Dr Anzaan Dippenaar
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.
Dr Shatha Omar
Dr Shatha Omar joined the Division of MBHG as a post-doctoral fellow in 2019. Her current research focuses on genetic characterization of NTM and their impact 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.
Dr Johannes (Hanno) Loubser
Dr Hanno Loubser 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, unknown variants of ethionamide resistance, 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.
Dr Nandi Niemand
Dr Nandi Niemand obtained her PhD in Molecular Biology and Human Genetics, 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 and primarily focuses on a study titled “Transmission of tuberculosis among illicit drug use linkages”, which aims to evaluate the proportion of TB cases derive from a recent transmission and define mechanisms responsible for efficient transmission in this population. In addition, she is also involved in the in vivo evaluation and characterization of single nucleotide polymorphism mutations and their association with phenotypic bedaquiline resistance.
Dr Emilyn Costa Conceicao
Dr Emilyn Costa Conceicao joined the Division of MBHG as a postdoctoral fellow in 2021. Her current research focuses on personalized medicine through WGS as part of “Sequencing Mycobacteria and Algorithm-Determined Resistant Tuberculosis Treatment (Smartt) Trial”. Emilyn is a Biologist (Federal University of Para), holding a masters degree in Infectious Disease (State University of Para) and PhD in Microbiology (Federal University of Rio de Janeiro/Paris-Sud University). Emilyn has experience in clinical trials and routine diagnostics with a focus on molecular biology applied to MTBC, NTM and Mycobacterium leprae. She is interested in epidemiology, genomics, drug-resistance, bioinformatics and science education.
Dr Brendon Mann
Dr Brendon joined the Division of MBHG as a postdoctoral fellow in 2021. He obtained his BSc Honours degree in environmental sciences, and MSc degree in Microbiology at the North-West University of Potchefstroom, working on environmental antimicrobial resistance. He did his PhD in Pharmaceutical Sciences at the DSI/NWU Preclinical Drug Development Platform (PCDDP) also at the North-West University, focussing on the human respiratory microbiome and its response to tuberculosis treatment, while also working on the development of a novel molecular TB diagnostic system. His current focus is to assess in-host M. tuberculosis genomic diversity to determine how this relates to treatment response and oversees the development of laboratory protocols for M. tuberculosis cellular and DNA enrichment from direct patient samples.
Justice Tresor N Ngom
Project Description: Justice’s project is based on using the Next-generation Sequencing (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.
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
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).
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).
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.
Project Description: Comparison of different outbreaks of MDR-TB in Western Cape province targeting genetic polymorphisms, drug-resistance conferring and compensatory mutations using WGS Analysis of the genomes of MDR-TB strains in the Western Cape Province, South Africa over a 12-year period will provide information about the changes in strain diversity, the potential to identify new possible outbreaks, and with early intervention, i.e. rapid diagnostics, early personalized treatment regimens, and close monitoring of patients. The study will also provide information on which drug combinations could potentially be more effective in specific communities, since there will be comparison of outbreaks amongst different communities.
Project Description: Resistance to the novel nitroimidazole drug class in M.tuberculosis – Novel clinical variants within the six target genes of pretomanid (PMD) and delamanid (DLM) were investigated to determine whether low levels of resistance between the two drugs exists between DLM-naïve patients through a genomic approach on resistance-associated genes (fbiA, fbiB, fbiC, fbiD fgd1 and ddn) and in vitro generated mutants to see whether they resemble resistant clinical strains and may serve as a proxy to investigate cross-resistance.
Project Description: Nanopore sequencing of M. tuberculosis – a handheld solution to comprehensive drug susceptibility testing: The aims of this project are to adapt and optimize workflows to enable DNA extraction directly from either decontaminated sputum or primary MGIT cultures, to compare manual library prep and automated library prep for MinION sequencing, and to build a bioinformatics analysis pipeline for MinION sequencing data. This project will move TB diagnosis closer to the point of care, enabling a more rapid prescription of treatment regimens to patients and thereby minimizing the spread of TB disease and drug-resistance.
Morwatshehla Paul Modjadji
Project Description: Portable diagnostics of M. tuberculosis: The aim of the study is to evaluate targeted deep sequencing to detect drug-resistance causing mutations in Mycobacterium tuberculosis using portable instruments which will be achieved by setting-up targeted deep sequencing on MinION using either purified DNA or DNA extracts from early positive cultures.
Magdalene Pine Adjei
Project Description: Method development for phenotypic isoniazid drug susceptibility testing in a high throughput setting. The aim of this study is to develop a phenotypic isoniazid drug susceptibility testing method that features ease of use, low cost and high accuracy to be used in practical clinical settings.
Project Description: Determining the role of an inhA genomic mutation in the cell wall of M. tuberculosis. The inhA promoter region contains genes involved in the synthesis of mycolic acid, which are an integral part of the M. tuberculosis cell wall. We are evaluating whether there is a difference in cell wall composition between M. tuberculosis wild type and an inhA promoter mutation by analyzing extracted mycolic acid, evaluating membrane fluidity and integrity; and comparing cell wall thickness using various microscopy techniques. This project will contribute to understanding the role of inhA promoter mutations as an additional compensatory mutation in drug-resistant isolates.