Electronic Theses and Dissertations (PhDs)

Permanent URI for this collectionhttps://hdl.handle.net/10539/38222

Browse

Now showing 1 - 20 of 29

Biomarkers to predict Tuberculosis treatment response
(2024) Boshielo, Itumeleng
Tuberculosis (TB) is a chronic disease caused by Mycobacterium tuberculosis (Mtb). Despite the implementation of multifaceted TB prevention and control efforts, a significant number of people still die from TB. Consistent with this, an uptick in TB-related mortality was recently noted, which has been ascribed to the negative effects of Coronavirus disease-2019 (COVID-19) on TB programs. The complex life cycle of Mtb is largely due to the use of immune evasion mechanisms to establish initial infection, remain dormant in the host, and reactivate pathogenicity under favourable circumstances. The prolonged TB treatment regimen is necessitated by the slow response of bacterial populations to standard TB chemotherapy, a phenomenon that may be caused by persistent, drug-tolerant bacteria. Scientific literature has provided evidence for these types of bacterial populations in the form of Differentially Culturable Tubercle Bacilli (DCTB). It has been demonstrated that DCTB represent drug tolerant bacteria that appear to be cleared at slower rate than organisms detected by routine culture methods. However, it remains unclear if DCTB populations elicit different immune responses when compared to their conventionally culturable counterparts. Herein, we address this question by optimizing a laboratory model for the generation of DCTB in vitro and test the capacity of clinical isolates of Mtb from Lineage 2 (Beijing) and Lineage 4 (LAM) to adopt the DCTB state. Using the Most probable number (MPN) assay, in the presence of culture filtrate (CF) as a source of growth factors to resuscitate DCTB, and colony forming units, the amount of DCTB in our model was quantified. As demonstrated by the limited growth on agar plates and increased growth in liquid media supplemented with CF from an axenic culture of Mtb, our findings demonstrated that carbon starvation was able to generate DCTB from clinical Mtb strains. After generating these populations, we stimulated whole blood with DCTB and conventionally culturable populations and report on the stimulation of a select set of cytokines (IFN-γ, IL-4, IL-5, IL-6, IL-12p70 and TNF-α) using a Bead Array Multiplex Immunoassay. In comparison to H37Rv-DCTB and LAM-DCTB, Beijing-DCTB induced significantly reduced levels of IL-5 and TNF-α. When comparing cytokine production between culturable and DCTB populations, within a single strain, we noted that LAMDCTB was delayed in the production of IFN-γ whilst Beijing-DCTB was not able to induce production of this cytokine when compared to conventionally culturable counterparts. These data suggest that shifting to a non-replicating DCTB state does indeed affect the ability of clinical isolates to induce immune responses. Based on these observations, we next set out to determine if DCTB affects immune responses during treatment of Mtb infected individuals. In prior work, using a prospective observational cohort, we demonstrated a substantive heterogeneity in clearance of DCTB in individuals with drug susceptible TB. We were able to classify these response patterns into three broad groups including (I) participants who were able to clear DCTB within the first two weeks of treatment (treatment-responsive); (II) those with delayed ability to clear these organisms (delayed-responsive) and (III) a group of individuals where DCTB did not change substantively during treatment (non-responders). Given these stark differences in treatment response patterns, we hypothesized that the immune responses associated with these patterns would be substantively different. In the second component of this work, we set out identify immune biomarkers that predict an effective response of DCTB to TB treatment. To quantify cytokines, chemokines and growth factors in plasma from these groups, we used a 65-plex Luminex assay, with a broad selection of targets. Statistically significant differences between these groups were analysed using the Kruskal-Wallis test with Dunn’s multiple comparisons, with p<0.05 was considered as statistically significant. When compared to patients who had TB and HIV co-infection, the number of cytokines that may possibly be used to report on the effectiveness of TB treatment was significantly higher in Mtbonly infected patients. This suggests that HIV infection significantly reduces the number of cytokines that can be used to report on TB treatment response. The ROC analysis of I-TAC, G-CSF and VEGFA showed that these cytokines have a significant discriminatory power to distinguish treatmentresponsive and non-responsive patients from HCs using DCTB as the measure of treatment response. No unifying cytokine signature that predicted DCTB response in all groups was identified. Together, our results indicate that some inflammatory markers are elevated in individuals with TB that rapidly clear bacteria during treatment. Given that these responses are based on DCTB, which represent drug tolerant populations, these select cytokines may be useful in evaluating the effectiveness of novel shorter TB treatment regimens.
Biomarkers to predict Tuberculosis treatment response
(University of the Witwatersrand, Johannesburg, 2023-06) Boshielo, Itumeleng Tania; Tiemessen, Caroline; Kana, Bavesh
Tuberculosis (TB) is a chronic disease caused by Mycobacterium tuberculosis (Mtb). Despite the implementation of multifaceted TB prevention and control efforts, a significant number of people still dee from TB. Consistent with this, an uptick in TB-related mortality was recently noted, which has been ascribed to the negative effects of Coronavirus disease-2019 (COVID 19) on TB programs. The complex life cycle of Mtb is largely due to the use of immune evasion mechanisms to establish initial infection, remain dormant in the host, and reactivate pathogenicity under favourable circumstances. The prolonged TB treatment regimen is necessitated by the slow response of bacterial populations to standard TB chemotherapy, a phenomenon that may be caused by persistent, drug-tolerant bacteria. Scientific literature has provided evidence for these types of bacterial populations in the form of Differentially Culturable Tubercle Bacilli (DCTB). It has been demonstrated that DCTB represent drug tolerant bacteria that appear to be cleared at slower rate than organisms detected by routine culture methods. However, it remains unclear if DCTB populations elicit different immune responses when compared to their conventionally culturable counterparts. Herein, we address this question by optimizing a laboratory model for the generation of DCTB in vitro and test the capacity of clinical isolates of Mtb from Lineage 2 (Beijing) and Lineage 4 (LAM) to adopt the DCTB state. Using the Most probable number (MPN) assay, in the presence of culture filtrate (CF) as a source of growth factors to resuscitate DCTB, and colony forming units, the amount of DCTB in our model was quantified. As demonstrated by the limited growth on agar plates and increased growth in liquid media supplemented with CF from an axenic culture of Mtb, our findings demonstrated that carbon starvation was able to generate DCTB from clinical Mtb strains. After generating these populations, we stimulated whole blood with DCTB and conventionally culturable populations and report on the stimulation of a select set of cytokines (IFN-γ, IL-4, IL-5, IL-6, IL-12p70 and TNF-α) using a Bead Array Multiplex Immunoassay. In comparison to H37Rv-DCTB and LAM-DCTB, Beijing-DCTB induced significantly reduced levels of IL-5 and TNF-α. When comparing cytokine production between culturable and DCTB populations, within a single strain, we noted that LAM-DCTB was delayed in the production of IFN-γ whilst Beijing-DCTB was not able to induce production of this cytokine when compared to conventionally culturable counterparts. These data suggest that shifting to a non-replicating DCTB state does indeed affect the ability of clinical isolates to induce immune responses. Based on these observations, we next set out to determine if DCTB affects immune responses during treatment of Mtb infected individuals. In prior work, using a prospective observational cohort, we demonstrated a substantive heterogeneity in clearance of DCTB in individuals with drug susceptible TB. We were able to classify these response patterns into three broad groups including (I) participants who were able to clear DCTB within the first two weeks of treatment (treatment-responsive); (II) those with delayed ability to clear these organisms (delayed-responsive) and (III) a group of individuals where DCTB did not change substantively during treatment (non-responders). Given these stark differences in treatment response patterns, we hypothesized that the immune responses associated with these patterns would be substantively different. In the second component of this work, we set out identify immune biomarkers that predict an effective response of DCTB to TB treatment. To quantify cytokines, chemokines and growth factors in plasma from these groups, we used a 65-plex Luminex assay, with a broad selection of targets. Statistically significant differences between these groups were analysed using the Kruskal-Wallis test with Dunn’s multiple comparisons, with p<0.05 was considered as statistically significant. When compared to patients who had TB and HIV co-infection, the number of cytokines that may possibly be used to report on the effectiveness of TB treatment was significantly higher in Mtb-only infected patients. This suggests that HIV infection significantly reduces the number of cytokines that can be used to report on TB treatment response. The ROC analysis of I-TAC, G-CSF and VEGF-A showed that these cytokines have a significant discriminatory power to distinguish treatment-responsive and non-responsive patients from HCs using DCTB as the measure of treatment response. No unifying cytokine signature that predicted DCTB response in all groups was identified. Together, our results indicate that some inflammatory markers are elevated in individuals with TB that rapidly clear bacteria during treatment. Given that these responses are based on DCTB, which represent drug tolerant populations, these select cytokines may be useful in evaluating the effectiveness of novel shorter TB treatment regimens.
