Publications

Antimicrobial usage among acutely ill hospitalised children aged 2‒23 months in sub-Saharan Africa and South Asia

Journal article

Tigoi C. et al, (2025), Open Forum Infectious Diseases

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, (2025), Wellcome Open Research, 9, 349 - 349

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

Community-acquired pneumonia identification from electronic health records in the absence of a gold standard: A Bayesian latent class analysis.

Journal article

Wei J. et al, (2025), PLOS digital health, 4

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

Establishing laboratory reference ranges for haematological and biochemical blood parameters in adults and children in Kilifi, Kenya

Journal article

Downs LO. et al, (2025), Wellcome Open Research, 10, 312 - 312

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

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

Journal article

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

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

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

Journal article

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Breadth of Fc-mediated effector function correlates with clinical immunity following human malaria challenge.

Journal article

Nkumama IN. et al, (2024), Immunity, 57, 1215 - 1224.e6

No evidence of difference in mortality with amoxicillin versus co-amoxiclav for hospital treatment of community-acquired pneumonia

Journal article

Wei J. et al, (2024), Journal of Infection, 88, 106161 - 106161

A Phase I trial of Non-invasive Ventilation and seizure prophylaxis with levetiracetam In Children with Cerebral Malaria Trial (NOVICE-M Trial)

Journal article

Maitland K. et al, (2024), Wellcome Open Research, 9, 281 - 281

Assessment of three antibiotic combination regimens against Gram-negative bacteria causing neonatal sepsis in low- and middle-income countries

Journal article

Kakaraskoska Boceska B. et al, (2024), Nature Communications, 15

Evaluation of the accuracy of bacterial genome reconstruction with Oxford Nanopore R10.4.1 long-read-only sequencing

Journal article

Sanderson ND. et al, (2024), Microbial Genomics, 10

Tungiasis among children in Kenya is associated with poor nutrition status, absenteeism, poor school performance and high impact on quality of life.

Journal article

Elson L. et al, (2024), PLoS neglected tropical diseases, 18

Distinct patterns of vital sign and inflammatory marker responses in adults with suspected bloodstream infection

Journal article

Gu Q. et al, (2024), Journal of Infection, 88, 106156 - 106156

Rifampicin resistant Mycobacterium tuberculosis in Vietnam, 2020-2022.

Journal article

Van Nguyen H. et al, (2024), Journal of clinical tuberculosis and other mycobacterial diseases, 35

Author Correction: The plasmidome associated with Gram-negative bloodstream infections: a large-scale observational study using complete plasmid assemblies

Journal article

Lipworth S. et al, (2024), Nature Communications, 15

Distinct patterns of vital sign and inflammatory marker responses in adults with suspected bloodstream infection.

Journal article

Gu Q. et al, (2024), The Journal of infection

Feasibility, safety, and impact of the RTS,S/AS01E malaria vaccine when implemented through national immunisation programmes: evaluation of cluster-randomised introduction of the vaccine in Ghana, Kenya, and Malawi

Journal article

Asante KP. et al, (2024), The Lancet, 403, 1660 - 1670

Rapid antigen testing for SARS-CoV-2 by lateral flow assay: A field evaluation of self- and professional testing at UK community testing sites.

Journal article

Futschik ME. et al, (2024), Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology, 171

SARS-CoV-2, influenza A/B and respiratory syncytial virus positivity and association with influenza-like illness and self-reported symptoms, over the 2022/23 winter season in the UK: a longitudinal surveillance cohort

Journal article

Dietz E. et al, (2024), BMC Medicine, 22

Prediction of pyrazinamide resistance in Mycobacterium tuberculosis using structure-based machine-learning approaches

Journal article

Carter JJ. et al, (2024), JAC-Antimicrobial Resistance, 6

The plasmidome associated with Gram-negative bloodstream infections: A large-scale observational study using complete plasmid assemblies

Journal article

Lipworth S. et al, (2024), Nature Communications, 15

Compensatory mutations are associated with increased in vitro growth in resistant clinical samples of Mycobacterium tuberculosis

