Publications
Latest publications
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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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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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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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Dissemination and persistence of antimicrobial resistance (AMR) along the wastewater-river continuum.
Read DS. et al, (2024), Water research, 264
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Comparison of direct cDNA and PCR-cDNA Nanopore sequencing of RNA from <i>Escherichia coli</i> isolates.
Rodger G. et al, (2024), Microbial genomics, 10
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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, 100913 - 100913
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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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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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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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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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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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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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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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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
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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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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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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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Nanopore sequencing of influenza A and B in Oxfordshire and the United Kingdom, 2022-23
Cane J. et al, (2024), Journal of Infection, 106164 - 106164
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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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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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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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Ribosome Phenotypes Enable Rapid Antibiotic Susceptibility Testing inEscherichia coli
Farrar A. 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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Global genomic epidemiology ofblaGES-5carbapenemase-associated integrons
Matlock W. et al, (2024)
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Comparison of direct cDNA and PCR-cDNA Nanopore sequencing ofEscherichia coliisolates
Rodger G. 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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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 Med, 21
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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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Factors associated with plasmid antibiotic resistance gene carriage revealed using large-scale multivariable analysis
Orlek A. et al, (2023), Scientific Reports, 13
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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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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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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
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Risk of SARS-CoV-2 reinfection during multiple Omicron variant waves in the UK general population
Wei J. et al, (2023)
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Compensatory mutations are associated with increasedin vitrogrowth in resistant clinical samples ofMycobacterium tuberculosis
Brunner V. and Fowler PW., (2023)
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Temporal trends and clinical characteristics of acute hepatitis with unknown aetiology and human adenovirus infections in Oxfordshire from 2016 to 2022
Tan CCS. et al, (2023)
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Patterns of antibiotic use, pathogens, and prediction of mortality in hospitalized neonates and young infants with sepsis: A global neonatal sepsis observational cohort study (NeoOBS).
Russell NJ. et al, (2023), PLoS medicine, 20
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COVID-19 vaccination, risk-compensatory behaviours, and contacts in the UK
Buckell J. et al, (2023), Scientific Reports, 13
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Challenges in the Implementation of the NeoOBS Study, a Global Pragmatic Observational Cohort Study, to Investigate the Aetiology and Management of Neonatal Sepsis in the Hospital Setting
Riddell A. et al, (2023), Antibiotics, 12, 923 - 923
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Protection against SARS-CoV-2 Omicron BA.4/5 variant following booster vaccination or breakthrough infection in the UK
Wei J. et al, (2023), Nature Communications, 14
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Justifying the More Restrictive Alternative: Ethical Justifications for One Health AMR Policies Rely on Empirical Evidence
Johnson T. and Matlock W., (2023), Public Health Ethics, 16, 22 - 34
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High-resolution characterization of short-term temporal variability in the taxonomic and resistome composition of wastewater influent
Chau KK. et al, (2023), Microbial Genomics, 9
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Reply: Epidemiological cut-off values for a 96-well broth microdilution plate for high-throughput research antibiotic susceptibility testing ofM. tuberculosis
(2023), European Respiratory Journal, 61, 2300426 - 2300426
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Rise in alanine aminotransferase after HCV treatment is a highly sensitive screen for treatment failure.
Flower B. et al, (2023), Clinical liver disease, 21, 138 - 142
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Bedaquiline and clofazimine resistance in Mycobacterium tuberculosis: an in-vitro and in-silico data analysis
Sonnenkalb L. et al, (2023), The Lancet Microbe, 4, e358 - e368
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Evaluation of Fourier Transform Infrared spectroscopy (IR Biotyper) as a complement to Whole genome sequencing (WGS) to characterise Enterobacter cloacae, Citrobacter freundii and Klebsiella pneumoniae isolates recovered from hospital sinks.
Aranega-Bou P. et al, (2023), medRxiv
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Risk of new-onset Long Covid following reinfection with SARS-CoV-2: community-based cohort study
Bosworth ML. et al, (2023)
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Penicillin Binding Protein Substitutions Cooccur with Fluoroquinolone Resistance in Epidemic Lineages of Multidrug-Resistant Clostridioides difficile
Dingle KE. et al, (2023), mBio
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Microbial Persistence, Replacement and Local Antimicrobial Therapy in Recurrent Bone and Joint Infection.
Young BC. et al, (2023), Antibiotics (Basel, Switzerland), 12
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Employment outcomes of people with Long Covid symptoms: community-based cohort study
Ayoubkhani D. et al, (2023)
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The quality of vital signs measurements and value preferences in electronic medical records varies by hospital, specialty, and patient demographics
Jackson N. et al, (2023), Scientific Reports, 13
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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, (2023)
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Inclusion of minor alleles improves catalogue-based prediction of fluoroquinolone resistance inMycobacterium tuberculosis
Brankin AE. and Fowler PW., (2023), JAC-Antimicrobial Resistance, 5
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Enterobacterales plasmid sharing amongst human bloodstream infections, livestock, wastewater, and waterway niches in Oxfordshire, UK.
Matlock W. et al, (2023), eLife, 12
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Evaluation of Nanopore sequencing for Mycobacterium tuberculosis drug susceptibility testing and outbreak investigation: a genomic analysis.
Hall MB. et al, (2023), The Lancet. Microbe, 4, e84 - e92
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Standard of care for viral haemorrhagic fevers (VHFs): a systematic review of clinical management guidelines for high-priority VHFs
Rigby I. et al, (2023), The Lancet Infectious Diseases
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Genomic Sequencing from Sputum for Tuberculosis Disease Diagnosis, Lineage Determination, and Drug Susceptibility Prediction.
Nilgiriwala K. et al, (2023), Journal of clinical microbiology
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Antibiotic review kit for hospitals (ARK-Hospital): a stepped-wedge cluster-randomised controlled trial
Llewelyn MJ. et al, (2023), The Lancet Infectious Diseases, 23, 207 - 221
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High number of SARS-CoV-2 persistent infections uncovered through genetic analysis of samples from a large community-based surveillance study
Ghafari M. et al, (2023)
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Impact of sub-optimal HIV viral control on activated T-cells: an earnest sub study.
Arrigoni FIF. et al, (2023), AIDS