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Recent Submissions

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    Molecular Characterisation and Population Structure Determination of Streptococcus pneumoniae in South Africa using Whole-Genome Analysis
    (University of the Witwatersrand, Johannesburg, 2025) Lekhuleni, Cebile Natasha Nolwazi
    Pneumococcal conjugate vaccines (PCV) have effectively reduced overall invasive pneumococcal disease (IPD) and antibiotic-nonsusceptible IPD in many countries. Ongoing invasive disease due to residual vaccine-targeted serotypes (VT) and non-vaccine serotypes (NVT) after PCV introduction remains a global concern. In South Africa, seven-valent PCV (PCV7) was introduced in 2009 and was replaced by 13-valent PCV (PCV13) in 2011. We aimed to evaluate changes in IPD lineages and antibiotic-nonsusceptibility before and after PCV introduction in South Africa. We analysed 54,199 IPD cases reported from 2005–2020 as part of the national, laboratory- based surveillance program. A randomly selected subset of approximately 4800 isolates underwent whole-genome sequencing. We determined in silico serotypes, sequence types, global pneumococcal sequence cluster (GPSC) lineages, and antimicrobial resistance determinants from the genomes of 4669 isolates. Vaccine periods were defined as pre-PCV (2005–2008), PCV7 (2009–2010), early-PCV13 (2011–2014), and late-PCV13 (2015–2020). Penicillin multidrug resistance (penicillin-MDR) was defined as nonsusceptibility to penicillin plus ≥2 other antibiotic classes. Other MDR was defined as nonsusceptibility to ≥3 antibiotic classes. Vaccine-type and non-vaccine-type lineages were defined as expressing ≥50% VTs and >50% NVTs, respectively, before PCV introduction. In silico serotype and lineage diversity trends were determined using Simpson’s diversity index (SDI). vii Significant incidence reductions occurred among vaccine-type lineages in the late-PCV13 period compared to the pre-PCV period. The five most common serotypes in the late-PCV13 period were NVTs 8, 12F, 15B/C, and residual VTs 19A and 19F, mainly expressed by GPSC3 (non-vaccine-type lineage), GPSC26 and GPSC56 (non-vaccine-type and vaccine- type), GPSC48 (non-vaccine-type), GPSC17 (vaccine-type), and GPSC1/21 (vaccine-types), respectively. Compared to the baseline period, significantly higher serotype diversity estimates were observed in the early-PCV13 period, with the highest estimate occurring during the PCV13 introduction year (2011, SDI 0.993, 95% confidence interval [CI] 0.991– 0.995). A significant increase in lineage diversity was also observed from the PCV7 period to the early-PCV13 period (SDI: 0.954, 95% CI 0.948–0.961 vs 0.965, 0.962–0.969) supporting intervention-driven population structure perturbation. Overall antibiotic-nonsusceptible IPD declined across the study period. Residual PCV13 serotypes 19A and 19F contributed 44% (977/2236) of penicillin-cotrimoxazole or penicillin-MDR IPD in the late-PCV13 period. Among NVTs, serotypes 10A, 15A, 15B/C, 16F, 23B, and 35B were common causes (61.9%, 545/881) of penicillin-cotrimoxazole or penicillin-MDR IPD after PCV13 introduction in children and adults. Overall, NVT 8 was the most common cause of IPD after PCV13 introduction with significant incidence increases among children ≤5 years (incidence rate ratio 2.3, 95% CI 1.3–4.1) and adults >64 years (2.8, 1.1–8.3) when comparing pre-PCV versus late-PCV13 periods. NVT 8 (GPSC3, sequence type 53) IPD was predicted to continue increasing despite remaining largely susceptible to first-line treatment. Incidence of IPD declined in all ages in South Africa after PCV introduction. Similarly, overall nonsusceptible IPD declined in the post-PCV era. Vaccine-type lineages, particularly those expressing VTs 19A (GPSC17) and 19F (GPSC21) continued to circulate after PCV introduction and were important contributors to penicillin-nonsusceptible IPD in addition to viii some pre-existing non-vaccine-type lineages. GPSC3 (NVT 8) caused substantial disease in children and adults in the post-PCV era. In 2024, South Africa switched to a lower-valency vaccine PCV10 (Pneumosil, Serum Institute of India). Given the expansion of non-vaccine- type lineages and the persistence of vaccine-type lineages that are predominantly expressing their NVT counterparts following PCV use, it is crucial to monitor the impact of this switch on the pneumococcal population structure and AMR to inform future PCV formulation considerations.