Journal article

Brunner VM. and Fowler PW., (2024), Microbial Genomics, 10

Risk of SARS-CoV-2 reinfection during multiple Omicron variant waves in the UK general population

Journal article

Wei J. et al, (2024), Nature Communications, 15

Fourth Controlled Human Infection Model (CHIM) meeting – CHIMs in endemic countries, May 22–23, 2023

Journal article

Kapulu M. et al, (2024), Biologicals, 85, 101747 - 101747

Safety and efficacy of malaria vaccine candidate R21/Matrix-M in African children: a multicentre, double-blind, randomised, phase 3 trial

Journal article

Datoo MS. et al, (2024), The Lancet, 403, 533 - 544

A workflow for the detection of antibiotic residues, measurement of water chemistry and preservation of hospital sink drain samples for metagenomic sequencing

Journal article

Rodger G. et al, (2024), Journal of Hospital Infection, 144, 128 - 136

Quantitative measurement of antibiotic resistance in Mycobacterium tuberculosis reveals genetic determinants of resistance and susceptibility in a target gene approach

Journal article

Barilar I. et al, (2024), Nature Communications, 15

Distinct transcriptomic signatures define febrile malaria depending on initial infective states, asymptomatic or uninfected.

Journal article

Kimenyi KM. et al, (2024), BMC infectious diseases, 24

Comparative performance of the InBios SCoV-2 Detect TM 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

Age-dependent acquisition of IgG antibodies to Shigella serotypes-a retrospective analysis of seroprevalence in Kenyan children with implications for infant vaccination.

Journal article

Kapulu MC. et al, (2024), Frontiers in immunology, 15

Bi-isotype immunoglobulins enhance antibody-mediated neutrophil activity against Plasmodium falciparum parasites.

Journal article

Ogwang R. et al, (2024), Frontiers in immunology, 15

A consensus statement on dual purpose pathogen surveillance systems: The always on approach.

Journal article

van der Westhuizen H-M. et al, (2024), PLOS global public health, 4

Rapid identification of bacterial isolates using microfluidic adaptive channels and multiplexed fluorescence microscopy

Journal article

Chatzimichail S. et al, (2024), Lab on a Chip, 24, 4843 - 4858

Epidemiology and microbiology of recurrent UTI in women in the community in Oxfordshire, UK

Journal article

Vazquez-Montes MDLA. et al, (2023), JAC-Antimicrobial Resistance, 6

Discordance between different bioinformatic methods for identifying resistance genes from short-read genomic data, with a focus on Escherichia coli

Journal article

Davies TJ. et al, (2023), Microbial Genomics, 9

Model-based evaluation of admission screening strategies for the detection and control of carbapenemase-producing Enterobacterales in the English hospital setting

Journal article

Pople D. et al, (2023), BMC Medicine, 21

A new variant of the colistin resistance gene MCR-1 with co-resistance to β-lactam antibiotics reveals a potential novel antimicrobial peptide.

Journal article

Liang L. et al, (2023), PLoS biology, 21

Hostile: accurate decontamination of microbial host sequences.

Journal article

Constantinides B. et al, (2023), Bioinformatics (Oxford, England), 39

Global blood miRNA profiling unravels early signatures of immunogenicity of Ebola vaccine rVSVΔG-ZEBOV-GP

Journal article

Vianello E. et al, (2023), iScience, 26, 108574 - 108574

Antibody responses to recombinant vesicular stomatitis virus-Zaire Ebolavirus vaccination for Ebola virus disease across doses and continents: 5-year durability.

Journal article

Huttner A. et al, (2023), Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases, 29, 1587 - 1594

Erratum: Comparison of R9.4.1/Kit10 and R10/Kit12 Oxford Nanopore flowcells and chemistries in bacterial genome reconstruction

Journal article

Sanderson ND. et al, (2023), Microbial Genomics, 9

Safety and immunogenicity of ChAdOx1 nCoV-19 (AZD1222) vaccine in adults in Kenya: a phase 1/2 single-blind, randomised controlled trial

Journal article

Hamaluba M. et al, (2023), Wellcome Open Research, 8, 182 - 182

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