Browsing by Faculty "Health Science"

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    Changes in trauma-related emergency medical services during the COVID-19 lockdown in the Western Cape, South Africa
    (BioMed Central, 2023-06-27) Pettke, Aleksandra; Stassen, Willem; Laflamme, Lucie; Wallis, Lee A.; Hasselberg, Marie
    Abstract Background To limit virus spread during the COVID pandemic, extensive measures were implemented around the world. In South Africa, these restrictions included alcohol and movement restrictions, factors previously linked to injury burden in the country. Consequently, reports from many countries, including South Africa, have shown a reduction in trauma presentations related to these restrictions. However, only few studies and none from Africa focus on the impact of the pandemic restrictions on the Emergency Medical System (EMS). Methods We present a retrospective, observational longitudinal study including data from all ambulance transports of physical trauma cases collected during the period 2019–01-01 and 2021–02-28 from the Western Cape Government EMS in the Western Cape Province, South Africa (87,167 cases). Within this timeframe, the 35-days strictest lockdown level period was compared to a 35-days period prior to the lockdown and to the same 35-days period in 2019. Injury characteristics (intent, mechanism, and severity) and time were studied in detail. Ambulance transport volumes as well as ambulance response and on-scene time before and during the pandemic were compared. Significance between indicated periods was determined using Chi-square test. Results During the strictest lockdown period, presentations of trauma cases declined by > 50%. Ambulance transport volumes decreased for all injury mechanisms and proportions changed. The share of assaults and traffic injuries decreased by 6% and 8%, respectively, while accidental injuries increased by 5%. The proportion of self-inflicted injuries increased by 5%. Studies of injury time showed an increased share of injuries during day shift and a reduction of total injury volume during the weekend during the lockdown. Median response- and on-scene time remained stable in the time-periods studied. Conclusion This is one of the first reports on the influence of COVID-19 related restrictions on EMS, and the first in South Africa. We report a decline in trauma related ambulance transport volumes in the Western Cape Province as well as changes in injury patterns, largely corresponding to previous findings from hospital settings in South Africa. The unchanged response and on-scene times indicate a well-functioning EMS despite pandemic challenges. More studies are needed, especially disaggregating the different restrictions.
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    Clinical and Experimental Determination of Protection Afforded by BCG Vaccination against Infection with Non-Tuberculous Mycobacteria: A Role in Cystic Fibrosis?
    (Multidisciplinary Digital Publishing Institute, 2023-08-01) Warner, Sherridan; Blaxland, Anneliese; Counoupas, Claudio; Verstraete, Janine; Zampoli, Marco; Marais, Ben J.; Fitzgerald, Dominic A.; Robinson, Paul D.; Triccas, James A.
    Mycobacterium abscessus is a nontuberculous mycobacterium (NTM) of particular concern in individuals with obstructive lung diseases such as cystic fibrosis (CF). Treatment requires multiple drugs and is characterised by high rates of relapse; thus, new strategies to limit infection are urgently required. This study sought to determine how Bacille Calmette-Guérin (BCG) vaccination may impact NTM infection, using a murine model of Mycobacterium abscessus infection and observational data from a non-BCG vaccinated CF cohort in Sydney, Australia and a BCG-vaccinated CF cohort in Cape Town, South Africa. In mice, BCG vaccination induced multifunctional antigen-specific CD up sup T cells circulating in the blood and was protective against dissemination of bacteria to the spleen. Prior infection with M. abscessus afforded the highest level of protection against M. abscessus challenge in the lung, and immunity was characterised by a greater frequency of pulmonary cytokine-secreting CD4 T cells compared to BCG vaccination. In the clinical CF cohorts, the overall rates of NTM sampling during a three-year period were equivalent; however, rates of NTM colonisation were significantly lower in the BCG-vaccinated (Cape Town) cohort, which was most apparent for M. abscessus. This study provides evidence that routine BCG vaccination may reduce M. abscessus colonisation in individuals with CF, which correlates with the ability of BCG to induce multifunctional CD4T cells recognising M. abscessus in a murine model. Further research is needed to determine the optimal strategies for limiting NTM infections in individuals with CF.
