Correction: Molecular detection of airborne Emergomyces africanus, a thermally dimorphic fungal pathogen, in Cape Town, South Africa.
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ABSTRACT:
SUBMITTER: PLOS Neglected Tropical Diseases Staff
PROVIDER: S-EPMC5931619 | biostudies-literature | 2018 May
REPOSITORIES: biostudies-literature
Publications
Correction: Molecular detection of airborne Emergomyces africanus, a thermally dimorphic fungal pathogen, in Cape Town, South Africa.
PLoS neglected tropical diseases 20180502 5
[This corrects the article DOI: 10.1371/journal.pntd.0006174.]. ...[more]
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Project description:Emergomyces africanus is a thermally dimorphic fungus that causes a systemic mycosis in immunocompromised persons in South Africa. Infection is presumed to follow inhalation of airborne propagules. We developed a quantitative PCR protocol able to detect as few as 5 Es. africanus propagules per day. Samples were collected in Cape Town, South Africa over 50 weeks by a Burkard spore trap with an alternate orifice. We detected Es. africanus in air samples from 34 days (10%) distributed over 11 weeks. These results suggest environmental exposure to airborne Es. africanus propagules occurs more commonly in endemic areas than previously appreciated.
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Project description:Cape Town was the first city in South Africa to experience the full impact of the coronavirus disease 2019 (COVID-19) pandemic. We acquired samples from all suspected cases and their contacts during the first month of the pandemic from Tygerberg Hospital. Nanopore sequencing generated SARS-CoV-2 whole genomes. Phylogenetic inference with maximum likelihood and Bayesian methods were used to determine lineages that seeded the local epidemic. Three patients were known to have travelled internationally and an outbreak was detected in a nearby supermarket. Sequencing of 50 samples produced 46 high-quality genomes. The sequences were classified as lineages: B, B.1, B.1.1.1, B.1.1.161, B.1.1.29, B.1.8, B.39, and B.40. All the sequences from persons under investigation (PUIs) in the supermarket outbreak (lineage B.1.8) fall within a clade from the Netherlands with good support (p > 0.9). In addition, a new mutation, 5209A>G, emerged within the Cape Town cluster. The molecular clock analysis suggests that this occurred around 13 March 2020 (95% confidence interval: 9-17 March). The phylogenetic reconstruction suggests at least nine early introductions of SARS-CoV-2 into Cape Town and an early localized transmission in a shopping environment. Genomic surveillance was successfully used to investigate and track the spread of early introductions of SARS-CoV-2 in Cape Town.
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Project description:This paper analyzes whether children born to teen mothers in Cape Town, South Africa are disadvantaged in terms of their health outcomes because their mother is a teen. Exploiting the longitudinal nature of the Cape Area Panel Study, we assess whether observable differences between teen mothers and slightly older mothers can explain why first-born children of teen mothers appear disadvantaged. Our balanced regressions indicate that observed characteristics cannot explain the full extent of disadvantage of being born to a teen mother, with children born to teen mothers continuing to have significantly worse child health outcomes, especially among coloured children. In particular, children born to teens are more likely to be underweight at birth and to be stunted with the disadvantage for coloured children four times the size for African children.
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Project description:This paper reports a study from Cape Town, South Africa, that tested an existing framework of everyday health system resilience (EHSR) in examining how a local health system responded to the chronic stress of large-scale organizational change. Over two years (2017-18), through cycles of action-learning involving local managers and researchers, the authorial team tracked the stress experienced, the response strategies implemented and their consequences. The paper considers how a set of micro-governance interventions and mid-level leadership practices supported responses to stress whilst nurturing organizational resilience capacities. Data collection involved observation, in-depth interviews and analysis of meeting minutes and secondary data. Data analysis included iterative synthesis and validation processes. The paper offers five sets of insights that add to the limited empirical health system resilience literature: 1) resilience is a process not an end-state; 2) resilience strategies are deployed in combination rather than linearly, after each other; 3) three sets of organizational resilience capacities work together to support collective problem-solving and action entailed in EHSR; 4) these capacities can be nurtured by mid-level managers' leadership practices and simple adaptations of routine organizational processes, such as meetings; 5) central level actions must nurture EHSR by enabling the leadership practices and micro-governance processes entailed in everyday decision-making.
