​​​​​​​​​​​​​​​​​TEAM MEMBERS

Rob Warren

​​Distinguished Professor

Head of TB Genomics Research Group

rw1@sun.ac.za

 ​

Rob obtained a PhD degree in Biochemistry from the University of Cape Town in 1995 and subsequently joined the Department of Medical Biochemistry, Stellenbosch University. 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 450 papers in international peer-reviewed journals in the fields of molecular epidemiology, drug resistance and bacterial evolution since 1996. These studies have given him excellent experience in managing grant-related outputs and established infrastructure for conduct of ongoing research. 

In January 2017, He was appointed as the Unit director for the South African Medical Research flagship Centre for Tuberculosis Research which is housed within the Division. He is currently appointed as a distinguished Professor in the Division of Molecular Biology and Human Genetics. 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 apply 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 to enhance the resolution of molecular epidemiological interpretation to impact on treatment and policy.​​​

Elizabeth (Lizma) Streicher

​​Professor

lizma@sun.ac.za

 ​

Lizma joined the Division of MBHG in 2001 as a postgraduate student, followed by a postdoctoral fellowship, research scientist, and currently as a professor. She established a culture bank of drug-resistant M. tuberculosis isolates from patients from the Western Cape Province. Lizma continues to manage this resource, which currently has more than 60000 TB cultures. This very valuable resource forms the basis for various student research and collaborations that contributed significantly to our current understanding and molecular epidemiology, exogenous reinfection, dual infections, and mechanisms and the spread of drug-resistant TB. A special area of interest is the acquisition of drug resistance and specifically the influence of hetero-resistance on molecular-based drug resistance diagnostics.​

Marisa Klopper

​​Senior Researcher

marisat@sun.ac.za

 

M​arisa used whole genome sequencing analysis to study the drug-resistant TB epidemic in South Africa. She has shown that an endemic strain has repeatedly acquired resistance to all standard first- and second line drugs and is spreading in such highly resistant forms and that isoniazid mono resistance is often missed due to complex diagnosis. She is also interested in various mycobacterial cell wall components and the role of iron and lipids in virulence. Addition​ally, she collaborates with SU Electronic Engineering and the CLIME group of MBHG to investigate the use of cough sound analysis in diagnosis of TB and COVID-19​

​

Melanie Grobbelaar

​​Research Scientist

melgrob@sun.ac.za

 

Melanie is involved in various research initiatives, including investigating rpoB resistance mutations and their effects on RNA polymerase function, stress response, fitness, and resistance acquisition using OMICs approaches. She also contributes to testing a point-of-care diagnostic assay for rapid TB detection, identifies RNA signatures in response to antibiotic treatment, and explores co-culturing devices for studying cell-cell interactions. Additionally, she oversees research projects, supervises biomedical engineering and molecular biology students, and manages a clinical trial utilizing targeted next-generation sequencing for patient diagnosis and management.​

​​

Nabila Ismail

​​Research Scientist

nabilai@sun.ac.za

 

Nabila, a Y-rated, HPCSA-registered medical scientist, specialized in drug-resistance mechanisms for novel and repurposed drugs, with a strong focus on bedaquiline. She plays a key role in regulatory and liaison administration for research projects and clinical trials. After working as a research assistant at NICD, she completed her PhD on resistance to linezolid, clofazimine, and bedaquiline. She joined TBG in 2019 and actively contributes to its research. She holds BSc, BSc (Hons), and MSc degrees in Biochemistry (all cum laude) from the University of Pretoria, is a 2023 Lindau Nobel Laureate Meetings alum, and was a Fulbright Visiting Scientist at Harvard Medical School (2023–2024).

Felicia (Wells) Hunter

​​Project Coordinator/NGS consultant​

fbwells@sun.ac.za

​ 

Felicia joined the Division of MBHG as a sequencing assistant in 2020. Her current research focuses on integrating NGS into the standard of care routine workflow of TB treatment in Western Cape. Felicia achieved her degrees in BSc Molecular Biology and Biotechnology, BSc (Hons) in Biochemistry and MSc in Biochemistry at the University of Stellenbosch. During her MSc degree, she worked as a research assistant at the Department of Horticulture in testing different packaging materials that prevent ethylene damage and several mixed flower trails to determine shelf life and water uptake. During this time, she also assisted with GC-MS analyses for PhD students and postdocs at CAF GC-MS under the supervision of Mr. William Arries (Supervisor) and Mr. Lucky Mokwena (Manager). 

