| 1. |
- Munk, P., et al.
(author)
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Genomic analysis of sewage from 101 countries reveals global landscape of antimicrobial resistance
- 2022
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In: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 13:1
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Journal article (peer-reviewed)abstract
- Antimicrobial resistance (AMR) is a major threat to global health. Understanding the emergence, evolution, and transmission of individual antibiotic resistance genes (ARGs) is essential to develop sustainable strategies combatting this threat. Here, we use metagenomic sequencing to analyse ARGs in 757 sewage samples from 243 cities in 101 countries, collected from 2016 to 2019. We find regional patterns in resistomes, and these differ between subsets corresponding to drug classes and are partly driven by taxonomic variation. The genetic environments of 49 common ARGs are highly diverse, with most common ARGs carried by multiple distinct genomic contexts globally and sometimes on plasmids. Analysis of flanking sequence revealed ARG-specific patterns of dispersal limitation and global transmission. Our data furthermore suggest certain geographies are more prone to transmission events and should receive additional attention.
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| 2. |
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| 3. |
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| 4. |
- Burn, E., et al.
(author)
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Deep phenotyping of 34,128 adult patients hospitalised with COVID-19 in an international network study
- 2020
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In: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 11:1
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Journal article (peer-reviewed)abstract
- Comorbid conditions appear to be common among individuals hospitalised with coronavirus disease 2019 (COVID-19) but estimates of prevalence vary and little is known about the prior medication use of patients. Here, we describe the characteristics of adults hospitalised with COVID-19 and compare them with influenza patients. We include 34,128 (US: 8362, South Korea: 7341, Spain: 18,425) COVID-19 patients, summarising between 4811 and 11,643 unique aggregate characteristics. COVID-19 patients have been majority male in the US and Spain, but predominantly female in South Korea. Age profiles vary across data sources. Compared to 84,585 individuals hospitalised with influenza in 2014-19, COVID-19 patients have more typically been male, younger, and with fewer comorbidities and lower medication use. While protecting groups vulnerable to influenza is likely a useful starting point in the response to COVID-19, strategies will likely need to be broadened to reflect the particular characteristics of individuals being hospitalised with COVID-19. Detailed knowledge of the characteristics of COVID-19 patients helps with public health planning. Here, the authors use routinely-collected data from seven databases in three countries to describe the characteristics of >30,000 patients admitted with COVID-19 and compare them with those admitted for influenza in previous years.
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| 6. |
- Lane, J. C. E., et al.
(author)
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Risk of hydroxychloroquine alone and in combination with azithromycin in the treatment of rheumatoid arthritis: a multinational, retrospective study
- 2020
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In: Lancet Rheumatology. - : Elsevier BV. - 2665-9913. ; 2:11
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Journal article (peer-reviewed)abstract
- Background Hydroxychloroquine, a drug commonly used in the treatment of rheumatoid arthritis, has received much negative publicity for adverse events associated with its authorisation for emergency use to treat patients with COVID-19 pneumonia. We studied the safety of hydroxychloroquine, alone and in combination with azithromycin, to determine the risk associated with its use in routine care in patients with rheumatoid arthritis. Methods In this multinational, retrospective study, new user cohort studies in patients with rheumatoid arthritis aged 18 years or older and initiating hydroxychloroquine were compared with those initiating sulfasalazine and followed up over 30 days, with 16 severe adverse events studied. Self-controlled case series were done to further establish safety in wider populations, and included all users of hydroxychloroquine regardless of rheumatoid arthritis status or indication. Separately, severe adverse events associated with hydroxychloroquine plus azithromycin (compared with hydroxychloroquine plus amoxicillin) were studied. Data comprised 14 sources of claims data or electronic medical records from Germany, Japan, the Netherlands, Spain, the UK, and the USA. Propensity