Magister Public Health - MPH / Background: The recognition of HIV/AIDS as a chronic life-long condition globally in recent years has demanded a different perception and an alignment to its association with other chronic diseases. Both HIV and other chronic non-communicable diseases are significant causes of morbidity and mortality. Their combined DALY contributions for Botswana would be significant if research and strategies in controlling these conditions are not put in place. Natural aging and specific HIV-related accelerated aging of patients who are on antiretroviral treatment means that age-related diseases will adversely affect this population. Princess Marina Hospital Infectious Diseases Care Clinic has been in operation since 2002. The clinic has initiated over 16 000 patients on anti-retroviral treatment (ART) since 2002. The current study estimated the prevalence of non-AIDS defining conditions (NADCs) in the attendees of the clinic in 2013. The majority of patients that attended the clinic had been on treatment for over three years with some patients more than ten years. These ART experienced patients were more likely to be susceptible to chronic non-communicable diseases, including non-AIDS defining conditions. The nomenclature used in classification of NADCs in the current study was appropriate for resource-limited settings; because the study setting offered HIV treatment under resources constraints. Aim: The current study characterised non-AIDS defining conditions, and determined their associations with virologic treatment failure in a cohort of patients that were enrolled at Princess Marina Hospital antiretroviral clinic in Gaborone, Botswana. Methods: A retrospective cross sectional study of records of patients who attended the Princess Marina Infectious Diseases Care Clinic in 2013. Stratified random sampling of a total of 228 patients’ records was achieved from a total population of 5,781 records. Data was transcribed into a Microsoft Excel Spreadsheet and then exported to Epi-Info statistical software for analysis. Results: Eighty (35%) cases of NADCs were reported/diagnosed in the study sample; with 27% (n=62) of the patients having at least one condition, 6.7% (n=17) two conditions, and 0.4% (n=1) three conditions. The top prevalent conditions were hypertension (n= 40), hyperlipidaemia (n=7) and lipodystrophy (n=7). The prevalence of NADCs on the various categories of patients compared with the total sample population was as follows: active patients (prevalence ratio= 0.70), transferred out patients (prevalence ratio = 1.24), patients who died (prevalence ratio=2.04) and patients who were lost to follow-up (prevalence ratio =2.86). The prevalence of NADCs was significantly associated with increasing age (p<0.001); having social problems (p=0.028); having been on treatment for over three years (p=0.007); an outcome of death (p = 0.03) and being lost to follow-up (p=0.007). The study showed that being controlled on second line or salvage regimen (p=0.014) and the presence of adherence problems in the past was associated with virologic failure (p=0.008). There was no association of presence of NADCs to virologic failure. Conclusions: There was significant morbidity of non-AIDS defining conditions in the Princess Marina Infectious Diseases Care Clinic shown by a prevalence of NADCs in the clinic of 35% in 2013.The significant associations of the presence of NADCs and virologic failure with outcomes of death and loss to follow-up illustrate the adverse effects that NADCs are having, and calls for strategies to address multi-morbidities in HIV patients on antiretroviral treatment.

The development and implementation of policy guidelines remains a contentious issue. Over the past few years, difficulty still exists in implementing the Department of Education (DoE) 1999, National Education Policy Act, 1996 (No. 27 of 1996): National Policy on HIV/AIDS for learners and educators in public schools, and students and educators in further education and training institutions [here after referred to as DoE HIV/AIDS policy (1999)], while at the same time trying to transform the entire education system. This research explored the perceptions of educators in the Port Elizabeth District regarding the implementation of DoE HIV/AIDS (1999) policy guidelines. A secondary objective was to provide a reflection of how the implementation of guidelines on HIV/AIDS interventions within the schools of the Port Elizabeth District either conformed to or deviated from the guidelines outlined in the DoE HIV/AIDS policy (1999). The study was executed within the paradigm of qualitative research and employed an exploratory, descriptive and contextual design. The researcher conducted a pilot study to enhance the trustworthiness of the study. Purposive sampling was employed to recruit research participants, consisting of 12 educators from 10 schools in the Port Elizabeth District where HIV/AIDS interventions were being implemented. Data was gathered through semi-structured interviewing and analysed using Tesch’s (1990) in De Vos, Strydom, Fouché & Delport (2005:340-341) framework for analysis of qualitative data. Guba’s model (in Krefting, 1991) was used to ensure the trustworthiness of the study. Three themes emerged from the results of the in-depth semi-structured interviews: (1) Educators’ views on the DoE HIV/AIDS policy (1999) guidelines and its implementation (2) Gaps or shortcomings in implementation of the DoE HIV/AIDS policy (1999) and (3) Educator suggestions’ to inform implementation of the DoE HIV/AIDS policy (1999) in schools. The results from the study indicate that there is inconsistency in the policy implementation approach employed by DoE district level representatives and there is a need for knowledge and capacity development at district and school level. The value of the study is outlined as well as recommendations.

