Epidemiology and Biostatistics
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- ItemAssessment of point-of-care testing for prediction of aromatase inhibitor-associated side effects in obese postmenopausal breast cancer patients screened for cardiovascular risk factors(Stellenbosch : Stellenbosch University, 2021-12) Milambo, Jean Paul Muambangu; Akudugu, John M.; Nyasulu, Peter S.; Stellenbosch University. Faculty of Medicine and Health Sciences. Dept. of Global Health. Epidemiology and Biostatistics.ENGLISH SUMMARY : Background: Aromatase inhibitors (AIs) constitute a standard of care for post- and premenopausal patients with estrogen receptor-positive breast cancer (BC). Obesity and mediators of inflammation have been identified as the most important risk and predictive factors in postmenopausal breast cancer survivors (BCS) using AIs. However, data on the feasibility of point-of-care (POC) genotyping using high sensitivity C-reactive protein (hs-CRP) and body mass index (BMI) as predictors of drug toxicity among postmenopausal BCS in African clinical settings are lacking. Aim: The study was conducted to assess the impact of AIs on hs-CRP and BMI, which are used at POC for prediction of therapy-associated side effects among obese postmenopausal breast cancer patients in Africa. Methods: One hundred and twenty-six female BC patients with cancer stages ranging from 0-III were recruited at Tygerberg Hospital (TBH) in the Western Cape Province of South Africa, between August 2014 and February 2017, for the study. A Quasi-experimental study was conducted. Patients were initially subjected to AIs and subsequently followed up at months 4, 12, and 24. Baseline clinical and biomedical assessments were conducted at commencement of study to predict hs-CRP and BMI at months 12 and 24, using a multiple imputation model. A random effects model was used to monitor the changes over the time. Statistical analyses were performed using SPSS 18.0 software (SPSS Inc., Chicago, IL, USA) and STATA version 16. Analyses were two-tailed and a p-value < 0.05 was considered statistically significant. Results: The mean age of the participants was 61 years (SD = 7.11 years; 95% CI: 60-62 years). Linear regression revealed that hs-CRP was associated with waist circumference (OR: 7.5; p= 0. 0116; 95%CI: 1.45 to 39.61) and BMI (OR: 2.15; p=0.034, 95%CI: 1.02 to 4.56). Waist circumference was associated with hypertension (OR: 3, 83; p= 0.003, 95%CI: 1.56 to 9.39), and chemotherapy was associated with waist circumference by (p= 0. 016; 95%CI: 0.11 to 0. 79). hs-CRP levels were significantly correlated with BMI and total body fat (TBF) among postmenopausal using aromatase inhibitors. Random linear effects modelling revealed stronger statistical association between BMI and homocysteine (p=0.021, 95%CI: 0.0083 to 0.1029). Weight and TBF were strongly associated after 24 months of follow-up. In addition, hs-CRP was associated with BMI (p=0.0001) and other inflammatory markers such as calcium (p=0.021, 95%CI: 0.0083 to 0.1029), phosphate (p=0.039, 95%CI: 0.0083 to 0.1029), and ferritin (p=0.002, 95%CI: 0.0199 to 0.084). Multiple imputation modelling indicated that there were statistically significant variations in TBF, weight, homocysteine, ferritin, and calcium between baseline and after 24 months of follow-up. Mathematical modeling Comparison of genotyping from HyBeacon® probe technology to Sanger sequencing showed that yielded sensitivity of 99% (95% CI: 94.55 to 99.97%), specificity of 89.44% (95% CI: 87.25 to 91.38%), PPV of 51% (95%: 43.77 to 58.26%), and NPV of 99.88% (95% CI: 99.31 to 100.00%). Based on the mathematical model, the assumptions revealed that incremental cost-effective ratio (ICER) was R7 044.55. Conclusion: This study revealed that hs-CRP and BMI are predictors of CVD-related adverse events in obese postmenopausal patients. Calcium, phosphate, homocysteine, and ferritin should also be incorporated in POCT. There were statistically significant variations in TBF, weight, hs-CRP, BMI, homocysteine, ferritin, and calcium between baseline and after 24 months of follow-up. HyBeacon® probe technology at POC for AI-associated adverse events maybe cost-effective in Africa while adjunct to standard practice. The appropriate pathways for implementation of POC testing in postmenopausal breast cancer survivors need further investigation in different clinical settings with real data for external validation.
- ItemThe association between taking HAART and hypertension(Stellenbosch : Stellenbosch University, 2017-12) Mangunda, Tichatonga John; Machekano, Rhoderick; Stellenbosch University. Faculty of Medicine and Health Sciences. Dept. of Global Health. Epidemiology and Biostatistics.ENGLISH SUMMARY: Prevalence of hypertension in patients on HAART compared to pre-ART patients at Sithobela Hospital. Background: The use of Highly Active Anti-retroviral Therapy (HAART) has improved the quality of life among people with HIV/AIDS, but there are concerns about its effect on hypertension and other cardiovascular diseases. Objectives: In this study we sought to find out if HAART is associated with hypertension and to describe lifestyle and socio-demographic factors among people on pre-ART and HAART. Methods: We conducted a cross sectional study of HIV infected patients initiated on HAART and pre-ART at Sithobela health centre. Results: We enrolled a total of 410 participants, 205 in the ART group and 205 in the pre-ART group. The estimated prevalence of hypertension among those on ART was 14.2% [95% CI: 9.3-18.9] and 19%[95% CI: 13.6-24.4] among pre-ART patients. There was no significant difference in the prevalence of hypertension between the two groups (p=0.185). However, after adjusting for age, marital status, level of education, stage of disease, smoking history, waist to hip ratio, occupation, income level, history of smoking and alcohol use, HAART was significantly associated with hypertension (AOR= 0.43 [95% CI: 0.23-0.83]). Patients who reported drinking alcohol were likely to be hypertensive (AOR 10.96 [95% CI: 2.36-50.92]). Smokers were 3 times more likely to be hypertensive compared to non-smokers but this association was found not to be statistically significant on multivariate analysis. Conclusion: our study demonstrated a potential beneficial effect of HAART in reducing hypertension among HIV infected people in Sithobela, Swaziland.
- ItemAssociation of home hygienic practice and diarrhoeal presence in low-cost housing in Cape Town, South Africa(Stellenbosch : Stellenbosch University, 2017-12) Brand, Amanda; Esterhuizen, Tonya; Stellenbosch University. Faculty of Medicine and Health Sciences. Dept. of Global Health. Epidemiology and Biostatistics.ENGLISH SUMMARY: Background: Good home hygiene in key high-risk areas shows potential to be a simple and cost-effective intervention for preventing infectious disease transmission in low income homes. Knowledge of good home hygiene does not, however, always translate to practice due to complex factors which hinder translation. The objective of the study was to investigate whether an association between cleanliness and diarrhoeal disease exists, and to understand the factors which impede knowledge translation. Method: This cross-sectional study in low-income areas in Cape Town, South Africa took the format of an administered questionnaire focusing on health, and hygienic behaviour. Interviewer-assessed cleanliness was also recorded for each home. Results: Gastrointestinal symptoms were significantly associated with unclean kitchens and toilets (odds ratio (OR)=5.93 (1.98 – 19.78) and OR=17.67 (5.20 – 63.90), respectively). The presence of diarrhoea was significantly associated with dirty toilet areas (OR=8.94 (2.34 – 40.96)), despite its relatively low prevalence (17% (11 – 25%)). While knowledge of home hygiene and health was high, a lack of association between knowledge and observed cleanliness indicated a gap in the translation of knowledge to practice. Proposed emotional drivers of this process could not be substantiated, but evidence suggested that lack of understanding of underlying reasons plays an important role, but it may be effectively overcome by education. Conclusions: Good home hygiene shows potential for preventing infectious disease risk in low-income areas, but knowledge does not translate to effective practice. This is likely attributable to a lack of understanding of underlying principles, specifically among persons with low levels of formal schooling.
