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Journal articleHowes A, Stringer A, Flaxman SR, et al., 2026,
Fast approximate Bayesian inference of HIV indicators using PCA adaptive Gauss-Hermite quadrature
, Journal of Theoretical Biology, Vol: 618, ISSN: 0022-5193Naomi is a spatial evidence synthesis model used to produce district-level HIV epidemic indicators in sub-Saharan Africa. Multiple outcomes of policy interest, including HIV prevalence, HIV incidence, and antiretroviral therapy treatment coverage are jointly modelled using both household survey data and routinely reported health system data. The model is provided as a tool for countries to input their data to and generate estimates with during a yearly process supported by UNAIDS. Previously, inference has been conducted using empirical Bayes and a Gaussian approximation, implemented via the TMB R package. We propose a new inference method based on an extension of adaptive Gauss-Hermite quadrature to deal with more than 20 hyperparameters. Using data from Malawi, our method improves the accuracy of inferences for model parameters, while being substantially faster to run than Hamiltonian Monte Carlo with the No-U-Turn sampler. Our implementation leverages the existing TMB C++ template for the model’s log-posterior, and is compatible with any model with such a template.
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Journal articleBose I, Hadida G, Green R, et al., 2026,
Rainfall and water-related diseases, malnutrition and mortality in Low- and Middle- Income Countries: a systematic review of the epidemiological evidence
, Heliyon, Vol: 12Background Climate change is altering rainfall patterns. Rainfall has been linked to numerous health outcomes, through the impacts on water quality and quantity, but the coherence and strength of evidence across outcomes remain unclear. Objectives Understand and evaluate the strength of evidence on associations between rainfall (both low and heavy events) and health outcomes in Low- and Middle- Income Countries (LMICs). Methods A systematic review of peer-reviewed epidemiological studies quantifying associations between rainfall and human health outcomes in LMIC populations was conducted. Seven databases were searched including MEDLINE and EMBASE. Study quality was evaluated using 9 modified criteria that were previously used to assess environmental epidemiology studies. The strength of evidence for each health outcome was assessed across rainfall exposures. Results Of 23,579 papers identified, 177 met the inclusion criteria. Health outcomes included diarrheal diseases (n = 119); malnutrition (n = 35); mortality (n = 21); helminth infections (n = 6), and eye infections (n = 4). There was moderately strong evidence for positive associations between both heavy and low rainfall and all-cause diarrhea. Evidence for undernutrition was mixed, with moderate evidence of a positive association with low rainfall. Despite sharing causal pathways, diarrheal disease and nutrition studies found contrasting results for heavy rainfall, likely due to differing study designs. Studies were heterogenous in design, rainfall exposure definitions, and lag times. Studies also often lacked a clear hypothesis. Discussion There is substantial evidence that rainfall affects health in LMICs through multiple pathways. Limitations in the data (often from cross-sectional surveys) and study designs, limit the strength of evidence for several health outcomes. Specifically, studies frequently used inappropriate exposures or lags to reflect the causal pathways. In future studies, efforts should be dir
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Journal articleLamberte LE, Darby EM, Kiu R, et al., 2025,
<i>Staphylococcus haemolyticus</i> is a reservoir of antibiotic resistance genes in the preterm infant gut
, GUT MICROBES, Vol: 17, ISSN: 1949-0976 -
Journal articleTapsoba M, Guelbeogo WM, Sanou A, et al., 2025,
Differential effects of dual and synergist-based insecticide-treated bed nets on pyrethroid resistance and L995F/S knockdown resistance mutation dynamics in Anopheles gambiae s.l. populations in south-western Burkina Faso
, Parasites & Vectors<jats:title>Abstract</jats:title> <jats:sec> <jats:title>Background</jats:title> <jats:p> The introduction of next-generation insecticide-treated nets (ITNs) in Burkina Faso aims to mitigate pyrethroid resistance in malaria vectors. This study evaluated the impact of different ITN types on phenotypic resistance and <jats:italic>kdr</jats:italic> mutation frequencies in <jats:italic>Anopheles gambiae</jats:italic> sensus lacto (s.l.) populations across three health districts over 3 years. </jats:p> </jats:sec> <jats:sec> <jats:title>Methods</jats:title> <jats:p> Annual mosquito collections were conducted in Banfora (where pyrethroid–chlorfenapyr nets had been distributed), Gaoua (pyrethroid-only ITNs) and Orodara (pyrethroid–piperonyl butoxide [PBO] ITNs). Two populations were analysed: adult females collected directly from the field and those reared from field-collected larvae. World Health Organization (WHO) susceptibility bioassays measured 24-h mortality after exposure to 1×, 5× and 10× concentrations of deltamethrin and alphacypermethrin, with and without pre-exposure to piperonyl butoxide. Frequencies of <jats:italic>kdr</jats:italic> mutations <jats:italic>L995F</jats:italic> and <jats:italic>L995S</jats:italic> were determined by polymerase chain reaction (PCR). </jats:p> </jats:sec> <jats:sec> <jats:title&
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Journal articleGifford H, Bedekovic T, Helmstetter N, et al., 2025,
Xenosiderophore transporter gene expression and clade-specific filamentation in Candida auris killifish (Aphanius dispar) infection.
