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Journal articleWariri O, Utazi CE, Okomo U, et al., 2025,
Multi-level determinants of timely routine childhood vaccinations in The Gambia: Findings from a nationwide analysis
, Vaccine, Vol: 43, ISSN: 0264-410XIntroduction: Achieving the ambitious goals of the Immunisation Agenda 2030 (IA2030) requires a deeper understanding of factors influencing under-vaccination, including timely vaccination. This study investigates the demand- and supply-side determinants influencing the timely uptake of key childhood vaccines scheduled throughout the first year of life in The Gambia. Methods: We used two nationally-representative datasets: the 2019–20 Gambian Demographic and Health Survey and the 2019 national immunisation facility mapping. Using Bayesian multi-level binary logistic regression models, we identified key factors significantly associated with timely vaccination for five key vaccines: birth dose of hepatitis-B (HepB0), first, second, and third doses of the pentavalent vaccine (Penta1, Penta2, Penta3), and first-dose of measles-containing vaccine (MCV1) in children aged 12–35 months. We report the adjusted Odds Ratios (aORs) and 95 % Credible Intervals (95 % CIs) in each case. Results: We found that demand-side factors, such as ethnicity, household wealth status, maternal education, maternal parity, and the duration of the household's residency in its current location, were the most common drivers of timely childhood vaccination. However, supply-side factors such as travel time to the nearest immunisation clinic, availability of cold-storage and staffing numbers in the nearest immunisation clinic were also significant determinants. Furthermore, the determinants varied across specific vaccines and the timing of doses. For example, delivery in a health facility (aOR = 1.58, 95 %CI: 1.02–2.53), living less than 30 min (aOR = 2.11, 95 %CI: 1.2–8.84) and living between 30 and 60 min (aOR = 3.68, 95 %CI: 1.1–14.99) from a fixed-immunisation clinic was associated with timely HepB0, a time-sensitive vaccine that must be administered within 24 h of birth. On the other hand, children who received Penta1 and Penta2 on time were three- to five-fold more
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Journal articleHallett TB, Mangal TD, Tamuri AU, et al., 2025,
Estimates of resource use in the public-sector health-care system and the effect of strengthening health-care services in Malawi during 2015–19: a modelling study (Thanzi La Onse)
, The Lancet Global Health, Vol: 13, Pages: E28-E37, ISSN: 2572-116XBackgroundIn all health-care systems, decisions need to be made regarding allocation of available resources. Evidence is needed for these decisions, especially in low-income countries. We aimed to estimate how health-care resources provided by the public sector were used in Malawi during 2015–19 and to estimate the effects of strengthening health-care services.MethodsFor this modelling study, we used the Thanzi La Onse model, an individual-based simulation model. The scope of the model was health care provided by the public sector in Malawi during 2015–19. Health-care services were delivered during health-care system interaction (HSI) events, which we characterised as occurring at a particular facility level and requiring a particular number of appointments. We developed mechanistic models for the causes of death and disability that were estimated to account for approximately 81% of deaths and approximately 72% of disability-adjusted life-years (DALYs) in Malawi during 2015–19, according to the Global Burden of Disease (GBD) estimates; we computed DALYs incurred in the population as the sum of years of life lost and years lived with disability. The disease models could interact with one another and with the underlying properties of each person. Each person in the Thanzi La Onse model had specific properties (eg, sex, district of residence, wealth percentile, smoking status, and BMI, among others), for which we measured distribution and evolution over time using demographic and health survey data. We also estimated the effect of different types of health-care system improvement.FindingsWe estimated that the public-sector health-care system in Malawi averted 41·2 million DALYs (95% UI 38·6–43·8) during 2015–19, approximately half of the 84·3 million DALYs (81·5–86·9) that the population would otherwise have incurred. DALYs averted were heavily skewed to children aged 0–4 years due to s
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Journal articleOliveira LMA, Costa NS, Mestrovic T, et al., 2025,
The battle against antimicrobial resistance is more important now than ever: time to educate, advocate and act
, International Journal of Infectious Diseases, Vol: 150, ISSN: 1201-9712 -
Journal articlePaschoalotto MAC, Cima J, Costa E, et al., 2024,
Politics and confidence toward the COVID-19 vaccination: A Brazilian cross-sectional study.
, Hum Vaccin Immunother, Vol: 20This study has the aim of assessing the Brazilian perceptions, influencing factors and political positioning on the confidence concerning COVID-19 vaccination. To achieve the objective, the methods rely on a cross-sectional survey of Brazilian citizens, distributed through different social networks. The sample is composed of 1,670 valid responses, collected from almost all Brazilian states and state capitals. To analyze the data and give a clear view of the variables' relationship, the study used bivariate and comparative graphs. Results show a higher level of confidence in vaccines from Pfizer and AstraZeneca, while the lower level of confidence is associated with vaccines from Sinopharm and Sputinik5. Vaccine efficacy is the most significant influencing factor that helps in the decision to get vaccinated. Also, individuals are less willing to get vaccinated if their political preferences are related to the right-wing. The results led to three main health and social implications: i) the vaccination strategy campaigns should take in count vaccine efficacy and political aspects; ii) the vaccination process should be adapted to regions with different political positions; and iii) a reinforcement in the educational policies of the vaccine's importance to the public health, to avoid the politization of a health issue.