- ItemBarriers and facilitators to linkage, adherence and retention in care among HIV positive patients : an overview of qualitative systematic reviews using mega-aggregation framework synthesis(Stellenbosch : Stellenbosch University, 2019-04) Hendricks, Lynn Avril; Rohwer, Anke; Stellenbosch University. Faculty of Medicine and Health Sciences. Dept. of Global Health. Epidemiology and Biostatistics.ENGLISH SUMMARY : Background: People living with Human Immunodeficiency Virus (PLHIV) continue to struggle with the complexities related to having a chronic disease and integrating antiretroviral treatment (ART) and care into their daily lives. This overview aimed to assess existing evidence related to self-reported barriers and facilitators to linkage to ART, adherence to ART and retention in care for PLHIV and to identify gaps in the evidence. Methods: The novel pragmatic approach of mega-aggregation framework synthesis was developed, described and applied in this overview using Kaufman’s interpretation of the socio-ecological framework. We included qualitative systematic reviews, up to July 2018, and used a systematic and rigorous approach to select reviews and extract data. We assessed methodological quality using an amended version of the Joanna Briggs Institute Critical Appraisal Checklist for Systematic Reviews. Results: We included 33 systematic reviews, from low, middle and high income countries and included 1 111 964 HIV positive children and adults. Methodological quality varied considerably across reviews. Using the mega-aggregative framework approach, we found 544 unique third order concepts, from the included systematic reviews, and reclassified the third order concepts into 45 fourth order themes within the individual, interpersonal, community, institutional and structural levels of the Kaufman HIV Behaviour Change model. Our overview found that the main barriers and facilitators to linkage, adherence and retention such as psychosocial personal characteristics of perceptions of ART, desires, fears, experiences of HIV and ART, coping strategies and mental health, were interwoven with other factors on the interpersonal, community, institutional and structural level. Conclusions: High quality qualitative review level evidence on self-reported barriers and facilitators of linkage, adherence and retention in care is lacking for adults and even more so for children. Overviews are useful in the identification of evidence gaps to inform new review questions and researchers are encouraged to build on the method of mega-aggregative framework synthesis as the place of overviews become more prominent with the growing body of qualitative reviews. Systematic review registration: The protocol of this overview was registered on PROSPERO (CRD42017078155) on 17 December 2017.
- ItemBurden of congenital rubella syndrome and potential impact of rubella vaccine introduction in South Africa(Stellenbosch : Stellenbosch University, 2021-12) Motaze, Nkengafac Villyen; Wiysonge, Charles S.; Suchard, Melinda S.; Metcalf, C. Jessica E.; Stellenbosch University. Faculty of Medicine and Health Sciences. Dept. of Global Health. Epidemiology and Biostatistics.ENGLISH SUMMARY : Background: Introduction of rubella vaccines into public vaccination schedules of all countries is necessary if global rubella elimination is to be achieved. Rubella is targeted for elimination in five World Health Organization (WHO) regions and several international organizations, under the stewardship of the WHO, are working towards this goal. Although there is no rubella elimination or control target for the WHO Africa region, there has been accelerated introduction of rubella vaccination on the continent. South African government is planning to introduce rubella vaccination in its Expanded Programme on Immunization (EPI) schedule and several epidemiological studies have been conducted to aid preparation of this public health intervention. In the absence of vaccination, rubella is mainly a mild endemic childhood viral illness that is asymptomatic in up to 50% of cases. The most severe consequences of rubella occur when infection occurs during pregnancy. These include miscarriages, stillbirths, intra-uterine growth restriction and congenital rubella syndrome. Rubella vaccines are therefore intended to prevent rubella and associated complications. In South Africa, rubella vaccines are not part of the EPI schedule and there is limited information on the epidemiology of rubella and its complications. In addition, the South African government has to cover the cost of introducing rubella vaccination. Therefore, the aim of this research project was to characterize the epidemiology of rubella and congenital rubella syndrome in South Africa, to assess the potential impact of introducing rubella vaccination in the EPI schedule. Methods: Four different studies were carried out as part of this PhD project: a cross-sectional descriptive study, a sero-survey, a mathematical modelling study and a systematic review. Results: The findings of a newly established CRS surveillance system to provide data on disease trends in the absence of rubella vaccination are presented in the first research component. We provided baseline data on laboratory-confirmed CRS that will enable planning and monitoring of RCV implementation in the South African EPI program. Ninety-eight percent of mothers of infants with CRS were young women 14 to 30 years old, indicating a potential immunity gap in this age group for consideration during introduction of RCV. In the second research component, we present results of testing on residual samples collected from public health facilities to identify immunity gaps in various age groups and genders. The bulk of individuals susceptible to rubella are children under sixteen years old and about 20% of individuals 16 to 49 years old are susceptible to rubella. In multivariable logistic regression, age and province of residence were found to be associated with rubella susceptibility.Webuilt on a previously published mathematical model adapted to the South African context in the third research component and provide insights into optimal scenarios for RCV introduction into the South African public immunization schedule. We simulated a number of scenarios that combined infant vaccination with vaccination of older individuals. Routine vaccination at 12 months of age coupled with vaccination of nine-year-old children was associated with the lowest RCV cost per CRS case averted for a similar percentage CRS reduction. Interestingly, at 80% RCV coverage, all vaccine introduction scenarios could achieve rubella and CRS elimination in South Africa.In the final research component, we systematically reviewed mathematical modelling studies to identify the most effective approach for countries introducing RCV into their public immunization schedules. There were variations in the manner in which individual studies reported outcomes. However, we found that better outcomes are obtained when rubella vaccination is introduced into public vaccination schedules at coverage figures of 80%, as recommended by WHO, or higher. Conclusion: The results from these different studies support the implementation of a strategy involving infant vaccination in combination with vaccination of older individuals. Further research projects are required to provide more detail on the burden of CRS and the economic impact of RCV introduction into the EPI schedule.
- ItemComparative, cross-sectional study describing agreement and accuracy of emergency centre triage using either a mobile application or manual triage(Stellenbosch : Stellenbosch University, 2016-03) Khan, Yaseen; Govender, Thashlin; Stellenbosch University. Faculty of Medicine and Health Sciences. Dept. of Global Health. Epidemiology and Biostatistics.ENGLISH SUMMARY: Background and Purpose: Unacceptable patient waiting times and misidentification of critically ill patients are significant problems within Emergency Centres (ECs). Triage, when performed correctly, is acritical process to address this. The South African Triage Scale (SATS) is widely used. Manually performed triage may be prone to inaccuracies and prolonged triage time. A mobile tablet application to facilitate use of the SATS by automating triage calculation and guiding nurses has been developed. Methods: This is a comparative cross-sectional study to observe the accuracy of triage using the mobile tablet application compared with triage performed manually. Under classroom examination conditions, nurses calculated triage scores on written case scenarios of typical EC presentations. A total of 59 nurses across five hospitals in the Western Cape Province, South Africa were randomized into an ‘app group’ and a ‘manual group’. Results: The app group scored a 23% higher level of agreement with the expert-validated results than the manual group. Kappa of 0.735 (0.719 - 0.770) and 0.597 (0.545 - 0.656) were found respectively. One in five patients are triaged more correctly using the app. Sensitivity for emergency cases was 65.5% and 53% respectively, with and without the app. Conclusions: Nurses triaging written scenarios with the aid of the app were observed to have a higher agreement with the expert-validated results than nurses performing traditional manual triage. The effect size is considerable and of practical relevance. The app could have significant benefit in busy Emergency Centres of public sector hospitals. A larger study involving real patients is recommended.