, Commun Biol, Vol: 8Candida auris is a critical priority fungal pathogen (World Health Organization). Clinical management is challenging, with high associated mortality, rapidly increasing antifungal resistance, and frequent nosocomial outbreaks. A critical bottleneck in understanding virulence is the lack of gene expression profiling models during infection. We developed a fish embryo yolk-sac microinjection model using Aphanius dispar (Arabian killifish; AK) at human body temperature. This enabled interrogation of infection dynamics via dual host-pathogen RNA-seq across five major clades of C. auris (I-V). Host responses included heat shock, complement activation, and nutritional immunity, notably haem oxygenase (HMOX) expression during clade IV infection. We identified a pathogen transcriptional signature across all five clades, strongly enriched for putative xenosiderophore transmembrane transporter candidate (XTC) genes. We describe this family and a sub-clade of five putative haem transport-related (HTR) genes. Only the basal clade V isolate formed filaments, associated with canonical and atypical regulators of morphogenesis. Clades I and IV demonstrated increased virulence, accompanied by up-regulation of three HTR genes in clade IV, and the non-mating mating-type locus (MTL) gene PIKA in both clades. Our study provides insights into C. auris pathogenesis, highlighting species-wide in vivo up-regulation of XTC genes during host tissue infection.
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Journal articleBasanez M-G, Amaral LJTDMD, Walker M, et al., 2025,
Reaching elimination of onchocerciasis transmission with long-term vector control and ivermectin treatment in togo
, Nature Communications, ISSN: 2041-1723The Onchocerciasis Control Programme in West Africa implemented vector control (VC) and ivermectin mass drug administration (MDA) to eliminate blindness, intensifying efforts in Special Intervention Zones (SIZ). Togo aims to eliminate onchocerciasis transmission (EOT) by 2030. We use the EPIONCHO-IBM model to project microfilarial prevalence trends across Togo’s five regions by SIZ status, MDA coverage (65%-80%) and VC efficacy (60%-100%). We compare projections with prevalence surveys (400 villages, 1970-2017) stratified by hypoendemic, mesoendemic, hyperendemic, and holoendemic baseline endemicity, and calculate EOT probabilities for 2024, 2027, and 2030. Combined VC and MDA reduced prevalence nationwide. After cessation of VC, prevalence continued to decline in hypo-to mesoendemic areas under annual MDA, while hyperendemic areas required biannual MDA. In holoendemic areas, prevalence rebounded even with biannual MDA, indicating that alternative strategies are needed. EPIONCHO-IBM reproduces Togo’s onchocerciasis trends throughout five decades of intervention and provides a transferable framework to guide policy towards 2030 goals.
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Journal articleGrégoire V, Zhu AW, Brown CM, et al., 2025,
Public reporting guidelines for outbreak data: Enabling accountability for effective outbreak response by developing standards for transparency and uniformity.
, Public Health, Vol: 251OBJECTIVES: There are few standards for what information about an infectious disease outbreak should be reported to the public and when. To address this problem, we undertook a consensus process to develop recommendations for what epidemiological information public health authorities should report to the public during an outbreak. STUDY DESIGN: We conducted a Delphi study following the steps outlined in the ACcurate COnsensus Reporting Document (ACCORD) for health-related activities or research. METHODS: We assembled a steering committee of nine experts representing federal and state public health, academia, and international partners to develop a candidate list of reporting items. We then invited 45 experts, 35 of whom agreed to participate in a Delphi panel. Of those, 25 participated in voting in the first round, 25 in the second round, and 25 in the third round, demonstrating consistent engagement in the consensus-building process. The final stage of the Delphi process consisted of a hybrid consensus meeting to finalize the voting items. RESULTS: The Delphi process yielded nine core reporting items representing a minimum standard for public outbreak reporting: numbers of new confirmed cases, new hospital admissions, new deaths, cumulative confirmed cases, cumulative hospital admissions, and cumulative deaths, each reported weekly and at Administrative Level 1 (typically state or province), and stratified by sex, age group, and race/ethnicity. CONCLUSIONS: This minimum reporting standard creates a strong framework for uniform sharing of outbreak information and promotes consistency of data between jurisdictions, enabling effective response by promoting access to information about an unfolding epidemic.