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Journal articleBottery MJ, van Rhijn N, Chown H, et al., 2024,
Elevated mutation rates in multi-azole resistant Aspergillus fumigatus drive rapid evolution of antifungal resistance.
, Nat Commun, Vol: 15The environmental use of azole fungicides has led to selective sweeps across multiple loci in the Aspergillus fumigatus genome causing the rapid global expansion of a genetically distinct cluster of resistant genotypes. Isolates within this cluster are also more likely to be resistant to agricultural antifungals with unrelated modes of action. Here we show that this cluster is not only multi-azole resistant but has increased propensity to develop resistance to next generation antifungals because of variants in the DNA mismatch repair system. A variant in msh6-G233A is found almost exclusively within azole resistant isolates harbouring the canonical cyp51A azole resistance allelic variant TR34/L98H. Naturally occurring isolates with this msh6 variant display up to 5-times higher rate of mutation, leading to an increased likelihood of evolving resistance to other antifungals. Furthermore, unlike hypermutator strains, the G233A variant conveys no measurable fitness cost and has become globally distributed. Our findings further suggest that resistance to next-generation antifungals is more likely to emerge within organisms that are already multi-azole resistant due to close linkage between TR34/L98H and msh6-G233A, posing a major problem due to the prospect of dual use of novel antifungals in clinical and agricultural settings.
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Journal articleWalters M, Korenromp E, Yakusik A, et al., 2024,
Guidance for triangulating data and estimates of HIV prevalence among pregnant women and coverage of PMTCT using the Spectrum AIDS Impact Module
, JAIDS: Journal of Acquired Immune Deficiency Syndromes, Vol: 97, Pages: 439-449, ISSN: 1525-4135Background: Most countries use the Spectrum AIDS Impact Module (Spectrum-AIM), antenatal care routine HIV testing, and antiretroviral treatment data to estimate HIV prevalence among pregnant women. Non-representative programme data may lead to inaccurate estimates HIV prevalence and treatment coverage for pregnant women. Setting: 154 countries and subnational locations across 126 countries.Methods: Using 2023 UNAIDS HIV estimates, we calculated three ratios: (1) HIV prevalence among pregnant women to all women 15-49y (prevalence), (2) ART coverage before pregnancy to women 15-49y ART coverage (ART pre-pregnancy), and (3) ART coverage at delivery to women 15-49y ART coverage (PMTCT coverage). We developed an algorithm to identify and adjust inconsistent results within regional ranges in Spectrum-AIM, illustrated using Burkina Faso’s estimates.Results: In 2022, the mean regional ratio of prevalence among pregnant women to all women ranged from 0.68 to 0.95. ART coverage pre-pregnancy ranged by region from 0.40 to 1.22 times ART coverage among all women. Mean regional PMTCT coverage ratios ranged from 0.85 to 1.51. The prevalence ratio in Burkina Faso was 1.59, above the typical range 0.62-1.04 in western and central Africa. Antenatal clinics reported more PMTCT recipients than estimated HIV-positive pregnant women from 2015 to 2019. We adjusted inputted PMTCT programme data to enable consistency of HIV prevalence among pregnant women from programmatic routine HIV testing at antenatal clinics with values typical for Western and central Africa. Conclusion: These ratios offer Spectrum-AIM users a tool to gauge the consistency of their HIV prevalence and treatment coverage estimates among pregnant women with other countries in the region.
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Journal articleMonteirinho Leitao RA, Leitao R, Wan IU, et al., 2024,
Detection of fungal sequences in human brain: rDNA locus amplification and deep sequencing
, Scientific Reports, ISSN: 2045-2322The aetiology of Alzheimer’s disease (AD) and Parkinson’s disease (PD) are unknown and tend to manifest at a late stage in life; eventhough these neurodegenerative diseases are caused by different affected proteins, they are both characterized by neuroinflammation.Links between bacterial and viral infection and AD/PD has been suggested in several studies, however, few have attempted to establisha link between fungal infection and AD/PD. In this study we adopted a nanopore-based sequencing approach to characterise thepresence or absence of fungal genera in both human brain tissue and cerebrospinal fluid (CSF). We observed the presence of smallfungal burden DNA in two AD brains and a control case (extensive amyloid angiopathy). This approach would be well-placed toinvestigate potential links between microbial infection and neurodegenerative disease.
