Publications

A novel framework for quantifying the clinical impact of substandard and falsified antimicrobials: application to typhoid fever.

Preprint

Cavany SM. et al, (2025)

The impact of different antimicrobial exposures on the gut microbiome in the ARMORD observational study

Preprint

Peto L. et al, (2025)

Timeliness of a potential automated system for national surveillance of healthcare-associated infections in England

Journal article

Quan TP. et al, (2025), Journal of Hospital Infection, 161, 10 - 12

Pf8: an open dataset of Plasmodium falciparum genome variation in 33,325 worldwide samples

Journal article

Abdel Hamid MM. et al, (2025), Wellcome Open Research, 10, 325 - 325

An improved catalogue for whole-genome sequencing prediction of bedaquiline resistance in Mycobacterium tuberculosis using a reproducible algorithmic approach

Journal article

Adlard D. et al, (2025), Microbial Genomics, 11

Epidemiology and excess mortality of antimicrobial resistance in bacteraemias among cancer patients: a cohort study using routinely collected health data from regional hospital trusts in Oxford and Oslo, 2008-2018.

Journal article

Danielsen AS. et al, (2025), BMJ Open, 15

To heal or harm: a systematic review of the role of fluoroquinolones in periprosthetic joint infections

Journal article

Tevell S. et al, (2025), CMI Communications, 105103 - 105103

COVID-19 mortality in Africa and Asia - Authors' reply.

Journal article

Bejon P. et al, (2025), Lancet Infect Dis

A pragmatic randomized controlled trial of standard care versus corticosteroids plus standard care for treatment of pneumonia in adults admitted to Kenyan hospitals (SONIA)

Journal article

Lucinde R. et al, (2025), Wellcome Open Research, 7, 269 - 269

An Electronic Health Record-Wide Association Study to identify populations at increased risk ofE. colibloodstream infections

Preprint

Pritchard E. et al, (2025)

Identification of undetected SARS-CoV-2 infections by clustering of Nucleocapsid antibody trajectories

Journal article

Zwerwer LR. et al, (2025), Nature Communications, 16

Benchmarking transformer-based models for medical record deidentification: A single centre, multi-specialty evaluation

Preprint

Kuo R. et al, (2025)

Subpopulations in clinical samples ofM. tuberculosiscan give rise to rifampicin resistance and shed light on how resistance is acquired

Preprint

Brunner VM. and Fowler PW., (2025)

Degradation of circular RNA by the ribonuclease DIS3.

Journal article

Tao X. et al, (2025), Molecular cell, 85, 1674 - 1685.e8

Key SARS-CoV-2 testing strategies implemented in the UK: rationale and impact.

Journal article

Fowler T. et al, (2025), Journal of the Royal Society of Medicine, 118, 112 - 120

Timeliness of a potential automated system for national surveillance of healthcare-associated infections in England

Preprint

Quan TP. et al, (2025)

Transformers and large language models are efficient feature extractors for electronic health record studies

Journal article

Yuan K. et al, (2025), Communications Medicine, 5

Dissemination of OXA-23 carbapenemase-producingProteus mirabilisandEscherichia coliis driven by transposon-carrying lineages in the UK

Preprint

Zamudio R. et al, (2025)

Nanopore adaptive sampling for bacterial identification from periprosthetic joint replacement tissue

Preprint

Street TL. et al, (2025)

Molecular clock complexities of Clostridioides difficile.

Journal article

Vernon JJ. et al, (2025), Anaerobe

Publisher Correction: Muscle abnormalities in Long COVID.

Journal article

Ranque B. et al, (2025), Nature communications, 16

Low-Dose Yellow Fever Vaccine in Adults in Africa

Journal article

Kimathi D. et al, (2025), New England Journal of Medicine, 392, 788 - 797

Deep Learning-based Framework for Mycobacterium Tuberculosis Bacterial Growth Detection for Antimicrobial Susceptibility Testing

Preprint

Vo H-AT. et al, (2025)

The effect of population selection criteria on model estimates and data missingness in electronic health record studies

Preprint

Pritchard E. et al, (2025)

The impact of antimicrobial stewardship ward rounds on antimicrobial use and predictors of advice, uptake, and outcomes

Journal article

Eyre DW. et al, (2025), Journal of Infection, 90, 106419 - 106419

Multi-antigen serology and a diagnostic algorithm for the detection of arbovirus infections as novel tools for arbovirus preparedness in southeast Europe (MERMAIDS-ARBO): a prospective observational study

Journal article

Kasbergen LMR. et al, (2025), The Lancet Infectious Diseases

Prevalence, clinical management, and outcomes of adults hospitalised with endemic arbovirus illness in southeast Europe (MERMAIDS-ARBO): a prospective observational study

Journal article

Sigfrid L. et al, (2025), The Lancet Infectious Diseases

Reply: Muscle abnormalities in Long COVID.