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Journal articleTapsoba M, Guelbeogo WM, Sanou A, et al., 2025,
Three-year trends in malaria transmission parameters under deployment of Interceptor®G1, Interceptor®G2 and PermaNet®3.0 insecticide-treated bed nets in South-Western Burkina Faso
, Malaria Journal, ISSN: 1475-2875BackgroundIn South-Western Burkina Faso, where malaria remains highly endemic, the widespread resistance of Anopheles mosquitoes to pyrethroid is reducing the effectiveness of insecticide-treated nets (ITNs). This study assessed 3-year trends in key entomological indicators following the deployment of standard pyrethroid-only (Interceptor®G1), dual-AI pyrethroid-chlorfenapyr (Interceptor®G2) and pyrethroid-PBO (PermaNet®3.0).MethodsA longitudinal entomological study was conducted from August 2019 to February 2022 in three malaria-endemic health districts, each receiving a different ITN type. Weekly mosquito sampling was conduct in three villages per district using Human Landing Catches at two households and CDC light traps at six households. Mosquitoes were morphologically and molecularly identified, and Plasmodium falciparum infection was detected by PCR. Key indicators included mosquito density, biting behaviour, sporozoite infection rate (SIR), and entomological inoculation rate (EIR).ResultsA total of 73,101 female Anopheles mosquitoes were collected. The dominant vector species was An. gambiae s.l. (> 59%), with An. coluzzii prevalent in Banfora (65.5%) and An. gambiae s.s. in Gaoua (91%) and Orodara (83.3%). In Banfora, where Pyr-CFR Interceptor G2 nets were deployed, Anopheles density declined by 88.7% over the 3 years. In Gaoua (Pyr-only ITNs), mosquito density declined initially but rebounded in year 3. In Orodara (Pyr-PBO ITNs), densities remained relatively stable. Trends in SIR and EIR mirrored those in vector density, with decline in year 2 followed by resurgences in Banfora and Gaoua during year 3.ConclusionDual-AI nets, particularly Pyr-CFR Interceptor®G2, were associated with sustained reductions in mosquito density and transmission indicators over 2 years. However, resurgence of entomological indices by the third year highlights the need for improved ITN durability and complementary vector control strategies. Continuous ent
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Journal articleKatsiferis A, Joensen A, Petersen LV, et al., 2025,
"Developing machine learning models of self-reported and register-based data to predict eating disorders in adolescence".
, Npj Ment Health Res, Vol: 4Early detection and prevention of eating disorders (EDs) in adolescence are crucial yet challenging. We developed and validated diagnostic and prognostic models to predict EDs using data from 44,357 Danish National Birth Cohort participants. Models were trained to identify ED presence in early and late adolescence (11- and 18-year follow-up), utilizing approximately 100 predictors from self-reported and registry-based data. The machine learning model demonstrated strong discrimination for both tasks (diagnostic Area Under the receiver operating characteristic Curve = 81.3; prognostic AUC = 76.9), while a logistic regression model using the top 10 predictors achieved comparable performance. Sex, emotional symptoms, peer relationship and conduct problems, stress levels, parental BMI values, body dissatisfaction, and BMI at the 7-year follow-up emerged as key predictors. Our models showed potential utility in supporting clinical risk assessment, particularly for low-risk preventive interventions, though further validation studies are needed to evaluate their effectiveness in real-world clinical settings.
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Journal articleBouchali R, Sentenac H, Bates KA, et al., 2025,
Unraveling the disease pyramid: the role of environmental micro-eukaryotes in amphibian resistance to the deadly fungal pathogen Batrachochytrium dendrobatidis.
, mSystemsThe disease pyramid conceptualizes the predictors of host infection risk, linking the host, the pathogen, environmental conditions, and both host and environmental microbiomes. However, the importance of the interaction between environmental and host-associated microbiomes in shaping infectious disease dynamics remains poorly understood. While the majority of studies have focused on bacteria, the role of micro-eukaryotes has been seldom investigated. Here, we explore three axes of the disease pyramid using an 18S rRNA gene metabarcoding approach to analyze the micro-eukaryotic assemblages of biofilm, water, and skin samples from three European amphibian species. Skin bacterial communities of the investigated amphibian populations have already been shown to be impacted by the presence of the lethal fungal pathogen Batrachochytrium dendrobatidis (Bd), with a higher abundance of protective bacteria in infected populations and a greater environmental microbial contribution to the skin microbiota in Bd-positive lakes. Here, we explored the relationships between the micro-eukaryotic skin communities of these tadpole populations with their surrounding environment. Tadpoles were sampled at 22 mountain lakes located in the Pyrenees (France), 8 of which harbored amphibian populations infected by Bd. We found that biofilms from Bd-negative lakes had higher environmental micro-eukaryotic diversity and a greater abundance of putative anti-Bd fungi, both in the environment and on the skin microbiota of Bufo spinosus and Rana temporaria, but not of Alytes obstetricans. Bayesian SourceTracker analysis further showed that the environmental contribution from biofilms to amphibian skin micro-eukaryotic assemblages was higher in Bd-positive lakes for B. spinosus and R. temporaria, but not for A. obstetricans.IMPORTANCEResearch on host-associated microbiomes and infectious diseases has mostly focused on bacteria, overlooking the potential contributions of micro-eukaryotes to infection d
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