Infectious diseases such as pneumonia still pose a major global health concern. Currently, the world is facing widespread emergence of acquired bacterial resistance to antibiotics which constitute one of the chief causes of infectious diseases. The accumulation of different antibiotic resistance mechanisms within the same strains has induced the appearance of the so called “superbugs”, or “multiple-drug resistant bacteria”. Due to antibiotic resistance, attention is currently being drawn towards biologically active components isolated from plant species commonly used as herbal medicine, as they may offer a new source of antibacterial, antifungal and antiviral activities. This is the basis of this study. In this study four medicinal plants namely, Cassia abbreviata, Geranium incanum, Pelargonium hortorum and Tecoma capensis were investigated for their antimicrobial potential. In vitro antimicrobial activity using agar disc diffusion method, agar dilution method and broth microdilution plate determination of minimum inhibitory concentration (MIC), were carried out against ATCC (American Type Culture Collection) strains and clinical isolates known to cause pneumonia. Aqueous, methanol and acetone extracts from the selected plants were thus tested against strains of Streptococcus pneumoniae, Haemophilus influenzae, Staphylococcus aureus, Klebsiella pneumoniae, Pseudomonas aeruginosa, Acinetobacter baumannii, Escherichia coli and Candida albicans. The plants exhibited pronounced antimicrobial activity and were more active against Gram-positive bacteria than Gram-negative bacteria. During agar disc diffusion method, the highest inhibition zone was demonstrated by the acetone extract of P. hortorum (IZ=22mm and AI=0.73) against the reference strain of S. pneumoniae (ATCC 49619). The range of zones of inhibition in diameter across strains of S. pneumoniae and H. influenzae was 7mm to 22mm with activity index range of 0.23 to 0.74. The lowest MIC produced by medicinal plants in the study during agar disc diffusion method against S. pneumoniae and H. influenzae strains, was 2.5mg/ml. In broth microdilution plate assay, the lowest MIC demonstrated by C. abbreviata, T. capensis and P. hortorum extracts on tested bacteria was 0.031mg/ml and that of G. incanum was 0.063mg/ml. Candida albicans strains were only inhibited at 20mg/ml by the study plants. The highest activity among the individual extracts was shown by P. hortorum methanol extract which inhibited 71% of the studied bacteria. T. capensis methanol extract was the least and inhibited only 17% of the tested bacteria. The strains of Klebsiella pneumoniae showed the highest resistance to medicinal plants employed in this study. Traditional preparation of selected medicinal plants did not show any significant antimicrobial activity. Bioactive analysis of compounds on study plants was carried out using standard methods which revealed the presence of anthraquinones, flavonoids, phytosterol, saponins, tannins and triterpenoids. Comparison of the inhibitory effect of the plant extracts against some broad spectrum antibiotics revealed that the tested medicinal plants showed greater antimicrobial activity than standard antibiotics. However, there was no correlation between the antibiotic susceptibility patterns of the bacteria and the effects of the plants, signifying that plants probably function through different mechanisms. Bioautographic findings on thin-layer chromatography plate, exhibited clear zones of inhibition of bacterial growth with the Rf value range of 0.09 to 0.94. Anti-mutagenic activity was assayed by the Ames mutagenicity test in the plate-incorporation method using histidine mutants of S. typhimurium strains TA 100. The selected plant extracts at 2.5mg/ml and 5mg/ml did not induce mutagenesis in the absence of liver-metabolizing enzymes. The study results indicated that the selected plants are capable of inhibiting the growth of the studied pathogenic microorganisms to a varied degree. The leaves of G. incanum, P. hortorum, T. capensis as well as the stem bark of C. abbreviata could be novel sources of antimicrobial agents that might have broad spectrum activity. The anti-mutagenic properties of the studied medicinal plants may also provide additional health supplemental value to the other claimed therapeutic properties of the plants.