Defining Fc-mediated Functions in People Living with HIV during Respiratory Viral Infection and Vaccination
(University of the Witwatersrand, Johannesburg, 2024) Motsoeneng, Boitumelo Madika; Moore, Penny
There are approximately 39 million people living with human immunodeficiency virus (HIV) (PLWH) worldwide. Furthering our understanding of humoral immune responses to respiratory viral infection and vaccination in PLWH is essential for reducing the burden of these diseases, in high HIV prevalence settings, and informing vaccine implementation in this population. Influenza virus hemagglutinin (HA) stalk-specific antibodies have been associated with protection and shown to mediate Fc-mediated functions. This thesis describes HA stalk-specific antibody- dependent cellular phagocytosis (ADCP), cellular cytotoxicity (ADCC) and complement deposition (ADCD) between PLWH and people without HIV (PWOH) following immunization with a seasonal trivalent inactivated influenza vaccine (TIV). Irrespective of HIV status, ADCD was boosted while ADCC was not. ADCP was only enhanced in PWOH. The coordination of these functions differed by HIV status. Additionally, differences in the regulation of these HA stalk Fc responses by HIV infection was reported. Furthermore, ADCC was not associated with protection in this study. Pre- existing ADCP reduced the risk of influenza virus infection while TIV-induced ADCD provided protection against influenza-illness. Overall, PLWH have unique responses to TIV and HA stalk- specific ADCD correlated with protection following TIV. For SARS-CoV-2, antiretroviral treatment (ART)-naïve PLWH had reduced humoral responses to respiratory infection. The infecting variants D614G and Beta differentially triggered ADCC, ADCD and antibody-dependent cellular trogocytosis (ADCT). Regarding the kinetics, PLWH infected with D614G had delayed neutralization and ADCP while Beta infection delayed ADCT, regardless of HIV status. PLWH showed improved coordination between immune responses following respiratory infection. ChAdOx-1 nCoV-19 vaccination differed from infection in that PLWH had delayed IgG binding while neutralization and ADCP were not delayed, and ADCC was substantially enhanced than in PWOH. In conclusion, despite the delayed and differential kinetics, PLWH on ART developed equivalent responses to PWOH, supporting the rapid rollout of ART and SARS-CoV-2 vaccines to PLWH. This thesis highlights the need to include high-risk groups with different responses in future vaccination trials and also supports the assessment of novel correlates of protection for future vaccines. Overall, this thesis provided insights into the mechanisms required for protection against severe respiratory diseases and improved our understanding of vaccine-induced immunity in PLWH
Defining the development of gp120-gp41 interface directed broadly neutralizing antibodies in HIV-1 infection
(2024) Hlatshwayo, Vincent Nkosinathi
A prophylactic HIV-1 vaccine will likely need to elicit broadly neutralizing antibodies (bNAbs) against conserved HIV-1 envelope epitopes such as the gp120-gp41 interface which includes the FP. The isolation of gp120-gp41 interface-, and FP-directed bNAbs from chronically HIVinfected donors has made this epitope an appealing vaccine target. Moreover, promising preclinical immunogenicity animal studies have shown the possibility of eliciting such responses in animals. However, little is known about the population prevalence or kinetics of gp120-gp41 interface responses, including FP-directed responses. Lastly, few FP-directed antibodies have been isolated from people living with HIV (PLWH), limiting our understanding of common developmental pathways that can be explored for vaccine purposes. Here, we first assessed the prevalence of bNAbs in participants previously enrolled in the CAPRISA 004 Tenofovir gel trial (CAP004). We show that in this cohort, only 12% of individuals developed breadth at three years post-infection, and that high viral load and low CD4 count were associated with bNAb development, as previously reported. ELISA screening showed that only 13% of individuals developed FP-directed responses at three years postinfection. Of the 13% (n=9), only two donors had broad plasma responses, including donor CAP312, whose plasma exhibited 64% neutralization breadth at three years post-infection. In CAP312, FP binding and heterologous neutralization against a multi-clade 22 virus panel appeared simultaneously, within one year (~ 50 weeks post-infection). Taken together, our findings suggest that gp120-gp41 interface- and FP-directed responses are infrequently elicited during infection. As few FP-specific bNAbs have been isolated to date, little is known about their shared features that could be exploited for eliciting FP-specific bNAbs by vaccination. We next isolated three FP-specific mAbs from donor CAP312 at three years post-infection; AIRU-F8, AIRU-G9 and AIRU-G4 with 64, 45 and 5% breadth, respectively. We showed that our mAbs, and previously isolated bNAbs PGT151 and ACS202 share gene usage and have a similar unusually long CDRH3, as a result of a conserved motif inherited from the germline IGHJ6*02 gene. Furthermore, we showed that CAP312 mAbs have even longer CDRH3s compared to PGT151 and ACS202 despite this shared motif. We also showed, using point mutants and glycan mutants that our FP-specific mAbs have a unique neutralization profile compared to published mAbs. Overall, these results suggest that FP-specific mAbs share structural and genetic features that could be explored further for lineage vaccine development. Lastly, we delineated the ontogeny of the gp120-gp41 interface-directed nAb CAP248-2B by tracing the evolutionary pathways utilising longitudinal samples from 11-281 weeks postinfection (wpi). CAP248-2B interacts with the HIV-1 Env trimer through a long light chain CDRL3 that inserts into the viral membrane, and a heavy chain CDRH1 32ED33 motif that interacts with gp41. We showed that the unusually long light chain CDRL3 and the heavy chain 32ED33 motif are functionally redundant against heterologous viruses. We also showed that affinity maturation mutations in this lineage selected a lineage with limited heterologous neutralization breadth. In summary, these findings support further research into gp120-gp41- and FP-specific responses in multiple cohorts. Furthermore, future studies should aim to elucidate mechanisms governing the development of these responses so that productive developmental pathways can be identified and exploited for vaccine design.
Development of a multi-disease targeted next generation sequencing panel to study genetic aetiology of rasopathies
(2024) Mudau, Maria Mabyalwa
With Next Generation Sequencing (NGS), technologies it is now possible to screen a large number of genes simultaneously through massively parallel sequencing, significantly reducing costs and time generally associated with mutation screening. After an informal survey of the diagnostic needs of the clinicians in the Division of Human Genetics, National Health Laboratory Service (NHLS), it was established that the aetiology of genetic disorders called facial dysostoses, RASopathies and Cohesinopathies (FRASC) could be understood better using NGS. These are developmental disorders that are phenotypically different and are commonly referred to our genetic clinic, currently there is limited genetic testing for these conditions in South Africa. A NGS panel targeting genes associated with the FRASC disorders was designed and optimised. Upon successful optimisation the panel was then utilised to sequence samples from patients presenting with features suggestive of RASopathies. An overall detection rate of 56.6% (34/60) was obtained for all RASopathy patients sequenced in the current study. Detection rate of 46.7% (7/15) for neurofibromatosis type 1 (NF1) patients and 60% (27/45) for patients with non-NF1 RASopathies was obtained. No clinically significant variants were identified in 26 of the 60 patients (43.3%), two of the 26 had a VUS in the MAP2K1 gene. Seven patients of the panel negatives were successfully sequenced using whole exome sequencing (WES), one patient had a pathogenic variant and the rest had variants of uncertain significance identified. This is the first report profiling mutations and clinical features in patients with RASopathies as a whole in South Africa, compared to a study focusing on NS patients only. The detection rates obtained were comparable to other international studies using NGS, except for detection rate of LZTR1 and BRAF1 gene variants observed in Noonan syndrome patients. The (35/60) 58.3% (panel and WES) of patients with a disease causing variant identified in this study now have a molecular confirmation that they previously did not have. Our results show that a targeted panel could be an effective first-line diagnostic testing for RASopathies in SA. The development of the multi-disease targeted panel in the current study has contributed to the design of the 500 gene inherited disease NGS targeted panel (IDP) that is currently being utilised in our facility for diagnostic testing of various monogenic disorders.
