Tuberculosis infection control practices in a high-burden metro in South Africa : a perpetual bane for efficient primary health care service delivery

Background: Tuberculosis (TB) prevention, including infection control, is a key element in the strategy to end the global TB epidemic. While effective infection control requires all health system components to function well, this is an area that has not received sufficient attention in South Africa despite the availability of policy and guidelines. Aim: To describe the state of implementation of TB infection control measures in a high-burden metro in South Africa. Setting: The research was undertaken in a high TB-and HIV-burdened metropolitan area of South Africa. More specifically, the study sites were primary health care facilities (PHC), that among other services also diagnosed TB. Methods: A cross-sectional survey, focusing on the World Health Organization levels of infection control, which included structured interviews with nurses providing TB diagnosis and treatment services as well as observations, at all 41 PHC facilities in a high TB-burdened and HIV-burdened metro of South Africa. Results: Tuberculosis infection control was poorly implemented, with few facilities scoring 80% and above on compliance with infection control measures. Facility controls: 26 facilities (63.4%) had an infection control committee and 12 (29.3%) had a written infection control plan. Administrative controls: 26 facilities (63.4%) reported separating coughing and non-coughing patients, while observations revealed that only 11 facilities (26.8%) had separate waiting areas for (presumptive) TB patients. Environmental controls: most facilities used open windows for ventilation (n = 30; 73.2%); however, on the day of the visit, only 12 facilities (30.3%) had open windows in consulting rooms. Personal protective equipment: 9 facilities (22%) did not have any disposable respirators in stock and only 9 respondents (22%) had undergone fit testing. The most frequently reported barrier to implementing good TB infection control practices was lack of equipment (n = 22; 40%) such as masks and disposable respirators, as well as the structure or layout of the PHC facilities. The main recommendation to improve TB infection control was education for patients and health care workers (n = 18; 33.3%). Conclusion: All levels of the health care system should be engaged to address TB prevention and infection control in PHC facilities. Improved infection control will address the nosocomial spread of TB in health facilities and keep health care workers and patients safe from infection

Patient- and delivery-level factors related to acceptance of HIV counseling and testing services among tuberculosis patients in South Africa: a qualitative study with community health workers and program managers

<p>Abstract</p> <p>Background</p> <p>South Africa has a high tuberculosis (TB)-human immunodeficiency virus (HIV) coinfection rate of 73%, yet only 46% of TB patients are tested for HIV. To date, relatively little work has focused on understanding why TB patients may not accept effective services or participate in programs that are readily available in healthcare delivery systems. The objective of the study was to explore barriers to and facilitators of participation in HIV counseling and testing (HCT) among TB patients in the Free State Province, from the perspective of community health workers and program managers who offer services to patients on a daily basis. These two provider groups are positioned to alter the delivery of HCT services in order to improve patient participation and, ultimately, health outcomes.</p> <p>Methods</p> <p>Group discussions and semistructured interviews were conducted with 40 lay counselors, 57 directly observed therapy (DOT) supporters, and 13 TB and HIV/acquired immune deficiency syndrome (AIDS) program managers in the Free State Province between September 2007 and March 2008. Sessions were audio-recorded, transcribed, and thematically analyzed.</p> <p>Results</p> <p>The themes emerging from the focus group discussions and interviews included four main suggested barrier factors: (1) fears of HIV/AIDS, TB-HIV coinfection, death, and stigma; (2) perceived lack of confidentiality of HIV test results; (3) staff shortages and high workload; and (4) poor infrastructure to encourage, monitor, and deliver HCT. The four main facilitating factors emerging from the group and individual interviews were (1) encouragement and motivation by health workers, (2) alleviation of health worker shortages, (3) improved HCT training of professional and lay health workers, and (4) community outreach activities.</p> <p>Conclusions</p> <p>Our findings provide insight into the relatively low acceptance rate of HCT services among TB patients from the perspective of two healthcare workforce groups that play an integral role in the delivery of effective health services and programs. Community health workers and program managers emphasized several patient- and delivery-level factors influencing acceptance of HCT services.</p

Considerations for preparing a randomized population health intervention trial: lessons from a South African–Canadian partnership to improve the health of health workers