Isolation of those ill with contagious disease has been a fundamental infection control concept for hundreds of years. However, recent studies suggest that fewer than 50% of health—care workers comply with their hospitals' isolation precaution policies and that efficacy of some of those policies is questionable. In response, two new systems, based upon fundamentally different goals, were promoted. The Centers for Disease Control, prompted by health—care worker& concerns about occupational risk of human immunodeficiency virus (HIV) from a growing number of patients with acquired immunodeficiency disease syndrome (AIDS), issued formal guidelines in 1987. This formed the basis for Universal Precautions (UP), a unifying strategy for precautions with all patients regardless of diagnosis intended to reduce risk to hospital staff members. Also in 1987, one hospital issued guidelines for Body Substance Isolation (BSI), hygienic precautions to be used with all patients based on recognition that colonized body substances are important reservoirs for cross—infection to both patients and staff members. These new strategies have been promoted widely, but there have been no formal assessments to reconcile controversies they raised nor to confirm their effectiveness. Further, necessary assessment tools have not been validated. This thesis provides new tools and new information to address three vital questions: Have hospitals adopted Universal Precautions or Body Substance Isolation? Do their staff members use the new system of precautions in daily practice? Has reliable use of a new system led to decreased risk of infection? A confidential mailed survey of all acute—care Canadian hospitals was conducted to measure rates of guideline receipt and adoption. It also obtained information on motivations for and perceived effectiveness of strategies adopted. A self—selected group of responding hospitals subsequently participated in standardized covert observation of their nurses infection control practices, then had the observed nurses complete a test examining their knowledge and beliefs. Employee health records were also examined to determine whether needlestick injury rates had changed since adoption of a new infection control strategy. Most Canadian hospitals adopted and modified new strategies based upon reasonable but unproven extensions of logic to protect health—care workers from HIV. 74% claimed UP (65%) or BSI (9%) but only 5% of 359 claiming UP and 0 of 50 claiming BSI adopted all policies expected. Many hospitals had not received key guideline publications. Guideline source, hospital size, and other variables were significantly associated with receipt. Nurses in 35 hospitals were observed to wear gloves during only z60% of procedures in which gloving was expected; rates varied widely among hospitals. Direct examination of sharps disposal containers confirmed compliance with a policy to not recap used needles (taken as recapping rate of 25%) in only 47% of 32 hospitals. Paired analysis of needlestick injury rates in 11 hospitals during comparable 90—day periods before versus after implementing UP/BSI showed no significant difference. 489 nurses completing a written test achieved their highest scores and least discordance among questions regarding procedural issues established long before UP/BSI, and lower scores or greater discordance on UP/BSJ concepts of philosophy, risk recognition and newer procedures. Positive correlation between knowledge and practice was not evident. UP and BSI now mean different things in different hospitals and have not been effective in harmonizing health—care workers’ infection control practices. Carefully standardized assessment methods are needed to guide their evolution to cost—effectiveness. / Graduate and Postdoctoral Studies / Graduate

Thesis(Ph.D.(Medical Science)) -- University of Limpopo, 2016 / Background: Chronic disease management (CDM) is an approach to health care that keeps people as healthy as possible through the prevention, early detection and management of chronic diseases. This approach offers holistic and comprehensive care, with a focus on rehabilitation, to achieve the highest level of independence possible for individuals.The aim of this study was to develop an integrated, evidence-based model for the management of chronic non-communicable diseases in a rural community of the Limpopo Province, South Africa. Methods: The study was conducted at Dikgale Health and Demographic Surveillance System (HDSS) site is situated in Capricorn District of Limpopo Province in South Africa. This study followed mixed methods methodology with an aim on integrating quantitative and qualitative data collection and analysis in a single study to develop an intervention program in a form of model to improve management of chronic diseases in a rural area. Therefore, this included literature review and WHO STEPwise approach to surveillance of NCD risk factors for quantitative techniques and focus group discussions, semi-structures interviews and quality circles for