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    Developing, implementing, and monitoring tailored strategies for integrated knowledge translation in five sub-Saharan African countries
    (BioMed Central, 2023-09-04) Sell, Kerstin; Jessani, Nasreen S.; Mesfin, Firaol; Rehfuess, Eva A.; Rohwer, Anke; Delobelle, Peter; Balugaba, Bonny E.; Schmidt, Bey-Marrié; Kedir, Kiya; Mpando, Talitha; Niyibizi, Jean B.; Osuret, Jimmy; Bayiga-Zziwa, Esther; Kredo, Tamara; Mbeye, Nyanyiwe M.; Pfadenhauer, Lisa M.
    Background Integrated knowledge translation (IKT) through strategic, continuous engagement with decision-makers represents an approach to bridge research, policy and practice. The Collaboration for Evidence-based Healthcare and Public Health in Africa (CEBHA +), comprising research institutions in Ethiopia, Malawi, Rwanda, South Africa, Uganda and Germany, developed and implemented tailored IKT strategies as part of its multifaceted research on prevention and care of non-communicable diseases and road traffic injuries. The objective of this article is to describe the CEBHA + IKT approach and report on the development, implementation and monitoring of site-specific IKT strategies. Methods We draw on findings derived from the mixed method IKT evaluation (conducted in 2020–2021), and undertook document analyses and a reflective survey among IKT implementers. Quantitative data were analysed descriptively and qualitative data were analysed using content analysis. The authors used the TIDieR checklist to report results in a structured manner. Results Preliminary IKT evaluation data (33 interviews with researchers and stakeholders from policy and practice, and 31 survey responses), 49 documents, and eight responses to the reflective survey informed this article. In each of the five African CEBHA + countries, a site-specific IKT strategy guided IKT implementation, tailored to the respective national context, engagement aims, research tasks, and individuals involved. IKT implementers undertook a variety of IKT activities at varying levels of engagement that targeted a broad range of decision-makers and other stakeholders, particularly during project planning, data interpretation, and output dissemination. Throughout the project, the IKT teams continued to tailor IKT strategies informally and modified the IKT approach by responding to ad hoc engagements and involving non-governmental organisations, universities, and communities. Challenges to using systematic, formalised IKT strategies arose in particular with respect to the demand on time and resources, leading to the modification of monitoring processes. Conclusion Tailoring of the CEBHA + IKT approach led to the inclusion of some atypical IKT partners and to greater responsiveness to unexpected opportunities for decision-maker engagement. Benefits of using systematic IKT strategies included clarity on engagement aims, balancing of existing and new strategic partnerships, and an enhanced understanding of research context, including site-specific structures for evidence-informed decision-making.
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    Enhancing linkage to HIV care in the “Universal Test and Treat” era: Barriers and enablers to HIV care among adults in a high HIV burdened district in KwaZulu-Natal, South Africa
    (BioMed Central, 2023-09-09) Nicol, Edward; Jama, Ngcwalisa A.; Mehlomakulu, Vuyelwa; Hlongwa, Mbuzeleni; Pass, Desiree; Basera, Wisdom; Bradshaw, Debbie
    Ending AIDS by 2030 would depend on how successful health systems are in linking people living with HIV (PLHIV) into care. The World Health Organization recommended the ‘Universal Test and Treat’ (UTT) strategy – initiating all individuals testing positive on antiretroviral therapy (ART) irrespective of their CD4 count and clinical staging. This study aimed to explore the enablers and barriers to linkage to HIV care among adults with a new HIV diagnosis in a high-HIV prevalent rural district in South Africa. A qualitative study was undertaken to explore patients’ perceptions of enablers and barriers of linkage-to-care, using a life-story narration and dialogue approach. In-depth interviews were conducted with 38 HIV-positive participants sampled from a cohort of 1194 HIV-positive patients recruited from December 2017 to June 2018. Participants were selected based on whether they had been linked to care or not within 3 months of positive HIV diagnosis. Interviews were thematically analysed using a general inductive approach. Of the 38 participants, 22 (58%) linked to care within three months of HIV-positive diagnosis. Factors that facilitated or inhibited linkage-to-care were found at individual, family, community, as well as health systems levels. Enablers included a positive HIV testing experience, and assistance from the fieldwork team. Support from family, and friends, as well as prior community-based education about HIV and ART were also noted. Individual factors such as acceptance of HIV status, previous exposure to PLHIV, and fear of HIV progressing, were identified. Barriers to linkage included, denial of HIV status, dislike of taking pills, and preference for alternative medicine. Negative experiences with counselling and health systems inefficiency were also noted as barriers. Perceived stigma and socio-economic factors, such as lack of food or money to visit the clinic were other barriers. Community-based and health system-level interventions would need to focus on clinic readiness in providing patients with necessary and effective health services such as proper and adequate counselling. This could increase the number of patients who link to care. Finally, interventions to improve linkage-to-care should consider a holistic approach, including training healthcare providers, community outreach and the provision of psychological, social, and financial support.