- ItemCompleteness of HIV intervention trial protocols : a systematic survey(Stellenbosch : Stellenbosch University, 2019-04) Samupindi, Shingirayi Irene; Dzikiti, Moleen; Stellenbosch University. Faculty of Medicine and Health Sciences. Dept. of Global Health. Epidemiology and Biostatistics.ENGLISH SUMMARY : Introduction: The Standard Protocol Items: Recommendations for Interventional Trials (SPIRIT1) 2013 guideline provides guidance to improve the quality of protocols. The aim of this study was to determine the completeness of randomised controlled trial protocols evaluating the efficacy or effectiveness of HIV prevention, treatment and care strategies using the SPIRIT 2013 checklist, and to identify factors associated with completeness of trial protocols. Methods: We searched MEDLINE, EMBASE, LILACS, Africa-wide information (EBSCOhost), Web of Science, Clinicaltrials.gov and CENTRAL (Wiley Cochrane Library) for randomized controlled trial protocols in May and June 2018. We included protocols for interventions in the HIV prevention, treatment and care fields published between 2008 and 2018. Two individuals independently screened the titles and abstracts. The adapted SPIRIT checklist was pilot tested independently in duplicate on the first 4 (5%) protocols. The rest of the data was collected by a single individual and verified by second reviewer. Disagreements were resolved by consensus. We summarized categorical data using count (percent) and continuous variables using mean (standard deviation). Generalised estimation equations assuming a Poisson distribution were used to assess association of protocol factors with number of checklist items reported. Results: Seventy-nine protocols met the eligibility criteria and were included in the analysis. A mean of 32 (SD= 5) of the possible 51 SPIRIT checklist items were reported in the protocols. Detailed methodological aspects relating to intervention allocation, blinding, data management, study monitoring and dissemination policy information were often missing in the protocols. Intervention category, period of publication (before or after SPIRIT 2013 publication) and study setting were not significantly associated with protocol completeness. Conclusion: There is need for improvement in the reporting of recommended SPIRIT 2013 checklist items in HIV intervention protocols. We recommend active implementation strategies of the SPIRIT guideline from publishing journals and HIV trialists to ensure more improvement in protocol quality.
- ItemThe effects of longitudinal HIV viral load exposure on immune outcomes, mortality, and opportunistic infections in people on ART in sub-Saharan Africa(Stellenbosch : Stellenbosch University, 2017-12) Sempa, Joseph Bukulu; Nieuwoudt, Martin; Stellenbosch University. Faculty of Medicine and Health Sciences. Dept. of Global Health. Epidemiology and Biostatistics.ENGLISH SUMMARY : Introduction: Longitudinal viral load monitoring is used as a cross-sectional marker for treatment failure in HIV infected people receiving antiretroviral therapy. Cumulative viral load, as quantified by area under the viral load curve during combination antiretroviral therapy, has been correlated with treatment outcomes in studies outside, but not within, sub-Saharan Africa. We investigate the effects of exposure to longitudinal viral load on, the incidence of opportunistic infections, mortality and immune recovery in local, previously combination antiretroviral therapy naïve, cohorts. Further, we systematically review statistically derived immune response models and use this to define priors for Bayesian models for application on a previously undescribed treatment cohort. Methods: We analyze data from the Infectious Diseases Institute (IDI) cohort, Kampala-Uganda, and the Antiretroviral Clinic at Tshwane District Hospital in Gauteng-South Africa. For the systematic review, we use ‘Preferred Reporting Items for Systematic Review and Meta- Analyses’ guidelines. We also compare cumulative viral load as numerically estimated using two methods: area under the viral load curve, which is then log-transformed, named, ‘untransformed cumulative viral load’; and area under the log-transformed viral load curve, above the kit-based detection limit of 400 copies/mL, named, ‘transformed cumulative viral load’. We use Cox Proportional Hazards and Bayesian Generalized Mixed Effects to define treatment outcome models. Results: In the IDI cohort most recent viral load, not cumulative viral load, is associated with a 1.34-fold (95% confidence interval: 1.12, 1.61) increase in the risk of opportunistic infections. Transformed, not untransformed, cumulative viral load is associated with mortality and immune response. Each log10 copy-yr/mL increase corresponds to a 1.63-fold (95% confidence interval: 1.02, 2.60) increase in risk of mortality. Systematic review of immune response statistical models also reveals many differences in the number and type of variables adjusted-for, variable transformations and scales and scant details regarding the modelling methods employed. In the Tshwane cohort, using Bayesian methods, for the slope of longitudinal CD4 counts, each log10 copy-yr/mL increase cumulative viral load corresponds to a mean annual CD4 count decrease of -19.5 cells/μL (95% credible interval: -28.34, -10.72). Further, in the asymptote model, each log10 copy-yr/mL increase reduced the odds of having a CD4 count ≥500 cells/μL to 0.42 (95% credible interval: 0.242, 0.724). Modelling inherently variable absolute CD4 count using a Student’s t-distribution produced better fits than assuming a Gaussian normal distribution. Discussion: Transformed cumulative viral load is associated with both mortality and long-term immune response, while most recent viral load is associated with incidence of opportunistic infections. This thesis emphasizes the need for the review of existing literature prior to any statistical analyses, so that more comparable and robust statistical models than have been available to date will be constructed. In particular, comparing immunological outcomes (CD4 counts), statistical models for sub-Saharan African cohorts would benefit from the application of more uniform modelling techniques. Adjusting for transformed cumulative viral load and the use of appropriate distributional assumptions, improves the modelling of immune response to antiretroviral therapy. Future statistical immune response models would benefit from the use of Bayesian methods owing to their flexibility in the selection of prior distributions and hierarchical model designs.