qualitative techniques. In the surveillance of NCD risk factors standardised international protocols were used to assess behavioural risk factors (smoking, alcohol consumption, fruit and vegetable consumption, physical activity) and physical characteristics (weight, height, waist and hip circumferences, and blood pressure). A purposive sampling method was used for qualitative research to determine knowledge, experience and barriers to chronic disease management in respect of patients, nurses, community health workers (CHWs), traditional health practitioners (THPs) and managers of chronic disease programmes. Data were analysed using STATA 12 for Windows, INVIVO and Excel Spreadsheets. Results: The study revealed that epidemiological transition is occurring in Dikgale HDSS. This rural area already demonstrates a high burden of risk factors for non-communicable diseases, especially smoking, alcohol consumption, low fruit and vegetable intake, physical inactivity, overweight and obesity, hypertension and dyslipidaemia, which can lead to cardiovascular diseases. The barriers mostly mentioned by the nurses, patients with chronic disease, CHWs and THPs include lack of knowledge of NCDs, shortages of medication and shortages of nurses in the clinics which cause patients to stay for long periods of time in a clinic. Lack of training on the management of chronic diseases, supervision by the district and provincial health managers, together with poor dissemination of guidelines, were contributing factors to lack of knowledge of NCDs management among nurses and CHWs. THPs revealed that cultural insensitivity on the part of nurses (disrespect) makes them unwilling to collaborate with the nurses in health service delivery. x The model developed in this study which was the main aim of the study describes four interacting system components which are health care providers, health care system, community partners and patients with their families. The main feature of this model is the integration of services from nurses, CHWs and THPs including a well-established clinical information system for health care providers to have better informed patient care. The developed model also has an intervention such as establishment of community ambassadors. Conclusion: Substantially high levels of the various risk factors for NCDs among adults in the Dikgale HDSS suggest an urgent need for adopting healthy life style modifications and the development of an integrated chronic care model. This highlights the need for health interventions that are aimed at controling risk factors at the population level in order to slow the progress of the coming non-communicable disease epidemic. Our study highlights the need for health interventions that aim to control risk factors at the population level, the need for availability of NCD-trained nurses, functional equipment and medication and a need to improve the link with traditional healers and integrate their services in order to facilitate early detection and management of chronic diseases in the community. The developed model will serve as a contribution to the improvement of NCD management in rural areas. Lastly, concerted action is needed to strengthen the delivery of essential health services in a health care system based on this model which will be tasked to organize health care in the rural area to improve management and prevention of chronic illnesses. Support systems in a form of supervisory visits to clinics, provision of medical equipments and training of health care providers should be provided. Contribution from community partners in a form of better leadership to mobilise and coordinate resources for chronic care is emphasized in the model. This productive interaction will be supported by the district and provincial Health Departments through re-organization of health services to give traditional leaders a role to take part in leadership to improve community participation. / Medical Science Department, University of Limpopo in South Africa,International Health Unit, and Antwerp University

Master of Public Health - MPH / Non-communicable diseases (NCDs) are the leading causes of deaths worldwide and are shown to be responsible for approximately 71% of deaths globally. NCDs mainly affect individuals of working age, resulting in high sick leave absences and loss of productivity in the working environment. This presents a major barrier to economic growth, particularly in low- and middle-income countries where the impact is greatest. Among the interventions identified in the South African Strategic Plan for the control of NCDs, is the implementation of wellness initiatives (i.e. diet and exercise interventions) in the workplace. This has been to improve overall productivity and decrease absenteeism. This study was therefore aimed at investigating the effect that participating in workplace wellness initiatives targeted at employees, particularly those that are overweight, hypertensive and diabetic at Nestlé, had on the number of working days lost due to sick leave from NCDs.

