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.

 

 

 

 

 

 

 

 

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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.






Nabila Ismail 

image.pngNabila Ismail joined the Department of Biomedical Sciences at Stellenbosch University as a post-doctoral fellow early in 2019. Her current research focuses on culture-free or early detection of TB infection and resistance profile information using whole genome sequencing technologies. Nabila achieved all three of her BSc, BSc (Hons) and MSc degrees in Biochemistry cum laude from the University of Pretoria. Following this, she worked as a research assistant at the NICD Centre for Tuberculosis (a WHO supranational laboratory) where she was actively involved in whole genome sequencing of isolates received from the National Drug Resistance Survey. During this time, she also assisted with the standardization of bedaquiline MIC testing on solid media. She then pursued her PhD in Medical Microbiology through the University of Pretoria and in association with the NICD Centre for Tuberculosis. Her doctoral thesis focused on identifying the optimal method for generation of in vitro mutants to novel and repurposed drugs and she successfully created a number of bedaquiline-, clofazimine- and linezolid-resistant mutants to uncover the genetic basis of resistance. All of the mutants were subjected to whole genome sequencing analysis and phenotypic screening. She published four articles during the course of her PhD.