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Journal articleMacià D, Pons-Salort M, Moncunill G, et al., 2025,
The effect of disease transmission on time-aggregated treatment efficacy estimates: a critical analysis of factors influencing the RTS,S and R21 malaria vaccine phase 3 trials
, The Lancet Infectious Diseases, ISSN: 1473-3099 -
Journal articleMorris KAL, Turner H, Checkley A, et al., 2025,
Malaria chemoprophylaxis provision in the UK: a call to evaluate the cost-effectiveness and equity implications of universal provision.
, J Travel Med, Vol: 32 -
Journal articleTrotter C, Diallo K, 2025,
Another step towards defeating meningitis.
, Lancet, Vol: 405, Pages: 1030-1031 -
Journal articleNiamsi-Emalio Y, Nana-Djeunga HC, Fronterrè C, et al., 2025,
Model-based geostatistical mapping of the prevalence of Onchocerca volvulus in Cameroon between 1971 and 2020
, PLoS Neglected Tropical Diseases, Vol: 19, ISSN: 1935-2727BackgroundAfter the closure of the African Programme for Onchocerciasis Control (APOC) in 2015, the Ministry of Public Health of Cameroon has continued implementing annual community-directed treatment with ivermectin (CDTI) in endemic areas. The World Health Organization has proposed that 12 countries be verified for elimination (interruption) of transmission by 2030. Using Rapid Epidemiological Mapping of Onchocerciasis, a baseline geostatistical map of nodule (onchocercoma) prevalence had been generated for APOC countries, indicating high initial endemicity in most regions of Cameroon. After more than two decades of CDTI, infection prevalence remains high in some areas. This study aimed at mapping the spatio-temporal evolution of Onchocerca volvulus prevalence from 1971 to 2020 to: i) identify such areas; ii) indicate where alternative and complementary interventions are most needed to accelerate elimination, and iii) improve the projections of transmission models.MethodologyA total of 1,404 georeferenced (village-level) prevalence surveys were obtained from published articles; the Expanded Special Project for Elimination of Neglected Tropical Diseases portal for Cameroon; independent researchers and grey literature. These data were used together with bioclimatic layers to generate model-based geostatistical (MBG) maps of microfilarial prevalence for 1971–2000; 2001–2010 and 2011–2020.Principal findingsTime-period was negatively and statistically significantly associated with prevalence. In 1971–2000 and 2001–2010, prevalence levels were high in most regions and ≥60% in some areas. Mean predicted prevalence declined in 2011–2020, reaching <20% in most areas, but data for this period were sparse, leading to substantial uncertainty. Hotspots were identified in South West, Littoral and Centre regions.Conclusions/SignificanceOur results are broadly consistent with recent MBG studies and can be used to intensify onchocerciasis
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Journal articleHorsfield ST, Fok B, Fu Y, et al., 2025,
Optimizing nanopore adaptive sampling for pneumococcal serotype surveillance in complex samples using the graph-based GNASTy algorithm.
, Genome ResSerotype surveillance of Streptococcus pneumoniae (the pneumococcus) is critical for understanding the effectiveness of current vaccination strategies. However, existing methods for serotyping are limited in their ability to identify co-carriage of multiple pneumococci and detect novel serotypes. To develop a scalable and portable serotyping method that overcomes these challenges, we employed nanopore adaptive sampling (NAS), an on-sequencer enrichment method that selects for target DNA in real-time, for direct detection of S. pneumoniae in complex samples. Whereas NAS targeting the whole S. pneumoniae genome was ineffective in the presence of nonpathogenic streptococci, the method was both specific and sensitive when targeting the capsular biosynthetic locus (CBL), the operon that determines S. pneumoniae serotype. NAS significantly improved coverage and yield of the CBL relative to sequencing without NAS and accurately quantified the relative prevalence of serotypes in samples representing co-carriage. To maximize the sensitivity of NAS to detect novel serotypes, we developed and benchmarked a new pangenome-graph algorithm, named GNASTy. We show that GNASTy outperforms the current NAS implementation, which is based on linear genome alignment, when a sample contains a serotype absent from the database of targeted sequences. The methods developed in this work provide an improved approach for novel serotype discovery and routine S. pneumoniae surveillance that is fast, accurate, and feasible in low-resource settings. Although NAS facilitates whole-genome enrichment under ideal circumstances, GNASTy enables targeted enrichment to optimize serotype surveillance in complex samples.
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Journal articleGmeiner A, Ivanova M, Njage PMK, et al., 2025,
Quantitative prediction of disinfectant tolerance in Listeria monocytogenes using whole genome sequencing and machine learning.
, Sci Rep, Vol: 15Listeria monocytogenes is a potentially severe disease-causing bacteria mainly transmitted through food. This pathogen is of great concern for public health and the food industry in particular. Many countries have implemented thorough regulations, and some have even set 'zero-tolerance' thresholds for particular food products to minimise the risk of L. monocytogenes outbreaks. This emphasises that proper sanitation of food processing plants is of utmost importance. Consequently, in recent years, there has been an increased interest in L. monocytogenes tolerance to disinfectants used in the food industry. Even though many studies are focusing on laboratory quantification of L. monocytogenes tolerance, the possibility of predictive models remains poorly studied. Within this study, we explore the prediction of tolerance and minimum inhibitory concentrations (MIC) using whole genome sequencing (WGS) and machine learning (ML). We used WGS data and MIC values to quaternary ammonium compound (QAC) disinfectants from 1649 L. monocytogenes isolates to train different ML predictors. Our study shows promising results for predicting tolerance to QAC disinfectants using WGS and machine learning. We were able to train high-performing ML classifiers to predict tolerance with balanced accuracy scores up to 0.97 ± 0.02. For the prediction of MIC values, we were able to train ML regressors with mean squared error as low as 0.07 ± 0.02. We also identified several new genes related to cell wall anchor domains, plasmids, and phages, putatively associated with disinfectant tolerance in L. monocytogenes. The findings of this study are a first step towards prediction of L. monocytogenes tolerance to QAC disinfectants used in the food industry. In the future, predictive models might be used to monitor disinfectant tolerance in food production and might support the conceptualisation of more nuanced sanitation programs.