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    Healthcare worker perceived barriers and facilitators to implementing a tuberculosis preventive therapy program in rural South Africa: a content analysis using the consolidated framework for implementation research
    (BioMed Central, 2023-08-30) van de Water, Brittney J.; Wilson, Michael; le Roux, Karl; Gaunt, Ben; Gimbel, Sarah; Ware, Norma C.
    Background South African national tuberculosis (TB) guidelines, in accordance with the World Health Organization, recommend conducting routine household TB contact investigation with provision of TB preventive therapy (TPT) for those who qualify. However, implementation of TPT has been suboptimal in rural South Africa. We sought to identify barriers and facilitators to TB contact investigations and TPT management in rural Eastern Cape, South Africa, to inform the development of an implementation strategy to launch a comprehensive TB program. Methods We collected qualitative data through individual semi-structured interviews with 19 healthcare workers at a district hospital and four surrounding primary-care clinics referring to the hospital. The consolidated framework for implementation research (CFIR) was used to develop interview questions as well as guide deductive content analysis to determine potential drivers of implementation success or failure. Results A total of 19 healthcare workers were interviewed. Identified common barriers included lack of provider knowledge regarding efficacy of TPT, lack of TPT documentation workflows for clinicians, and widespread community resource constraints. Facilitators identified included healthcare workers high interest to learn more about the effectiveness of TPT, interest in problem-solving logistical barriers in provision of comprehensive TB care (including TPT), and desire for clinic and nurse-led TB prevention efforts. Conclusion The use of the CFIR, a validated implementation determinants framework, provided a systematic approach to identify barriers and facilitators to TB household contact investigation, specifically the provision and management of TPT in this rural, high TB burden setting. Specific resources—time, trainings, and evidence—are necessary to ensure healthcare providers feel knowledgeable and competent about TPT prior to prescribing it more broadly. Tangible resources such as improved data systems coupled with political coordination and funding for TPT programming are essential for sustainability.
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    HIV Viral Load Testing in the South African Public Health Setting in the Context of Evolving ART Guidelines and Advances in Technology, 2013 - 2022
    (Multidisciplinary Digital Publishing Institute, 2023-08-22) Hans, Lucia; Cassim, Naseem; Sarang, Somayya; Hardie, Diana; Ndlovu, Silence; Venter, W.D. Francois; Da Silva, Pedro; Stevens, Wendy
    HIV viral load (VL) testing plays a key role in the clinical management of HIV as a marker of adherence and antiretroviral efficacy. To date, national and international antiretroviral treatment recommendations have evolved to endorse routine VL testing. South Africa (SA) has recommended routine VL testing since 2004. Progressively, the centralised HIV VL program managed by its National Health Laboratory Service (NHLS) has undergone expansive growth. Retrospective de-identified VL data from 2013 to 2022 were evaluated to review program performance. Test volumes increased from 1,961,720 performed in 2013 to 45,334,864 in 2022. The median total in-laboratory turnaround time (TAT) ranged from 94 h (2015) to 51 h (2022). Implementation of two new assays improved median TATs in all laboratories. Samples of VL greater than 1000 copies/mL declined steadily. Despite initial increases, samples of fewer than 50 copies/mL stagnated at about 70% from 2019 and declined to 68% in 2022. Some variations between assays were observed. Overall, the SA VL program is successful. The scale of the VL program, the largest of its kind in the world by some margin, provides lessons for future public health programs dependent on laboratories for patient outcome and program performance monitoring.
