Background: The epidemiological studies investigating environmental risk factors associated with asthma among children living in informal settlements are scant as are studies on the independent and co-pollutant effect of short- and long-term exposures to ambient air pollutants as well as fungal spores on asthma-associated outcomes. This study systematically investigated these factors among schoolchildren residing in informal settlements in the Western Cape province of South Africa. Methods: A cohort study of grade-4 schoolchildren (n=590) recruited from six primary schools in four informal settlements was conducted over 12 months. In addition, a panel study, investigated the children for 2 consecutive school weeks in both summer and winter. Spirometry and fractional-exhaled nitric oxide (FeNO) measurements were conducted during the school day, while the International Study on Asthma and Allergy in Children (ISAAC) standardised questionnaire was administered to the parent or guardian at the child’s home at baseline and follow-up. The presence of atopy was determined based on a positive Phadiatop test on sera. In the cohort study, annual NO2 and PM2.5 levels were computed for each child’s address using a land-use regression model. Daily PM10 levels obtained from a stationary monitor near two of the study areas were used for the panel study. Airborne pollen and fungal spore measurements were obtained directly from a stationary monitor placed in each study area. Results: The prevalence of doctor-diagnosed asthma was 3.4% and only half of them were on asthma treatment. The prevalence of wheezing in the past 12 months (12.9%), airway obstruction (17.6%) and airway inflammation (10.2%) was much higher. The presence of damp conditions, visible mould growth, passive smoking as well as paraffin-use for cooking and heating were significant indoor risk factors for asthma. The estimated annual average NO2 level of 16.6 µg/m3 was below the WHO annual exposure standards, however more than a third of children were exposed to annual PM2.5 levels above the 10 µg/m3 WHO standard and the allergic symptom threshold level of 100 spores/m3 for Alternaria spores. In the panel study, daily exposure of schoolchildren to Alternaria and Cladosporium spores independently decreased FEV1 (-27.56 ml, 95% CI: -50.60 to -4.51 ml per 10 spores/m3 increase in Alternaria; and -86.19ml, 95% CI: -131.69 to -40.70 ml per 50 spores/m3 increase in Cladosporium respectively) from lag day-0 to lag day-5, especially in the winter monitoring period. In the cohort study, an interquartile range increase of 14.2 µg/m3 in annual NO2 was associated with an risk of new onset ocular-nasal symptoms (adjusted odds ratio – aOR: 1.63, 95% CI: 1.01 – 2.60), wheezing (aOR: 3.57, 95% CI: 1.18 – 10.92), more than two or more asthma symptom score (aOR: 1.71, 95% CI: 1.02 – 2.86), and airway inflammation defined as FeNO > 35ppb (aOR: 3.10, 95% CI: 1.10 – 8.71), independent of PM2.5 exposures. In addition, an interquartile increase of 83.1 spores/m3 in 24-hour annual Alternaria spore levels was associated with an increased risk of airway inflammation incidence and having a ≥ 10% increase in FeNO at follow-up both in the single-pollutant model and two-pollutant model. Conclusion: This study demonstrated a large proportion of undiagnosed and untreated asthma in schoolchildren living in informal settlements, with both indoor and outdoor mould exposures playing an important role in addition to ambient chemical pollutants. The incidence of new onset asthma symptoms and airway inflammation associated with NO2 at levels below the WHO Air Quality Standards raises the issue of the adequacy of these standards in protecting respiratory health. Raised long-term levels of airborne Alternaria spores contributing to increased airway inflammation is likely to form the basis for the increased risk of acute symptoms and airway effects observed in association with exposure peaks.

