Publications
Latest publications
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Subpopulations in clinical samples ofM. tuberculosiscan give rise to rifampicin resistance and shed light on how resistance is acquired
Brunner VM. and Fowler PW., (2025)
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Timeliness of a potential automated system for national surveillance of healthcare-associated infections in England
Quan TP. et al, (2025)
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Dissemination of OXA-23 carbapenemase-producingProteus mirabilisandEscherichia coliis driven by transposon-carrying lineages in the UK
Zamudio R. et al, (2025)
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Nanopore adaptive sampling for bacterial identification from periprosthetic joint replacement tissue
Street TL. et al, (2025)
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Deep Learning-based Framework for Mycobacterium Tuberculosis Bacterial Growth Detection for Antimicrobial Susceptibility Testing
Vo H-AT. et al, (2025)
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Machine learning and clinician predictions of antibiotic resistance in Enterobacterales bloodstream infections
Yuan K. et al, (2025), Journal of Infection, 90, 106388 - 106388
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An improved catalogue for whole-genome sequencing prediction of bedaquiline resistance inM. tuberculosisusing a reproducible algorithmic approach
Adlard D. et al, (2025)
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P-260. Antibiotic residues in hospital sink p-trap water in Kilifi, Kenya
Hookham L. et al, (2025), Open Forum Infectious Diseases, 12
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Predicting rifampicin resistance inM. tuberculosisusing machine learning informed by protein structural and chemical features
Lynch CI. et al, (2025), ERJ Open Research, 00952 - 2024
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Multiple introductions of NRCS-A Staphylococcus capitis to the neonatal intensive care unit drive neonatal bloodstream infections: a case-control and environmental genomic survey
Lees EA. et al, (2025), Microbial Genomics, 11
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Developing a framework for tracking antimicrobial resistance gene movement in a persistent environmental reservoir
Mathers AJ. et al, (2024), npj Antimicrobials and Resistance, 2
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Addition of Macrolide Antibiotics for Hospital Treatment of Community-Acquired Pneumonia
Wei J. et al, (2024), The Journal of Infectious Diseases
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Validation of the Baseline Recurrence Risk in Cellulitis (BRRISC) score and the added impact of acute clinical response
Cross ELA. et al, (2024)
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Assessing skin temperature over time in a cohort of lower limb cellulitis: A methods comparison study
Cross ELA. et al, (2024)
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Detecting changes in population trends in infection surveillance using community SARS-CoV-2 prevalence as an exemplar
Pritchard E. et al, (2024), American Journal of Epidemiology, 193, 1848 - 1860
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Erratum: Towards quantifying plasmid similarity.
Matlock W. et al, (2024), Microbial genomics, 10
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Global genomic epidemiology of <i>bla</i> <sub>GES-5</sub> carbapenemase-associated integrons.
Matlock W. et al, (2024), Microbial genomics, 10
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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]
Wei J. et al, (2024), Journal of Infection, 89, 106361 - 106361
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Predicting individual patient and hospital-level discharge using machine learning
Wei J. et al, (2024), Communications Medicine, 4
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Enhancement and validation of the antibiotic resistance prediction performance of a cloud-based genetics processing platform for Mycobacteria
Westhead J. et al, (2024)
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A Comparison of Causative Pathogens in Bone and Prosthetic Joint Infections: Implications for Antimicrobial Therapy.
Unsworth A. et al, (2024), Antibiotics (Basel, Switzerland), 13
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The use of antibiotic-loaded calcium sulphate beads in debridement, antibiotics, and implant retention (DAIR) for periprosthetic infections: a retrospective comparative cohort on outcome.