Development of a multiplex HIV/TB point-of-care diagnostic assay based on the microarray
(University of the Witwatersrand, Johannesburg, 2023) Malatji, Kanyane Bridgett
HIV/AIDS mortality is caused by opportunistic illnesses/infections that take advantage ofthe weakened immune system in infected individuals. In Africa, the most common of these opportunistic illnesses include infection by Mycobacterium tuberculosis (M.tb) responsible for tuberculosis (TB). HIV co-infection with M.tb has negative implications for disease management given that each pathogen accelerates the morbidity caused by the other. The effective management of patients infected with both pathogens is restricted by the fact that their diagnosis is done separately. The situation is more difficult in remote areas where patients must wait for much longer to obtain their TB diagnostic results. In addition, the current diagnostic tests for the detection of TB such as chest X-ray and bacterial culture have a long turnaround time, are expensive to perform, and require sophisticated equipment and trained personnel. It is in this context that this project sought to develop an HIV and TB multiplex microarray-based assay for the detection of the two diseases using one test. The project used a 2.5 x 7.6 cm epoxy-coated glass slide as well as high- binding 96 well plates to which HIV-1 p24 and M.tb CFP10, ESAT6 and pstS1 antigens, known to be markers of active TB, were immobilized. The immobilized antigens were then incubated with anti-p24, anti-CFP10, anti-ESAT6 and anti-pstS1 primary antibodies diluted in human serum to mimic physiological conditions where the antibodies would exist in the presence of other proteins. Detection of binding between the antigens and primary antibodies was achieved by means of secondary antibodies conjugated to either a fluorescence dye or horseradish peroxidase (HRP). In chapter two of the study, the immobilization of the HIV and TB antigens on the epoxy-coated glass slides as capture molecules of the HIV and TB antibodies diluted in human serum was performed. The antigen-antibody reactions detection were achieved by means of fluorescence dye conjugated secondary antibodies. This chapter also covered the sensitivity and specificity of the technology where the epoxy-coated glass slides were compared to the gold standard 96 well high-binding plates. Data showed that the HIV and TB antigen-antibody reactions were specific, and the slides were more sensitive relative to the 96 well high-binding plates with limits of detection many folds lower. To be specific, the limit of detection from the slides averaged 0.954 ng/ml compared to 4474.6 ng/ml for the plates. The detection limit concentrations of the slides were lower than the reported physiological concentrations of HIV and TB antibodies in infected individuals. Chapter two also focused on the evaluation of the antigens’ stability on the epoxy-coated glass slides by determining the optimal experimental pH buffer, temperature, storage condition (dry or wet), as well as the shelf-life. Data showed that the optimal pH and temperature for the HIV and TB antigens immobilized on the slides were pH 7.4 and 25 ˚C. Moreover, the antigens could be stored dry for at least 90 days without losing their function. Overall, this chapter showed that the epoxy-coated microarray slides performed better than the gold standard 96 well high-binding plates in terms of sensitivity; and that the immobilized antigens could remain stable for a long period, and do not require specialized storage conditions; thus, making the microarray technology a potential diagnostic tool for the multiplex detection of HIV and TB in the case of co-infection. Chapter three of the study focused on the proof-of-concept of the technology using human serum samples infected with HIV. The chapter showed that the technology could detect p24 antibodies in six out of seven samples infected with HIV, i.e., it detected p24 antibodies in 85.7% of samples known to be HIV positive. Furthermore, HIV negative samples also proved to be negative with this technology, thus no false positives were observed. Moreover, the technology was specific for HIV detection as no binding was observed on TB antigens. Therefore, these data support what was observed in the previous chapter when the HIV antibodies were spiked in normal human serum. Chapter four explored the application of the diagnostic technology for the point-of-care (POC) detection of HIV and TB antigen- antibody reaction, using HRP conjugated secondary antibodies, as well as the 2,2′-azino- bis(3-ethylbenzothiazoline-6-sulfonicacid) (ABTS) and 3,3',5,5'-tetramethyl Benzidine (TMB) substrates for colour change based endpoint. This chapter also covered the sensitivity and specificity of the immunoassay in the high-binding 96 well plates and on epoxy-coated glass slides. Similar to what was observed in the previous chapter, the HIV and TB antigen-antibody interactions were specific, and the epoxy-coated microarray slides were more sensitive than the 96 well high-binding plates with limits of detection averaging 815-folds lower than the plates. Nevertheless, both platforms were found to be sensitive enough to be used for the POC detection of HIV and TB co infection using visual inspection. Furthermore, the stability of the antigens in the 96 well high-binding plates using colour change detection was also evaluated. The antigens were found to be stable in the high-binding plates at different pH and temperature conditions; however, pH 7.4 and 25 ˚C were optimal. In addition, the antigens were stable when stored dry in the plates for a period of three months. In addition, between the two HRP substrates used, TMB was faster and more sensitive to the HIV and TB antigen-antibody reactions than the ABTS substrate, and the difference was statistically significant (p<0.05). The importance of this chapter is that it eliminated the need for sophisticated equipment to detect the presence of HIV and TB antibodies, as the detection could be achieved by visual inspection. Overall, data in this chapter supported further development of the microarray technology for the POC HIV and TB co-infection diagnosis. Chapter five attempted to produce the CFP10, ESAT6, and pstS1 TB antigens in plants to reduce the cost associated with the current commercially available bacteria-produced antigens.
Development of an Anopheles arabiensis sex separation strain and optimisation of mosquito handling, packaging and transport conditions for the South African Mosquito Sterile Insect Technique programme
(University of the Witwatersrand, Johannesburg, 2023) Mashatola, Thabo; Munhenga, Givemore; Koekemoer, Lizette
South Africa is taking significant strides towards eliminating malaria transmission within its borders. However, existing vector control strategies that focus on indoor mosquito management face challenges with Anopheles arabiensis, the primary malaria vector. To bolster these efforts, the sterile insect technique (SIT) is being considered as an additional vector control strategy. SIT involves mass-rearing and sterilising specific pest insects, which are then released to mate with wild insects, effectively reducing the pest population. The South African SIT project faces a crucial challenge of efficiently separating female mosquitoes from the production line. This is because female mosquitoes are capable of transmitting the malaria parasite, making their elimination vital. Current methods like manual separation and resistance-based sorting have operational limitations and require further optimisation for field trials. To address this challenge, this thesis conducted optimisation and acclimatisation experiments on adult Anopheles arabiensis females, aiming to transition them to an artificial membrane feeding technique. Comparative assessments demonstrated that artificial blood-feeding methods utilising a Hemotek® membrane feeding system and hog casing could effectively replace conventional methods without significant detriment to reproductive fitness. Subsequently, the study explored the use of ivermectin, a toxicant, to spike blood during artificial feeding to target and eliminate females. An optimal concentration of ivermectin (7.5 ppm) was identified, showing potential for segregating females from males during laboratory rearing. However, complete female elimination within the desired timeframe was not achieved, indicating that this method serves as a secondary phase for female elimination. The study also investigated the use of genetic sexing strains (GSSs) to selectively eliminate females. Although efforts to induce temperature-sensitive lethal mutations temperature sensitive lethality mutations and random morphological variations were unsuccessful, further cross mating studies and insights from previous studies on thermosensitive strains from Cameroon informed future research aimed at developing GSSs tailored to the South African genetic background Another challenge addressed was the optimal temperature and compaction conditions for chilling and immobilising sterile males during handling and transport. This is crucial for maintaining the quality of sterile males. Optimal knockdown temperature ranges (4°C – 8°C for 20 minutes) and packaging conditions (1000 sterile, marked adult males per 27000 cm³ Bugdorm-1® cage) were identified for laboratory handling and transport, facilitating recent small-scale pilot trials with successful packaging and transportation of sterile males to field sites. These advancements signify significant strides in South Africa's malaria elimination endeavours, while also playing a pivotal role in shaping the development of efficient operational protocols for SIT. Furthermore, as the country remains steadfast in its commitment to eliminating malaria, these innovative approaches offer a promising trajectory forward and establish a robust framework for orchestrating the SIT operational phase.