Background: Community-based cluster-randomized controlled trials (RCTs) are increasingly being conducted to address pressing global health concerns. Preparations for clinical trials are well-described, as are the steps for multi-component health service trials. However, guidance is lacking for addressing the ethical and logistic challenges in (cluster) RCTs of population health interventions in low- and middle-income countries. Objective: We aimed to identify the factors that population health researchers must explicitly consider when planning RCTs within North–South partnerships. Design: We reviewed our experiences and identified key ethical and logistic issues encountered during the pre-trial phase of a recently implemented RCT. This trial aimed to improve tuberculosis (TB) and Human Immunodeficiency Virus (HIV) prevention and care for health workers by enhancing workplace assessment capability, addressing concerns about confidentiality and stigma, and providing onsite counseling, testing, and treatment. An iterative framework was used to synthesize this analysis with lessons taken from other studies. Results: The checklist of critical factors was grouped into eight categories: 1) Building trust and shared ownership; 2) Conducting feasibility studies throughout the process; 3) Building capacity; 4) Creating an appropriate information system; 5) Conducting pilot studies; 6) Securing stakeholder support, with a view to scale-up; 7) Continuously refining methodological rigor; and 8) Explicitly addressing all ethical issues both at the start and continuously as they arise. Conclusion: Researchers should allow for the significant investment of time and resources required for successful implementation of population health RCTs within North–South collaborations, recognize the iterative nature of the process, and be prepared to revise protocols as challenges emerge

Impacts of 1.5°C Global Warming on Natural and Human Systems

An IPCC Special Report on the impacts of global warming of 1.5°C above pre-industrial levels and related global greenhouse gas emission pathways, in the context of strengthening the global response to the threat of climate change, sustainable development, and efforts to eradicate povert

FungalTraits:A user-friendly traits database of fungi and fungus-like stramenopiles

The cryptic lifestyle of most fungi necessitates molecular identification of the guild in environmental studies. Over the past decades, rapid development and affordability of molecular tools have tremendously improved insights of the fungal diversity in all ecosystems and habitats. Yet, in spite of the progress of molecular methods, knowledge about functional properties of the fungal taxa is vague and interpretation of environmental studies in an ecologically meaningful manner remains challenging. In order to facilitate functional assignments and ecological interpretation of environmental studies we introduce a user friendly traits and character database FungalTraits operating at genus and species hypothesis levels. Combining the information from previous efforts such as FUNGuild and Fun(Fun) together with involvement of expert knowledge, we reannotated 10,210 and 151 fungal and Stramenopila genera, respectively. This resulted in a stand-alone spreadsheet dataset covering 17 lifestyle related traits of fungal and Stramenopila genera, designed for rapid functional assignments of environmental studies. In order to assign the trait states to fungal species hypotheses, the scientific community of experts manually categorised and assigned available trait information to 697,413 fungal ITS sequences. On the basis of those sequences we were able to summarise trait and host information into 92,623 fungal species hypotheses at 1% dissimilarity threshold

The genetic architecture of the human cerebral cortex

The cerebral cortex underlies our complex cognitive capabilities, yet little is known about the specific genetic loci that influence human cortical structure. To identify genetic variants that affect cortical structure, we conducted a genome-wide association meta-analysis of brain magnetic resonance imaging data from 51,665 individuals. We analyzed the surface area and average thickness of the whole cortex and 34 regions with known functional specializations. We identified 199 significant loci and found significant enrichment for loci influencing total surface area within regulatory elements that are active during prenatal cortical development, supporting the radial unit hypothesis. Loci that affect regional surface area cluster near genes in Wnt signaling pathways, which influence progenitor expansion and areal identity. Variation in cortical structure is genetically correlated with cognitive function, Parkinson's disease, insomnia, depression, neuroticism, and attention deficit hyperactivity disorder

Impact of COVID-19 on cardiovascular testing in the United States versus the rest of the world