- ItemAn evaluation of the effectiveness of task-shifting health systems approaches, including community-based and pharmaceutical care models, for HIV treatment and prevention programs in South Africa(Stellenbosch : Stellenbosch University, 2020-12) Fatti, Geoffrey; Chikte, Usuf M. E.; Nachega, Jean; Stellenbosch University. Faculty of Medicine and Health Sciences. Dept. of Global Health. Epidemiology and Biostatistics.ENGLISH SUMMARY : Southern Africa is the epicenter of the human immunodeficiency virus (HIV) pandemic having the highest burden of HIV globally. Although South Africa has made great strides with the roll-out of its antiretroviral treatment (ART) program, ongoing challenges include high attrition of patients from ART care and ongoing elevated HIV incidence. There is also a severe shortage of professional health workers in the region, which impacts HIV program delivery. Task-shifting health systems approaches have been developed in order for the health system to provide large-scale HIV program delivery with limited numbers of professional health workers. This thesis evaluates the effectiveness of task-shifting health systems interventions in HIV prevention and treatment programs in South Africa, including community-based programs utilizing community healthcare workers (CHWs), and pharmaceutical care models. Data were collected in cohort studies conducted between 2004 and 2015/2016 in four provinces of South Africa. The results chapters of the thesis are presented in the form of published papers. The first paper evaluates the effectiveness of a community-based support (CBS) program amongst a large cohort of adults living with HIV receiving ART up to five years after ART initiation. Adults who received CBS had improved ART outcomes, including improved patient retention with lower loss to follow-up and lower mortality, both of which were reduced by one third. The second paper evaluates the effectiveness of a community-based combination HIV prevention intervention delivered by CHWs for pregnant and postpartum women in a high HIV incidence district in KwaZulu-Natal. Maternal HIV incidence amongst participants who received the intervention was considerably lower compared to other studies from the region. The paper further recommends expanded roll-out of home-based couples HIV counselling and testing, and initiating oral pre-exposure prophylaxis for HIV particularly for pregnant women within serodiscordant couples, in order to reduce maternal HIV incidence. The third paper compares the effectiveness and cost of two task-shifting pharmaceutical care models for ART delivery in South Africa, namely the indirectly supervised pharmacist assistant (ISPA) model and the nurse-managed model. The ISPA model was found to have a higher quality of pharmaceutical care, was less costly to implement and was possibly associated with improved patient clinical outcomes. The fourth paper evaluates the effectiveness and cost-effectiveness of CBS for adolescents and youth receiving ART at 47 health facilities in South Africa. CBS was found to substantially reduce patient attrition from ART care in adolescents and youth, and was a low cost intervention with reasonable cost-effectiveness. Lastly, a published scientific letter is included as an appendix, which is a critique of findings from a cluster-randomized trial investigating the effectiveness of two interventions as part of the current South African National Adherence guidelines (AGL). The letter recommends the inclusion of long-term CBS for ART patients utilizing CHWs in a revised version of the AGL. The thesis concludes that task-shifting healthcare models including communitybased and pharmaceutical care models are effective and cost-efficient for HIV program delivery in South Africa, and can aid the greater Southern African regions’ progress toward several of the interrelated UNAIDS Sustainable Development Goals by 2030.
- ItemEvaluation of the Mean Duration of Recent Infection (MDRI) and the False Recent Rate (FRR) for the Limiting Antigen Avidity Enzyme Immune Assay (LAg) and Bio-Rad HIV ½ Plus O Avidity Incidence Assay (BRAI)(Stellenbosch : Stellenbosch University, 2017-12) Gonese, Elizabeth; Hargrove, John; Nachega, Jean; Van Zyl, Gert; Kilmarx, Peter H.; Stellenbosch University. Faculty of Medicine and Health Sciences. Dept. of Global Health. Epidemiology and Biostatistics.ENGLISH SUMMARY : Background: The evaluation of laboratory assays in estimating HIV incidence has become a priority because of the complexity of HIV epidemics and the need to measure the impact of public health interventions targeting reduction of HIV incidence. Biomarkers should have test properties that allow the lowest possible False Recent Rate (FRR, or probability of diagnosing a long-term infection as recently infected) over the longest possible period (Mean Duration of Recent Infection or MDRI) during which the case is considered as a recent infection. Methods: We compared the BED Capture Enzyme Immunoassay (BED), Sedia Limiting Antigen (LAg) and Bio-Rad HIV ½ Plus O Avidity Incidence Assay (BRAI) using samples from a prospective cohort trial, the Zimbabwe Vitamin A for Mothers and Babies Project (ZVITAMBO) 1997–2000. We determined MDRI using 591 samples from 184 seroconverting women, and determined FRR by testing 2825 cases known to be HIV- positive for >12 months. We used these results to estimate HIV incidence over the first 12 months postpartum, and during the period prior to childbirth. Results: At recommended cut-offs MDRI values were: BRAI, 135 days (120 – 151) at Avidity Index (AI) 30%; LAg, 104 days (98 - 110) at ODn cut-off 1.5; BED, 188 days (180 -196) at ODn cut-off 0.8. All error bounds in this thesis signify 95% confidence intervals. The coefficients of variation (CV) of the MDRI estimates for BRAI, LAg and BED were 5.9%, 2.9% and 2.1%, respectively. Corresponding FRRs were 1.1% (0.7-1.5) for BRAI, 0.6% (0.3-0.9) for LAg and 4.8% (4.1-5.7) for BED. MDRI and FRR estimates, all derived using postpartum women, were lower than in other published studies. Using original ZVITAMBO HIV diagnoses, adjusted HIV incidence over the first 12 months postpartum was estimated as; BRAI, 2.7% (1.8-3.7); LAg, 3.7% (2.7-4.8); BED, 3.6% (2.4 -4.9). Follow-up incidence was 3.4% (3.0-3.8). When cases with viral load <1000 copies/ml were defined as long-term infections, regardless of serological biomarker level, FRRs were; BRAI, 1.0% (0.7-1.5); LAg, 0.2% (0.2 -0.7); BED 3.8% (3.1-4.6). MDRIs were; BRAI, 133 days (113-154); LAg, 101 days (87-115); BED, 177 days (155 - 199). Corresponding incidences, unadjusted for FRR, were: BRAI, 3.9% (2.9-4.9); LAg, 3.1% (2.1-4.0); BED, 6.2 % (5.0-7.3). Adjusted estimates were 2.7% (1.5-4.0), 2.5% (1.6-3.5) and 2.6% (1.6-3.7) respectively. At baseline, with no follow-up estimate for comparison, adjusted incidence for serological biomarkers used alone were; BRAI, 8.1% (6.6-9.7); LAg, 6.9% (5.7-8.1); BED 6.7% (5.5-7.9). When viral load was also used, the adjusted and unadjusted incidence estimates were; BRAI, 7.3% (5.7-8.8) and 8.4% (6.8-10.0); LAg, 5.1% (3.9-6.3) and 5.7% (4.5-6.9); BED, 5.4% (4.1-6.7) and 8.6% (7.3-10.0). Conclusion: At recommended cut-offs; BRAI FRR was 1.9 times higher than that of LAg. BRAI MDRIs were also 1.3 times higher, but with a relative standard error 2.4 times as high. Postpartum BRAI incidence estimates were consistently lower than follow-up estimates. Adjusted biomarker estimates under-estimated follow-up incidence when we used viral load in combination with either serological test.