The unexpected and sudden death of an infant (SUDI) is a traumatic event. SUDI is defined as all deaths occurring suddenly and unexpectedly in infants under the age of one year. Molecular autopsy is used to determine the potential genetic contribution to SUDI and may lead to screening and interventions of at-risk family members. However, the potential of this may only be realised if the family members are willing to engage in the follow-up process. Next-of-kin experiences of participating in molecular autopsy research are unknown, and not previously done in South Africa. This study explored the experiences and perceptions of bereaved next-of-kin participating in forensic genetic research on SUDI at Salt River Mortuary, Cape Town. Methods Eleven participants, including the mothers and other family members for six SUDI cases participated in the study. These participants were recruited from a larger forensic molecular autopsy study conducted at the University of Cape Town. In order to explore the experiences and perceptions of next-of-kin, a qualitative approach was used and semi structured interviews were conducted. The interviews, transcribed verbatim, were analysed through thematic analysis. The perspective from the main researcher in the larger forensic molecular autopsy study was included to holistically explore the setting in which the genetics research took place. Results Four major themes were identified, namely (i) old wounds, (ii) my booboo, (iii) the sudden death and (iv) afterthought. Their main reasons for participating in the research were to find answers and to be of value in future cases of SUDI. Grief seemed to play a significant role in their understanding and engagement with regards to their research participation. Conclusion This study found that the grief and loss of at the time of obtaining consent may play a significant role in understanding and willingness for further engagement with molecular autopsy results. Understanding has previously been implicated in the willingness to engage with genetics results, however, it has not been explored in a mortuary setting. The understanding of genetics research is critical for further engagement that may have implications for the screening of other family members and future offspring. These findings may allow researchers to better engage with participants in genetics research on sensitive topics, including SUDI.

Urinary tract infections (UTI)are one of the most common human bacterial infections, caused by uropathogenic E. coli (UPEC). Conventionally, UTI’s are treated with antibiotics, such as sulpha-mathoxazole/trimethoprim and ampicillin. However, a significant proportion of UPEC strains have become resistant to these antibiotics, resulting in a significant burden on the health care system worldwide. Bacteriophages (phages) that target E. coli strains could provide an alternative treatment for UTIs, particularly those resistant to antibiotics. This study aimed to screen a variety of environmental samples for phages that target a UPEC strains and characterize these phenotypically and genotypically, towards the development of a candidate phage preparation for treatment for antibiotic-resistant UPEC. Environmental samples (including faeces cattle, sheep, horse, goat faeces, river water, raw cow milk and mud) were collected from various sources around the City of Cape Town and screened for phages using an E. coli laboratory strain; K-12 MG1655. Lytic phages against E. coli MG1655 were purified and host-range testing was conducted against a panel of 11 UPEC strains form the E. coli reference collection (ECOR). These lytic phages were characterized phenotypically using transmission electron microscopy (TEM) using negative staining and genotypically using restriction enzyme HaeIII. In total, 41 phages that were lytic against MG1655 were isolated from six different environmental samples. Of these, 31/41 (76%) were lytic against 7/11 (64%) UPEC strains tested. Four phages (16-3, 16-4, 16-5 and 16-7; all isolated from raw milk) had the broadest host range of all the phages screened, being lyticagainst4/11(36%) UPEC strains. UPEC strain ECOR-40 was the most susceptible of the E. coli strains tested, being susceptible to 18/31 (58%) of the lytic phages isolated. In contrast, four UPEC strains (including ECOR-14, -60, -62 and -64) were not susceptible to any of the phages isolated. Ninety percent (28/31) of the isolated phages were structurally similar to four known phage families; including Myoviridae, Siphoviridae, Inoviridae and Rudiviridae. The remaining 10% (3/31) had structures that did not resemble any ofthe known phage families. DNA was x isolated from all 31 phage isolates to screen for similarities in restriction patterns of isolates. Of these, RFLP banding was clear for 5/31 samples; which showed that 5/5 phages were unique based on their banding patterns. In conclusion, this study demonstrated the existence of several unique E. coli phages in nature and their ability to target several of the UPEC strains known to cause UTI. Although time did not allow for sequencing of the full genomes of those isolates with unique characteristics in this study, this should be a priority for this research going forward.

Includes abstract. / Includes bibliographical references. / Rheumatic Heart Disease (RHD) is a post-infectious immune disease ascribed to an interaction between a rheumatogenic strain of group A streptococcus, a susceptible host who lives in poor social conditions with limited access to medical facilities. The disease process begins with repeated group A streptococcal (GAS) infections, which, subsequently result in acute rheumatic fever (ARF). In the absence of intervention, repeated bouts of ARF in turn, may result in progression to RHD, particularly in those ARF patients with cardiac involvement. The prevalence of ARF and RHD in developed countries has shown considerable decline during the last century, largely attributed to improved living conditions and access to healthcare. Epidemiological data from developing countries, while scant, indicate a continued high prevalence of GAS-positive pharyngitis and RHD. Furthermore, while much is known about the social factors and the microbial agent that predispose individuals to ARF, little progress has been made in elucidating genetic susceptibility factors that are reproducible in different populations. This thesis aimed to establish determinants of RHD as well as to document the prevalence of RHD in South African school children. The specific objectives of each study component were as follows: To derive quantitative estimates of the size of the genetic contribution to the risk of developing ARF/RHD. To determine the prevalence of GAS carriage and emm strains of GAS isolates among asymptomatic children enrolled in primary and secondary school. To describe the epidemiology of GAS among 3- to 15-year old children with pharyngitis attending primary health care facilities. To develop a clinical prediction rule for diagnosis of GAS throat infection that is valid for children aged 5-15 years in the primary care setting within the South African context. To determine the prevalence of echocardiographically-proven rheumatic heart disease in school children.