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    How South Africa Used National Cycle Threshold (Ct) Values to Continuously Monitor SARS-CoV-2 Laboratory Test Quality
    (Multidisciplinary Digital Publishing Institute, 2023-08-01) Scott, Lesley Erica; Hsiao, Nei-yuan; Dor, Graeme; Hans, Lucia; Marokane, Puleng; da Silva, Manuel Pedro; Preiser, Wolfgang; Vreede, Helena; Tsoka, Jonathan; Mlisana, Koleka; Stevens, Wendy Susan
    The high demand for SARS-CoV-2 tests but limited supply to South African laboratories early in the COVID-19 pandemic resulted in a heterogenous diagnostic footprint of open and closed molecular testing platforms being implemented. Ongoing monitoring of the performance of these multiple and varied systems required novel approaches, especially during the circulation of variants. The National Health Laboratory Service centrally collected cycle threshold (Ct) values from 1,497,669 test results reported from 6 commonly used PCR assays in 36 months, and visually monitored changes in their median Ct within a 28-day centered moving average for each assays’ gene targets. This continuous quality monitoring rapidly identified delayed hybridization of in the Allplex & trade; SARS-CoV-2 assay due to the Delta (B.1.617.2) variant; gene target failure in the TaqPath & trade; COVID-19 assay due to B.1.1.7 (Alpha) and the B.1.1.529 (Omicron); and recently gene delayed hybridization in the Xpress SARS-CoV-2 due to XBB.1.5. This near ;real-time; monitoring helped inform the need for sequencing and the importance of multiplex molecular nucleic acid amplification technology designs used in diagnostics for patient care. This continuous quality monitoring approach at the granularity of Ct values should be included in ongoing surveillance and with application to other disease use cases that rely on molecular diagnostics.
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    Medical interns in district health services: an evaluation of the new family medicine rotation in the Western Cape of South Africa
    (BioMed Central, 2023-09-04) Hutton, Lauren; Jenkins, Louis S.; Mash, Robert; von Pressentin, Klaus; Reid, Steve; Morgan, Jennie; Kapp, Paul
    Background In 2021, South Africa introduced a 6-month internship rotation in family medicine, in the second year of a 2-year internship programme for newly qualified doctors. This was a major change from the previous 3-months training in family medicine, and expanded the training platform to smaller district hospitals and primary health care (PHC) facilities, many of which had never had interns. The medical disciplines in South Africa needed to know if this change in the internship programme was worthwhile and successful. The aim of this study was to assess the new family medicine rotation for medical interns at district health facilities in the Western Cape Province. Methods Descriptive exploratory qualitative research included six intern programmes across the province. Purposeful sampling identified a heterogeneous group with maximum variation in experience. Overall, eight interns, four managers, four supervisors and four intern curators were included. Individual semi-structured interviews were audio-recorded and the transcripts were thematically analysed using the framework method and Atlas-ti software. Results Four major themes emerged around the varied structure and organisational characteristics of the rotations, the orientation and arrival of interns, their learning during the rotation, and impact on health services. A programme theory was developed that defined the key inputs (i.e. infrastructure, communication, orientation, preparation, prior learning and guidelines), processes (i.e. model of the rotation, clinical training and supervision, clinical teaching), outputs (i.e. more independent decision making, approach to undifferentiated problems, approach to chronic care and continuity, development of procedural skills, approach to sequential coordination of care and referrals, working in a multidisciplinary team and inter-professional learning, integration of multiple competencies, as well as becoming more person and community orientated). Conclusions The new rotation in family medicine was positively experienced by most interns, supervisors and managers. It should lead to improved quality of care, better preparation for obligatory community service, and an increased likelihood of considering a career in district level health services. This study will form part of an exploratory sequential mixed methods study that incorporates the key issues into a questionnaire for a descriptive survey of all interns in a subsequent study.
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    Meta-analysis of African ancestry genome-wide association studies identified novel locus and validates multiple loci associated with kidney function
    (BioMed Central, 2023-08-29) Kintu, Christopher; Soremekun, Opeyemi; Machipisa, Tafadzwa; Mayanja, Richard; Kalyesubula, Robert; Bagaya, Bernard S.; Jjingo, Daudi; Chikowore, Tinashe; Fatumo, Segun
    Despite recent efforts to increase diversity in genome-wide association studies (GWASs), most loci currently associated with kidney function are still limited to European ancestry due to the underlying sample selection bias in available GWASs. We set out to identify susceptibility loci associated with estimated glomerular filtration rate (eGFRcrea) in 80027 individuals of African-ancestry from the UK Biobank (UKBB), Million Veteran Program (MVP), and Chronic Kidney Disease genetics (CKDGen) consortia. We identified 8 lead SNPs, 7 of which were previously associated with eGFR in other populations. We identified one novel variant, rs77408001 which is an intronic variant mapped to the ELN gene. We validated three previously reported loci at GATM-SPATA5L1, SLC15A5 and AGPAT3. Fine-mapping analysis identified variants rs77121243 and rs201602445 as having a 99.9% posterior probability of being causal. Our results warrant designing bigger studies within individuals of African ancestry to gain new insights into the pathogenesis of Chronic Kidney Disease (CKD), and identify genomic variants unique to this ancestry that may influence renal function and disease.