- ItemIdentifying gaps using the EPICOT+ framework and exploring the association between funding sources and author conclusions in primary nutrition research addressing non-communicable diseases from Cochrane nutrition reviews : a descriptive-analytical cross-sectional study(Stellenbosch : Stellenbosch University, 2021-03) Ruzive, Sheena; Naude, Celeste E.; Stellenbosch University. Faculty of Medicine and Health Sciences. Dept. of Global Health. Epidemiology and Biostatistics.ENGLISH SUMMARY : Background: With the rise in non-communicable diseases (NCDs) globally, we aimed to summarise the research gaps and describe the adequacy of the reporting of future research recommendations in Cochrane reviews of nutrition interventions addressing NCDs. We also aimed to explore the influence of funding sources and author- sponsor financial ties on author conclusions in a subset of primary studies included in these reviews. Methods: Two researchers independently screened a Cochrane nutrition reviews database (n=470, July 2015) to identify reviews addressing four NCDs (cardiovascular diseases, cancer, chronic respiratory diseases and diabetes). The “implications for research” section of eligible reviews was analysed using the evidence, population, intervention, comparison, outcome, timeframe, study design and burden of disease (EPICOT+) framework to describe the extent of reporting of research recommendations and to summarise gaps. A purposive sample of English full-text studies included in reviews addressing alternative nutrition supplements were analysed to assess reporting of conflict of interest (COI), funding sources and author-sponsor financial ties, and to explore influences of funding sources and author-sponsor financial ties on author conclusions. Results: Ninety-eight eligible reviews were analysed. The EPICOT+ reporting was as follows: evidence 34/98 (33.7%), population 68/98 (69.4%), intervention 90/98 (91.8%), comparison 26/98 (26.5%), outcomes 78/98 (79.6%), study design 85/98 (86.7%), time frame 52/98 (53.1%), and burden of disease 7/98 (7.1%). Studies requiring better quality, different interventions, and outcomes in low- and middle-income countries (LMICs) were highlighted. Seven reviews addressed alternative nutrition supplements, including 51 eligible primary studies. Conflicts of interest were disclosed in 10/51 (19.2%); funding in 27/51 (51.9%), of which, 11/27 (40.7%) were industry and 16/27 (59.3%) were non-industry sponsors; and author-sponsor financial ties in 9/51 (13.4%), of which 1/9 (11.1%) was industry and 8/9 (88.9%) were non-industry. There was no association between authors making favourable conclusions and having industry sponsors and author-sponsor financial ties (8/12) compared with non-industry sponsors and no author-sponsor financial ties (10/24), (Fisher exact p =0.289). Conclusions: EPICOT+ items were not well reported in most reviews. Future studies of better quality, different interventions, outcomes or populations in LMICs are needed. Authors should disclose all COI, funding sources and author-sponsor financial ties. Possible influences of funding sources and author-sponsor financial ties on author conclusions needs further investigation.
- ItemThe impact of caring for a school-going visually impaired child in Cape Town, Western Cape on the home caregiver and the rest of the family – the health, socio-economic and psychological health burdens(Stellenbosch : Stellenbosch University, 2021-03) St. Jerry, Marlyse; Barnes, J. M. (Johanna Maria); Nyasule, Peter S; Stellenbosch University. Faculty of Medicine and Health Sciences. Dept. of Global Health. Epidemiology and Biostatistics.ENGLISH SUMMARY : Background: Visually impaired (VI) children need additional care for daily tasks due to their diminished independent living skills (ILS). In learners in Special Educational Needs (LSEN) schools and specially-adapted mainstream schools, occupational therapy and trained assistants help to bridge the gap that diminished ILS pose to their education. However, in impoverished areas of the Cape Metropole, many families cannot afford trained caregivers in their homes. Typically a maternal figure fulfils the responsibilities of caring for the VI child as well as for the rest of the household; such a person then becomes the VI child’s primary home caregiver. Aims and Objectives: The main focus of the study was to determine the caregiving load and its impact on the caregiver's physical, mental and emotional well-being. Methods: The cross-sectional study used a questionnaire consisting of a self-designed questionnaire based on issues from literature on the subject and the validated Caregiver Strain Questionnaire – Short Form (CGSQ-SF). The CGSQ-SF provides qualitative data on the noticeable, emotional, and overall impact of caregiving. During prescheduled home interview sessions, the caregivers completed the questionnaires. The mixed research method used measurable data such as financial status and qualitative data, such as the emotional experiences associated with caring for a VI child. The University of Stellenbosch ethics committee (S13/03/049) and the Western Cape Education Department (20130704-13796) approved the study. Professor M. Kidd of the Centre for Statistical Services at the University of Stellenbosch carried out the statistical analyses, Mann-Whitney U tests and Kruskal-Wallis tests analysed the relationship of variables with CGSQ-SF scores. Results: Of the population of 320 VI learners from the only school for the VI in the Cape Metropole, 150 learners resided at home during the school term. According to the inclusion criteria, only 95 of the 150 home caregivers were eligible. The study obtained consent from 73 caregivers. The CGSQ-SF scoring showed that the majority of the 73 caregivers experienced moderate strain in terms of overall (55/73; 75.3%), objective (57/73; 78.1%) and subjective internalised caregiver strain (55/73; 75.3%). Elevated caregiver strain frequently occurred with these factors: financial difficulty; diminished ILS; and reluctance to spend time away from the VI child. Conclusion: All the caregivers experienced a considerable caregiving load and subsequently substantial caregiver strain level. All the participating households experienced both poverty and caring for a VI child. This bias in the design made it difficult to attribute what strainload was due to either of these variables. It was not possible to determine whether having a VI child increased the household’s strain compared to those who did not have a VI child. The confounding nature of the design made it challenging to unravel the relationship between poverty and caregiver strain due to the presence of a VI child. Qualitative information from the caregivers suggested that they did not view their child’s special needs as the only cause for the financial struggles they face and that their biggest concern was their child’s future as a disabled adult.
- ItemThe impact of missing data on estimating HIV/AIDS prevalence and incidence in demographic sentinel survey studies(Stellenbosch : Stellenbosch University, 2022-04) Mosha, Neema Ramadhani; Machekano, Rhoderick; Young, Taryn; Todd, Jim; Stellenbosch University. Faculty of Medicine and Health Sciences. Dept. of Global Health. Epidemiology and Biostatistics.ENGLISH SUMMARY: Background: Missing data is a challenge in most research, especially with observational population data such as demographic surveys. These studies often account for survey designs and clustering when estimating disease prevalence or incidence, but do not account for missing data. In other circumstances they do not explicitly state how they dealt with missing data during analysis or inappropriately handles them in practice. There are many challenges in conceptualising the pattern of missingness, its occurrence mechanism and complexity of methods for handling the problem of missing data. Ignoring the missingness of survey data can cause biased estimates and invalid conclusions. The primary aim of this PhD was to evaluate the impact of missing data on estimating HIV/AIDS prevalence in demographic sentinel surveillance studies. Methods: A systematic review of HIV studies to identify and describe methods used to analyse studies with missing data was done. A series of simulation studies to explore the precision and efficiency of the prevalence estimates using complete case analysis (CCA), multiple imputation (MI), inverse probability weighting (IPW) and double robust estimator (DR), when data are missing at random (MAR) in survey studies was done. A descriptive statistics and a complete case analysis to determine the incidence and population prevalence estimates ignoring the missingness on four different survey rounds of Magu Health Demographic Sentinel Surveillance (HDSS) was done.The surveys were conducted between 2006 and 2016, they included adults aged 15 years and above and about 50% of the population was tested for HIV in each survey. This was followed by data exploration assessing the missingness occurrence and association between missingness and other study characteristics. Finally, application of the statistical methods used in the simulations study was performed to re-estimate the prevalence of the surveys data taking into account the missingness. Results: The systematic review found 24 eligible articles from population, demographic and cross-sectional surveys that acknowledged the presence of missing data. In these studies, complete case analysis was the standard method of choice (100%) followed by multiple imputations (46%) and Heckman’s selection models (38%). A simulation study generated a hypothetical HIV survey with 32 different scenarios exploring data when an outcome is missing 20% and 55%. This simulation showed that when data are MAR, complete case analysis produces biased and inefficient estimates. Results showed that the three methods (MI, IPW and DR) were valid and efficient if the missingness or imputation models are correctly specified, but if either of the MI or IPW models are mis-specified, then the DR estimator can still be valid. Regarding to performance of the methods, provided that correct models are used, MI is more unbiased even when there is 55% of the data missing. However with 55% missingness all estimators are less reliable. In the complete case analysis, the overall population prevalence estimates for HIV decreased from 7.2% in 2006 to 6.6% in 2016. Cox models were used to determine HIV incidence rates and risk factor analysis by sex. The incidence rate was 5.5 per 1000 person - years in women compared to 4.6 per 1000 person-years in men. Residence, marital status, mobile individuals, and individuals with two or more partners were associated with the increase in incidence of HIV in bivariate analysis. The missingness OF HIV was as high as 60.3% (in the 2016 survey) and in all surveys(Sero 5 to 8) it was associated with age, sex, residence, and marital status. Further analysis using MI, IPW and DR assuming the outcome was MAR showed that the overall HIV prevalence was not significantly different from the complete case analysis in all four of the surveys. However, there were significant differences in the HIV estimates when stratified by the covariates. Looking at the confidence intervals width multiple imputations outperformed IPW and DR by producing more narrower estimates. Conclusion: Overall, this dissertation showed that despite the availability of methods to adjust for missing data, many surveys still ignore the missingness. The reporting among articles adjusted for missingness was below guideline standards. Understanding the mechanism of missingness enhances the proper application of advanced methods to account for the missingness. With data missing at random, IPW, MI, and DR can account for the missingness and produce unbiased and efficient estimates in HIV survey studies. Also, more simplified information and awareness are still needed to allow researchers to make informed choices, specifically on which method to apply and in which situation it works best for the estimates to be more reliable and representative.