Rotondwa Bubuluma

​​Research Assistant

rbubuluma@sun.ac.za

 

Rotondwa completed his BSc and BSc Honours in Microbiology (Virology) at University of Venda. He earned his Master of Science in Medicine (Medical Virology) with Cum Laude from Sefako Makgatho Health Sciences University. In 2022, he joined the National Health Laboratory Service (NHLS) as an Intern Medical Biological Scientist in the Division of Virology, which enabled him to register with the Health Professions Council of South Africa (HPCSA) as a qualified Medi​cal Biological Scientist specializing in Virology and Molecular Biology. Rotondwa has a keen interest in genomics and bioinformatics. He is currently working as a Research Assistant focusing on the research project titled “An RNA-based phenotypic assay for the Diagnosis of Antibiotic Resistance in M. tuberculosis.” His work involves the identification of Mycobacterium tuberculosis RNA signatures in response to antibiotic treatment.​

Taime Sylvester

​​Consultant Scientist

tashnicao@sun.ac.za​​​

 

Taime joined the Division of MBHG 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 Stellenbosch 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 o​n evaluating the cardio-protection of kolaviron in ischaemia-reperfusion. In 2018, Taime joined Prof Rob Warren's research group as a postdoctoral fellow, where she aims to investigate the molecular epidemiology of tuberculosis in Namibia.

Anzaan Dippenaar

​​Consultant Scientist

anzaan.dippenaar@uantwerpen.be​

 

Dr Anzaan Dippenaar has been a member of the TB Genomics group since 2011, first as a PhD student and later as a post-doctoral research fellow and member of the Tuberculosis Omics Research (TORCH) consortium. She is interested in using Next-Generation 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. As of July 2020, she works as part of the Antwerp-based team of the TORCH consortium. ​

​​​​​​​​​​​​​​​​​POSTDOCTORAL RESEARCHERS

Shatha Omar

​​Postdoctoral Researcher

shatha@sun.ac.za

Shatha joined the Division of MBHG as a post-doctoral fellow in 2019. Her current research focuses on genetic characterization of NTM and their impac​t on macrophages during coinfection with M. tuberculosis. Shatha finished her Masters in 2008 determining the relationship between heat shock proteins (HSP's) and cell cycle regulator's proteins. She completed her PhD at the University of Cape Town, assessing the relationship between in vivo viral outgrowth in HIV-1 subtype C dual-infected individuals and Env entry efficiency, and to identify functional determinants of viral fitness as novel targets for drug and vaccine design. ​ ​ 

​

Johannes (Hanno) Loubser​​

​​Postdoctoral Researcher

jloubser@sun.ac.za

Hanno is a molecular biologist with special interest in biotechnology, genetics, microbiology and bioinformatics. Since 2020, he is a postdoctoral researcher with the TB Genomics research group, where he is involved in next-generation sequencing analysis of MTBC. His projects of interest include the transmission dynamics of TB contacts, within-host microevolution of MDR-TB, the role of DNA methylation in drug resistance, optimizing nanopore sequencing for TB diagnostics, standardization of bioinformatic pipelines for MTBC epidemiology. He is also very passionate about capacity building and teaching.​

​

Nandi (Niemand​) Wolhuter

​​Postdoctoral Researcher

nniemand@sun.ac.za

Nandi obtained her PhD in Molecular Biology, focussing on mycobacterial physiology, investigating, and characterizing the role of a novel protein involved in the iron-sulfur cluster biogenesis system. She joined the TB Genomics group as part of her postdoctoral fellowship focussing on a study titled “Transmission of tuberculosis among illicit drug use linkages”. A specific area of interest is understanding M. tuberculosis and HIV transmission under at-risk key populations in high TB and HIV prevalent settings. To understand ongoing transmission in people who smoke illicit drugs, she is actively involved in the analysis of the mycobacterial and HIV viral whole genome sequences, and host-blood transcriptomic TB signatures.​

Emilyn Costa Conceicao

​​Postdoctoral Researcher​

emilyncosta@sun.ac.za

Emilyn is a Biologist (Federal University of Para), holding a masters degree in Infectious Disease (State University of Para) and a PhD in Microbiology (Federal University of Rio de Janeiro/Paris-Sud University). Emilyn joined the Division of MBHG as a postdoctoral fellow in 2021. Her current research focuses on NGS for precision medicine and precision public health under the consortia TORCH (SMARTT trial), GenPAth (PARR-TB) and REVIGET-Brazil. Emilyn has experience in clinical trials and routine diagnostics focusing on molecular biology applied to MTBC, NTM and Mycobacterium leprae. She is interested in genomic-epidemiology, drug-resistance, bioinformatics and scientific communication and dissemination.