score stratification and calibration using negative control outcomes were used to address confounding. Cox models were fitted to estimate calibrated hazard ratios (HRs) according to drug use. Estimates were pooled where the I-2 value was less than 0.4. Findings The study included 956 374 users of hydroxychloroquine, 310 350 users of sulfasalazine, 323 122 users of hydroxychloroquine plus azithromycin, and 351 956 users of hydroxychloroquine plus amoxicillin. No excess risk of severe adverse events was identified when 30-day hydroxychloroquine and sulfasalazine use were compared. Selfcontrolled case series confirmed these findings. However, long-term use of hydroxychloroquine appeared to be associated with increased cardiovascular mortality (calibrated HR 1.65 [95% CI 1.12-2.44]). Addition of azithromycin appeared to be associated with an increased risk of 30-day cardiovascular mortality (calibrated HR 2.19 [95% CI 1.22-3.95]), chest pain or angina (1.15 [1.05-1.26]), and heart failure (1.22 [1.02-1.45]). Interpretation Hydroxychloroquine treatment appears to have no increased risk in the short term among patients with rheumatoid arthritis, but in the long term it appears to be associated with excess cardiovascular mortality. The addition of azithromycin increases the risk of heart failure and cardiovascular mortality even in the short term. We call for careful consideration of the benefit-risk trade-off when counselling those on hydroxychloroquine treatment. Copyright (c) 2020 The Author(s). Published by Elsevier Ltd.
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| 7. |
- Abila, R., et al.
(author)
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Oil extraction imperils Africa’s Great Lakes
- 2016
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In: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 354:6312, s. 561-562
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Journal article (other academic/artistic)abstract
- As the world's demands for hydrocarbons increase (1), remote areas previously made inaccessible by technological limitations are now being prospected for oil and gas deposits. Virtually unnoticed by the public, such activities are ongoing in the East African Great Lakes region, threatening these ecosystems famed for their hyper-diverse biota, including the unique adaptive radiations of cichlid fishes (2). Countries in the region see exploitation of hydrocarbon reserves as a vital economic opportunity. In the Lake Albert region of Uganda, for example, the government foresees a $3.6 billion oil profit per year starting in 2018—a sum almost as high as the country's current annual budget (3). However, oil extraction in the East African Great Lakes region poses grave risks to the environment and local communities.
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| 8. |
- King, C, et al.
(author)
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Care-seeking patterns amongst suspected paediatric pneumonia deaths in rural Malawi
- 2020
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In: Gates open research. - : F1000 Research Ltd. - 2572-4754. ; 4, s. 178-
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Journal article (peer-reviewed)abstract
- Background: Pneumonia remains a leading cause of paediatric deaths. To understand contextual challenges in care pathways, we explored patterns in care-seeking amongst children who died of pneumonia in Malawi. Methods: We conducted a mixed-methods analysis of verbal autopsies (VA) amongst deaths in children aged 1-59 months from 10/2011 to 06/2016 in Mchinji district, Malawi. Suspected pneumonia deaths were defined as: 1. caregiver reported cough and fast breathing in the 2-weeks prior to death; or, 2. the caregiver specifically stated the child died of pneumonia; or 3. cause of death assigned as ‘acute respiratory infection’ using InterVA-4. Data were extracted from free-text narratives based on domains in the ‘Pathways to Survival’ framework, and described using proportions. Qualitative analysis used a framework approach, with pre-specified themes. Results: We analysed 171 suspected pneumonia deaths. In total, 86% of children were taken to a healthcare facility during their final illness episode, and 44% sought care more than once. Of children who went to hospital (n=119), 70% were admitted, and 25% received oxygen. Half of the children died within a healthcare setting (43% hospital, 5% health centre and 2% private clinics), 64 (37%) at home, and 22 (13%) in transit. Challenges in delayed care, transport and quality of care (including oxygen), were reported. Conclusions: Healthcare was frequently sought for children who died of suspected pneumonia, however several missed opportunities for care were seen. Sustained investment in timely appropriate care seeking, quick transportation to hospital and improved case management at all levels of the system is needed.
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| 9. |
- Morton, B, et al.