- ItemInfluence of previous tuberculosis treatment on time to culture conversion for patients receiving a bedaquiline-containing regimen at Sizwe Tropical Disease Hospital, South Africa(Stellenbosch : Stellenbosch University, 2021-03) Saimen, Amashnee; Esterhuizen, Tonya; Padanilam, Xavier; Stellenbosch University. Faculty of Medicine and Health Sciences. Dept. of Global Health. Epidemiology and Biostatistics.; Stellenbosch University. Faculty of Medicine and Health Sciences. Dept. of Global Health. Epidemiology and Biostatistics.ENGLISH SUMMARY : Tuberculosis remains one of the leading causes of death worldwide. There is a growing crisis concerning the number of drug resistant TB cases. New drug regimens were urgently needed to improve mortality and morbidity among drug resistant TB patients. Bedaqualine is a newly developed diarylquinoline with a unique mechanism of action. . Studies have reported varying time to culture conversion regarding RR/MDR-TB patients with history of previous TB treatment. The Rv0678 mutation found in patients with prior Rifampicin exposure has demonstrated a more than four-fold increase in the minimum inhibitory concentrations of Bedaquiline. Previously treated TB patients may be more likely to have higher bacterial load due to extensive parenchymal damage. This study will provide information on effective Bedaquiline treatment duration for those previously exposed to TB treatment. Aim: To determine whether previous exposure to TB treatment influences the time to culture conversion as compared to no previous TB treatment exposure in patients receiving a DR- TB regimen containing Bedaquiline. Primary Objective: To compare the time to culture conversion for previously treated and new DR-TB patients receiving the Bedaquiline containing regimen. Secondary Objectives: 1.To evaluate treatment regimens at time of culture conversion for previously treated andnew DR-TB patients 2.To compare the rate of relapse in previously treated and new DR-TB patients receivingthe Bedaquiline containing regimen. 3.To compare the duration of Bedaquiline therapy in previously treated and new DR-TBpatients 4.To establish the severity of disease of previously treated and new DR-TB patients. Setting and Study Population: The study will be conducted at Sizwe Tropical Disease Hospital in Gauteng Province. Sizwe Tropical Disease Hospital serves as a referral centre for complicated MDR/XDR-TB cases in Gauteng. Study Design: A retrospective cohort study will be undertaken for confirmed DR-TB patients who were initiated on DR-TB regimen containing Bedaquiline from April 2016 to March 2019. Inclusion Criteria: Bacteriologically confirmed DR-TB All patients receiving DR-TB Regimens containing Bedaquiline including new DR-TB with no previous history of TB treatment Documented culture conversion Variables: Culture Conversion; Time to culture conversion; Duration of Bedaquiline treatment Sampling Technique: The group sample sizes were determined to be 76 (Previous treatment group) and 304 (New treatment group), power of 80% with a level of significance of α 0.05. Time Frame: The study will be conducted from June 2020 to November2020.
- ItemKnowledge, attitudes and practices regarding the prevention of type 2 Diabetes Mellitus among overweight and obese adults in Manzini, Eswatini : a cross-sectional study(Stellenbosch : Stellenbosch University, 2020-12) Chideme-Chinovhiringa, Karen; Chivese, Tawanda; Dudley, Lilian; Stellenbosch University. Faculty of Medicine and Health Sciences. Dept. of Global Health. Epidemiology and Biostatistics.ENGLISH SUMMARY : Introduction: Being overweight or obese is one of the strongest risk factors for type 2 diabetes. Eswatini has a high prevalence of undiagnosed type 2 diabetes and half of its adults are either overweight or obese. However, there is a paucity of data on knowledge, attitudes and practices towards the prevention of type 2 diabetes in people at risk in Eswatini. This study aims to assess knowledge, attitudes and practices towards the prevention of type 2 diabetes mellitus among overweight and obese adults presenting at an urban outpatient clinic in Manzini, Eswatini. Methods: A cross-sectional study of adults who were either overweight or obese attending the clinic was carried out. Knowledge, attitudes and practices towards the prevention of type 2 diabetes mellitus were assessed using a validated researcher administered questionnaire. Knowledge, attitudes and practices were compared between overweight and obese participants. In addition, the correlation between knowledge, attitudes and practices was evaluated using a correlation matrix. Results: A total of 105 participants, with a mean age of 35.2 (SD 10.7) years participated in the study. Of these, 55 (52.4%) and 50 (47.6%) were overweight and obese, respectively. The majority of the participants showed acceptable knowledge levels, with 61% of the participants having good knowledge and 30% excellent knowledge. Participants showed positive attitudes towards diabetes prevention, 69.5% of participants had satisfactory attitudes, 21.0% had excellent attitudes and 9.5% had neutral attitudes towards the prevention of type two diabetes mellitus. Practices were generally poor with only 33.3% meeting the World Health Organisation recommended 150 minutes of physical activity per week. Just over half (53.0%) of participants who met the criteria for screening had screened for diabetes. Dietary practices were poor with just over a third (36.2%) of participants meeting the World Health Organisation recommended daily vegetable and/or fruit intake of five servings a day and 85.7% exceeding the World Health Organisation daily recommended limit of sugar intake. There were no significant differences between participants who were overweight and those who were obese in their knowledge, attitudes and practices towards preventing type 2 diabetes mellitus. There was a significant, positive correlation between total knowledge scores and total attitude scores (r= 0.42, p<0.01). Conclusion: Overweight and obese adults visiting the outpatient clinic had satisfactory knowledge and attitude levels towards the prevention of type 2 diabetes. Practices towards prevention were generally poor with few participants meeting the World Health Organisation recommendations for physical activity and fruit and/or vegetable daily intake. Just over half of the eligible participants had screened for diabetes prior to the study. In addition to information, interventions are needed to motivate patients at high risk to adopt healthier dietary and physical activity practices.
