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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 articleDuchêne DA, Chowdhury A-A, Yang J, et al., 2025,
Drivers of avian genomic change revealed by evolutionary rate decomposition.
, NatureModern birds have diversified into a striking array of forms, behaviours and ecological roles. Analyses of molecular evolutionary rates can reveal the links between genomic and phenotypic change1-4, but disentangling the drivers of rate variation at the whole-genome scale has been difficult. Using comprehensive estimates of traits and evolutionary rates across a family-level phylogeny of birds5,6, we find that genome-wide mutation rates across lineages are predominantly explained by clutch size and generation length, whereas rate variation across genes is driven by the content of guanine and cytosine. Here, to find the subsets of genes and lineages that dominate evolutionary rate variation in birds, we estimated the influence of individual lineages on decomposed axes of gene-specific evolutionary rates. We find that most of the rate variation occurs along recent branches of the tree, associated with present-day families of birds. Additional tests on axes of rate variation show rapid changes in microchromosomes immediately after the Cretaceous-Palaeogene transition. These apparent pulses of evolution are consistent with major changes in the genetic machineries for meiosis, heart performance, and RNA splicing, surveillance and translation, and correlate with the ecological diversity reflected in increased tarsus length. Collectively, our analyses paint a nuanced picture of avian evolution, revealing that the ancestors of the most diverse lineages of birds underwent major genomic changes related to mutation, gene usage and niche expansion in the early Palaeogene period.
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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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Journal articleMeier-Scherling CPG, Watson OJ, Asua V, et al., 2025,
Selection of Plasmodium falciparum kelch13 mutations in Uganda in comparison with southeast Asia: a modelling study
, The Lancet Microbe, ISSN: 2666-5247BackgroundArtemisinin partial resistance, mediated by mutations in the Plasmodium falciparum kelch13 gene (k13), rapidly spread in southeast Asia, undermining the antimalarial effectiveness of artemisinin-based combination therapies. k13 mutations have also arisen in Africa, but their rates of increase are not well characterised. We aimed to quantify the selection of k13 mutations in Africa and compare the selection with that in southeast Asia.MethodsIn this modelling study, we investigated k13 mutation allele frequency at 16 sites in Uganda (2016–22) and five sites in southeast Asia (in Cambodia, Thailand, and Viet Nam; 2003–14). The Ugandan data were obtained from annual clinical surveillance studies and the southeast Asian data were obtained from the MalariaGEN Pf7 dataset. We investigated five validated and candidate k13 mutations: Pro441Leu, Cys469Phe, Cys469Tyr, Arg561His, and Ala675Val. We calculated annual selection coefficients using Bayesian mixed-effect linear models. We then tested whether the k13 mutation allele frequency in southeast Asia could have been forecast accurately using up to the first 5 years of available data and forecast future k13 mutation allele frequency in Uganda.FindingsWe used data from 7564 samples from Uganda and 6568 samples from southeast Asia. The annual selection coefficient of evaluable k13 mutations (Pro441Leu, Cys469Phe/Tyr, Arg561His, and Ala675Val) across all sites was estimated at 0·381 (95% credible interval 0·298 to 0·472) per year, a 38% increase in relative allele frequency. Selection coefficients across Uganda were 0·494 (−0·462 to 1·410) for Pro441Leu, 0·324 (−0·629 to 1·150) for Cys469Phe, 0·383 (0·207 to 0·591) for Cys469Tyr, and 0·237 (0·087 to 0·403) for Ala675Val. In southeast Asia, the selection coefficients were 0·627 (−0·088 to 1·312) for Cys580Tyr, 0&mid
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Journal articleDjaafara B, Sherrard-Smith E, Churcher T, et al., 2025,
Spatiotemporal heterogeneity in malaria transmission across Indonesia: analysis of routine surveillance data 2010-2019
, BMC Medicine, Vol: 23, ISSN: 1741-7015BackgroundIndonesia faces challenges in achieving its goal of eliminating malaria by 2030, with cases stagnating between 2015 and 2019. This study analysed regional epidemiological trends and demographic changes in malaria cases from 2010 to 2019, considering differences in surveillance across the country.MethodsWe analysed national and sub-national malaria routine surveillance data using generalised additive and generalised linear models to assess temporal trends in case reporting, test positivity, demographics, and parasite species distribution while accounting for surveillance variations.ResultsAfter adjusting for increased testing from 2015 onwards, we estimated declining malaria incidence in six of seven Indonesian regions. These regions showed a demographic shift toward older, predominantly male cases, suggesting a transition from household to occupational transmission. In contrast, Papua maintained high transmission with cases concentrated in children. Despite comprising only 2% of Indonesia’s population, Papua’s contribution to national malaria cases rose from 40 to 90% (2010–2019).ConclusionWhile most Indonesian regions progress toward elimination by addressing mobile and migrant populations and P. vivax transmission, Papua shows different patterns with persistently high transmission among children. Achieving nationwide elimination requires enhanced control measures, improved healthcare access, and strengthened multisectoral collaboration to address these region-specific challenges.
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ReportWinskill P, Haile L, Ruybal-Pesántez S, et al., 2025,
Rapid response modelled estimates of the effect of the US global aid freeze on President’s Malaria Initiative impact in sub-Saharan Africa
The current freeze on US global aid has the potential to disrupt critical live-saving activities of the President’s Malaria Initiative (PMI). Disruptions or cessation of planned PMI activities in 2025, with no mitigation, could result in an estimated additional 84,200 (95% CI: 69,300, 98,100) malaria deaths in sub-Saharan Africa over the course of 2025. Empirical observations and modelled scenarios highlight the speed at which malaria can resurge following the cessation of core interventions.
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Journal articleKulkarni SG, Laurent S, Miotto P, et al., 2025,
Multivariable regression models improve accuracy and sensitive grading of antibiotic resistance mutations in Mycobacterium tuberculosis.
, Nat Commun, Vol: 16Rapid genotype-based drug susceptibility testing for the Mycobacterium tuberculosis complex (MTBC) relies on a comprehensive knowledgebase of the genetic determinants of resistance. Here we present a catalogue of resistance-associated mutations using a regression-based approach and benchmark it against the 2nd edition of the World Health Organisation (WHO) mutation catalogue. We train multivariate logistic regression models on over 52,000 MTBC isolates to associate binary resistance phenotypes for 15 antitubercular drugs with variants extracted from candidate resistance genes. Regression detects 450/457 (98%) resistance-associated variants identified using the existing method (a.k.a, SOLO method) and grades 221 (29%) more total variants than SOLO. The regression-based catalogue achieves higher sensitivity on average (+3.2 percentage points, pp) than SOLO with smaller average decreases in specificity (-1.0 pp) and positive predictive value (-1.6 pp). Sensitivity gains are highest for ethambutol, clofazimine, streptomycin, and ethionamide as regression graded considerably more resistance-associated variants than SOLO for these drugs. There is no difference between SOLO and regression with regards to meeting the target product profiles set by the WHO for genetic drug susceptibility testing, except for rifampicin, for which regression specificity is below the threshold of 98% at 97%. The regression pipeline also detects isoniazid resistance compensatory mutations in ahpC and variants linked to bedaquiline and aminoglycoside hypersusceptibility. These results inform the continued development of targeted next generation sequencing, whole genome sequencing, and other commercial molecular assays for diagnosing resistance in the MTBC.
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