(author)
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Establishment of a high-dependency unit in Malawi
- 2020
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In: BMJ global health. - : BMJ. - 2059-7908. ; 5:11
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Journal article (peer-reviewed)abstract
- Adults admitted to hospital with critical illness are vulnerable and at high risk of morbidity and mortality, especially in sub-Saharan African settings where resources are severely limited. As life expectancy increases, patient demographics and healthcare needs are increasingly complex and require integrated approaches. Patient outcomes could be improved by increased critical care provision that standardises healthcare delivery, provides specialist staff and enhanced patient monitoring and facilitates some treatment modalities for organ support. In Malawi, we established a new high-dependency unit within Queen Elizabeth Central Hospital, a tertiary referral centre serving the country’s Southern region. This unit was designed in partnership with managers, clinicians, nurses and patients to address their needs. In this practice piece, we describe a participatory approach to design and implement a sustainable high-dependency unit for a low-income sub-Saharan African setting. This included: prospective agreement on remit, alignment with existing services, refurbishment of a dedicated physical space, recruitment and training of specialist nurses, development of context-sensitive clinical standard operating procedures, purchase of appropriate and durable equipment and creation of digital clinical information systems. As the global COVID-19 pandemic unfolded, we accelerated unit opening in anticipation of increased clinical requirement and describe how the high-dependency unit responded to this demand.
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| 10. |
- Kamtchum-Tatuene, J., et al.
(author)
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A 42-year-old woman with subacute reversible dementia: A cautionary tale
- 2017
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In: Malawi Medical Journal. - : African Journals Online (AJOL). - 1995-7262. ; 29:3, s. 265-267
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Journal article (peer-reviewed)abstract
- A 42-year-old woman presented with a 6-month history of diffuse headache of moderate intensity and gradual onset of generalized weakness, imbalance, apathy, memory decline, hypophonia, dysphagia, constipation and urinary incontinence. Clinical examination revealed several elements of a frontal lobe dysfunction including apathy with motor impersistence, presence of primitive reflexes, generalized hyperreflexia with bilateral Hoffman sign and ankle clonus. The biological workup was unremarkable and a brain computed tomography scan identified a giant olfactory groove meningioma. A prompt neurosurgical intervention helped to reverse the symptoms. This case illustrates the benefits of actively looking for treatable conditions in young patients presenting with acute or subacute dementia and emphasizes the pivotal role of early brain imaging.
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| 11. |
- Loh, P, et al.
(author)
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Added value of an open narrative in verbal autopsies: a mixed-methods evaluation from Malawi
- 2021
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In: BMJ paediatrics open. - : BMJ. - 2399-9772. ; 5:1, s. e000961-
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Journal article (peer-reviewed)abstract
- The WHO standardised verbal autopsy (VA) instrument includes closed questions, ascertaining signs and symptoms of illness preceding death, and an optional open narrative. As VA analyses increasingly use automated algorithms, inclusion of narratives should be justified. We evaluated the role of open narratives on VA processes, data quality and respondent’s emotional stress.MethodsA mixed-methods analysis was conducted using VA data for child deaths (0–59 months), between April 2013 and November 2016 in Mchinji district, Malawi. Deaths were prospectively randomised to receive closed questions only or open narrative followed by closed questions. On concluding the VA, interviewers self-completed questions on respondents’ emotional stress. Logistic regression was used to determine associations with visible emotional distress during VAs. A group discussion with interviewers was conducted at the project end, to understand field experiences and explore future recommendations; data were coded using deductive themes.Results2509 VAs were included, with 49.8% (n=1341) randomised to open narratives. Narratives lasted a median of 7 minuntes (range: 1–113). Interviewers described improved rapport and felt narratives improved data quality, although there was no difference in the proportion of deaths with an indeterminate cause using an automated algorithm (5.3% vs 6.1%). The majority of respondents did not display visible emotional stress (81%). Those with a narrative had higher, but not statistically significant, odds of emotional distress (adjusted OR: 1.20; 95% CI: 0.98 to 1.47). Factors associated with emotional stress were: infant deaths versus neonates; deaths at a health centre or en-route to hospital versus home; and higher socioeconomic status. Non-parental respondents and increased time between death and interview were associated with lower odds of emotional distress.ConclusionConducting an open narrative may help build rapport, something valued by the interviewers. However, additional time and emotional burdens should be further justified, with quality and utility of narratives promoted through standardised recommendations.