- ItemMechanical debridement with antibiotics in the treatment of chronic periodontitis : effect on systemic biomarkers : a systematic review(Stellenbosch : Stellenbosch University, 2019-04) Munasur, Sudhir L.; Chikte, Usuf M. E.; Turawa, Eunice B.; Stellenbosch University. Faculty of Medicine and Health Sciences. Dept. of Global Health. Epidemiology and Biostatistics.ENGLISH SUMMARY : Background: Chronic periodontitis is an inflammatory oral disease which leads to the destruction of the supporting tissues of the teeth, leading to bone resorption and tooth loss. Destruction of the periodontal attachment apparatus can result in gingival recession and root furcation exposure in advanced stages resulting in tooth mobility and tooth loss. Mechanical debridement is the most frequent treatment for chronic periodontitis, in severe cases systemic antibiotics in conjunction with mechanical debridement have been used. The efficacy and the beneficial effect of this combination on the inflammatory biomarkers require further investigation. Objectives: The aim of this systematic review was to assess the effectiveness of adjunctive antibiotics in the improvement of inflammatory systemic biomarkers in the treatment chronic periodontitis. Search methods: We searched the following electronic databases: Cochrane Oral Health Group Trials Register (30th June 2018). The Cochrane Central Register of Controlled Trials (CENTRAL) (Cochrane Library 2018 – current issue), MEDLINE (1966 to present), EMBASE (1982 to present), CINAHL via EBSCO (1990 -present), Google scholar (1990 - present). Web of Knowledge (1990 to May 2018), The meta-Register of Controlled Trials (www.controlled-trials.com), The US National Institutes of Health On-going Trials Register (www.clinicaltrials.gov). The World Health Organization International Clinical Trials Registry platform (www.who.int/trialsearch) was searched to identify relevant trials for inclusion in the review. Conference proceedings, on-going trials registers (02/06/2018) and reference list of included articles were assessed for relevant trials. No language or date of publication restrictions applied. Selection criteria: We searched for randomised controlled trials (RCTs that evaluated the effectiveness of adjunct antibiotic therapy on the systemic biomarkers in the treatment of chronic periodontitis. All trials that compared adjunctive systemic antibiotics with mechanical debridement or mechanical debridement alone, or scaling and root planning, oral hygiene and prophylaxis or placebo were included in the study. Data collection and analysis: Two reviewers independently examined the titles and abstracts retrieved by the search to identify relevant trials for inclusion in the review. All included trials were assessed for risk of bias and data were extracted for further analysis. The primary outcomes assessed include: changes in serum/blood levels of inflammatory biomarkers such as Matrix Metalloproteinases (MMPs), Tissue Inhibitors of MMPs(TIMs), Cytokines, C-Reactive Protein(CRP) and Glycated haemoglobin(HbA1c). Secondary outcomes include periodontal indices such as bleeding on probing (BOP), gingival index (GI), clinical attachment level (CAL), plaque index (PI) and probing pocket depth (PPD). Main results: Fourteen trials (n=1457 participants) were included in the review. Seven trials reported on MMP-8, with average of 3 months time to event. Five trials reported on IL-1β, three trials on IL-6 and two on IL-8 serum level. Four trials reported on CRP; while eight reported on HbA1c level and one on TIMP-1 level. Trials were assessed for risk of bias and judged as low, high, or unclear of risk of bias. Six studies showed no significant differences in MMP-8 concentration level between the two intervention groups. Significant decrease (60%) in odds of increased MMP-8 levels during 2-year study was reported in one trial (OR 0.40, 95%CI: 0.21 to 0.77, p=0.006). One study reported no significant difference for TIMP-1 (0.96, 95% CI: 0.78 to 1.18, p=0.7), while two studies showed significant reduction in HbA1c (10%) at 3 months. Other studies reported no difference in HbA1c levels (%): (Mean (SD) 7.00 (0.76) versus 7.11 (0.99); p=0.710), (Median (Interquartile Range [IQR]) 6.3 (5.5,7.3) versus 6.7 (6.3, 7.7); p=0.8), (p=0.35, 0.55, 0.33, and 0.62, at baseline, 3 months, 6 months, and after 1 year of treatment respectively. Metaanalysis showed a mean reduction of 0.24mm in the periodontal pockets (PD) at 3 months [MD, -0.25 with 95% CI -0.38 to -0.12]. Two trials revealed no significant difference PD≤3mm at 3 months, [MD, -1, 95% CI -22.54 to 20.53 (p=0.19)]. A decrease in periodontal pockets(PD≥4mm) and a reduction of 3.38mm in favour of SRP+antibiotics after 3 months [MD, -3.38, 95% CI -6.51 to -0.25 (p=0.93, I2=0%)] was observed for probing depth(PD). No significant difference in clinical attachment level (CAL) at 3 months [MD, -0.13, 95% CI -0.34 to 0.07; Chi2=0.98, df=3, p=0.81, I2=0%]. The overall quality of evidence was low largely because of attrition bias (24%; 32%) connoting high risk of bias and wide confidence intervals which suggests imprecision of results. Authors' conclusions: There is limited but low-level of evidence suggesting that systemic antibiotic therapy combined with mechanical debridement improves the systemic biomarker levels during the treatment of chronic periodontitis.
- ItemNursing students' knowledge, attitude and practices of infection prevention and control guidelines at a tertiary institution in the Western Cape : a cross sectional study(Stellenbosch : Stellenbosch University, 2017-12) Rahiman, Farzana; Chikte, Usuf; Stellenbosch University. Faculty of Medicine and Health Sciences. Dept. of Global Health. Epidemiology and Biostatistics.ENGLISH SUMMARY: Background: Nurses in sub-Saharan Africa are particularly at a higher risk of acquiring nosocomial infections, considering the increased prevalence of infectious diseases. It is therefore imperative that these nurses have a sound knowledge and understanding of infection prevention procedures. Objective: The main objective of this study was to describe the knowledge, attitudes and practices concerning infection prevention and control precautions among nursing students in a resource limited setting. Method: A cross sectional study design was employed. A self-administered questionnaire concerning infection prevention and control guidelines were made available to students enrolled in a mainstream programme for completion of an undergraduate nursing degree. Setting and participants: A total of 301 students at second, third and final years of study from a tertiary institution in the Western Cape were invited to participate. Results: The final cohort comprised of 301 students with the majority between the ages of 17-26 (88.2%), with a mean age of 23±4.7 (SD) years and the dominant gender being female (83.4%). According to the classification system used in this study, majority of the students were overall evaluated as having good level of knowledge (47.4%) and poor attitude (41.7%) scores, with little difference in practice scores observed between different years of study. There was a positive correlation found between students’ total attitude and total practice scores (r = 0.48 p<0.01). Results showed that a significant association between gender with knowledge (p<0.05), attitudes (p<0.05) and practice (p<0.05) exists. There was also a significant association between province and those who repeated a year with total knowledge scores (p<0.05). Conclusion: Based on the results of this study, it is recommended that interactive infection control courses that promotes critical thinking are implemented at undergraduate level along with more stringent forms of assessments focusing on infection prevention and control, during clinical training.