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    Towards Evidence-Based Implementation of Pharmacogenomics in Southern Africa: Comorbidities and Polypharmacy Profiles across Diseases
    (Multidisciplinary Digital Publishing Institute, 2023-07-26) Soko, Nyarai Desiree; Muyambo, Sarudzai; Dandara, Michelle T. L.; Kampira, Elizabeth; Blom, Dirk; Jones, Erika S. W.; Rayner, Brian; Shamley, Delva; Sinxadi, Phumla; Dandara, Collet
    Pharmacogenomics may improve patient care by guiding drug selection and dosing; however, this requires prior knowledge of the pharmacogenomics of drugs commonly used in a specific setting. The aim of this study was to identify a preliminary set of pharmacogenetic variants important in Southern Africa. We describe comorbidities in 3997 patients from Malawi, South Africa, and Zimbabwe. These patient cohorts were included in pharmacogenomic studies of anticoagulation, dyslipidemia, hypertension, HIV and breast cancer. The 20 topmost prescribed drugs in this population were identified. Using the literature, a list of pharmacogenes vital in the response to the top 20 drugs was constructed leading to drug–gene pairs potentially informative in translation of pharmacogenomics. The most reported morbidity was hypertension (58.4%), making antihypertensives the most prescribed drugs, particularly amlodipine. Dyslipidemia occurred in 31.5% of the participants, and statins were the most frequently prescribed as cholesterol-lowering drugs. HIV was reported in 20.3% of the study participants, with lamivudine/stavudine/efavirenz being the most prescribed antiretroviral combination. Based on these data, pharmacogenes of immediate interest in Southern African populations include ABCB1, CYP2B6, CYP2C9, CYP2C19, CYP2D6 CYP3A4, CYP3A5, SLC22A1, SLCO1B1 and UGT1A1. Variants in these genes are a good starting point for pharmacogenomic translation programs in Southern Africa.
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    Understanding diarrhoeal diseases in response to climate variability and drought in Cape Town, South Africa: a mixed methods approach
    (BioMed Central, 2023-08-18) Lee, Tristan T.; Dalvie, Mohamed A.; Röösli, Martin; Merten, Sonja; Kwiatkowski, Marek; Mahomed, Hassan; Sweijd, Neville; Cissé, Guéladio
    Background The climate of southern Africa is expected to become hotter and drier with more frequent severe droughts and the incidence of diarrhoea to increase. From 2015 to 2018, Cape Town, South Africa, experienced a severe drought which resulted in extreme water conservation efforts. We aimed to gain a more holistic understanding of the relationship between diarrhoea in young children and climate variability in a system stressed by water scarcity. Methods Using a mixed-methods approach, we explored diarrhoeal disease incidence in children under 5 years between 2010 to 2019 in Cape Town, primarily in the public health system through routinely collected diarrhoeal incidence and weather station data. We developed a negative binomial regression model to understand the relationship between temperature, precipitation, and relative humidity on incidence of diarrhoea with dehydration. We conducted in-depth interviews with stakeholders in the fields of health, environment, and human development on perceptions around diarrhoea and health-related interventions both prior to and over the drought, and analysed them through the framework method. Results From diarrhoeal incidence data, the diarrhoea with dehydration incidence decreased over the decade studied, e.g. reduction of 64.7% in 2019 [95% confidence interval (CI): 5.5–7.2%] compared to 2010, with no increase during the severe drought period. Over the hot dry diarrhoeal season (November to May), the monthly diarrhoea with dehydration incidence increased by 7.4% (95% CI: 4.5–10.3%) per 1 °C increase in temperature and 2.6% (95% CI: 1.7–3.5%) per 1% increase in relative humidity in the unlagged model. Stakeholder interviews found that extensive and sustained diarrhoeal interventions were perceived to be responsible for the overall reduction in diarrhoeal incidence and mortality over the prior decade. During the drought, as diarrhoeal interventions were maintained, the expected increase in incidence in the public health sector did not occur. Conclusions We found that that diarrhoeal incidence has decreased over the last decade and that incidence is strongly influenced by local temperature and humidity, particularly over the hot dry season. While climate change and extreme weather events especially stress systems supporting vulnerable populations such as young children, maintaining strong and consistent public health interventions helps to reduce negative health impacts.