Master of Public Health - MPH / Introduction: People with mental illness (PMI) are likely to die of chronic diseases, primarily cardiovascular, cerebrovascular and respiratory diseases at a younger age compared with the general population. The side-effects of psychotropic medications particularly weight gain and impaired glucose intolerance increase the risk of premature mortality in PMI. Behavioural risk factors for non-communicable diseases such as physical inactivity and unhealthy diet (diets high in fat and low in fruit and vegetables) are also thought to be consequences of negative symptoms of mental illness and emotional dysregulation.

Master of Public Health - MPH / Obesity is one of the critical problems that threatens not only health, but the economy at a global level. Among the factors associated with obesity is less than optimum level of nutrition literacy. Nutrition literacy is more than just the food knowledge, it is a combination of other essential factors that help individuals to maintain healthy a body size. These factors include the selection and consumption of nutritious food; acquiring knowledge and skills in the areas of meal planning and preparation; as well as using and knowing how to read food labels correctly.

Background: The health systems in many low-middle income countries are faced with an increasing number of patients with non-communicable diseases within a high prevalence of infectious diseases. Integrated chronic disease management programs have been recommended as one of the approaches to improve efficiency, quality of care and clinical outcomes at primary healthcare level. The South African Department of Health has implemented the Integrated Chronic Disease Management (ICDM) Model in Primary Health care (PHC) clinics since 2011. Some of the expected outcomes on implementing the ICDM model have not been achieved, and there is a dearth of studies assessing implementation outcomes of chronic care models, especially in low-middle income countries. This thesis aims to assess the degree of fidelity, moderating factors of fidelity and costs associated with the implementation of the ICDM model in South African PHC clinics. Methods: The study was a cross-sectional study design using mixed methods and following the process evaluation conceptual framework. A total of sixteen PHC clinics in the Dr. Kenneth Kaunda (DKK) health district of the North West Province as well as the West Rand (WR) health district of the Gauteng Province, that were ICDM pilot sites were included in the study. The degree of fidelity in the implementation of the ICDM model was evaluated using a fidelity criterion from the four major components of the ICDM model as follows: facility reorganization, clinical supportive management, assisted self-support and strengthening of the support systems. In addition, the implementation fidelity framework was utilized to guide the assessment of ICDM model fidelity moderating factors. The data on fidelity moderating factors were obtained by interviewing 30 purposively selected healthcare workers. The abbreviated Denison Organizational Culture (DOC) survey was administered to 90 healthcare workers to assess the impact of three cultural traits (involvement, consistency and adaptability) on fidelity. Cost data from the provider's perspective were collected in 2019. The costs of implementing the ICDM model current activities for three (facility reorganization, clinical supportive management and assisted self-management) components and additional costs of implementing with enhanced fidelity were estimated. Costs data was collected from budget reviews, interviews with management teams, and other published data. Descriptive statistics were used to describe participants and clinics. Fidelity scores were summarized using medians and proportions and compared by facilities and health districts. Qualitative data were analysed thematically. Pearson correlation coefficient was utilized to assess the association between fidelity and culture. The annual ICDM model implementation costs per PHC clinic and patient per visit were presented in 2019 US dollars. Results: The 16 PHC clinics had comparable patient caseload, and a median of 2430 (IQR: 1685-2942) patients older than 20 years received healthcare services in these clinics over six months. The overall implementation fidelity of the ICDM model median score was 79% (125/158, IQR: 117-132); WR was 80% (126/158, IQR: 123-132) while DKK was 74% (117/158, IQR: 106-130), p=0.1409. The highest clinic fidelity score was 86% (136/158), while the lowest was 66% (104/158). The fidelity scores for the four components of the ICDM model were very similar. A patient flow analysis indicated long (2-5 hours) waiting times and that acute and chronic care services were combined onto one stream. Interviews with healthcare workers revealed that the moderating factors of implementation fidelity of the ICDM model were the existence of facilitation strategies (training and clinical mentorship); intervention complexity (healthcare worker, time and space integration); and participant responsiveness (observing operational efficiencies, compliance of patients and staff attitudes). Participants also indicated that poor adherence to any one component of the ICDM model affected