Journal article

Ranque B. et al, (2025), Nature communications, 16

Machine learning and clinician predictions of antibiotic resistance in Enterobacterales bloodstream infections

Journal article

Yuan K. et al, (2025), Journal of Infection, 90, 106388 - 106388

An improved catalogue for whole-genome sequencing prediction of bedaquiline resistance inM. tuberculosisusing a reproducible algorithmic approach

Preprint

Adlard D. et al, (2025)

P-260. Antibiotic residues in hospital sink p-trap water in Kilifi, Kenya

Journal article

Hookham L. et al, (2025), Open Forum Infectious Diseases, 12

Humanity's Last Exam

Preprint

Phan L. et al, (2025)

Predicting rifampicin resistance inM. tuberculosisusing machine learning informed by protein structural and chemical features

Journal article

Lynch CI. et al, (2025), ERJ Open Research, 00952 - 2024

Rapid clinical diagnosis and treatment of common, undetected, and uncultivable bloodstream infections using metagenomic sequencing from routine blood cultures with Oxford Nanopore

Preprint

Govender KN. et al, (2025)

Multiple introductions of NRCS-A Staphylococcus capitis to the neonatal intensive care unit drive neonatal bloodstream infections: a case-control and environmental genomic survey

Journal article

Lees EA. et al, (2025), Microbial Genomics, 11

Leveraging base excision repair for efficient adenine base editing of mitochondrial DNA

Journal article

Fan Y. et al, (2025), Nature Biotechnology

Circular RNA aptamers targeting neuroinflammation ameliorate Alzheimer disease phenotypes in mouse models

Journal article

Feng X. et al, (2025), Nature Biotechnology

Specific and efficient RNA A-to-I editing through cleavage of an ADAR inhibitor

Journal article

Li G. et al, (2025), Nature Biotechnology

Comparative evaluation of swabbing sites for Omicron variant detection in PCR testing.

Journal article

Fowler T. et al, (2025), Diagnostic microbiology and infectious disease, 111

Effectiveness and user experience of nose and throat swabbing techniques for SARS-CoV-2 detection: results from the UK COVID-19 National Testing Programme.

Journal article

Futschik ME. et al, (2025), BMC global and public health, 3

Developing a framework for tracking antimicrobial resistance gene movement in a persistent environmental reservoir

Journal article

Mathers AJ. et al, (2024), npj Antimicrobials and Resistance, 2

Addition of Macrolide Antibiotics for Hospital Treatment of Community-Acquired Pneumonia

Journal article

Wei J. et al, (2024), The Journal of Infectious Diseases

Validation of the Baseline Recurrence Risk in Cellulitis (BRRISC) score and the added impact of acute clinical response

Preprint

Cross ELA. et al, (2024)

Assessing skin temperature over time in a cohort of lower limb cellulitis: A methods comparison study

Preprint

Cross ELA. et al, (2024)

Kinetics of naturally induced binding and neutralising anti-SARS-CoV-2 antibody levels and potencies among SARS-CoV-2 infected Kenyans with diverse grades of COVID-19 severity: an observational study

Journal article

Kimotho J. et al, (2024), Wellcome Open Research, 8, 350 - 350

Detecting changes in population trends in infection surveillance using community SARS-CoV-2 prevalence as an exemplar

Journal article

Pritchard E. et al, (2024), American Journal of Epidemiology, 193, 1848 - 1860

Global genomic epidemiology of bla GES-5 carbapenemase-associated integrons.

Journal article

Matlock W. et al, (2024), Microbial genomics, 10

Corrigendum to “No evidence of difference in mortality with amoxicillin versus co-amoxiclav for hospital treatment of community-acquired pneumonia” [J Infect 88 (2024) 106161]

Journal article

Wei J. et al, (2024), Journal of Infection, 89, 106361 - 106361

Predicting individual patient and hospital-level discharge using machine learning

Journal article

Wei J. et al, (2024), Communications Medicine, 4

Enhancement and validation of the antibiotic resistance prediction performance of a cloud-based genetics processing platform for Mycobacteria

Preprint

Westhead J. et al, (2024)

Footprints of innate immune activity during HIV-1 reservoir cell evolution in early-treated infection

Journal article

Sun W. et al, (2024), Journal of Experimental Medicine, 221

A Comparison of Causative Pathogens in Bone and Prosthetic Joint Infections: Implications for Antimicrobial Therapy.

