Clinical Mycobacteriology and Epidemiology
Welcome to Stellenbosch University

Division of Molecular Biology and Human Genetics

​Clinical Mycobacteriology and Epidemiology (CLIME) Group​​ 

Vacancies


PhD positions

PhD position in the Faculty of Medicine and Health Sciences, Stellenbosch University (Tygerberg Campus, Cape Town)
Project title: Investigating the role of the microbiome in tuberculosis pathogenesis
Duration: 3 years (depending on progress, with renewal possible beyond this period contingent on funding)
Project description: About 10 million people suffer from tuberculosis (TB), which is the single biggest infectious cause of death globally. TB – despite primarily being a lung disease - results in broad, systemic changes to microbial communities throughout the body. Furthermore, unlike most bacterial infections that are treatable with a short-course antibiotic regimen, TB requires multiple antibiotics for a prolonged period (at least 6 months for drug-susceptible TB). We know the human microbiota is associated (sometimes causatively) with many different diseases and plays an important role in health. However, despite TB’s importance as a global public health issue and the large-scale long-term use of broad-spectrum antibiotics required to treat TB, little is known about the identity and function of microbial communities in TB patients, how these change over treatment (including their driving of antimicrobial resistance), and any linkages between the microbiome, recurrence, and clinical outcome.

The successful candidate will join a growing team of individuals working on microbiome- and TB-related projects. The candidate will focus specifically on studying the microbiome at the site-of-disease (bronchoalveolar space), which is a unique environmental and immunological niche, in patients repeatedly over time. The candidate will, using multi-omic approaches, also study markers of the immune system and bacterial metabolism.

The candidate will primarily be responsible for initially leading and subsequently overseeing clinical specimen processing in a BSL-3 facility, DNA/RNA extractions (e.g. from sputum, stool and blood) and microbiome and transcriptome analyses. They will also be involved in the generation and analysis of data associated with mechanistic aspects of the microbiome (metabolome). Prospective candidates are encouraged to first familiarise themselves with the field (e.g., https://bit.ly/2x52oMT). Candidates will have opportunities to train overseas with our collaborators.

Application details:
Applicants should have attained an MSc within the last 5 years and have a strong background in molecular biology, microbiology, or bioinformatics. TB experience is helpful but not critical.

A tax-free bursary is provided. The successful candidate will be assisted in applying for additional funding that they will likely be entitled to keep in addition to the base bursary.
For more information, please contact Dr Charissa Naidoo (ccnaidoo@sun.ac.za) and copy Assoc. Prof Grant Theron (gtheron@sun.ac.za​)

To apply, please send a covering letter, a CV containing details of relevant experience, grades, and the email addresses and telephone numbers of 3 references to the above addresses before 31 November 2019. Early applications are encouraged.

The Faculty of Medicine and Health Sciences is situated about 20 minutes from central Cape Town and 30 minutes from the Stellenbosch campus by car.​


Post-doctoral positions

Post-doctoral positions in Tuberculosis Diagnostics (up to two positions available)
Faculty of Medicine and Health Sciences
Stellenbosch University (Tygerberg Campus, Cape Town, South Africa)
Duration: 4 years (renewed annually contingent on progress)
Description: The Clinical Mycobacteriology & Epidemiology (CLIME) group is seeking to fill two exciting post-doctoral scientist positions related to the diagnosis of tuberculosis (TB). TB, despite being readily curable, remains the single biggest infectious cause of death in the world. New diagnostics are key to reducing TB transmission.
The positions are part of long-term internationally-funded studies where novel non-sputum TB diagnostic tests will be evaluated across multiple African countries. The effect of using certain results for patient management will be measured on health outcomes. The first project involves tests for incipient TB, which is generally asymptomatic early stage disease. The second uses a novel point-of-care test for active TB. Both projects are in collaboration with multiple commercial test developers and health policy makers.
The successful candidate(s) will join a broader team of individuals working on different TB diagnostics projects. The candidate(s) will primarily be responsible for project implementation, day-to-day management and leadership, preliminary data analyses, site visits (annual international travel required), and the co-analysis and co-leadership of publications. The candidate will have the opportunity to co-supervise students.

Prospective candidates are encouraged to familiarise themselves with the field and CLIME’s track record.

Application details:
Applicants should have a PhD within the last 5 years and a background in epidemiology, microbiology, or related disciplines. TB and/or project management experience is helpful but not critical.

A competitive tax-free bursary is provided. The candidate(s) will be assisted in applying for additional funding that they are entitled to keep in conjunction with the base bursary.
For more information, please contact Dr Byron Reeve (byronreeve@sun.ac.za) and copy Assoc. Prof Grant Theron (gtheron@sun.ac.za)

To apply, please send a covering letter, a CV containing details of relevant experience, publications, grades, and the email addresses and telephone numbers of three references to the above addresses before 31 November 2019. Early applications are encouraged.

The Faculty of Medicine and Health Sciences is situated about 20 minutes from central Cape Town and 30 minutes from the Stellenbosch campus by car.