the implementation of the other components. Contextual factors that affected fidelity included supply chain management, infrastructure and adequate staff, and balanced patient caseloads. The overall mean score for the DOC was 3.63 (SD = 0.58), the involvement cultural trait had the highest (3.71; SD = 0.72) mean score, followed by adaptability (3.62; SD = 0.56), and consistency (3.56; SD = 0.63). Although there were no statistically significant differences in cultural scores between PHC clinics, culture scores for all three traits were significantly higher in WR (involvement 3.39 vs 3.84, p= 0.011; adaptability 3.40 vs 3.73, p= 0.007; consistency 3.34 vs 3.68, p= 0.034). The mean annual cost of implementing the ICDM model was $148 446.00 (SD: $65 125.00) per clinic, and 84% ($124 345.00) was for current costs while additional costs for higher fidelity accounted for were 16% ($24 102.00). The mean cost per patient per visit was $6.00 (SD:$0.77). Conclusion: There was some variability of fidelity scores on the components of the ICDM model by PHC clinics, and there are multiple (context, participant responsiveness, intervention complexity and facilitation strategies) interrelated moderating factors influencing implementation fidelity of the ICDM model. Organizational culture needs to be purposefully influenced to enhance adaptability and consistency cultural traits of clinics to enhance the ICDM model's principles of coordinated, integrated, patient-centred care. Small additional costs are required to implement the ICDM model with higher fidelity. Recommendations: Interventions to enhance the fidelity of chronic care models should be tailored to specific activities that have low degree of adherence to the guidelines. Addressing some of the moderating factors like training and mentoring of staff members, role clarification and supply chain management could contribute to enhanced fidelity. Organizational culture enhancements to ensure that the prevailing culture is aligned with the planned quality advancements is recommended prior to the implementation of new innovative interventions. Further research on the cost-effectiveness of the ICDM model in middle-income countries is recommended.

Malaria is still one of the most proli c communicable diseases in the world with more than 200 million infections annually, its greatest e ect is felt in the poor nations with-in sub-saharan Africa and south-east Asia. It is especially fatal for women and children where out of the 660 000 fatalities in 2010, 86% were below the age of 5. In the past decade the global fatality rate due to malaria has been signi cantly reduced, primarily due to proliferation of vector control using treated nets and indoor residual spraying of DDT. There have, however, been few innovations in anti-malarial therapeutics and with the threat of the spread of drug resistant strains a need still exists to develop novel drugs to combat malaria infections. One of the major hinderances to drug development is the huge cost of the drug development process, where candidate failures late in development are extremely costly. This is where post-genomic information has the potential of adding great value. By using all available data pertaining to a disease, one gains higher discerning power to select good drug candidates and identify risks early in development before serious investments are made. This need provided the motivation for the development of Discovery; a tool to aid in the identi cation of protein targets and viable lead compounds for the treatment of malaria. Discovery was developed at the University of Pretoria to be a platform for a large spectrum of biological data focused on the malaria causing Plasmodium parasite. It conglomerates various data types into a web-based interface that allows searching using logical lters or by using protein or chemical start points. In 2010 it was decided to rebuild Discovery to improve it's functionality and optimize query times. Also, since its inception various new datasources became available speci cally related to bio-active molecules, these include the ChEMBL database and TCAMS dataset of bio-active molecules and the focus of this project was the integration of said datasets into Discovery. Large quantities of high quality bioactivity data have never been available in the public domain and this has opened up the opportunity to gain even greater insight into the activity of chemical compounds in malaria. Due to conserved structural/functional similarities of proteins between di erent species it is possible to derive predictions about a malaria protein or a chemicals activity in malaria due to experiments carried out on other organisms. These comparisons can be leveraged to highlight potential new compounds that were previously not considered or prevent wasting resources persuing potential compounds that pose threats of toxicity to humans. This project has resulted in a web based system that allows one to search through the chemical space of the malaria parasite. Allowing them to view sets of predicted protein-ligand interactions for a given protein based on that proteins similarity to those existing in the bio-active molecule databases. / Dissertation (MSc)--University of Pretoria, 2014. / gm2014 / Biochemistry / unrestricted