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07 January 2018 Photo Charl Devenish
Researcher tackling drug-resistant TB through molecular methods
Dr Anneke van der Spoel van Dijk is invested in contributing to the global effort of stopping TB by 2035.

The work of Dr Anneke van der Spoel van Dijk investigates the spread of TB in the Free State population using techniques such as next generation sequencing, spoligotyping and MIRU-VNTR typing. Dr Van der Spoel van Dijk, a senior medical scientist in the Department of Medical Microbiology at the University of the Free State (UFS) also looks at drug resistance in her research. This work informs decisions about how best to treat patients with multidrug-resistant TB (MDR-TB). 

She employs rapid molecular techniques to track one of Africa’s most serious diseases, tuberculosis (TB). 

Drug resistance
Scientists assist the National Health Laboratory Service and Department of Health in trying to refine the diagnostic tools to identify these cases earlier. Dr Van der Spoel van Dijk explains: “Until recently, it took up to two years to fine-tune treatment decisions for patients with MDR-TB. Patients get a cocktail of anti-TB drugs, but it takes time to find the right combination. Re-infection and relapse (patients stopping treatment for several reasons) add to the diagnostic and treatment management challenges.

Enormous impact
“Now doctors can reduce the time needed for diagnostic certainty to about seven days, while new drugs allow reduction of treatment from more than 18 to nine months. This can have an enormous impact on the life of many patients.”

Dr Van der Spoel van Dijk’s work forms part of research in the faculty looking at resistance development in TB strains. She is currently also doing her doctoral thesis on the differences and incidence of MDR-TB among adolescents versus adults. Dr Van der Spoel van Dijk says: “It is a complicated picture, but we hope to unravel it to support better diagnostic tools and patient care.”

As part of the National Health Laboratory Service, her department is playing an important role in TB diagnostics and the training of scientists and future pathologists. “Our work is contributing to the global vision to stop TB by 2035,” Dr Van der Spoel van Dijk says.

News Archive

Newly operational sequencing unit in genomics at UFS
2016-09-09

Description: Next Generation Sequencing Tags: Next Generation Sequencing

Dr Martin Nyaga and his research assistant,
Tshidiso Mogotsi in the Next Generation
Sequencing Laboratory.
Photo: Charl Devenish

The Next Generation Sequencing (NGS) unit at the UFS was established as an interdisciplinary facility under the Directorate for Research Development, Faculty of Health Sciences and Faculty of Natural and Agricultural Sciences.

The aim of the NGS facility is to aid internal and external investigators undertaking studies on Deoxyribonucleic acid (DNA) sequencing, assembly and bioinformatics approaches using the more advanced Illumina MiSeq NGS platform.

The NGS unit became operational in 2016 and is managed by Dr Martin Nyaga and administered through the office of the Dean, Faculty of Health Sciences, under the leadership of Prof Gert Van Zyl. Dr Nyaga has vast experience in microbial genomics, having done his PhD in Molecular Virology.

He has worked and collaborated with globally recognised centres of excellence in Prokaryotic and Eukaryotic genomics, namely the J. Craig Venter Institute and the Laboratory of Viral Metagenomics, Rega Institute, among others.

The unit has undertaken several projects and successfully generated data on bacterial, viral and human genomes. Currently, work is ongoing on bacterial and fungal metagenomics studies through 16S rRNA sequencing.

In addition, the unit is also working on plasmid/insert sequencing and whole genome sequencing of animal and human rotaviruses. The unit has capacity to undertake other kinds of panels like the HLA, Pan-cancer and Tumor 15 sequencing, among others.

Several investigators from the UFS including but not limited to Prof Felicity Burt, Prof Wijnand Swart, Dr Frans O’Neil, Dr Trudi O'Neill, Dr Charlotte Boucher, Dr Marieka Gryzenhout and Dr Kamaldeen Baba are actively in collaboration with the NGS unit.

The unit has also invested in other specialised equipment such as the M220 Focused-ultrasonicator (Covaris), 2100 Bioanalyzer system (Agilent) and the real-time PCR cycler, the Rotor-Gene Q (Qiagen), which both the UFS and external investigators can use for their research.

Investigators working on molecular and related studies are encouraged to engage with Dr Nyaga on how they would like to approach their genomics projects at the UFS NGS unit. 

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