Journal article

Unsworth A. et al, (2024), Antibiotics (Basel, Switzerland), 13

The use of antibiotic-loaded calcium sulphate beads in debridement, antibiotics, and implant retention (DAIR) for periprosthetic infections: a retrospective comparative cohort on outcome.

Journal article

Sigmund IK. et al, (2024), Acta orthopaedica, 95, 707 - 714

Identification of complex Plasmodium falciparum genetic backgrounds circulating in Africa: a multicountry genomic epidemiology analysis.

Journal article

Miotto O. et al, (2024), The Lancet. Microbe

Prospective clinical surveillance for severe acute respiratory illness and COVID-19 vaccine effectiveness in Kenyan hospitals during the COVID-19 pandemic.

Journal article

Lucinde RK. et al, (2024), BMC infectious diseases, 24

Exploring uncatalogued genetic variation in antimicrobial resistance gene families in Escherichia coli: an observational analysis

Journal article

Lipworth S. et al, (2024), The Lancet Microbe, 5, 100913 - 100913

Comparison of direct cDNA and PCR-cDNA Nanopore sequencing of RNA from Escherichia coli isolates

Journal article

Rodger G. et al, (2024), Microbial Genomics, 10

Diversity, functional classification and genotyping of SHV β-lactamases in Klebsiella pneumoniae

Journal article

Tsang KK. et al, (2024), Microbial Genomics, 10

Identification of undetected SARS-CoV-2 infections by clustering of Nucleocapsid antibody trajectories

Preprint

Zwerwer LR. et al, (2024)

Effects of the COVID-19 pandemic on hospital admissions and inpatient mortality in Kenya: a retrospective cohort study

Journal article

Ogero MO. et al, (2024), Wellcome Open Research, 9, 582 - 582

Comparative evaluation of large-language models and purpose-built software for medical record de-identification

Preprint

Kuo R. et al, (2024)

How, why and when are delayed (back-up) antibiotic prescriptions used in primary care? A realist review integrating concepts of uncertainty in healthcare

Journal article

Mcleod M. et al, (2024), BMC Public Health, 24

Predicting future hospital antimicrobial resistance prevalence using machine learning

Journal article

Vihta K-D. et al, (2024), Communications Medicine, 4

Preference Fine-Tuning for Factuality in Chest X-Ray Interpretation Models Without Human Feedback

Preprint

Hein D. et al, (2024)

Establishing laboratory reference ranges for adults and children in Kilifi, Kenya

Preprint

Downs LO. et al, (2024)

Dissemination and persistence of antimicrobial resistance (AMR) along the wastewater-river continuum

Journal article

Read DS. et al, (2024), Water Research, 264, 122204 - 122204

Antibodies to PfEMP1 and variant surface antigens: Protection after controlled human malaria infection in semi-immune Kenyan adults.

Journal article

Kinyua AW. et al, (2024), The Journal of infection, 89

Long Covid: a global health issue - a prospective, cohort study set in four continents.

Journal article

Pazukhina E. et al, (2024), BMJ global health, 9

Overview of the First Shared Task on Clinical Text Generation: RRG24 and "Discharge Me!"

Preprint

Xu J. et al, (2024)

Developing a novel approach to complex evolution of antimicrobial resistance via mobile genetic elements from a persistent environmental biofilm

Preprint

Mathers A. et al, (2024)

Genomic epidemiology and longitudinal sampling of ward wastewater environments and patients reveals complexity of the transmission dynamics of blaKPC-carbapenemase-producing Enterobacterales in a hospital setting

Journal article

Stoesser N. et al, (2024), JAC-Antimicrobial Resistance, 6

Global, regional, and national incidence and mortality burden of non-COVID-19 lower respiratory infections and aetiologies, 1990-2021: a systematic analysis from the Global Burden of Disease Study 2021.

Journal article

GBD 2021 Lower Respiratory Infections and Antimicrobial Resistance Collaborators None., (2024), The Lancet. Infectious diseases, 24, 974 - 1002

A retrospective analysis of P. falciparum drug resistance markers detects an early (2016/17) high prevalence of the k13 C469Y mutation in asymptomatic infections in Northern Uganda.

Journal article

Ogwang R. et al, (2024), Antimicrobial agents and chemotherapy, 68

Expanding the use of mathematical modeling in healthcare epidemiology and infection prevention and control.

Journal article

Grant R. et al, (2024), Infection control and hospital epidemiology, 1 - 6

Double testing with lateral flow antigen test devices for COVID-19: does a second test in quick succession add value?