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Project description:Coccidioides spp. are fungal pathogens endemic to Southern California, Arizona, and other desert regions where they cause a spectrum of symptoms known as Valley Fever in otherwise healthy individuals. In the soil, Coccidioides grows in a hyphal form that produces vegetative spores (arthroconidia). When arthroconidia are inhaled by mammals they undergo an elaborate developmental transition consisting of germination, multiple rounds of nuclear division, and segmentation to form large spherules filled with vegetative endospores. Very little is understood about the molecular basis of spherule formation. Here we characterize the role of the conserved transcription factor Ryp1 in Coccidioides spherule formation. We show that Coccidioides ryp1 mutants are unable to form mature spherules, instead arresting at an early stage of spherulation. We analyze the transcriptional profile of wild-type and Δryp1 mutant cells under hyphal and spherule-promoting conditions, thereby defining a set of hyphal- or spherule-enriched transcripts that are dependent on Ryp1 for their expression. Ryp1-dependent transcripts include key virulence factors such as SOWgp, which encodes the spherule outer wall glycoprotein. In the mouse model of coccidioidomycosis, we find that the Δryp1 mutant is completely avirulent, indicating that Ryp1-dependent pathways are essential for the ability of Coccidioides to cause disease. Vaccination of C57BL/6 mice with live Δryp1 spores does not provide any protection from lethal C. posadasii intranasal infection, consistent with our findings that the Δryp1 mutant fails to make mature spherules. Taken together, this work identifies the first transcriptional regulator that drives mature spherulation and virulence in Coccidioides.
2022-03-03 | GSE178277 | GEO
Project description:Introduction:Crowding is a significant challenge for emergency centres (ECs) globally. While South Africa is not alone in reckoning with high patient demand and insufficient resources to treat these patients; staff-to-patient ratios are generally lower than in the Global North. The study of crowding and its consequences for patient care is a key research priority for strengthening the quality and efficacy of emergency care in South Africa. The study set out to understand frontline staff's perspectives on crowding in Cape Town public ECs to learn how they cope in such high- pressure working conditions, determine what they see as the factors contributing to crowding, and obtain their recommendations for reform. Methods:This research is a qualitative study from interviews and observations at five ECs in Cape Town, conducted in June and July 2017. In total 43 staff were interviewed individually or in pairs. The interviews included physicians of varying levels of experience (25), and registered or enrolled nurses (18). Data were analysed with the qualitative text-analysis software NVivo. Results:Both doctors and nurses saw crowding as a consequence of three factors: 1) limited bed space in the EC, 2) insufficient health professionals to care for admitted patients, and 3) the presence of boarders. Systemic or organizational factors as well as human resource scarcity were determined to be the key reasons for crowding. Discussion:With its high patient acuity and volume and its limited human and material resources, South Africa is an important case study for understanding how emergency care providers manage working in crowded conditions. The solutions to crowding recommended by interviewees were to expand the EC workforce and to add discharge lounges and examination tables.
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Project description:BackgroundMobile HIV screening may facilitate early HIV diagnosis. Our objective was to examine the cost-effectiveness of adding a mobile screening unit to current medical facility-based HIV testing in Cape Town, South Africa.Methods and findingsWe used the Cost Effectiveness of Preventing AIDS Complications International (CEPAC-I) computer simulation model to evaluate two HIV screening strategies in Cape Town: 1) medical facility-based testing (the current standard of care) and 2) addition of a mobile HIV-testing unit intervention in the same community. Baseline input parameters were derived from a Cape Town-based mobile unit that tested 18,870 individuals over 2 years: prevalence of previously undiagnosed HIV (6.6%), mean CD4 count at diagnosis (males 423/µL, females 516/µL), CD4 count-dependent linkage to care rates (males 31%-58%, females 49%-58%), mobile unit intervention cost (includes acquisition, operation and HIV test costs, $29.30 per negative result and $31.30 per positive result). We conducted extensive sensitivity analyses to evaluate input uncertainty. Model outcomes included site of HIV diagnosis, life expectancy, medical costs, and the incremental cost-effectiveness ratio (ICER) of the intervention compared to medical facility-based testing. We considered the intervention to be "very cost-effective" when the ICER was less than South Africa's annual per capita Gross Domestic Product (GDP) ($8,200 in 2012). We projected that, with medical facility-based testing, the discounted (undiscounted) HIV-infected population life expectancy was 132.2 (197.7) months; this increased to 140.7 (211.7) months with the addition of the mobile unit. The ICER for the mobile unit was $2,400/year of life saved (YLS). Results were most sensitive to the previously undiagnosed HIV prevalence, linkage to care rates, and frequency of HIV testing at medical facilities.ConclusionThe addition of mobile HIV screening to current testing programs can improve survival and be very cost-effective in South Africa and other resource-limited settings, and should be a priority.
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