Differential Gene Expression in Exfoliation Syndrome and Exfoliation Glaucoma in the Conjunctiva of Black South Africans
(University of the Witwatersrand, Johannesburg, 2024) Hulley, Michaella Robyn
Glaucoma is a heterogeneous group of clinically and genetically complex optic neuropathies. The most prevalent identifiable secondary cause of glaucoma is the ocular manifestation of exfoliation syndrome (XFS), known as exfoliation glaucoma (XFG), a severe form of glaucoma characterized by rapid progression. While XFS is systemic, XFG is defined by fibrillar extracellular matrix (ECM) deposits in the eye. XFG has a recognised genetic aetiology, specifically with contributions from LOXL1 variants, however the molecular pathogenesis remains unclear. Conjunctival cells have not previously been used for whole transcriptome sequencing, and gene expression studies on XFG are lacking, particularly in South Africa. The aim of this study was to validate the use of conjunctival cells for whole transcriptome sequencing and interrogate the gene expression profiles of individuals with XFS and XFG. Conjunctival cells were collected from 19 cases and 15 control participants for RNA extraction, cDNA library construction and sequencing. Differential gene expression was assessed between cells from cases and controls and 81 genes were found to be differentially expressed, with 80 upregulated in cases. Interestingly, LOXL1, which has shown contradictory expression results in previous studies, was not identified as differentially expressed. The most significant overexpression was of the CCN2 gene, which encodes a matricellular protein that interacts with structural ECM molecules. A potential novel pathway involving megakaryocytes and the activation of neutrophils was, however, identified. Megakaryocytes and neutrophils are both involved with interstitial fibrosis, with neutrophils also responding to chemotactic signals to induce inflammation. The inflammatory pathway has long been associated with XFS, XFG and other fibrotic disorders, such as Alzheimer's disease and rheumatoid arthritis. Genes involved in the inflammatory process were overexpressed in XFG, including TGF-β, IL-1β, IL- 33, EGR1 and EGR3. EGR1 and EGR3 are regulated by fibrotic signals and therefore play an important role in fibrosis, which may contribute to XFS fibrillar deposits. They are also regulated by TGF-β, thus supporting a complex interplay of the inflammatory process and fibrosis in XFS pathogenesis
Equitable access to vaccines: exploring the role of accessability, acceptability, affordabilityand availability with a focus on COVID-19
(University of the Witwatersrand, Johannesburg, 2024) Schwalbe, Nina; Cutland, Clare
The coronavirus disease (COVID-19) crisis brought to light many challenges, including “vaccine equity”. In other words, it raised the question: was the distribution of vaccines “fair”? While, on the one hand, there have been unprecedented advances in the science and technologies associated with vaccines, including extraordinary speed and scale-up of manufacturing, there were also significant barriers related to rollout and reaching those most at risk of severe COVID-19. These challenges have disproportionately affected low- and middle-income countries and low-income populations in high-income countries. Building on evidence from other vaccine preventable diseases, this thesis describes the challenges and opportunities concerning vaccine access with a focus on production and distribution (the “supply side”). It explores access using a “4A's” framework to conceptualise the components of access to medicines: affordability, availability, acceptability, and accessibility. The research identifies a range of access policy levers across the end-to-end process of vaccine research, development, and rollout (affordability, acceptability, accessibility, acceptability); reviews these levers as they apply to vaccine manufacturing (affordability, availability); explores the lever of financial incentives to increase coverage (acceptability); and explores the potential of using precision public health to improve vaccine impact by targeting vaccine distribution to groups most risk (accessibility). This thesis identifies several policy and program interventions ranging from regulatory harmonisation and intellectual property sharing, to using precision public health to target the delivery of vaccines to those most at risk. It also shows that while financial incentives may help, governments cannot “buy” coverage. It proposes that in future, vaccine development and deployment should start and end with a “4A’s” strategy and provides practical recommendations on how that can be achieved
Exploring the interplay of chemokine receptors ccr5 and cxcr6 in mechanisms of natural control in HIV-1- infected black South Africans
(2024) Koor, Gemma Whitney
In sub-Saharan Africa, HIV-1 is a significant cause of morbidity and mortality. However, research remains primarily focused on North American and European population groups, who have remarkably different genetic backgrounds to individuals from sub-Saharan Africa. HIV1 controllers represent a model of HIV-1 functional cure, with some individuals able to control viral replication, and some able to sustain immune function in the presence of high viral loads, both in the absence of antiretroviral therapy (ART). The chemokine receptors CCR5 and CXCR4 are the major coreceptors HIV-1 utilises to enter cells. The use of alternative coreceptors, such as the CXCR6 coreceptor, is thought to contribute to the lower pathogenicity exhibited by the HIV-2 and SIVsmm strains. Building on previous work conducted in our research unit on these two coreceptors in South African populations, this thesis firstly describes CCR5 genetic variants that associate with HIV-1 control or risk of progressive infection in black South Africans, and then explores constitutive expression levels of CCR5 and CXCR6 on various peripheral blood immune cell subsets in the absence of HIV-1 infection in ethnically divergent population groups. The effect of sex, age, and select CCR5 and CXCR6 single nucleotide polymorphisms (SNPs) on expression levels of these two receptors was also investigated. The CCR5 5’UTR and 3’UTR regions were PCR-amplified and sequenced from genomic DNA extracted from 145 ART-naive black South African individuals living with HIV-1 (71 HIV-1 controllers – 23 elite controllers, 37 viraemic controllers, 11 high viral load long-term nonprogressors and 74 progressors). Findings confirmed results from other studies in showing that the CCR5 HHE haplotype is deleterious for HIV-1 disease progression, and the HHA haplotype and HHA/HHC genotype associated with protection from HIV-1 disease progression. Novel haplotypes were characterised, both in the 3’UTR and spanning the CCR5 5’UTR and 3’UTR. Overall, findings suggest that two CCR5 promoter SNPs (-2459 G>A and -2135 T>C) and one CCR5 3’UTR SNP (+2919 T>G) may be key functional variants with regards to HIV-1 control in black South Africans. To gain further insight into the constitutive expression of CCR5 and CXCR6 on peripheral blood immune cells and explore the relationship between select genetic variants and expression, immunophenotyping by flow cytometry was conducted using whole blood from age- and sex-matched ethnically distinct South African HIV-uninfected individuals (17 black, 21 white). Expression levels of CCR5 and CXCR6 were assessed on CD4+ and CD8+ T cells, B cells, monocytes and NK cells, and their respective subsets. The effects of age and sex on expression levels of these two receptors was also investigated. Population-specific differences with regards to CCR5 expression on all cell types, except for B cells, were evident. Generally, black South Africans exhibited a lower expression level of CCR5 compared to white South Africans. CXCR6 expression only differed with regards to percentage of CXCR6-expressing cells, not CXCR6 density (numbers of cell surface receptors). Black individuals had a lower percentage of CXCR6-expressing CD8+ T cell subsets (naïve and effector memory) and a higher percentage of CXCR6-expressing CD14+CD16+ monocytes compared to white individuals. Overall, we found significant population-specific differences in expression levels of both CCR5 and CXCR6, multiple associations with cell activation (as measured by HLADR expression) and CCR5 and CXCR6 expression, and CCR5 and CXCR6 expression was positively significantly correlated on multiple cell subsets. Furthermore, both sex and age influenced CCR5 and CXCR6 expression, however results varied widely across the two population groups studied. Sex differences were only evident in white individuals; predominantly CXCR6 expression was increased in males compared to females. Age associations with CCR5 and CXCR6 expression were also primarily found in white individuals. Four CCR5-related SNPs that are associated with HIV-1 control in this or other studies (rs553615728 -4223 C>T SNP, rs1799987 −2459 G>A SNP, rs746492 +2919 T>G SNP and rs1015164 G>A SNP) were assessed for their potential association with CCR5 expression levels. The +2919 TG genotype significantly associated with a higher percentage of CCR5- expressing total CD8+ T cells, transitional memory and terminally differentiated CD8+ T cells compared to the GG genotype. The +2919 GG genotype associated with a lower percentage of CCR5-expressing B cells compared to the TT and TG+TT genotypes, however, only in white South Africans. The +2919 TG and TG+TT genotypes associated with significantly higher CCR5 density on all CD8+ T cell subsets, except for naïve CD8+ T cells, when compared to the GG genotype. When evaluating two CXCR6 genetic variants previously associated with HIV-1 viraemic control (rs2234355 G>A and rs2234358 G>T) in relation to CXCR6 expression, possession of the rs2234355 SNP GA genotype associated with lower CXCR6 expression on select CD4+ and CD8+ T cell subsets as well as on B cells, while possession of the rs2234358 SNP TT genotype associated with higher CXCR6 expression on multiple cell types, primarily in white South Africans. Possession of the -358TT/+355GA genotype combination associated with lower CXCR6 expression on select subsets of CD4+ T cells and monocytes. In summary, this study provides information on genetic variation in the CCR5 gene in a South African context, describes genetic variants associating with HIV-1 control in black South Africans, adds novel insight into constitutive CCR5 and CXCR6 expression levels on CD4+ and CD8+ T cells, B cells, monocytes and NK cells in HIV-1-uninfected black and white South Africans, and describes the potential associations of select genetic variants and expression. Black and white individuals differed in their baseline expression levels of CCR5 or CXCR6, which was partly driven by host genetic factors that were explored. This work highlights the importance of considering effects of ethnicity, age, and sex in any studies addressing any immune molecules in relation to differential HIV-1 outcomes of infection susceptibility/protection, disease progression, or HIV-1 virological control on antiretroviral therapy. Although conducted on small numbers of individuals, these variables clearly influenced constitutive expression of CCR5 and CXCR6, and further population-specific studies are warranted to gain further insights. Findings from this study have implications for risk of acquisition of HIV-1 infection and for disease progression in people living with HIV-1. Understanding the role of these molecules is important for informing strategies for both HIV1 prevention and HIV cure.