Introduction There is insufficient data to describe ST-elevation myocardial infarction (STEMI) in sub-Saharan African settings using common diagnostic criteria. This study describes the outcomes at discharge (survival, death or transferred) of patients thrombolysed for STEMI at a public hospital without primary percutaneous coronary intervention capability as well as associated ECG changes. Materials and methods A retrospective, cross- sectional study was conducted at an urban, public emergency centre in Cape Town, South Africa that did not have direct access to percutaneous coronary intervention for STEMI. Descriptive statistics for age, length of stay and the various timings surrounding thrombolysis were presented using proportions, mean and standard deviation. Assumptions were tested using the X2 - test or Fishers Exact test. A p-value less than 0.05 was considered significant. Results The study enrolled 104 patients of which 25 were excluded for insufficient data and two for thrombolysis of an incorrect STEMI diagnosis. Of the remaining patients, 56 (64%) survived to discharge, 26 (30%) required transfer and five (6%) died. There was no difference between regions affected and patient outcome (p=0.31). Resolution of ST-segments was seen in 48 (86%) survivors. It was not seen in 21 (81%) who were transferred and in none that died. The difference between resolution of ST-segments between survivors versus those transferred or dead was highly significant (p< 0.001). Conclusion This study described a higher than expected thrombolysis failure rate as well as a higher than expected association of poor outcome with inferior STEMI. It highlights the need for improved health care records to improve health research in low-resourced settings. The creation of a STEMI registry could contribute to research but will need funding. The use of clinical messaging apps to gain senior ECG interpretation may provide an additional layer toward quality care.

INTRODUCTION: Injury prevention programmes in rugby union are important to reduce the sport’s injury burden. The BokSmart Safe Six exercise-based injury prevention programme (“Safe Six”) was designed for this purpose. The programme incorporates six targeted exercises as a warm-up for rugby players. The effectiveness of the BokSmart Safe Six programme was assessed using the “Sequence of Prevention” Model. METHODS: The first study was a prospective cohort study using injury surveillance, of players at the South African Rugby (SA Rugby) Youth week tournaments. The study was conducted over six years to determine the injury incidence density (IID) youth players and also factors associated with the IID. The second study was a systematic review with the purpose of determining the effectiveness of exercise-based injury prevention interventions to reduce injury rates in collision sports. The next study was conducted over three years of SA Rugby Youth weeks and assessed the awareness of coaches and players of the BokSmart Safe Six following a targeted-marketing approach. This was followed by a study in which the BokSmart Safe Six programme was implemented in a cohort of apparently healthy non-rugby playing adults. The aim of this study was to determine the efficacy of the programme on injury risk profiles (Functional Movement Screening and Musculoskeletal Screening Assessments). The final study was a cluster-randomised controlled trial (cRCT) over eight weeks, using six schools (n = 210 players) in the Western Cape to determine the effectiveness of the BokSmart Safe Six on injury risk profiles and IID. RESULTS AND CONCLUSIONS: SA youth rugby cohort have a similar IID to other youth rugby cohorts (and in some instances lower). The systematic review identified only one highlevel study (out of three) that was effective for injury prevention. The players’ awareness of the BokSmart Safe Six was associated with the awareness of their specific coaches’ awareness. The awareness increased during the targeted marketing approach. The BokSmart Safe Six was associated with minimal significant improvements of the injury risk profiles in both the healthy adults and in the cRCT intervention group youth rugby players.

