Division of Molecular Biology and Human Genetics
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TB GENOMICS
Monique Barnard
Postdoctoral Researcher
Monique obtained her PhD degree in Biochemistry at Stellenbosch University, mainly focussing on the role of steroids in the development and progression of prostate cancer. She joined the TB genomics group in 2020 as a postdoctoral fellow under the supervision of Dr Klopper and Prof Warren until 2023. The focus of her postdoctoral study included investigating iron and heme in different M. tuberculosis strains. Furthermore, she is interested in the acquisition of bedaquiline resistance conferring mutations in patients diagnosed with Rifampicin resistant TB due to poor drug adherence, especially during COVID-19 lockdown periods in South Africa.
Zaahida Sheik Ismail
Postdoctoral Researcher
Zaahida joined the Department of Biomedical Sciences at Stellenbosch University as a post-doctoral fellow in July 2022. She obtained her PhD in Biochemistry and MSc Med at the University of Witwatersrand where she worked on HIV and TB. Her BSc and BSc Hons Biotechnology degrees were completed at the University of the Western Cape. Her current research focuses on using targeted next-generation sequencing to assess drug resistant profiles of Mtb clinical isolates to optimize treatment.
Jethro Sims-Handcock
Masters graduate
Investigating variants associated with INH resistance in multi-Drug resistant TB using Whole Genome Sequencing, – The mains aims of the project included the initial WGS and bioinformatic analysis of a MDR outbreak, this included establishing genomic drug resistances and phylogenetic relationships. Next, the identification of novel genomic variants in drug associated genes and those contributing to the IHN resistance phenotype. Followed by the purification and transformation of the variant genes into M. smegmatis and subsequent fitness assays. This work serves to add to known mechanisms of drug resistance as well as highlight targets for potential adjunctive therapeutics.
Leah Mwendwa
Masters graduate
Determination of the compensatory role and transcriptomic effects of inhA promoter mutations in M. tuberculosis. The project is based on the hypothesis that the inhA C-15T promoter mutation confers a fitness advantage over wild-type strains in the presence or absence of additional drug-resistance mutations. The purpose of the study is to assess fitness and gene expression in wild-type and inhA mutant M. tuberculosis strains under different growth conditions including iron depletion. By understanding the role of the inhA promoter mutations, we will gain insight into the potential compensatory role and transcriptomic effects of inhA promoter mutations in TB mutant strains.
Ilham Al-Talib
BSc Honours graduate
Genetic characterisation of nontuberculous mycobacteria isolated from urban and rural water sources. The aim of this project is to determine if there are pathogenic NTM present at any of the sampling sites identified near the Athlone treatment plant and further downstream, and then to identify and characterize any isolates found. Antimicrobial resistant properties of isolates will also be studied.
Mishka Ismail
BSc Honours graduate
Evaluation and optimization of DNA extraction methods from mycobacteria growth indicator tube (MGIT) early positive culture (EPC) of M. tuberculosis for whole-genome sequencing. The aim of this research project is to evaluate the performance of several commercial DNA extraction methods compared to the chemically based DNA extraction procedure known as CTAB, by evaluating the quality, quantity, and integrity of the produced DNA. The goal of this project is to decrease the time of WGS diagnosis of tuberculosis from approximately 1 to 2 months to only a few weeks.
Astrid Paulse
Masters graduate
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.
Magdalene Pine Adjei
Masters graduate
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.
Charne Glanz
Masters graduate
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.