Exploring the Interplay of Chemokine Receptors CCRS and CXCR6 in Mechanisms of Natural Control in HIV-1-lnfected Black South Africans
(University of the Witwatersrand, Johannesburg, 2023-06) Koor, Gemma Whitney; Tiemessen, Caroline T.; Paximadis, Maria; Shalekoff, Sharon
In sub-Saharan Africa, HIV-1 is a significant cause of morbidity and mortality. However, research remains primarily focused on North American and European population groups, who have remarkably different genetic backgrounds to individuals from sub-Saharan Africa. HIV-1 controllers represent a model of HIV-1 functional cure, with some individuals able to control viral replication, and some able to sustain immune function in the presence of high viral loads, both in the absence of antiretroviral therapy (ART). The chemokine receptors CCR5 and CXCR4 are the major coreceptors HIV-1 utilises to enter cells. The use of alternative coreceptors, such as the CXCR6 coreceptor, is thought to contribute to the lower pathogenicity exhibited by the HIV-2 and SIVsmm strains. Building on previous work conducted in our research unit on these two coreceptors in South African populations, this thesis firstly describes CCR5 genetic variants that associate with HIV-1 control or risk of progressive infection in black South Africans, and then explores constitutive expression levels of CCR5 and CXCR6 on various peripheral blood immune cell subsets in the absence of HIV-1 infection in ethnically divergent population groups. The effect of sex, age, and select CCR5 and CXCR6 single nucleotide polymorphisms (SNPs) on expression levels of these two receptors was also investigated. The CCR5 5’UTR and 3’UTR regions were PCR-amplified and sequenced from genomic DNA extracted from 145 ART-naive black South African individuals living with HIV-1 (71 HIV-1 controllers – 23 elite controllers, 37 viraemic controllers, 11 high viral load long-term non-progressors and 74 progressors). Findings confirmed results from other studies in showing that the CCR5 HHE haplotype is deleterious for HIV-1 disease progression, and the HHA haplotype and HHA/HHC genotype associated with protection from HIV-1 disease progression. Novel haplotypes were characterised, both in the 3’UTR and spanning the CCR5 5’UTR and 3’UTR. Overall, findings suggest that two CCR5 promoter SNPs (-2459 G>A and -2135 T>C) and one CCR5 3’UTR SNP (+2919 T>G) may be key functional variants with regards to HIV-1 control in black South Africans. To gain further insight into the constitutive expression of CCR5 and CXCR6 on peripheral blood immune cells and explore the relationship between select genetic variants and expression, immunophenotyping by flow cytometry was conducted using whole blood from age- and sex-matched ethnically distinct South African HIV-uninfected individuals (17 black, 21 white). Expression levels of CCR5 and CXCR6 were assessed on CD4+ and CD8+ T cells, B cells, monocytes and NK cells, and their respective subsets. The effects of age and sex on expression levels of these two receptors was also investigated. Population-specific differences with regards to CCR5 expression on all cell types, except for B cells, were evident. Generally, black South Africans exhibited a lower expression level of CCR5 compared to white South Africans. CXCR6 expression only differed with regards to percentage of CXCR6-expressing cells, not CXCR6 density (numbers of cell surface receptors). Black individuals had a lower percentage of CXCR6-expressing CD8+ T cell subsets (naïve and effector memory) and a higher percentage of CXCR6-expressing CD14+CD16+ monocytes compared to white individuals. Overall, we found significant population-specific differences in expression levels of both CCR5 and CXCR6, multiple associations with cell activation (as measured by HLA-DR expression) and CCR5 and CXCR6 expression, and CCR5 and CXCR6 expression was positively significantly correlated on multiple cell subsets. Furthermore, both sex and age influenced CCR5 and CXCR6 expression, however results varied widely across the two population groups studied. Sex differences were only evident in white individuals; predominantly CXCR6 expression was increased in males compared to females. Age associations with CCR5 and CXCR6 expression were also primarily found in white individuals. Four CCR5-related SNPs that are associated with HIV-1 control in this or other studies (rs553615728 -4223 C>T SNP, rs1799987 −2459 G>A SNP, rs746492 +2919 T>G SNP and rs1015164 G>A SNP) were assessed for their potential association with CCR5 expression levels. The +2919 TG genotype significantly associated with a higher percentage of CCR5-expressing total CD8+ T cells, transitional memory and terminally differentiated CD8+ T cells compared to the GG genotype. The +2919 GG genotype associated with a lower percentage of CCR5-expressing B cells compared to the TT and TG+TT genotypes, however, only in white South Africans. The +2919 TG and TG+TT genotypes associated with significantly higher CCR5 density on all CD8+ T cell subsets, except for naïve CD8+ T cells, when compared to the GG genotype. When evaluating two CXCR6 genetic variants previously associated with HIV-1 viraemic control (rs2234355 G>A and rs2234358 G>T) in relation to CXCR6 expression, possession of the rs2234355 SNP GA genotype associated with lower CXCR6 expression on select CD4+ and CD8+ T cell subsets as well as on B cells, while possession of the rs2234358 SNP TT genotype associated with higher CXCR6 expression on multiple cell types, primarily in white South Africans. Possession of the -358TT/+355GA genotype combination associated with lower CXCR6 expression on select subsets of CD4+ T cells and monocytes. In summary, this study provides information on genetic variation in the CCR5 gene in a South African context, describes genetic variants associating with HIV-1 control in black South Africans, adds novel insight into constitutive CCR5 and CXCR6 expression levels on CD4+ and CD8+ T cells, B cells, monocytes and NK cells in HIV-1-uninfected black and white South Africans, and describes the potential associations of select genetic variants and expression. Black and white individuals differed in their baseline expression levels of CCR5 or CXCR6, which was partly driven by host genetic factors that were explored. This work highlights the importance of considering effects of ethnicity, age, and sex in any studies addressing any immune molecules in relation to differential HIV-1 outcomes of infection susceptibility/protection, disease progression, or HIV-1 virological control on antiretroviral therapy. Although conducted on small numbers of individuals, these variables clearly influenced constitutive expression of CCR5 and CXCR6, and further population-specific studies are warranted to gain further insights. Findings from this study have implications for risk of acquisition of HIV-1 infection and for disease progression in people living with HIV-1. Understanding the role of these molecules is important for informing strategies for both HIV-1 prevention and HIV cure.
HIV infection, antiretroviral therapy and the haemostasis of pregnancy
(University of the Witwatersrand, Johannesburg, 2023-07) Schapkaitz, Elise; Libhaber, Elena; Jacobson, Barry; Büller, Harry
The human immunodeficiency virus (HIV) epidemic affects an estimated 30% of pregnant women living in South Africa. Increasing evidence suggests that women living with HIV are at a heightened risk for venous thrombo-embolism (VTE), which is a significant contributor to maternal mortality. In addition to a higher prevalence of obstetric and venous risk factors, this increased risk of VTE has been attributed to the effects of HIV and/or its treatment. HIV is characterized by immune activation and inflammation, which promote endothelial dysfunction and activation of coagulation. This is more pronounced with untreated HIV, yet this pro-inflammatory and pro-thrombotic balance may persist with long-term suppressive antiretroviral therapy (ART). However, the extent to which ongoing inflammation disrupts maternal haemostasis and predisposes pregnant women living with HIV to its prothrombotic consequences, is currently unknown. The aims of the work presented in this thesis in women living with HIV with access to ART were firstly to identify antepartum and postpartum risk factors for VTE; secondly to assess procoagulant changes in maternal haemostasis; and thirdly to determine risks of thrombosis and bleeding associated with thromboprophylaxis for VTE prevention. An epidemiological case-control study was performed in 128 cases with pregnancy related VTE and 640 matched controls. This study found at least a two-fold increased risk for VTE among pregnant and postpartum women living with HIV. In addition, antepartum risk factors, that may explain the disproportion of VTE risk in HIV, included medical co-morbidities and chronic hypertension, while postpartum risk factors included a personal history of VTE, medical co-morbidities, systemic infection, prolonged hospital admission and postpartum haemorrhage. Opportunistic infections, ART and the degree of immunosuppression were not associated with VTE risk. A sub-study followed and investigated antiphospholipid antibodies (aPL) in 215 women with thrombosis and/or obstetric complications. In this study, 15 (13.2%) of the women with HIV were positive at baseline for one of the five criteria aPL. The prevalence of aPL was not significantly increased among women with HIV, as compared to HIV negative women. Furthermore, the aPL profiles were not significantly different between the two groups. Lupus anticoagulant (LAC) positivity, on a single occasion, was associated with thrombosis (p < 0.003). Subsequently two prospective cross-sectional studies were conducted which assessed endothelial activation as well as fibrinolysis, coagulation and platelet activation in pregnant women with HIV, in each trimester. The studies included three groups: HIV negative, HIV with virological suppression (< 50 copies/mL) and HIV with viral load (VL) of >50 copies/mL. Endothelial activation was evaluated by measuring von Willebrand factor (VWF) antigen, VWF propeptide, multimer patterns and ADAMTS-13 antigen, activity, and antibody levels. The results showed an increase in the ratio of VWF propeptide to VWF antigen in the first, second and third trimester, in the HIV virologically suppressed group (1.7 ± 0.7, 1.7 ± 0.4, 1.6 ± 0.5) and the HIV group with VL > 50 copies/mL (1.9 ± 0.9, 1.7 ± 0.9, 1.6 ± 1.1) compared to the HIV negative group (1.4 ± 0.6, 1.3 ± 0.4, 1.2 ± 0.3, p < 0.05). Virological suppression was not associated with a significant reduction in this ratio, in each trimester. In addition, increased high molecular weight multimers were observed in the HIV groups, despite only a mild reduction in ADAMTS-13 activity compared to the HIV negative group (p < 0.001). Thereafter, fibrinolytic activity was evaluated by measuring d-dimer and plasminogen activator inhibitor-1 (PAI-1). Coagulation activity was determined by measuring thrombin-antithrombin (TAT) complex concentrations, and platelet factor-4 and platelet indices, namely mean platelet volume (MPV) and platelet distribution width as a measure of platelet activation. The results showed increased log d-dimer levels in the first, second and third trimester, in the HIV virologically suppressed group (-1.2 ± 0.5, -0.9 ± 0.4, -0.5 ± 0.3) and the HIV group with VL > 50 copies/mL (- 1.1 ± 0.4, -0.7 ± 0.4, -0.5 ± 0.5) compared to the HIV negative group (-1.4 ± 0.2, -1.1 ± 0.3, -0.8 ± 0.3, p < 0.05). Additionally, log PAI-1 levels were increased in the first, second, and third trimester, in the HIV virologically suppressed group (1.0 ± 0.4, 1.3 ± 0.4, 1.5 ± 0.4) and the HIV with VL > 50 copies/mL (0.8 ± 0.5, 1.2 ± 0.4, 1.5 ± 0.3) compared to the HIV negative group (0.4 ± 0.5, 0.8 ± 0.3, 1.3 ± 0.3, p < 0.05). Virological suppression was not associated with a significant reduction in first and third trimester d-dimer and PAI-1 levels. Thrombin-antithrombin complex levels were not increased, in the HIV virologically suppressed group as compared to the HIV negative group, beyond the first trimester. With regard to platelet parameters, only log MPV measured in the third trimester was decreased in in the HIV virologically suppressed group (2.3 ± 0.1) and the HIV group with VL > 50 copies/mL (2.3 ± 0.1) compared to the HIV negative group (2.5 ± 0.2) (p < 0.001). The last study was a longitudinal study of 129 pregnant women at intermediate or high risk of VTE, who received thromboprophylaxis. Venous thrombo-embolism occurred antepartum in 1.4%, 95% confidence interval (CI) 0.04-7.7 of intermediate and 3.4%, 95% CI 0.4-11.7 of high risk pregnancies. Major, clinically relevant non-major and minor bleeding events occurred in 7.1%, 95% CI 2.4-15.9 of intermediate and 8.5%, 95% CI 2.8-18.7 of high risk pregnancies. Owing to the small number of events, this study could not assess for HIV as a predictor of thrombosis and bleeding. Thus, in conclusion, the findings described in the studies in this thesis contribute to our knowledge in pregnant women living with HIV in the following ways. Firstly, HIV emerged as a significant antepartum and postpartum risk factor for VTE. Traditional obstetric and venous risk factors were also linked to the risk of thrombosis and could be useful for identifying women with HIV, who may benefit from postpartum and/or antepartum thromboprophylaxis. Secondly, this thesis identified heightened markers of endothelial activation and impaired fibrinolysis. Markers such as the ratio of VWF propeptide to VWF antigen, d-dimer and PAI-1 may provide a biological mechanism for the increased risk of pregnancy-related VTE in in HIV. Finally, this thesis provided rates of thrombosis and bleeding in women who received thromboprophylaxis in pregnancy and the postpartum period which can be used to advise women with HIV of the associated risks.
Investigation of Contamination of Community Groundwater Sources with Antibiotics in Informal Settlements of Kisumu, Kenya
(University of the Witwatersrand, Johannesburg, 2023-09) Karimi, Kellen Joyce; Ahmad, Aijaz; Duse, Adriano; Mwanthi, Mutuku
Antibiotics have been used to cure diseases, but there are growing concerns about the risk to human health caused by inadvertent exposure to low levels of antibiotics in the environment. Despite extensive reporting from the developed world on antibiotic pollution of groundwater, relatively little study has been conducted on antibiotic contamination of groundwater in the developing countries, particularly informal settlements. Antibiotic usage and misuse have long been seen as clinical events, with little understanding of the role of disposal in the development of environmentally induced resistance. Exposure pathways that contribute to groundwater contamination in informal settlements put residents at odds because they already face inequalities, such as a high disease burden exacerbated by antibiotic resistance; thus, proper antibiotic disposal is critical in protecting human and environmental health. The purpose of this cross-sectional study was to establish the prevalence of groundwater contamination with the common antibiotics’ such as sulfamethoxazole, trimethoprim, and metronidazole, and the related antibiotic resistance and the human health risk of exposure. Ethical clearance to conduct research was obtained from three institutions as follows: - the Health Research Ethic Committee of the university of the Witwatersrand (HREC. Protocol Number M190412); the Kenyatta National Hospital and University of Nairobi Ethics and Research Committee (KNH/UoN-ERC. Ref No. P71910/2018); and the National Commission for Science, Technology, and Innovation (Ref No. NACOSTI/P/19/3232/28732). Each respondent gave informed consent to participate in the study. Anonymity was maintained at all levels of the study to protect the study participants from identification. Antibiotic use, which is connected to antibiotic disposal, was evaluated in a random sample of 447 families. From the 188 mapped groundwater sources, a random sample of 49 groundwater sources was chosen, and water samples were taken for antibiotic concentration analysis utilising a solid-phase extraction and liquid chromatography coupled to magnetic sector high resolution mass spectrometry (SPE-LC-MS/MS). The Kirky-Bauber diffusion method was used to test antibiotic resistance in Escherichia coli. The community's potential groundwater contamination routes were assessed by determining antibiotic use and disposal among households as well as assessing the environmental risk of exposure. In the households visited, 75% (n=337) were female and 25% (n=110) were male. The prevalence of antibiotic use in informal settlements was 43% (n=193), with 70% (n=137) users reporting that they obtained the antibiotics through a prescription from a health practitioner. A significant relationship was observed between having HIV/AIDS and acquiring antibiotics through a prescription; p=0.001. An association was also observed among the informal settlements, where a lower number of MNY B dwellers did not receive a prescription for the antibiotics acquired. There was no statistically significant difference in antibiotic use between males and females; odds ratio=1.33; whereas there was a difference in HIV/AIDS status; odds ratio=0.313; and among informal settlements where the odds of using antibiotics were reduced in NY B; odds ratio=0.42. Respondents who used antibiotics either kept the unused antibiotics for future use 87.1% (n=27) or disposed them. Among the disposals 51.6% (n=16) disposed in pit latrines, 16.1% (n=5) dispose in compost pits, and 6.5% (n=2) dispose the remaining antibiotics by burning. Females completed their antibiotic doses at a higher rate (36.3%; n=117) than males (32.5%; n=39). Significant difference was observed in completion rate among the HIV/AIDS positive and negative respondents as well as among informal settlements; p<0.000 and p=0.001 respectively. On the other hand, groundwater use in these communities is widespread. Respondents used it for a variety of purposes, including drinking (9%; n=39), though they declined to report. Awareness of the health consequences of drinking antibiotic-contaminated water was also low (35%; n=158), especially among households that reported antibiotic use; p=0.003. Only Sulfamethoxazole was detected in 7 out of 49 groundwater samples at a detection frequency of 14.3%; with concentrations ranging from nd to 258 ng/L. Escherichia coli and Cryptosporidium parvum were isolated from all the 49 water samples and E. coli isolates from 3 (6%) water samples were resistant to sulfamethoxazole with Inhibition Zone Diameters of 0.8 mm, 10.5 mm, and 11.5 mm. The 3 water samples were however not among samples where sulfamethoxazole was detected. The Hazard Quotient was 0 (zero), and therefore no risk of exposure to sulfamethoxazole in the environment, but the level of antibiotics that trigger antibiotic resistance is not known. Because of the rising problem of antibiotic resistance due to overuse and incorrect disposal, teaching on safe antibiotic prescription should be incorporated into medical training for all cadres. In addition to educating patients on proper use and disposal, the ministries of health should ensure the antimicrobial stewardship standards are adhered to both locally and worldwide. Follow-up research of antibiotic resistance discovered in three groundwater sources must be done to eliminate the possible sources and prevent further spread. This study is instrumental in informing the inclusion of antibiotics on the list of frequently monitored contaminants during water treatment, as well as serving as a starting point for antibiotic surveillance in Kenya.
Life History Trade-offs associated with Evolution of Cancer
(University of the Witwatersrand, Johannesburg, 2023-07) Worsley, Catherine Mary; Durand, Pierre; Mayne, Elizabeth; Veale, Rob
The evolution of multicellularity requires cooperation between single cells to form new multicellular individuals. Changes in levels of selection occur during this process, with selection at the multicellular level overriding that at the single cell level. For a multicellular individual to function, somatic mutations and selection must be under tight regulation. Nevertheless, mutations and selective environmental pressures can select for cells with fitness advantages relative to normal cells, resulting in cancer. Therapeutic drugs and radiation are forms of artificial selection that can drive the development and selection of cell populations that are resistant to treatment. Cancer occurs because of the failure of multicellular systems to suppress somatic evolution. This somatic evolution results in tumour cells with a wide range of phenotypes with either fast (proliferating) or slow (quiescent) life history strategies. Evolutionary theory provides a framework for understanding what drives the formation of these phenotypes and the ecological niche that supports them, and helps in predicting tumour progression and response to therapy. The key hypothesis of this study was that selective pressures in the tumour microenvironment drive trade-offs between tumour cell survival, proliferation, and apoptosis. An extensive literature review was conducted to identify key selective pressures affecting tumour progression. Low extracellular pH was identified as a component of the tumour microenvironment that affects life history trade-offs, and particularly drives escape from immune-mediated destruction. A protocol was then developed to expose cancer cells to low pH in cell culture. Breast carcinoma and oesophageal squamous cell carcinoma cell lines were selected for these experiments based on the prevalence of these cancers and because of their different anatomical locations. Exposure to low pH induced different levels of apoptosis in each cell line. This also affected cell cycle progression and the secretion of growth factors and immunomodulatory cytokines. The oesophageal cell line, WHCO6, adapted to moderate acidity levels with some cells undergoing apoptosis. Factors released by these cells supported the growth and survival of related cells. In contrast, in the breast carcinoma MCF-7 cell line, low pH induced high rates of apoptosis, and factors released by dying cells stimulated death in related cells. This study highlights that different life history strategies are employed by different cancer types. It also shows the importance of the tumour microenvironment, and acidity in particular, in driving tumour cell adaptation and survival. This study also identifies apoptosis as a pro-tumorigenic driver of cancer progression which has important therapeutic implications.
