Med Microbiology
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​​​​​​Division of Medical Microbiology



​Medical Microbiology:

Antibiotic resistance, epidemiology, and virulence of bacterial pathogens
Antimicrobial resistance is a global health problem that threatens the effective prevention and treatment of an ever-increasing range of infections caused by microorganisms. Surveillance of the prevalence and mechanisms of resistance in bacterial pathogens is critical to inform treatment guidelines, infection control practices and antibiotic stewardship. The dissemination of antimicrobial resistance in hospitals, communities, agriculture and the environment leads to increased antibiotic resistance in hospital- and community-acquired infections, and further impacts the efficacy of available antibiotics. Our research investigates the epidemiology of resistance in a number of important bacterial pathogens, including Gram-negatives such as Escherichia coli, Klebsiella pneumoniae, Acinetobacter baumannii and Gram-positives such as Staphylococcus aureus and coagulase negative staphylococci. We also take a One Health Approach to investigate the interplay between resistance in clinical, community, environmental and agricultural niches, and the roles that these environments and other non-pathogenic bacteria play as reservoirs of resistance. Many of these bacterial species are opportunistic pathogens, however the production of virulence factors increases the frequency and extent to which the organism can cause disease. Our research is expanding to explore virulence factors involved in both Gram-positive and Gram-negative bacterial infections. Collaborations with clinical partners in the Faculty of Medicine and Health Sciences allow us to investigate risk factors associated with resistance and virulence, and the impact of resistance and virulence on clinical outcomes.
There is growing appreciation of the influence of the human microbiome on health. Disruption or dysbiosis of human microbial communities has a significant impact on human health and has been linked to multiple metabolic, immunological, and developmental disorders. The impact of antibiotics on the microbiome is of particular concern. Currently we are investigating the impact of levofloxacin prophylaxis on the gut microbiome in children, as part of the Tuberculosis Child Multidrug-resistant Preventive Therapy Trial (TB-CHAMP) being conducted by the Department of Paediatrics and Child Health, Stellenbosch University & Desmond Tutu Tuberculosis Centre. We have also recently investigated the impact of tuberculosis treatment on the respiratory microbiome in a cohort of children from Cape Town and the oral microbiome in individuals with metabolic syndrome and are interested in expanding our microbiome related research. We are associated with the African Microbiome Institute, a cross faculty initiative at Stellenbosch University that recognised the important of the microbiome across multiple disciplines.
We have recently started to use some of the techniques more commonly associated with microbiome research to investigate the resistome – the entire collection of resistance genes and determinants that may be present in a bacterial community.
Diagnostic development
The core function of the NHLS clinical microbiology laboratory is to identify pathogens and provide antibiotic susceptibility profiles to guide the clinical management of patients. The ability to perform these tests accurately and rapidly remains central in attaining the best outcome for patients. Conventional techniques such as culture and microscopy have a poor sensitivity, long turnaround time and culture requires the pathogen to be viable. Advanced molecular techniques for the diagnosis and molecular characterisation of infectious disease pathogens may overcome some of these limitations. Current projects are investigating the use of real-time polymerase chain reaction (PCR) based platforms such as in-house real-time PCR for the identification of bacterial meningitis pathogens, and multi-pathogen syndromic platforms for the simultaneous identification of bacterial, viral and fungal causes of meningitis, respiratory illnesses and bacteraemia. We are also exploring the use of next generation sequencing, including clinical metagenomics, for the identification and characterisation of causes of infectious diseases. Further studies to determine the clinical impact of molecular and NGS diagnostics are critical to assess their feasibility, especially in resource limited settings.


HIV immunology
Inflammation and immune activation play a role in chronic HIV infection, particularly in children on long-term antiretroviral therapy. The focus of this research, in collaboration with FAMCRU, is to establish the nature of immune dysfunction in people on long-term therapy. In performing this research in the well-characterised and well-maintained CHER cohort, we have been able to longitudinally track immune status and function over time. Particular areas of investigation include persisting innate immune stimulation, myeloid cell-derived cytokines and the role of gastrointestinal damage and gut translocation in driving persisting immune defects. Additional work has investigated novel markers of gut damage, and also changes in the T follicular helper (Tfh) cell subset, identified as a key HIV reservoir cell type. Much of the data generated is being used in analysis of how aberrant immunity in chronic HIC relates to the development of both neurocognitive impairment and cardiovascular diseases.

Inflammatory and immune biomarkers for monitoring autoimmune disease (and treatment response)
Autoimmune diseases are characterized by chronic inflammation and immune activation, either persistently or in sporadic “flare-ups”. Treatment often aims to control the hyper-inflammatory state, and symptom changes do not necessarily directly mirror immune status. The focus of this research is currently in Juvenile Arthritis (JA), in which use of standard laboratory measures of inflammation (such as ESR and CRP) do not provide accurate measures, particularly of joint inflammation. This research is assessing S100A8/A9 (calprotectin) as a biomarker of joint inflammation in JA patients initiating therapy. This research will give us an indication of levels of calprotectin in JA patients, and how they respond to therapy. Correlation with standard laboratory markers as well as a range of other immune biomarkers will aid in generating comprehensive in-depth comparative data.

Functional immune changes in TB-related primary immunodeficiency disorders (PIDs), particularly MSMD
Mendelian susceptibility to Mycobacterial Disease (MSMD) is a PID which involves genetic defects in the host impacting on the interferon-γ (IFN-γ) and IL-12 immune pathways. Classically these patients present with severe, persistent, unusual or recurrent mycobacterial infections. The focus of our research is in investigating the functional immune defects in the pathways that are flagged following whole genome sequencing (WGS) of patient DNA. Both previously described and novel genetic variants need to be validated functionally to determine the extent of the impact of the genetic defect on the overall immune functioning of the patients. In addition to assessing relative numbers of key immune cell types, their function (cytokine secretion) and signalling profile is assessed. A specific focus has been on key transcription factors in this pathway (T-bet). This work has enabled the identification of novel genetic variants in South African patients, and is contributing to our understanding of how a disease like MSMD manifests in a high prevalence TB area.