Brendon Mann

​​Postdoctoral Researcher​

bcmann@sun.ac.za

Brendon joined the Division of MBHG as a postdoctoral fellow in 2021. He earned his BSc Honours in Environmental Sciences and MSc in Microbiology from North-West University, where he investigated environmental antimicrobial resistance in wastewater. He then completed his PhD in Pharmaceutical Sciences at the DSI/NWU PCDDP, focusing on the human respiratory microbiome and its response to tuberculosis treatment. His current research explores M. tuberculosis genomic diversity and its link to treatment outcomes while developing protocols for M. tuberculosis cellular and DNA enrichment from direct patient samples, aiming to improve diagnostic and genomic analysis methods for tuberculosis​

​Justice Tresor N Ngom

​​Postdoctoral Researcher​​

justicengom@sun.ac.za

​​​

Justice joined the TB Genomics group in 2021 as a PhD student and earned his degree in 2024. He seeks to integrate Molecular Biology and Bioinformatics techniques to elucidate molecular epidemiology, resistance mechanisms, and the evolution of strains responsible for drug-resistant tuberculosis. The Justice’s current focus is on using the NGS method (WGS) to decipher the impact of changes in treatment strategies on the XDR-TB population structure in the Western Cape Province over time.​

​​

STUDENTS​​

Janré Steyn

​​Doctoral candidate​​

janre@sun.ac.za​

​​ 

Project Description: To evaluate a targeted sequencing-based approach using Deeplex for rapid determination of drug resistance profiles of M. tuberculosis as part of the clinical trial Pragmatic Use of Next-generation Sequencing for Management of Drug-resistant Tuberculosis (TSELiOT).​

Christoffel J Opperman

​​Doctoral candidate​​

14487616@sun.ac.za

Project Description:​ ​The study aims to: 1) Describe NTMs that are clinically relevant using descriptive epidemiology, spatial mapping, and clinical analysis of cases diagnosed in the Western Cape - a retrospective study over six years. 2) Prospectively, characterize Mycobacterium species with WGS, Sanger sequencing, and proteomics (MALDI-TOF) that remained unidentified following the Mycobacterium CM/AS line probe assay (LPA) performed on clinical samples within the NHLS, Green Point complex, TB-laboratory, Cape Town. 3) Illustrate the antibiotic susceptibility profiles of clinically relevant NTM isolates in the Western Cape, collected prospectively, with the NTM-DR LPA, Sensititre Mycobacteriaplates, and proportional method (BACTEC MGIT 960 system).   ​​

Sarishna Singh

​​Doctoral candidate​​

sarishna.singh@nhls.ac.za

​​

Project Description:​ Isoniazid-resistant (INH-R) tuberculosis in the Western Cape, a descriptive study of clinical characteristics and outcomes. We aim to describe the epidemiology of NH-R in patients living in the Western Cape Province with the objectives: 1) a retrospective description of the  NH-R in patients diagnosed over a five-year period (2017-2022);  2) Identify the percentage of patients within this cohort that gained additional resistance; 3) Prospectively determine the burden of NH-R; 4) Compare treatment outcomes in patients with NH-R to treatment outcomes in patients with drug-susceptible TB  in both periods; and  5) Determine the areas where NH-R is concentrated (hotspots).​

Tuelo Mogashoa

​​Doctoral candidate​​

22385924@sun.ac.za

​​

Project Description:​ Tuelo’s project is based on using next-generation sequencing to characterize rifampicin-resistant M. tuberculosis strains circulating in Botswana. Her project will also evaluate transmission dynamics of rifampicin-resistant M. tuberculosis strains as well as evaluate treatment outcomes and factors associated with unsuccessful treatment outcomes among people diagnosed with rifampicin-resistant tuberculosis (RR-TB). Data from this project will provide insights into the molecular epidemiology of RR-TB in Botswana. She is interested in TB molecular epidemiology, drug resistance, and bioinformatics and is very passionate about capacity building.​