Molecular profiling of colorectal cancer within South Africa
(2024) McCabe, Michelle
There is a global requirement to characterize colorectal cancer (CRC) by molecular subtyping within subpopulations for the assignment of relevant therapies to improve prediction outcomes. Previous CRC studies conducted within South Africa (SA) have mainly been epidemiological, and subtyping limited to immunohistochemistry (IHC) protein expression analysis. The conclusions from these reports provided limited insight and lacked supportive molecular investigations in the development of CRC specifically within our population. CRC develops through 3 main molecular pathways; i.e. (1) Chromosomal instability (CIN) (75- 85%), (2) Microsatellite Instability (MSI) (~15%), and (3) CpG Island Methylator Phenotype (CIMP) (15-20%) pathway. This study descriptively analyses histopathological and molecular information of CRC patients in a 5-year study cohort (2011-2015), by assessing MSI status to ascertain unique features associated with different population groups, particularly within the African population. This study showed a large proportion (37%) of African CRC patients present with early disease onset (<50 years) in comparison to other ethnic group (OEG) patients (15%). Molecular characterization of CRC revealed MSI CRC within African patients occurred at an increased frequency compared to other ethnic groups (15% vs 8%), lacked a BRAFV600E mutation, and the dominant deficient (d) mismatch repair (MMR) profile was dMSH2 and dMSH6, suggesting hereditary Lynch Syndrome (LS) as the dominant pathway of disease development. These results are unique, as international findings demonstrate, 75% of MSI-CRC are sporadic, associated with dMLH1 and BRAFV00E mutations. OEG SA patients however were mostly associated with MLH1 and BRAFV600E mutations, and therefore follow the more wellestablished sporadic MSI pathway. Further insight gained through universal MSI screening was the ability to differentiate MSI-H versus MSS and MSI-L CRC. MSS/MSI-L CRC categorized by tumour site (left versus right) and ethnicity revealed unique histopathological features associated with left-sided CRC (LCC) in African patients compared to OEG patients. In addition, a higher proportion of MSI-L LCC was seen in African patients associated with more advanced disease stage and unique molecular and histopathological features. These findings suggest MSI CRC found in African patients is predominantly of a hereditary form, and further variant screening analysis to determine causative germline pathogenic variants are required. MSS CRC particularly within the left colon, was associated with unique histopathological features in the African population group, suggesting an alternative carcinogenic pathway of development when compared to OEG patients. MSI-L CRC also illustrated unique features at this site in African patients, and suggest this to be a completely separate molecular subtype. Deeper molecular characterization by next generation sequencing, including somatic and germline cancer gene screening is required to provide more insight into the different molecular subtypes and pathways in the development of CRC within the SA. This research will therefore direct better clinical management strategies, improving diagnosis, genetic counselling and testing strategies, prognosis, treatment outcomes, survival, and the overall burden associated with the disease within SA.
Optimising laboratory-rearing parameters for anopheles funestus to enhance scalability toward the sterile insect technique
(University of the Witwatersrand, Johannesburg, 2023-11) Niain’ny Felamboahangy, Lalasoa; Koekemoer, Lizette; Munhenga, Givemore; Kaiser, Maria
The plateauing of gains in the fight against malaria, partly due to insecticide resistance in malaria vector mosquitoes, is a threat to malaria control. Additional vector control tools like the sterile insect technique (SIT) are being evaluated. Anopheles funestus, a main malaria vector in Africa, has not yet been evaluated for control using SIT partly due to difficulties in its colonisation. To proceed with SIT for this species, knowledge of their optimal laboratory-rearing conditions is critical. To optimise An. funestus laboratory-rearing conditions, this study investigated the effect of using an artificial blood-feeding system or anaesthetised guinea pig on fecundity and fertility. Different larval diet doses and larval rearing densities were determined using a life-table approach. Finally, a range of irradiation doses were used to determine the optimal dose which induces sterility in An. funestus males without impacting the ability of the sterile males’ to compete with fertile males to mate with fertile females. Subsequently, mating competitiveness under laboratory conditions of An. funestus males irradiated at 120 Gy across three different ratios of fertile: irradiated males were performed. Results showed that fecundity was three times higher in females blood-fed on anaesthetised guinea pig compared to those blood-fed on the artificial blood-feeding system using bovine blood. Increasing the blood-meal frequency using the artificial blood-feeding system increased egg production, although it was not statistically significant. There were no significant differences between the egg fertility from females that fed on guinea pig or those fed on the artificial blood-feeding system using bovine blood. Anopheles funestus larvae fed with a food dose of 0.04 mg/larva and reared at a density of 0.48 larvae/cm2 resulted in optimal developmental time and pupal production. Furthermore, irradiation of male pupae at different doses did not affect adult emergence regardless of the dose used, however, it correlated negatively with longevity and fertility. Irradiation at doses greater than 100 Gy resulted in a significant difference in both fecundity and fertility. The average mating competitiveness value of An. funestus males irradiated at 120 Gy was 1.24, decreased from 2.63 to 0.27 for different ratios of sterile male: fertile male: fertile female 1:1:1 to 3:1:1. In conclusion, these findings can be used to improve the rearing of An. funestus under laboratory conditions, improving evaluations for SIT. Feeding defibrinated bovine blood through an artificial system will reduce the dependency on live animals for blood-feeding. Optimised larval feeding and rearing density will reduce developmental time and ensure maximal pupal production. An irradiation dose of 100 Gy can be used to induce sterility of An. funestus without significantly affecting mating competitiveness.
Peptidoglycan amidation enzymes in Mycobacterium tuberculosis are new drug targets for Tuberculosis treatment and development of a novel TB vaccine
(2024) Shaku, Moagi Tube
Mycobacteria assemble a complex cell wall with cross-linked peptidoglycan (PG) playing an essential role for maintenance of cell wall integrity and tolerance of osmotic pressure. In previous work, it was demonstrated that various hydrolytic enzymes are required to remodel PG during essential processes such as cell elongation and septal hydrolysis. In this thesis work, we explore the chemistry associated with PG cross-linking, specifically the requirement for amidation of the D-glutamate residue found in PG precursors. In Mycobacterium smegmatis, an experimental surrogate for Mycobacterium tuberculosis (Mtb), we confirm the essentiality of Dglutamate amidation in PG cross-linking by labeling cells with synthetic fluorescent PG probes that require amidated side chains for stable incorporation. We also use CRISPRi targeted knockdown of genes encoding the MurT-GatD complex, previously implicated in D-glutamate amidation in other bacterial species, and demonstrate that these genes are essential for mycobacterial growth. We show that MurT-GFP co-localizes with mRFP-GatD at the cell poles and septum, which are the sites of cell wall synthesis in mycobacteria and that these enzymes interact to form the PG amidation complex. Furthermore, time-lapse microscopic analysis of MurT-GFP localization in fluorescent D-amino acid (FDAA) - labeled mycobacterial cells during growth demonstrated co-localization with maturing PG, suggestive of a role for PG amidation during cell wall remodeling and repair. Depletion of MurT and GatD caused reduced PG cross-linking and increased sensitivity to lysozyme and β-lactam antibiotics. Cell growth cessation was found to be the result of a shutdown of PG biosynthesis mediated by the serine/threonine protein kinase B (PknB) which senses uncross-linked PG. Collectively, the first component of this work in M. smegmatis demonstrates the importance of D-glutamate amidation in mycobacterial PG precursors. We further exploit this enzyme complex in the second part of the dissertation to develop a novel CRISPRi-based recombinant BCG (rBCG) vaccine named rBCG::iE-DAP. This rBCG vaccine is based on the depletion of MurT-GatD, which results in reduced PG side chain amidation. As amidation masks detection of PG by the NOD1 pathogen recognition receptor, we postulate that this novel recombinant BCG will facilitate enhanced immunity against TB disease. As expected, the recombinant BCG induced increased immune activation and protection against Mtb infection in a mouse model of TB infection. This work highlights the MurT-GatD complex as a novel drug target and as a target for development of a next generation TB vaccine targeting innate immune responses against Mtb infection.
