom, North-West Province, South Africa, where she completed her BSc (Microbiology and Biochemistry), BSc (Hons, Biochemistry) and MSc in Biochemistry.
Anzaan is currently a post-doctoral research fellow in the Department of Biomedical Sciences at Stellenbosch University and is a member of the Centre of Whole Genome Sequencing. She is interested in using whole genome sequencing approaches to investigate the microevolution of M.tuberculosis during transmission, the mycobacterial genomics of treatment response during tuberculosis disease, and to explore the genomic characteristics of various mycobacterial strains causing tuberculosis in a variety of animal host species.

 

 

Melanie Grobbelaar

Melanie.pngMelanie is interested in the transcriptome of Mycobacterium tuberculosis, especially the effect of different rpoB mutations on the transcriptomic map of M. tuberculosis using qPCR and RNA-seq. She started her MSc in 2010 at the Centre of Excellence for Biomedical Tuberculosis Research and the Centre for Tuberculosis Research in the Division of Molecular Biology and Human Genetics at Stellenbosch University. Her PhD centred around the transcriptomic effect of rifampicin on different mono-resistant isolates.

 

 

 

 

 

 

 

 

Michael Whitfield

Michael.pngMichael began his MSc in Molecular Biology in 2013 as part of the Department of Biomedical Sciences at Stellenbosch University. Two years later he successfully upgraded his MSc into a PhD. The focus of his research was on Pyrazinamide (PZA) resistance in MTB. He investigated genotypic and phenotypic associations as well as prevalence of PZA resistance across a spectrum of drug resistance cohorts. Michael successfully graduated in December 2016; his interests include drugresistance and improving whole genome sequencing (WGS) of Mycobacterium tuberculosis (MTB). Michael who is currently based at Stellenbosch University is a postdoctoral research fellow and is a member of the Centre for Whole Genome Sequencing of MTB. He is working on culture free and sputum free sampling for WGS of MTB. The aim of this research is to eliminate the culturing step in WGS allowing us to have a better perspective of the patient's infection.

 

 

 

 

Serej Ley

Serej.pngSerej is a molecular epidemiologist with an MSc in molecular biology and a PhD in microbiology. She has several years of international (Switzerland, Papua New Guinea, Australia, South Africa) work exposure in multidisciplinary environments. She has experience in various fields including laboratory and field work implementation and coordination, different molecular methods used in molecular parasitology and infection biology, qualitative and quantitative data analysis, as well as contributing to the development of national and international health policy. Serej joined the Department of Biomedical Sciences at Stellenbosch University in 2016 when she started her current position as a postdoc in the Division of Molecular Biology and Human Genetics. Her work focuses on the evolution and population structure of drug resistant Mycobacterium tuberculosis (Mtb) within and between hosts, using whole genome sequencing.

 

 

 

Taime Sylvester

Taime.pngTaime Sylvester joined the Department of Biomedical Sciences at Stellenbosch University in 2014 when she started her PhD in Molecular Biology, focusing on characterizing the immune response of African lions to Mycobacterium bovis infection. Before joining Stellenosch University she did her undergraduate training in Biomedical Technology at the Cape Peninsula University of Technology. Here she also completed her Masters in Biomedical Technology, focusing on evaluating the cardio-protection of kolaviron in ischaemia-reperfusion. In 2018, Taime joined Prof Rob Warren's research group as a post-doctoral fellow, where she aims to investigate the molecular epidemiology of tuberculosis in Namibia.