Objectives: This study sought to quantify and compare the decline in volumes of cardiovascular procedures between the United States and non-US institutions during the early phase of the coronavirus disease-2019 (COVID-19) pandemic. Background: The COVID-19 pandemic has disrupted the care of many non-COVID-19 illnesses. Reductions in diagnostic cardiovascular testing around the world have led to concerns over the implications of reduced testing for cardiovascular disease (CVD) morbidity and mortality. Methods: Data were submitted to the INCAPS-COVID (International Atomic Energy Agency Non-Invasive Cardiology Protocols Study of COVID-19), a multinational registry comprising 909 institutions in 108 countries (including 155 facilities in 40 U.S. states), assessing the impact of the COVID-19 pandemic on volumes of diagnostic cardiovascular procedures. Data were obtained for April 2020 and compared with volumes of baseline procedures from March 2019. We compared laboratory characteristics, practices, and procedure volumes between U.S. and non-U.S. facilities and between U.S. geographic regions and identified factors associated with volume reduction in the United States. Results: Reductions in the volumes of procedures in the United States were similar to those in non-U.S. facilities (68% vs. 63%, respectively; p = 0.237), although U.S. facilities reported greater reductions in invasive coronary angiography (69% vs. 53%, respectively; p < 0.001). Significantly more U.S. facilities reported increased use of telehealth and patient screening measures than non-U.S. facilities, such as temperature checks, symptom screenings, and COVID-19 testing. Reductions in volumes of procedures differed between U.S. regions, with larger declines observed in the Northeast (76%) and Midwest (74%) than in the South (62%) and West (44%). Prevalence of COVID-19, staff redeployments, outpatient centers, and urban centers were associated with greater reductions in volume in U.S. facilities in a multivariable analysis. Conclusions: We observed marked reductions in U.S. cardiovascular testing in the early phase of the pandemic and significant variability between U.S. regions. The association between reductions of volumes and COVID-19 prevalence in the United States highlighted the need for proactive efforts to maintain access to cardiovascular testing in areas most affected by outbreaks of COVID-19 infection

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Factors Associated with Limited Vaccine Literacy: Lessons Learnt from COVID-19

Compared to many other developed countries, South Africa has a lower uptake of COVID-19 vaccinations. Although not widely researched, there is evidence that vaccine literacy (VL) is positively associated with vaccination uptake. Therefore, this study aimed to assess levels of VL among the adult population in South Africa, as well as to identify factors associated with limited VL. A cross-sectional, anonymous online survey was conducted during September 2021. The survey, which included the standardized Health Literacy about Vaccination in adulthood (HLVa) Scale, was widely advertised, yielding a total of 10,466 respondents. The average scores for the two HLVa sub-scales were relatively high: functional (M = 2.841, SD 0.799) and interactive-critical (M = 3.331, SD 0.559) VL. A proposed &lsquo;limited&rsquo; VL score (score value &le; 2.50) was observed in 40% of respondents for functional literacy and 8.2% of respondents for interactive-critical literacy. The main factors associated with limited VL included lower levels of education, lower socio-economic status, not being vaccinated against COVID-19, self-identifying as Black/African or Colored (i.e., people of mixed ethnic descent), having poorer health, and being a woman. The significant association between VL and vaccination uptake provides an impetus for policy makers such as the South African Department of Health to promote VL in the attempt to increase COVID-19 vaccination uptake

Post-Traumatic Stress and Coping Strategies of South African Nurses during the Second Wave of the COVID-19 Pandemic

Prior to the 2019 novel coronavirus (COVID-19) outbreak, the South African healthcare system was already under severe strain due to amongst others, a lack of human resources, poor governance and management, and an unequal distribution of resources among provinces and between the public and private healthcare sectors. At the center of these challenges are nurses, the backbone of the healthcare system, and the first point of call for most patients in the country. This research investigated post-traumatic stress and coping strategies of nurses during the second wave of COVID-19 in the country. A structured self-administered questionnaire captured the biographic characteristics, perceived risk factors for COVID-19, and views on infection control of 286 nurses Data were subjected to descriptive and binomial logistic regression analyses. More than four in every 10 nurses screened positive for higher levels of post-traumatic disorder (PTSD). Self-reported risk for contracting COVID-19 mainly centered on being a health worker and patients’ non-adherence to infection prevention guidelines. Unpreparedness to manage COVID-19 patients, poorer health, and avoidant coping were associated with PTSD. Nurses voiced a need for emotional support and empathy from managers. Emotional, psychological, and debriefing intervention sessions that focus on positive coping strategies to actively address stress are recommended