Sigmund IK. et al, (2024), Acta orthopaedica, 95, 707 - 714
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Exploring uncatalogued genetic variation in antimicrobial resistance gene families in Escherichia coli: an observational analysis
Lipworth S. et al, (2024), The Lancet Microbe, 5, 100913 - 100913
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Comparison of direct cDNA and PCR-cDNA Nanopore sequencing of RNA from Escherichia coli isolates
Rodger G. et al, (2024), Microbial Genomics, 10
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Diversity, functional classification and genotyping of SHV β-lactamases in Klebsiella pneumoniae
Tsang KK. et al, (2024), Microbial Genomics, 10
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Identification of undetected SARS-CoV-2 infections by clustering of Nucleocapsid antibody trajectories
Zwerwer LR. et al, (2024)
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How, why and when are delayed (back-up) antibiotic prescriptions used in primary care? A realist review integrating concepts of uncertainty in healthcare
Mcleod M. et al, (2024), BMC Public Health, 24
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Predicting future hospital antimicrobial resistance prevalence using machine learning
Vihta K-D. et al, (2024), Communications Medicine, 4
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Dissemination and persistence of antimicrobial resistance (AMR) along the wastewater-river continuum
Read DS. et al, (2024), Water Research, 264, 122204 - 122204
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Developing a novel approach to complex evolution of antimicrobial resistance via mobile genetic elements from a persistent environmental biofilm
Mathers A. et al, (2024)
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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
Stoesser N. et al, (2024), JAC-Antimicrobial Resistance, 6
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Double testing with lateral flow antigen test devices for COVID-19: does a second test in quick succession add value?
Futschik ME. et al, (2024), Journal of Virological Methods, 329
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Global burden of bacterial antimicrobial resistance 1990–2021: a systematic analysis with forecasts to 2050
Naghavi M. et al, (2024), The Lancet, 404, 1199 - 1226
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Infection Inspection: using the power of citizen science for image-based prediction of antibiotic resistance in Escherichia coli treated with ciprofloxacin
Farrar A. et al, (2024), Scientific Reports, 14
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Why Was the Azithromycin “for Life” Trial Necessary?
Maitland K. and Walker AS., (2024), New England Journal of Medicine, 391, 760 - 762
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Predicting rifampicin resistance inM. tuberculosisusing machine learning informed by protein structural and chemical features
Lynch CI. et al, (2024)
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Quantitative drug susceptibility testing for Mycobacterium tuberculosis using unassembled sequencing data and machine learning
(2024), PLOS Computational Biology, 20, e1012260 - e1012260
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MmpR5 protein truncation and bedaquiline resistance in Mycobacterium tuberculosis isolates from South Africa: a genomic analysis.
Roberts LW. et al, (2024), The Lancet. Microbe, 5
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The impact of different antimicrobial exposures on the gut microbiome in the ARMORD observational study
Peto L. et al, (2024)
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The impact of different antimicrobial exposures on the gut microbiome in the ARMORD observational study
Peto L. et al, (2024)
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Retrospective analysis of hospital electronic health records reveals unseen cases of acute hepatitis with unknown aetiology in adults in Oxfordshire
Tan CCS. et al, (2024), BMC Public Health, 24
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The implementation of whole-genome sequencing for <i>Mycobacterium tuberculosis</i> in Vietnam.
Huong DT. et al, (2024), IJTLD open, 1, 320 - 322
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Improving the representativeness of UK’s national COVID-19 Infection Survey through spatio-temporal regression and post-stratification
Pouwels KB. et al, (2024), Nature Communications, 15
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Ribosome Phenotypes Enable Rapid Antibiotic Susceptibility Testing inEscherichia coli
Farrar A. et al, (2024)
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Nanopore sequencing of influenza A and B in Oxfordshire and the United Kingdom, 2022–23
Cane J. et al, (2024), Journal of Infection, 88, 106164 - 106164
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No evidence of difference in mortality with amoxicillin versus co-amoxiclav for hospital treatment of community-acquired pneumonia
Wei J. et al, (2024), Journal of Infection, 88, 106161 - 106161
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A Phase I trial of Non-invasive Ventilation and seizure prophylaxis with levetiracetam In Children with Cerebral Malaria Trial (NOVICE-M Trial)
Maitland K. et al, (2024), Wellcome Open Research, 9, 281 - 281
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Estimating the effect of antimicrobial resistance genes on minimum inhibitory concentration inEscherichia coli
Lipworth S. et al, (2024)
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Assessment of three antibiotic combination regimens against Gram-negative bacteria causing neonatal sepsis in low- and middle-income countries
Kakaraskoska Boceska B. et al, (2024), Nature Communications, 15
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Evaluation of the accuracy of bacterial genome reconstruction with Oxford Nanopore R10.4.1 long-read-only sequencing
Sanderson ND. et al, (2024), Microbial Genomics, 10
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Distinct patterns of vital sign and inflammatory marker responses in adults with suspected bloodstream infection
Gu Q. et al, (2024), Journal of Infection, 88, 106156 - 106156
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Rifampicin resistant Mycobacterium tuberculosis in Vietnam, 2020-2022.