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    The CARE Principles for Indigenous Data Governance
    (Ubiquity Press, 2020) Carroll, Stephanie; Garba, Ibrahim; Figueroa-Rodríguez, Oscar; Holbrook, Jarita; Lovett, Raymond; Materechera, Simeon; Parsons, Mark; Raseroka, Kay; Rodriguez-Lonebear, Desi; Rowe, Robyn; Sara, Rodrigo; Walker, Jennifer; Anderson, Jane; Hudson, Maui
    Concerns about secondary use of data and limited opportunities for benefit-sharing have focused attention on the tension that Indigenous communities feel between (1) protecting Indigenous rights and interests in Indigenous data (including traditional knowledge) and (2) supporting open data, machine learning, broad data sharing, and big data initiatives. The International Indigenous Data Sovereignty Interest Group (within the Research Data Alliance) is a network of nation-state based Indigenous data sovereignty networks and individuals that developed the ‘CARE Principles for Indigenous Data Governance’ (Collective Benefit, Authority to Control, Responsibility, and Ethics) in consultation with Indigenous Peoples, scholars, non-profit organizations, and governments. The CARE Principles are people and purpose-oriented, reflecting the crucial role of data in advancing innovation, governance, and self-determination among Indigenous Peoples. The Principles complement the existing data-centric approach represented in the ‘FAIR Guiding Principles for scientific data management and stewardship’ (Findable, Accessible, Interoperable, Reusable). The CARE Principles build upon earlier work by the Te Mana Raraunga Maori Data Sovereignty Network, US Indigenous Data Sovereignty Network, Maiamnayri Wingara Aboriginal and Torres Strait Islander Data Sovereignty Collective, and numerous Indigenous Peoples, nations, and communities. The goal is that stewards and other users of Indigenous data will ‘Be FAIR and CARE.’ In this first formal publication of the CARE Principles, we articulate their rationale, describe their relation to the FAIR Principles, and present examples of their application.
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    The strategies to enable, and challenges faced with implementation of quality electronic health records in South Africa
    (University of the Witwatersrand, Johannesburg, 2025) Zharima, Campion
    Background: As many middle-income countries move towards universal health coverage, the expansion of health care services using public funds has become more common. Electronic health records (EHRs) are critical for monitoring provider performance, enabling strategic purchasing and guiding the allocation of health care funds. South Africa, in its pursuit of the national health insurance (NHI), envisions EHRs as essential for informing purchasing decisions and tracking health outcomes. Despite the country’s policy efforts, the progress in implementation of EHRs has been slow. Primary aim: To examine the implementation challenges and identify potential strategies to ensure high quality EHRs in South Africa. Methods: Data were collected between 2021 and 2023 using qualitative methods. At first, in- depth interviews were conducted with 18 key stakeholders, including academics, private sector managers, and government officials, to explore the barriers and facilitators of EHR implementation in South Africa. Secondly, 38 interviews were conducted with managers, implementers, and end-users to investigate the stalling of an electronic health record system, using the Consolidated Framework for Implementation Research (CFIR). Lastly, through a rapid review of global evidence examined 41 studies on EHR implementation to identify effective end- user engagement strategies for EHR adoption in healthcare settings, guided by the Normalization Process Theory (NPT). Thematic analysis was applied in all data sets. Findings: Results revealed that while South Africa has a favorable policy landscape, the capacity and resources for a national EHR implementation, efforts have been hindered by leadership gaps, limited technical expertise, and insufficient investment in necessary infrastructure. However, the Western Cape, a province of South Africa, demonstrated significant progress, having developed a functioning EHR system through efforts spanning over two decades. A case study of a piloted EHR system further revealed some of the factors and complexities of implementation in South Africa. In this case, while the system initially showed promise, supported by strong stakeholder engagement and consultative development, it eventually stalled due to external factors such as changes in developers, funding cuts and lack of provincial support. xi Moreover, political interference in key appointments led to corruption and mismanagement of funds, further highlighting how contextual and systemic barriers can undermine a well-designed and adopted system. Lastly, the review also identified effective user engagement strategies for successful user adoption, which include early user involvement, tailored training, and continuous technical support. Moreover, the successful adoption of EHRs is best achieved when engagement strategies aligned with NPT principles of coherence, cognitive participation, collective action, and reflexive monitoring. These principles guide implementers in ensuring that users understand the purpose of the system, actively engage in learning how to use it, collaborate and continuously contribute to improving it. Conclusion: This study identified the multifaceted barriers and facilitators shaping implementation of EHRs in South Africa. The findings emphasize the need for balancing between top-down and bottom-up approaches through integrating strong policy leadership with meaningful stakeholder engagement to navigate contextual and systemic challenges. Together, a top-down approach provides centralized and strategic direction with resource allocation while bottom-up fosters user engagement which promotes adaptability and local ownership. To advance EHR implementation, it is essential to address leadership gaps, investing in infrastructure, creating a pathway for system interoperability and adopting user centered design principles are critical steps to achieving a robust national electronic health record system, a key pillar in realizing Suth Africa’s vision for national health insurance.