Prognostic influence of myc aberrations and other clinicopathological factors of aggressive b-cell non-Hodgkin lymphomas
(2024) Pather, Sugeshnee
Introduction: Up to 30% of cancers in Africa are linked to infectious agents and in the context of the aggressive B-cell non-Hodgkin lymphomas (NHL), human immunodeficiency virus (HIV) infection is an established risk factor. Aggressive B-cell NHLs are frequently confirmed at the Chris Hani Baragwanath Academic Hospital due to the high seroprevalence of HIV infection. Therefore, an array of clinicopathological characteristics of these tumours was evaluated with the aim of identifying poor prognostic factors. Materials and methods: HIV-associated plasmablastic lymphoma (PBL), HIV-associated diffuse large B-cell lymphoma (DLBCL) and DLBCL, not otherwise specified (NOS) were included from October 2013 to June 2017. Formalin-fixed paraffin-embedded tissue sections were subjected to c-MYC immunohistochemistry (IHC), dual-colour chromogenic and fluorescence in situ hybridisation (CISH and FISH) for assessment of MYC gene rearrangement and MYC gene copy number enumeration. Thereafter, the clinicopathological characteristics were explored. Results: The study included 67 PBL patients and 63/64 (98%) were HIV-seropositive. HIVassociated PBL was typified by a mean age of 41 (standard deviation [SD] ± 10.1) years and a 54% female predominance. The patients received combination antiretroviral therapy (c-ART) prior to, or shortly after, the lymphoma diagnosis was confirmed. The median CD4 count was 170 (interquartile range [IQR] 249) cells/mm3 and 37% of the patients had CD4 counts y (P=0.02). Expression of c-MYC protein (i.e., ≥40%) occurred in 81% of PBL. Epstein-Barr virus (EBV) latent infection was detected in 90% of these tumours by utilising CISH. MYC gene aberrations included MYC rearrangement (70%) and a low-level increase in MYC gene copy numbers (43%). Concurrent MYC rearrangement with increased MYC gene copy numbers (49%) were also detected. In addition, there was low-level polysomy of chromosome (C) 8 (6%). MYC aberrations in HIV PBLs were significantly associated with a SS appearance (P=0.01), monomorphic morphology (P=0.03), c-MYC protein expression (P=0.03) and mortality (P=0.03). The median overall survival (OS) for HIV PBL was 75 days (95% CI 14–136). MYC aberrations in HIV PBL did not significantly influence the median OS [MYC+ 65 days (95% CI 0–143 days) and MYC- 71 days (95% CI 3–139 days), P=0.61] There were 22 HIV seronegative DLBCL, NOS patients (19%) with a mean age of 57 (SD ±16.7) years and a 59% male predominance. There were 93 patients (81%) with HIV-associated DLBCL, typified by a mean age of 42 (SD ±10.8) years and a 55% male predominance. The HIV seropositive patients were significantly younger at the time of presentation with lymphoma (P <0.01). c-ART was commenced prior to, or shortly after, the lymphoma diagnosis was confirmed. The median CD4 count was 162 (IQR 215) cells/mm3 and 33% of the patients had CD4 counts <100 cells/mm3 . The median viral load was 217 (IQR 182 981) copies/mL and 30% of the patients had a lower than detectable limit viral load. An advanced stage of lymphoma, i.e., stage III-IV, at presentation occurred in 87% of the patients. HIV DLBCL demonstrated a germinal centre (GC) and non-germinal centre (NGC) immunophenotypic cell of origin (COO) in 53% and 47%, respectively. Expression of c-MYC protein occurred in 58% of the HIV DLBCLs and this was significantly associated with a SS appearance (P=0.04) and high tumour proliferation indices, i.e., Ki-67 ≥90%, (P<0.01). Double expression of c-MYC and BCL2 proteins were significantly associated with the NGC COO immunophenotype (P<0.01). MYC aberrations included a low-level increase of MYC gene copy numbers (57%) and MYC rearrangements (12%). Infrequently, C8 polysomy, MYC gene clusters and concurrent MYC rearrangement with increased MYC gene copies were also identified in HIV DLBCL. The median OS was 228 days (95% CI 54–402) and 825 days (95% CI 309–1341) in the HIV seropositive and seronegative DLBCL groups, respectively (P=0.08). Compared with the HIV seronegative DLBCL group, an inferior median OS outcome occurred in the HIV seropositive group when the CD4 counts were <100 cells/mm3 (P=0.04) and when the Internal Prognostic Index (IPI) was 3–5 (P=0.01). MYC aberrations did not significantly influence the median OS [MYC+ DLBCL 155 days (95% CI 0–356) and MYC- DLBCL 154 days (95% CI 53–256), P=0.67]. In the multivariate regression analysis, the presence of concomitant infections negatively impacted the overall survival (hazard ratio 4.01 [95% CI 1.86–12.20], P=0.02).
Synthetic cytology image generation to augment teaching and quality assurance in pathology
(2024) McAlpine, Ewen David
INTRODUCTION- Urine cytology offers rapid and relatively inexpensive screening for the detection of high-grade urothelial neoplasia in patients with haematuria. In our setting of a public sector laboratory in South Africa, however, there is a paucity of such specimens with which to train cytotechnologists and cytopathologists. Advancements in Generative Adversarial Networks present a potential solution to this problem by allowing for the generation of synthetic urine cytology images to supplement teaching and training. We illustrate an end-to-end machine learning model – from dataset creation to testing synthetic images in pathology personnel – to assess this technology in a real-world setting. METHODS- Two hundred and fourteen urine cytology slides were digitised and processed to construct a morphologically balanced dataset containing examples of benign, atypical and malignant urine cytology images. This dataset was used to train a StyleGAN3 model to generate synthetic urine cytology images. These synthetically generated images were then tested in a group of pathology personnel – both pathologists and trainees – to assess whether a difference between real and synthetic urine cytology images exists. Diagnostic error rate and subject image assessment were tested. RESULTS- StyleGAN3 was able to generate a wide morphological diversity of realistically appearing benign, atypical and malignant urine cytology images. When testing how these synthetic images were perceived by pathology personnel, there was no significant difference in diagnostic error rate, subjective image quality or inclusion of synthetic images in a cytology teaching set. DISCUSSION This work presents a proof-of-concept illustration of the feasibility of the use of synthetic cytology images to supplement pathology teaching when real examples may be difficult to obtain. Furthermore, this work presents important insights into the dynamics of pathology dataset creation and discusses the use of synthetic data in health education and the ethical and legal issues that arise with the use of synthetic patient data. CONCLUSION- Our work demonstrates that realistic, morphologically diverse urine cytology images can be generated using existing GANs technology and that human observers find such synthetic data visually acceptable. Additionally, our data indicate that there is no significant difference in synthetic data in terms of subjective image quality or diagnostic classification as determined by pathology personnel.
Synthetic cytology image generation to augment teaching and quality assurance in pathology
(University of the Witwatersrand, Johannesburg, 2023-05) McAlpine, Ewen David; Michelow, Pamela; Celik, Turgay
INTRODUCTION: Urine cytology offers rapid and relatively inexpensive screening for the detection of high-grade urothelial neoplasia in patients with haematuria. In our setting of a public sector laboratory in South Africa, however, there is a paucity of such specimens with which to train cytotechnologists and cytopathologists. Advancements in Generative Adversarial Networks present a potential solution to this problem by allowing for the generation of synthetic urine cytology images to supplement teaching and training. We illustrate an end-to-end machine learning model – from dataset creation to testing synthetic images in pathology personnel – to assess this technology in a real-world setting. METHODS: Two hundred and fourteen urine cytology slides were digitised and processed to construct a morphologically balanced dataset containing examples of benign, atypical and malignant urine cytology images. This dataset was used to train a StyleGAN3 model to generate synthetic urine cytology images. These synthetically generated images were then tested in a group of pathology personnel – both pathologists and trainees – to assess whether a difference between real and synthetic urine cytology images exists. Diagnostic error rate and subject image assessment were tested. RESULTS: StyleGAN3 was able to generate a wide morphological diversity of realistically appearing benign, atypical and malignant urine cytology images. When testing how these synthetic images were perceived by pathology personnel, there was no significant difference in diagnostic error rate, subjective image quality or inclusion of synthetic images in a cytology teaching set. DISCUSSION: This work presents a proof-of-concept illustration of the feasibility of the use of synthetic cytology images to supplement pathology teaching when real examples may be difficult to obtain. Furthermore, this work presents important insights into the dynamics of pathology dataset creation and discusses the use of synthetic data in health education and the ethical and legal issues that arise with the use of synthetic patient data. CONCLUSION: Our work demonstrates that realistic, morphologically diverse urine cytology images can be generated using existing GANs technology and that human observers find such synthetic data visually acceptable. Additionally, our data indicate that there is no significant difference in synthetic data in terms of subjective image quality or diagnostic classification as determined by pathology personnel.