Van Nguyen H. et al, (2024), Journal of clinical tuberculosis and other mycobacterial diseases, 35
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Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny
Hunt M. et al, (2024)
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Leveraging transformers and large language models with antimicrobial prescribing data to predict sources of infection for electronic health record studies
Yuan K. et al, (2024)
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Author Correction: The plasmidome associated with Gram-negative bloodstream infections: a large-scale observational study using complete plasmid assemblies
Lipworth S. et al, (2024), Nature Communications, 15
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Distinct patterns of vital sign and inflammatory marker responses in adults with suspected bloodstream infection.
Gu Q. et al, (2024), The Journal of infection
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Target enrichment improves culture-independent detection of Neisseria gonorrhoeae and antimicrobial resistance determinants direct from clinical samples with Nanopore sequencing
Street TL. et al, (2024), Microbial Genomics, 10
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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
Dietz E. et al, (2024), BMC Medicine, 22
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The impact of different antimicrobial exposures on the gut microbiome in the ARMORD observational study
Peto L. et al, (2024)
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Prediction of pyrazinamide resistance in Mycobacterium tuberculosis using structure-based machine-learning approaches
Carter JJ. et al, (2024), JAC-Antimicrobial Resistance, 6
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The plasmidome associated with Gram-negative bloodstream infections: A large-scale observational study using complete plasmid assemblies
Lipworth S. et al, (2024), Nature Communications, 15
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Anti-inflammatory effects of oral prednisolone at stable state in people treated with mepolizumab: a proteomic and bulk transcriptomics analysis
Howell I. et al, (2024)
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Global genomic epidemiology ofblaGES-5carbapenemase-associated integrons
Matlock W. et al, (2024)
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Compensatory mutations are associated with increased in vitro growth in resistant clinical samples of Mycobacterium tuberculosis
Brunner VM. and Fowler PW., (2024), Microbial Genomics, 10
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Risk of SARS-CoV-2 reinfection during multiple Omicron variant waves in the UK general population
Wei J. et al, (2024), Nature Communications, 15
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Development and validation of the Baseline Recurrence Risk in Cellulitis (BRRISC) score.
L A Cross E. et al, (2024), The Journal of infection, 88, 103 - 111
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A workflow for the detection of antibiotic residues, measurement of water chemistry and preservation of hospital sink drain samples for metagenomic sequencing
Rodger G. et al, (2024), Journal of Hospital Infection, 144, 128 - 136
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Comparison of direct cDNA and PCR-cDNA Nanopore sequencing ofEscherichia coliisolates
Rodger G. et al, (2024)
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Evaluation of the accuracy of bacterial genome reconstruction with Oxford Nanopore R10.4.1 long-read-only sequencing
Sanderson ND. et al, (2024)
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Quantitative measurement of antibiotic resistance in Mycobacterium tuberculosis reveals genetic determinants of resistance and susceptibility in a target gene approach
Barilar I. et al, (2024), Nature Communications, 15
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Target enrichment improves culture-independent detection ofNeisseria gonorrhoeaedirect from sample with Nanopore sequencing
Street TL. et al, (2024)
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E. coliphylogeny drives co-amoxiclav resistance through variable expression ofblaTEM-1
Matlock W. et al, (2024)
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A consensus statement on dual purpose pathogen surveillance systems: The always on approach.