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    Gliogenesis in the Male Japanese Quail (Coturnix japonica) Brain
    (University of the Witwatersrand, Johannesburg, 2025) Shehu, Asmau Muhammad; Ihunwo, Amadi
    Gliogenesis is a process that involves the generation of new glial cells (astrocytes, oligodendrocytes, and microglia) from neural stem cells (NSCs) or neural progenitor cells (NPCs) in both developing and adult individuals. The process of gliogenesis is essential for the preservation of the functional integrities of the central nervous system (CNS) from development to adulthood. The present thesis aimed to study gliogenesis and neurogenesis in the male Japanese quail (Coturnix japonica) brain at three different developmental stages: juvenile, subadult, and adult. This line of study used a multidisciplinary approach including histology (Nissl and myelin silver staining), revealed the cytoarchitecture in different brain regions, myelination fibers and patterns. Immunohistochemistry (IHC) using markers for neural and glial progenitors (SOX2), cell proliferation (PCNA), astrocytes (GFAP, S100A1), oligodendrocytes (OLIG2), microglia (IBA-1) and immature neurons (DCX). Immunofluorescence double-labeling IHC, which revealed colocalization of neural stem cells and GFAP the in ventricular zones, pial surface, optic tectum and cerebellum. Transmission electron microscopy (TEM) revealed detailed ultrastructural insights into mitochondria, glial and neuronal features. Findings highlight the distribution, characterization, timing, regional differences, and cellular mechanisms of gliogenesis, contributing to a deeper understanding of avian brain development. The study also showed dynamic neuronal and glial population changes during brain maturation and indicate a process of temporal and spatial regulation of gliogenesis during brain maturation. These insights contribute to a greater understanding of cellular dynamics within the quail brain and, thus, are important for our more comprehensive understanding of avian development and brain evolution.
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    Journal indexing and scientific impact of Africa’s public health research: current status, barriers, facilitators and opportunities
    (University of the Witwatersrand, Johannesburg, 2025) Selemani, Apatsa
    Background: African health research has limited global visibility due to underrepresentation of African journals in major citation databases, which reduces their scholarly impact. However, there is limited evidence concerning barriers and enablers of African health science journal indexing, hindering efforts to improve their visibility and impact. Aim: This thesis sought to investigate challenges, enablers, and opportunities for improving journal indexing and the scientific impact of African public health research. Methodology: A sequential mixed-methods approach was used, incorporating a scoping review, scientometric analysis, analytical cross-sectional analysis, in-depth interviews (IDIs), and a discrete choice experiment (DCE). The scoping review analyzed bibliometric and scientometric studies of African health research. The scientometric and analytical cross-sectional studies utilized the web scraping technique, and manual collection of journal metrics for the former, and country- specific data for the latter. The analytical cross-sectional study compared African health science journals with western European health science journals. The IDIs purposively recruited 18 editors from 7 African countries while the DCE recruited 86 African journal editors. The study was guided by the research impact payback model and the post-colonial theory. Findings: The study found limited representation of African journals in indexing services such as Web of Science, Scopus, and PubMed. Some countries were entirely absent in the indexes, highlighting the restricted visibility of African health research. A country’s economic status was a significant determinant of journal indexing between African and western European health science journals. Barriers and facilitators were multifaceted; structural inequalities influenced by post- colonial legacies that shaped funding, infrastructure, and access to indexing services. Development of alternative inclusive research evaluation indicators, and indexing services for African context, was seen as an important direction to take. Conclusion: The study highlights the need for systemic reforms to address existing structural inequities in knowledge production and dissemination. It recommends developing inclusive research evaluation indicators and establishing context-specific indexing platforms to enhance the visibility and impact of African health research.