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Journal articleHanley-Cook GT, Deygers J, Daly AJ, et al., 2025,
Dietary species richness provides a comparable marker for better nutrition and health across contexts.
, Nat FoodEcological diversity indices such as Hill numbers have been developed to estimate effective species numbers, yet the ability of Hill numbers to compare food biodiversity across contexts is unclear. Here we computed the between- and within-country variability of similarity-insensitive Hill numbers using dietary intake collected from prospective cohorts in nine European countries and cross-sectional studies in five low- and middle-income countries. We also assessed the relationships between more biodiverse diets, mortality rates and micronutrient adequacy. Only Hill0, better known as dietary species richness (DSR), showed strong heterogeneity between countries and individuals within countries. Higher DSR was most strongly associated with lower mortality rates in Europe as compared to Hill1, Hill2 and Hill∞, whereas relationships with micronutrient adequacy were comparable across Hill numbers in the global south. DSR can be used to assess progress towards more biodiverse diets, while also serving as a marker for the deleterious nutrition and health impacts associated with non-diverse diets.
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Journal articleWeiss DJ, Dzianach PA, Saddler A, et al., 2025,
Mapping the global prevalence, incidence, and mortality of Plasmodium falciparum and Plasmodium vivax malaria, 2000-22: a spatial and temporal modelling study.
, Lancet, Vol: 405, Pages: 979-990BACKGROUND: Malaria remains a leading cause of illness and death globally, with countries in sub-Saharan Africa bearing a disproportionate burden. Global high-resolution maps of malaria prevalence, incidence, and mortality are crucial for tracking spatially heterogeneous progress against the disease and to inform strategic malaria control efforts. We present the latest such maps, the first since 2019, which cover the years 2000-22. The maps are accompanied by administrative-level summaries and include estimated COVID-19 pandemic-related impacts on malaria burden. METHODS: We initially modelled prevalence of Plasmodium falciparum malaria infection in children aged 2-10 years in high-burden African countries using a geostatistical modelling framework. The model was trained on a large database of spatiotemporal observations of community infection prevalence; environmental and anthropogenic covariates; and modelled intervention coverages for insecticide-treated bednets, indoor residual spraying, and effective treatment with an antimalarial drug. We developed an additional model to incorporate disruptions to malaria case management caused by the COVID-19 pandemic. The resulting high-resolution maps of infection prevalence from 2000 to 2022 were subsequently translated to estimates of case incidence and malaria mortality. For other malaria-endemic countries and for Plasmodium vivax estimates, we used routine surveillance data to model annual case incidence at administrative levels. We then converted these estimates to infection prevalence and malaria mortality, and spatially disaggregated administrative-level results to produce high-resolution maps. Lastly, we combined the modelled outputs to produce global maps and summarised tables that are suitable for assessing changing malaria burden from subnational to global scales. FINDINGS: We found an ongoing plateau in rates of malaria infection prevalence and case incidence within sub-Saharan Africa, with consistent year-on-ye
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Journal articleChabuka L, Choga WT, Mavian CN, et al., 2025,
Genomic surveillance of a climate amplified cholera outbreak in Malawi 2022-2023
, Emerging Infectious Diseases, ISSN: 1080-6040 -
Journal articleAdams L, Karachaliou Prasinou A, Trotter C, 2025,
Modelling the impact and cost effectiveness of universal varicella vaccination in England.
, Vaccine, Vol: 50INTRODUCTION: Two distinct diseases are attributable to the varicella zoster virus, varicella (chickenpox) and zoster (shingles). This study assesses the impact and cost-effectiveness of a childhood varicella vaccination program in England. METHODS: We use an age-structured dynamic transmission model and a health economic decision tree. The model incorporates recent data on varicella and zoster epidemiology, including the effects of exogenous boosting on zoster incidence. By simulating various vaccination strategies, including routine and catch-up programs, the study evaluates the potential reduction in varicella and zoster cases due to vaccination and the associated vaccine cost-effectiveness (from the NHS perspective). RESULTS: We find that a two-dose varicella vaccination program could significantly reduce varicella incidence, potentially achieving near-elimination if high coverage rates are maintained. However, the model also predicts a temporary increase in zoster incidence due to reduced natural boosting from varicella exposure; this is partly mitigated by the current zoster vaccination program and the effect is much less substantial than previously estimated. Cost-effectiveness analyses reveal that all vaccination strategies modelled are cost-effective at typical thresholds, with the routine vaccination scenario being the most economically advantageous. Sensitivity analyses demonstrate that vaccine price and varicella treatment costs are the primary drivers of cost-effectiveness. CONCLUSION: The study supports the introduction of a childhood varicella vaccination program in England, which offers substantial health benefits and is highly likely to be cost-effective.
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