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Journal articleHuong NHT, Toan ND, Thien TB, et al., 2024,
In children, N-Methyl-D-Aspartate receptor antibody encephalitis incidence exceeds that of Japanese encephalitis in Vietnam
, Open Forum Infectious Diseases, ISSN: 2328-8957BackgroundThe recognition of autoimmune causes of encephalitis has led to epidemiological shifts in the worldwide characteristics. N-Methyl-D-Aspartate receptor antibody encephalitis leads to well-established complex neuropsychiatric manifestations. In low- and middle-income countries, including Vietnam, its relative incidence, especially in children, is unknown and most neurologists currently consider infectious encephalitis prior to autoimmune etiologies.MethodsThe study was prospectively conducted at Children’s Hospital 1 in Ho Chi Minh City between March 2020 and December 2022. Any child admitted to the Department of Infectious Diseases and Neurology fulfilling the case definition of encephalitis, was eligible to participate. Cerebrospinal fluid samples were collected alongside meta-clinical data for analysis.ResultsWe recruited 164 children with a clinical diagnosis of encephalitis. Etiologies were determined as N-Methyl-D-Aspartate receptor antibody encephalitis in 23/164 cases (14.0%), Japanese Encephalitis Virus in 14/164 (8.5%) and Herpes Simplex Virus in 4/164 (2.4%). Clinical categorizations suggested idiopathic viral encephalitis in another 71 (43.3%), and autoimmune encephalitis of unknown origin in the remaining 52. Factors including demographics, specific clinical features, cerebrospinal fluid and electroencephalogram findings, and length of hospital stay were significantly different between N-Methyl-D-Aspartate receptor antibody encephalitis and Japanese encephalitis.ConclusionsAt a tertiary children’s hospital in Vietnam, the prevalence of N-Methyl-D-Aspartate receptor antibody encephalitis exceeds that of Japanese encephalitis, the most common infectious encephalitis cause in Southeast Asia. N-Methyl-D-Aspartate receptor antibody encephalitis is associated with long hospital stay and poor outcomes. These findings should change paediatric diagnostics, to earlier consider autoimmune treatments in this clinical setting.
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Journal articleAvraam D, Hadjichrysanthou C, 2024,
The impact of contact-network structure on important epidemiological quantities of infectious disease transmission and the identification of the extremes.
, J Theor BiolWe developed an individual-based stochastic model to simulate the spread of an infectious disease on all possible contact-networks of size between six and nine nodes. We assessed systematically the impact of the change in the population contact structure on four important epidemiological quantities: i) the epidemic duration, ii) the maximum number of infected individuals at a time point during the epidemic, iii) the time at which the maximum number of infected individuals is reached, and iv) the total number of individuals that have been infected during the epidemic. We identified the networks that maximise and minimise each of these quantities in the case of an epidemic outbreak. Chain-like networks minimise the peak and final epidemic size, but the disease spread is slow on such contact structures which leads to the maximisation of the epidemic duration. Star-like networks maximise the time to the peak whereas highly connected networks lead to faster disease transmission, and higher peak and final epidemic size. While the pairwise relationship of most of the quantities becomes almost linear, or inverse linear, as the network connectivity increases and approaches the complete network, where every individual is connected to each other, the relationships are non-linear towards networks of low connectivity. In particular, the pairwise relationship between the final epidemic size and other quantities is changed in a 'bow-shaped' manner. There is a strong inverse linear relationship between epidemic duration and peak epidemic size with increasing network connectivity. The (inverse) linear relationships between quantities are more pronounced in cases of high disease transmissibility. All the values of the quantities change in a non-linear way with the increase of network connectivity and are characterised by high variability between networks of the same degree. The variability decreases as network connectivity increases.
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Journal articleMills C, Donnelly CA, 2024,
Climate-based modelling and forecasting of dengue in three endemic departments of Peru.
, PLoS Negl Trop Dis, Vol: 18Amid profound climate change, incidence of dengue continues to rise and expand in distribution across the world. Here, we analysed dengue in three coastal departments of Peru which have recently experienced public health emergencies during the worst dengue crises in Latin American history. We developed a climate-based spatiotemporal modelling framework to model monthly incidence of new dengue cases in Piura, Tumbes, and Lambayeque over 140 months from 2010 to 2021. The framework enabled accurate description of in-sample and out-of-sample dengue incidence trends across the departments, as well as the characterisation of the timing, structure, and intensity of climatic relationships with human dengue incidence. In terms of dengue incidence rate (DIR) risk factors, we inferred non-linear and delayed effects of greater monthly mean maximum temperatures, extreme precipitation, sustained drought conditions, and extremes of a Peruvian-specific indicator of the El Niño Southern Oscillation. Building on our model-based understanding of climatic influences, we performed climate-model-based forecasting of dengue incidence across 2018 to 2021 with a forecast horizon of one month. Our framework enabled representative, reliable forecasts of future dengue outbreaks, including correct classification of 100% of all future outbreaks with DIR ≥ 50 (or 150) per 100,000, whilst retaining relatively low probability of 0.12 (0.05) for false alarms. Therefore, our model framework and analysis may be used by public health authorities to i) understand climatic drivers of dengue incidence, and ii) alongside our forecasts, to mitigate impacts of dengue outbreaks and potential public health emergencies by informing early warning systems and deployment of vector control resources.
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