van der Westhuizen H-M. et al, (2024), PLOS global public health, 4
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Rapid identification of bacterial isolates using microfluidic adaptive channels and multiplexed fluorescence microscopy
Chatzimichail S. et al, (2024), Lab on a Chip, 24, 4843 - 4858
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Epidemiology and microbiology of recurrent UTI in women in the community in Oxfordshire, UK
Vazquez-Montes MDLA. et al, (2023), JAC-Antimicrobial Resistance, 6
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Discordance between different bioinformatic methods for identifying resistance genes from short-read genomic data, with a focus on Escherichia coli
Davies TJ. et al, (2023), Microbial Genomics, 9
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Retrospective analysis of hospital electronic health records reveals unseen cases of acute hepatitis with unknown aetiology in adults in Oxfordshire
Tan CCS. et al, (2023)
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Model-based evaluation of admission screening strategies for the detection and control of carbapenemase-producing Enterobacterales in the English hospital setting
Pople D. et al, (2023), BMC Medicine, 21
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Infection Inspection: Using the power of citizen science to help with image-based prediction of antibiotic resistance inEscherichia coli
Farrar A. et al, (2023)
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A new variant of the colistin resistance gene MCR-1 with co-resistance to β-lactam antibiotics reveals a potential novel antimicrobial peptide.
Liang L. et al, (2023), PLoS biology, 21
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Hostile: accurate decontamination of microbial host sequences.
Constantinides B. et al, (2023), Bioinformatics (Oxford, England), 39
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OA-225 Optimising second line anchor drug options for children with HIV in Africa: 96 week results of the CHAPAS-4 randomised trial
Lugemwa A. et al, (2023), Abstracts of Oral Presentations, A8.1 - A8
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Predicting future hospital antimicrobial resistance prevalence using machine learning
Vihta K-D. et al, (2023)
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Erratum: Comparison of R9.4.1/Kit10 and R10/Kit12 Oxford Nanopore flowcells and chemistries in bacterial genome reconstruction
Sanderson ND. et al, (2023), Microbial Genomics, 9
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A validated cloud-based genomic platform for co-ordinated, expedient global analysis of SARS-CoV-2 genomic epidemiology
Amoako D. et al, (2023)
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Nanopore sequencing of influenza A and B in Oxfordshire and the United Kingdom, 2022-23
Cane J. et al, (2023)
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Persistence of SARS-CoV-2 antibodies over 18 months following infection: UK Biobank COVID-19 Serology Study.
Bešević J. et al, (2023), Journal of epidemiology and community health
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Deep learning and single-cell phenotyping for rapid antimicrobial susceptibility detection in Escherichia coli.
Zagajewski A. et al, (2023), Communications biology, 6
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Increasing test specificity without impairing sensitivity: lessons learned from SARS-CoV-2 serology
Perkmann T. et al, (2023), Journal of Clinical Pathology, 76, 770 - 777
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Defining normal inflammatory marker and vital sign responses to suspected bloodstream infection in adults with positive and negative blood cultures
Gu Q. et al, (2023)
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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
Dietz E. et al, (2023)
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When should factorial designs be used for late-phase randomised controlled trials?
White IR. et al, (2023), Clinical trials (London, England)
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Swab pooling enables rapid expansion of high-throughput capacity for SARS-CoV-2 community testing.
Fagg J. et al, (2023), Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology, 167
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Cycle Threshold Values as Indication of Increasing SARS-CoV-2 New Variants, England, 2020-2022.
Harrison RE. et al, (2023), Emerging infectious diseases, 29, 2024 - 2031
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Lineage replacement and evolution captured by 3 years of the United Kingdom Coronavirus (COVID-19) Infection Survey.
Lythgoe KA. et al, (2023), Proceedings. Biological sciences, 290
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A workflow for the detection of antibiotic residues, measurement of water chemistry and preservation of hospital sink drain samples for metagenomic sequencing
Rodger G. et al, (2023)
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Evaluation of sequence hybridization for respiratory viruses using the Twist Bioscience Respiratory Virus Research panel and the OneCodex Respiratory Virus sequence analysis workflow
Kapel N. et al, (2023), Microbial Genomics, 9
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A second update on mapping the human genetic architecture of COVID-19.
COVID-19 Host Genetics Initiative None., (2023), Nature, 621, E7 - E26
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[A global core outcome measurement set for snakebite clinical trials].
Abouyannis M. et al, (2023), Medecine tropicale et sante internationale, 3
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Performance of antigen lateral flow devices in the UK during the alpha, delta, and omicron waves of the SARS-CoV-2 pandemic: a diagnostic and observational study
Eyre DW. et al, (2023), The Lancet Infectious Diseases, 23, 922 - 932