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| 12. |
- Spyridonis, F., et al.
(author)
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A study on the state-of-the-art of e-infrastructures uptake in Africa
- 2015
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In: Palgrave Communications. - : Palgrave Macmillan Ltd.. - 2055-1045. ; 1
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Journal article (peer-reviewed)abstract
- e-Science is a pioneering method that uses integrated collections of Information and Communication Technologies (ICTs), or e-Infrastructures, to enable scientists across the world to collaboratively work on more and more ambitious projects. Have advances and access to ICTs enabled African e-Infrastructure development? This paper aims to understand the current state of e-Infrastructure uptake in Africa and present some of these initiatives across the African continent by exploring the current landscape emerging from a survey of early consumers. These initiatives are discussed in terms of key projects and user communities that they are addressing. In line with wider perceptions that e-Infrastructures will re-shape the ways research is performed, this study yielded 34 current or planned e-Infrastructure projects across 13 African countries addressing a range of research domains, and identified 7 user communities across these disciplines. Our findings suggest that the African research community is increasingly interested and involved in e-Infrastructure development activities in response to the issue of limited access to dedicated global research and education resources. The study can contribute to the ongoing discussion on how e-Infrastructures can positively promote the research, technological development and innovation potential of developing countries.
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| 13. |
- Tebaldini, S., et al.
(author)
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Biomass Level-2 Products - Part II: Processing Schemes and AGB Estimation Results from Campaign Data
- 2021
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In: International Geoscience and Remote Sensing Symposium (IGARSS). ; 2021-July, s. 783-786
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Conference paper (peer-reviewed)abstract
- Scheduled for launch in 2023, ESA's seventh Earth Explorer Mission, BIOMASS, will carry the first P-band synthetic aperture radar (SAR) to be flown in space, to gather fully polarimetric acquisitions over forested areas worldwide in interferometric and tomographic modes. This paper presents the algorithms developed to estimate biophysical parameters from BIOMASS measurements and their implementation in the BIOMASS level 2 (L2) prototype processor. The L2 processor will generate global maps of forest Above Ground Biomass (AGB), Forest Height (FH), Forest disturbance (FD). Accurate generation of these products requires the L2 processor to be closely inter-linked with the BIOMASS interferometric processor, in order to produce phase-calibrated interferometric stacks, retrieve sub-canopy terrain topography, and generate a 3D representation of forest structure by use of SAR tomography. AGB estimation results are here shown using BIOMASS-like acquisitions derived from campaign data acquired over six tropical forests in South America and Equatorial Africa.
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| 14. |
- Ulander, Lars, 1962, et al.
(author)
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BIOMASS LEVEL-2 PRODUCTS - PART I: RATIONALE AND APPLICATIONS
- 2021
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In: International Geoscience and Remote Sensing Symposium (IGARSS). ; 2021-July, s. 779-782
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Conference paper (peer-reviewed)abstract
- This paper describes the rationale and development of the estimation techniques for the level-2 data products of the European Space Agency's 7th Earth Explorer BIOMASS mission. BIOMASS is planned for launch in 2023 and will carry the first-ever P-band synthetic aperture radar (SAR) onboard a satellite. It has been designed to produce consistent global maps of the Earth's forests during a nominal five-year lifetime. Fully polarimetric SAR data will be collected and the satellite orbit will be selected for repeat-pass interferometry and tomography in separated mission phases. Mission requirements call for three level-2 data products: above-ground biomass, forest height and forest disturbance. The paper also discusses the expected limitations of the estimation techniques and remaining problems to be addressed.
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