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• Journal article
  Gmeiner A, Ivanova M, Njage PMK, Hansen LT, Chindelevitch L, Leekitcharoenphon Pet al., 2025,

  Quantitative prediction of disinfectant tolerance in <i>Listeria monocytogenes</i> using whole genome sequencing and machine learning

  , SCIENTIFIC REPORTS, Vol: 15, ISSN: 2045-2322
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• Journal article
  Auzenbergs M, Abbas K, Peak CM, Voorman A, Jit M, O'Reilly KMet al., 2025,

  Vaccination strategies against wild poliomyelitis in polio-free settings: outbreak risk modelling study and cost-effectiveness analysis

  , BMJ GLOBAL HEALTH, Vol: 10, ISSN: 2059-7908
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• Journal article
  Weiss DJ, Dzianach PA, Saddler A, Lubinda J, Browne A, McPhail M, Rumisha SF, Sanna F, Gelaw Y, Kiss JB, Hafsia S, Jayaseelen R, Baggen HS, Amratia P, Bertozzi-Villa A, Nesbit O, Whisnant J, Battle KE, Nguyen M, Alene KA, Cameron E, Penny MA, Bhatt S, Smith DL, Symons TL, Mosser JF, Murray CJL, Hay S, Gething PWet 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: 979-990, ISSN: 0140-6736
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  • Citations: 9
• Journal article
  Chabuka L, Choga WT, Mavian CN, Moir M, Morgenstern C, Tegally H, Sharma A, Wilkinson E, Naidoo Y, Inward R, Bhatt S, Wint GRW, Khan K, Bogoch II, Kraemer MUG, Lourenço J, Baxter C, Tagliamonte M, Salemi M, Lessells R, Mitambo C, Chitatanga R, Bitilinyu-Bango J, Chiwaula M, Chavula Y, Bukhu M, Manda H, Chitenje M, Malolo I, Mwanyongo A, Mvula B, Nyenje M, de Oliveira T, Kagoli Met al., 2025,

  Genomic surveillance of a climate amplified cholera outbreak in Malawi 2022-2023

  , Emerging Infectious Diseases, ISSN: 1080-6040
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• Journal article
  Ahmed AN, Fornace KM, Iwamura T, Murray KAet al., 2025,

  Human animal contact, land use change and zoonotic disease risk: a protocol for systematic review.

  , Syst Rev, Vol: 14

  BACKGROUND: Zoonotic diseases pose a significant risk to human health globally. The interrelationship between humans, animals, and the environment plays a key role in the transmission of zoonotic infections. Human-animal contact (HAC) is particularly important in this relationship, where it serves as the pivotal interaction for pathogen spillover to occur from an animal reservoir to a human. In the context of disease emergence linked to land-use change, increased HAC as a result of land changes (e.g., deforestation, agricultural expansion, habitat degradation) is frequently cited as a key mechanism. We propose to conduct a systematic literature review to map and assess the quality of current evidence linking changes in HAC to zoonotic disease emergence as a result of land-use change. METHOD: We developed a search protocol to be conducted in eight (8) databases: Medline, Embase, Global Health, Web of Science, Scopus, AGRIS, Africa-Wide Info, and Global Index Medicus. The review will follow standard systematic review methods and will be reported according to the Preferred Reporting Items for Systematic reviews and Meta-Analysis (PRISMA) guidelines. The search will consist of building a search strategy, database search, and a snowballing search of references from retrieved relevant articles. The search strategy will be developed for Medline (through PubMed) and EMBASE databases. The search strategy will then be applied to all eight (8) databases. Retrieved articles will be exported to EndNote 20 where duplicates will be removed and exported to Rayyan®, to screen papers using their title and abstract. Screening will be conducted by two independent reviewers and data extraction will be performed using a data extraction form. Articles retrieved will be assessed using study quality appraisal tools (OHAT-Office for Health Assessment and Technology Risk of Bias Rating Tool for Human and Animal Studies, CCS-Case Control Studies, OCCSS-Observational Cohort and Cross-Sectio

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• Journal article
  Adams L, Prasinou AK, Trotter C, 2025,

  Modelling the impact and cost effectiveness of universal varicella vaccination in England

  , VACCINE, Vol: 50, ISSN: 0264-410X
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  • Citations: 1
• Journal article
  Meier-Scherling CPG, Watson OJ, Asua V, Ghinai I, Katairo T, Garg S, Conrad MD, Rosenthal PJ, Okell LC, Bailey JAet al., 2025,

  Selection of Plasmodium falciparum kelch13 mutations in Uganda in comparison with southeast Asia: a modelling study

  , The Lancet Microbe, ISSN: 2666-5247

  BackgroundArtemisinin 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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• Report
  Winskill P, Haile L, Ruybal-Pesántez S, Simmons O, Topazian H, Okell Let 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 article
  Djaafara B, Sherrard-Smith E, Churcher T, Fajariyani SB, Prameswari HD, Herdiana H, Puspadewi RT, Lestari KD, Elyazar IRF, Walker Pet al., 2025,

  Spatiotemporal heterogeneity in malaria transmission across Indonesia: analysis of routine surveillance data 2010-2019

  , BMC Medicine, Vol: 23, ISSN: 1741-7015

  BackgroundIndonesia 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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• Journal article
  Kulkarni SG, Laurent S, Miotto P, Walker TM, Chindelevitch L, Nathanson C-M, Ismail N, Rodwell TC, Farhat MRet al., 2025,

  Multivariable regression models improve accuracy and sensitive grading of antibiotic resistance mutations in <i>Mycobacterium tuberculosis</i>

  , NATURE COMMUNICATIONS, Vol: 16
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  • Citations: 2

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