Journal article

Futschik ME. et al, (2024), Journal of virological methods, 329

Global burden of bacterial antimicrobial resistance 1990–2021: a systematic analysis with forecasts to 2050

Journal article

Naghavi M. et al, (2024), The Lancet, 404, 1199 - 1226

Infection Inspection: using the power of citizen science for image-based prediction of antibiotic resistance in Escherichia coli treated with ciprofloxacin

Journal article

Farrar A. et al, (2024), Scientific Reports, 14

Why Was the Azithromycin “for Life” Trial Necessary?

Other

Maitland K. and Walker AS., (2024), New England Journal of Medicine, 391, 760 - 762

The mRNA content of plasma extracellular vesicles provides a window into molecular processes in the brain during cerebral malaria

Journal article

Kioko M. et al, (2024), Science Advances, 10

Predicting rifampicin resistance inM. tuberculosisusing machine learning informed by protein structural and chemical features

Preprint

Lynch CI. et al, (2024)

R21 malaria vaccine is protective against intradermal but not intravenousPlasmodium falciparumsporozoites in a randomized controlled human malaria infection study in Kenyan adults

Preprint

Kapulu MC. et al, (2024)

Quantitative drug susceptibility testing for Mycobacterium tuberculosis using unassembled sequencing data and machine learning

Journal article

(2024), PLOS Computational Biology, 20, e1012260 - e1012260

Full-length MSP1 is a major target of protective immunity after controlled human malaria infection.

Journal article

Rosenkranz M. et al, (2024), Life science alliance, 7

MmpR5 protein truncation and bedaquiline resistance in Mycobacterium tuberculosis isolates from South Africa: a genomic analysis.

Journal article

Roberts LW. et al, (2024), The Lancet. Microbe, 5

Self-swabbing versus assisted swabbing for viral detection by qRT-PCR: the experience from SARS-CoV-2 based on a meta-analysis of six prospectively designed evaluations conducted in a UK setting.

Journal article

Fowler T. et al, (2024), European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology, 43, 1621 - 1630

Optimising Clinical Epidemiology in Disease Outbreaks: Analysis of ISARIC-WHO COVID-19 Case Report Form Utilisation.

Journal article

Merson L. et al, (2024), Epidemiologia (Basel, Switzerland), 5, 557 - 580

The impact of different antimicrobial exposures on the gut microbiome in the ARMORD observational study

Preprint

Peto L. et al, (2024)

The impact of different antimicrobial exposures on the gut microbiome in the ARMORD observational study

Preprint

Peto L. et al, (2024)

Retrospective analysis of hospital electronic health records reveals unseen cases of acute hepatitis with unknown aetiology in adults in Oxfordshire

Journal article

Tan CCS. et al, (2024), BMC Public Health, 24

Improving nitrofurantoin resistance prediction in Escherichia coli from whole-genome sequence by integrating NfsA/B enzyme assays

Journal article

Dulyayangkul P. et al, (2024), Antimicrobial Agents and Chemotherapy, 68

The implementation of whole-genome sequencing for Mycobacterium tuberculosis in Vietnam.

Journal article

Huong DT. et al, (2024), IJTLD open, 1, 320 - 322

Linking Cerebral Malaria Pathogenesis to APOE-Mediated Amyloidosis: Observations and Hypothesis.

Journal article

Kioko M. et al, (2024), Molecular neurobiology

At-admission prediction of mortality and pulmonary embolism in an international cohort of hospitalised patients with COVID-19 using statistical and machine learning methods.

Journal article

Mesinovic M. et al, (2024), Scientific reports, 14

Comparative performance of the InBios SCoV-2 DetectTM IgG ELISA and the in-house KWTRP ELISA in detecting SARS-CoV-2 spike IgG antibodies in Kenyan populations

Journal article

Kutima B. et al, (2024), Wellcome Open Research, 9, 349 - 349

ACES: Automatic Cohort Extraction System for Event-Stream Datasets

Preprint

Xu J. et al, (2024)

Improving the representativeness of UK’s national COVID-19 Infection Survey through spatio-temporal regression and post-stratification

Journal article

Pouwels KB. et al, (2024), Nature Communications, 15

Ribosome Phenotypes Enable Rapid Antibiotic Susceptibility Testing inEscherichia coli

Preprint

Farrar A. et al, (2024)

Utility of MALDI-TOF MS for determination of species identity and blood meal sources of primary malaria vectors on the Kenyan coast

Journal article

Karisa J. et al, (2024), Wellcome Open Research, 8, 151 - 151

Nanopore sequencing of influenza A and B in Oxfordshire and the United Kingdom, 2022–23

Journal article

Cane J. et al, (2024), Journal of Infection, 88, 106164 - 106164

Harvesting and amplifying gene cassettes confers cross-resistance to critically important antibiotics.

Journal article

Dulyayangkul P. et al, (2024), PLoS pathogens, 20

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