- ItemOptimisation and benchmarking of analytical approaches to estimation of population level HIV incidence from survey data(Stellenbosch : Stellenbosch University, 2022-04) Mhlanga, Laurette; Welte, Alex; Grebe, Eduard; Stellenbosch University. Faculty of Medicine and Health Sciences. Dept. of Global Health. Epidemiology and Biostatistics.ENGLISH SUMMARY: Disease prevalence (the proportion of a population with a condition of interest) is conceptually and procedurally much more straightforward to estimate than disease incidence (the rate of occurrence of new cases - for example, infections). For long-lasting conditions, incidence is fundamentally more difficult to estimate than prevalence, but also more interesting, as it sheds light on current epidemiological trends such as the emerging burden on health systems and the impact of recent policy interventions. Progress towards reducing reliance on questionable assumptions in the analysis of large population based surveys (for the estimation of HIV incidence) has been slow. The work of Kassanjee et al and the work of Mahiane et al, in particular, provide rigorous ways of estimating incidence by using 1) markers of ‘recent infection’, 2) the ‘gradient’ of prevalence, and 3) ‘excess mortality’ associated with HIV infection, without the need for simplifying assumptions to the effect that any particular parameters are constant over ranges of time and/or age. To date, the use of these methods has largely ignored 1) the rich details of the age and time structure of survey data, and 2) the opportunities for combining the two methods. The primary objective of this work was to find stable approaches to applying the Mahiane and Kassanjee methods to large age/time structured population survey data sets which include HIV status, and optionally, ‘recent infection’ status. In order to evaluate proposed methods, a sophisticated simulation platform was created to simulate HIV epidemics and generate survey data sets that are structured like real population survey data, with the underlying incidence, prevalence, and mortality explicitly known. The first non-trivial step in the analysis of survey data amounts essentially to performing a smoothing procedure from which the (age/time specific) prevalence of HIV infection, the prevalence of ‘recent infection’, and the gradient of prevalence of infection can be inferred without recourse to ‘epidemiological’ assumptions. The second step involves the correct accounting for uncertainty in a context-specific weighted mean of the Mahiane and Kassanjee estimators. These two steps are approached incrementally, as there are numerous details which have not previously been systematically elucidated. The investigation culminates in a proposed generic ‘once size fits most’ algorithm based on: 1) fitting survey data to generalised linear models defined by simple link functions and high order polynomials in age and time; 2) the use of a ‘moving window’ rule for data inclusion into a separate analysis for each age/time point for which incidence is to be estimated; 3) a ‘variance optimal’ weighting scheme for the combination of the Mahiane and Kassanjee estimators (when both are applicable); 4) flexible use of a delta method expansion or bootstrapping to estimate confidence intervals and p values. We find it is relatively easy to obtain estimates with practically negligible bias, but samplesizes/ sampling-density requirements are always considerable. We also make numerous observations on survey design and the inherent challenges faced by all attempts to estimate HIV incidence using surveys of reasonable size.
- ItemPrevalence of non-communicable diseases in adults living with Human Immunodeficiency Virus : an overview of systematic reviews(Stellenbosch : Stellenbosch University, 2019-04) Jaffer, Shahista Mustafa; Young, Taryn; Stellenbosch University. Faculty of Medicine and Health Sciences. Dept. of Global Health. Epidemiology and Biostatistics.ENGLISH SUMMARY : Background: Non-communicable diseases (NCD’s) are on the rise in patients with HIV and this has been partly attributed to the increasing use of Antiretroviral therapy (ART). Our aim was to consolidate findings on prevalence of NCD in those with HIV, from systematic reviews, to inform the existing body of research and provide evidence to inform planning of healthcare services. Methods: We undertook a comprehensive search in February 2018, with no date limitations, in 7 databases to identify systematic reviews on the prevalence of NCD’s in HIV patients on ART. We included systematic reviews with participants over the age of 13years who were on ART and had one or more of the specified NCD’s including diabetes mellitus type 2, hypertension, dyslipidemia and depression. We then assessed the quality of these systematic reviews using the AMSTAR 2 tool and extracted prevalence’s of the NCD’s from each one of them. Results: We identified 10 systematic reviews meeting our inclusion criteria of which 3 are ongoing. The methodological quality of the seven systematic reviews assessed varied in many aspects. Only one systematic review assessed prevalence of multi-morbidity defined as the presence of two or more NCD’s in people living with HIV (PLHIV) which ranged from 8.4% to 47%, the remaining six only assessed the prevalence of comorbidity of any one NCD in PLHIV. Diabetes mellitus type 2 had the lowest prevalence especially in African countries and it ranged between 7% to 48.6% globally while dyslipidemia had the highest prevalence globally ranging from 6.3% to 100%. Depression in PLHIV who were on ART was considerably high ranging from 25.81% to 64% while hypertension ranged from as low as 4.0% to as high as 67.0%. Conclusions: This overview highlights that NCD’s are highly prevalent in PLHIV on ART. There is a lack of systematic reviews and primary studies focusing on multi-morbidity in the HIV population on ART. PROSPERO registration number - CRD42018104420.
- ItemQuality of systematic reviews in African emergency medicine : a cross-sectional methodological study(Stellenbosch : Stellenbosch University, 2023-03) Van Niekerk, Hendrik Jacques; McCaul, Michael; Rohwer, Anke; Stellenbosch University. Faculty of Medicine and Health Sciences. Dept. of Global Health. Epidemiology and Biostatistics.ENGLISH SUMMARY: Introduction: Reliable systematic reviews are essential to inform clinical practice guidelines, policies and further research priorities in Africa. For systematic review findings to be trustworthy, they need to be conducted with methodological rigour and reported transparently. We assessed the methodological quality of systematic reviews published in African emergency medicine journals, comparing them to those published in international emergency medicine journals. Additionally, we describe the types of review literature published in the African journals. Methods: We performed a cross-sectional methodological study of systematic reviews published in selected African and international emergency medicine journals from 2012 to 2021. Studies were eligible for inclusion if they were i) published in one of the top five emergency medicine journals in the African region or internationally, ii) a review article on an emergency medicine topic and iii) published between January 2012 and December 2021 in English or French. We searched PubMed, Web of Science and Scopus databases and hand-searched selected journals. Two authors screened titles, abstracts and full texts independently and in duplicate to select reviews for inclusion. Data extraction was performed by one reviewer, using a standardised form, after completing a calibration exercise. We described the characteristics of systematic reviews and assessed methodological quality using AMSTAR II. Results: We identified 34 (37%) African and 511 (54%) international systematic reviews from 92 and 948 review articles respectively across 10 journals. We included all 34 African and a random sample of 100 international systematic reviews. Methodological quality was low or critically low for all the African systematic reviews (n=34, 100%) and all but three international systematic reviews (n=97, 97%). The median number of critical domain weaknesses was 4 (IQR 4;5) and 2 (IQR 2;4) for African and international systematic reviews respectively. The most common weaknesses across both African and international systematic reviews were i) not establishing a priori review protocols, ii) unclear selection of study designs iii) not providing a list of excluded studies and iv) unclear reporting on funding sources for included studies. Conclusion: Emergency medicine systematic reviews published in African and international journals are lacking in methodological quality. Reporting an a priori protocol, developing a comprehensive search strategy, appropriate evidence synthesis and adequate assessment of the risk of bias, heterogeneity and evidence certainty will improve the quality of systematic reviews.