Background Human immunodeficiency virus (HIV) invades the central nervous system (CNS) as early as 8 days after HIV infection, causing a wide spectrum of neuropathological changes including HIV associated neurocognitive disorders (HAND). HAND is a spectrum of cognitive impairment, which in its most severe form cause marked interference with day-to-day functioning (HIV-associated dementia). Antiretroviral therapy (ART) has substantially reduced the incidence of HIV-associated dementia, but has not had an impact on the overall prevalence of HAND. The prevalence of milder stages of HAND in ART experienced individuals varies from 15 - 50%. Transporters expressed in the blood brain barrier and blood cerebrospinal fluid (CSF) barrier affect influx and efflux of drugs including antiretrovirals. Antiretrovirals that have better penetration into the CNS may result in improved cognitive function in patients with HAND, however this has not yet been conclusively shown. On the other hand, prolonged CNS exposure to high antiretroviral concentrations has been proposed as a cause of secondary decline in cognitive function as several antiretrovirals are neurotoxic. Efavirenz in particular, but also tenofovir and emtricitabine, have been shown to have direct neurotoxicity in preclinical models. Polymorphisms in genes that encode these enzymes or transporters may therefore affect antiretroviral CSF concentrations. Africans are the most genetically diverse population worldwide and South Africa has the world’s largest ART programme, with most of patients currently receiving efavirenz-tenofovir-emtricitabine. The impact of pharmacogenetic polymorphisms on the pharmacokinetics of efavirenz-tenofovir-emtricitabine CNS penetration are lacking. A number of adjunctive pharmacotherapies for HAND have been studied, including lithium. Multiple mechanisms have been suggested for the potential beneficial cognitive effect of lithium, including the inhibition of glycogen synthase kinase-3- beta, which mediates inflammation signaling pathways and neuronal apoptosis. Lithium has been used in mood disorders and other neuropsychiatric conditions for more than 40 years. In addition, lithium is a low-cost drug and widely available in public service settings in low and middle-income countries. There is a need for controlled data to evaluate the efficacy of lithium as adjunctive therapy for HAND. Finally, it is unknown whether lithium causes additive nephrotoxicity in combination with tenofovir. Methods We conducted a 24-week randomised placebo-controlled trial of lithium as adjunctive pharmacotherapy in participants with moderate to severe HAND established on ART for at least 6 months, with suppressed viral loads. We randomised 66 participants to lithium (n=32) or placebo (n= 34). Our primary efficacy endpoint was the change in Global Deficit Score (GDS) from baseline to 24 weeks, while our secondary endpoint was the change in proton magnetic resonance spectroscopy (1 H-MRS) brain metabolite concentrations. We collected paired plasma-CSF samples in 47 adult participants with and without HAND treated with efavirenz-tenofovir-emtricitabine. We considered 2049 single-nucleotide polymorphisms (SNPs), including SNPs known to affect plasma efavirenz exposure, from potentially relevant genes (ABCC5, ABCG2, ABCB1, SLCO2B1, SCLO1A2, ABCC4, CYP2B6 and CYP2A6) and 880 met a linkage disequilibrium (LD)-pruning threshold. We investigated genetic polymorphisms associated with CSF exposure of efavirenz and its metabolites, tenofovir and emtricitabine. The secondary objective was to explore the pharmacokineticpharmacodynamic relationships with neurocognitive performance. Finally, we investigated the change in estimated glomerular filtration rate (eGFR) in participants who received concomitant tenofovir and lithium. Results The median change in GDS between baseline and week 24 for the lithium and placebo arms were -0.57 (95% confidence interval [CI] -0.77, -0.32) and -0.56 (-0.69, -0.34) respectively, with a mean difference of -0.054 (95% CI -0.26, 0.15); p = 0.716. The improvement remained similar when analysed according to age, severity of impairment, CD4+ count, time on ART and ART regimen. Standard 1 H-MRS metabolite concentrations were similar between the treatment arms. The study drug was well tolerated in both study arms. There was no statistically significant difference in the reduction in eGFR or in potassium between the two arms during the 24 weeks. A model that included the composite CYP2B6 15582/516/983 genotype in univariate analyses best predicted the log10-transformed concentrations of plasma efavirenz, plasma 7-hydroxy-efavirenz, plasma 8-hydroxyefavirenz-to-efavirenz ratio and CSF efavirenz. Lower plasma 7-hydroxy-efavirenz concentrations were independently associated with CYP2A6 rs10853742, ABCB1 rs115780656 and CYP2A6 -48A→C. The CYP2A6 -48A→C polymorphism was independently associated with higher CSF 8-hydroxy-efavirenz-to-efavirenz ratio. The CYP2B6 rs2279345 polymorphism was associated with lower plasma 7-hydroxy-efavirenzto-efavirenz ratio in univariate on multivariate analyses adjusting for CYP2B6 516G→T and 983T→C. No polymorphisms were associated with CSF-to-plasma ratios of all 3 drugs, plasma or CSF 8-hydroxy-efavirenz, tenofovir or emtricitabine concentrations, or neurocognitive performance. Conclusion Adjunctive lithium pharmacotherapy in patients on ART with HAND was well tolerated but had no additional benefit on neurocognitive impairment. We found that 24-week treatment of HIV-infected patients with lithium and tenofovir did not result in increased nephrotoxicity. We identified novel genetic associations with plasma efavirenz, plasma 7-hydroxy-efavirenz, plasma 7-hydroxy-efavirenz-to-efavirenz ratio, plasma 8-hydroxy-efavirenz-to-efavirenz ratio, CSF 8-hydroxy-efavirenz-to-efavirenz ratio and CSF efavirenz.

Background Cerebrovascular disease remains one of the leading causes of morbidity and mortality globally. In South Africa, cerebrovascular disease was the fourth leading cause of death in 2016, responsible for 5.1 % of all deaths - the leading cause of death in individuals 65 years and older. Atrial fibrillation accounts for 15% of all strokes and a 25% of patients with AF-related stroke have this arrhythmia diagnosed at the time of the stroke. Objectives This study sets out to determine the prevalence of atrial fibrillation in patients with ischaemic stroke, as confirmed on CT scan, at a district level hospital in the Western Cape, South Africa. Methods This descriptive study was conducted at Mitchell’s Plain Hospital in Cape Town and data was collected over a year. Patients diagnosed with a stroke were identified from an electronic patient register and relevant radiology and clinical data was sourced retrospectively. The diagnosis of ischaemic stroke was confirmed by a CT scan report and ECGs were independently screened by two Emergency Physicians. Categorical data was described in percentages and descriptive statistics. Continuous variables were described by median and interquartile range (IQR). Statistical significance is defined as a p< 0.05. Categorical data was compared using the Fisher’s exact test. This project has been approved by UCT Human Research Ethics Committee [790/2018]. Results The proportion of adult patients with a diagnosis of stroke was 2%. Of those, 64% had ischaemic strokes, 9% had intracranial bleeds, 20% did not have a CT scan and 7% had stroke mimics. 11% of all participants with ischaemic stroke had atrial fibrillation, 67% of those presumed new. A total of 90 (22%) of all participants with ischaemic stroke was less than 51 years of age. The mortality rate was statistically higher in patients who had AF. Conclusion The results from this study suggests that screening practices to detect both Atrial Fibrillation in asymptomatic patients, as well as in those with an ischaemic stroke, are not effective. With the increasing population life expectancy, and prevalence of cardiovascular disease, the prevalence of AF and its complications will increase. Since the risk of stroke related to AF can be reduced significantly by oral anticoagulation, further studies should aim to explore barriers and challenges to effective screening.

Background Bedaquiline is used as a substitute for second-line injectable (SLI) intolerance in the treatment of multidrug-resistant tuberculosis (MDR-TB), but the efficacy and safety of this strategy is unknown. Methods We performed a retrospective cohort study to evaluate treatment outcomes for MDR-TB patients who substituted bedaquiline for SLIs. Adults receiving bedaquiline substitution for MDR-TB therapy, plus a matched control group who did not receive bedaquiline, were identified from the electronic TB register in the Western Cape Province, South Africa. The primary outcome measure was the proportion of patients with death, loss to follow up, or failure to achieve sustained culture conversion at 12 months of treatment. Results Data from 162 patients who received bedaquiline substitution and 168 controls were analyzed; 70.6% were HIV-infected. Unfavorable outcomes occurred in 35/146 (23.9%) patients in the bedaquiline group versus 51/141 (36.2%) in the control group (relative risk, 0.66; 95% confidence interval [CI], 0.46 to 0.95). The number of patients with culture reversion was lower in those receiving bedaquiline (1 patient, 0.8%) compared to controls (12 patients, 10.3%; P = 0.001). Delayed initiation of bedaquiline was independently associated with failure to achieve sustained culture conversion (adjusted odds ratio, 1.5; 95% CI, 1.1 – 1.9, for every 30-day delay). Mortality was similar at 12 months (11 deaths in each group; P = 0.973). Conclusions Substituting bedaquiline for SLIs in MDR-TB treatment resulted in improved outcomes at 12 months compared with patients who remained on SLIs, supporting the use of bedaquiline for MDR-TB treatment in programmatic settings.

Bibliography: leaves 156-174.