Publications

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)

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

Preprint

Zwerwer LR. 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

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

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

Journal article

Read DS. et al, (2024), Water research, 264

Comparison of direct cDNA and PCR-cDNA Nanopore sequencing of RNA from <i>Escherichia coli</i> isolates.

Journal article

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

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, 100913 - 100913

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)

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

Why Was the Azithromycin “for Life” Trial Necessary?

Other

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

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

Preprint

Lynch CI. 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

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

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

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 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

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

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

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

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

Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny

Preprint

Hunt M. et al, (2024)

Leveraging transformers and large language models with antimicrobial prescribing data to predict sources of infection for electronic health record studies

Preprint

Yuan K. et al, (2024)

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

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, 106164 - 106164

Target enrichment improves culture-independent detection of Neisseria gonorrhoeae and antimicrobial resistance determinants direct from clinical samples with Nanopore sequencing

Journal article

Street TL. et al, (2024), Microbial Genomics, 10

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

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

Preprint

Peto L. et al, (2024)

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

Anti-inflammatory effects of oral prednisolone at stable state in people treated with mepolizumab: a proteomic and bulk transcriptomics analysis

Preprint

Howell I. et al, (2024)

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

Development and validation of the Baseline Recurrence Risk in Cellulitis (BRRISC) score.

Journal article

L A Cross E. et al, (2024), The Journal of infection, 88, 103 - 111

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

Preprint

Sanderson ND. et al, (2024)

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

Target enrichment improves culture-independent detection ofNeisseria gonorrhoeaedirect from sample with Nanopore sequencing

Preprint

Street TL. et al, (2024)

Ribosome Phenotypes Enable Rapid Antibiotic Susceptibility Testing inEscherichia coli

Preprint

Farrar A. et al, (2024)

Global genomic epidemiology ofblaGES-5carbapenemase-associated integrons

Preprint

Matlock W. et al, (2024)

Comparison of direct cDNA and PCR-cDNA Nanopore sequencing ofEscherichia coliisolates

Preprint

Rodger G. et al, (2024)

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

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 Med, 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

Factors associated with plasmid antibiotic resistance gene carriage revealed using large-scale multivariable analysis

Journal article

Orlek A. et al, (2023), Scientific Reports, 13

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

Predicting future hospital antimicrobial resistance prevalence using machine learning

Preprint

Vihta K-D. et al, (2023)

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

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

Preprint

Cane J. et al, (2023)

Persistence of SARS-CoV-2 antibodies over 18 months following infection: UK Biobank COVID-19 Serology Study.

Journal article

Bešević J. et al, (2023), Journal of epidemiology and community health

Deep learning and single-cell phenotyping for rapid antimicrobial susceptibility detection in Escherichia coli.

Journal article

Zagajewski A. et al, (2023), Communications biology, 6

Increasing test specificity without impairing sensitivity: lessons learned from SARS-CoV-2 serology

Journal article

Perkmann T. et al, (2023), Journal of Clinical Pathology, 76, 770 - 777

Defining normal inflammatory marker and vital sign responses to suspected bloodstream infection in adults with positive and negative blood cultures

Preprint

Gu Q. et al, (2023)

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

Preprint

Dietz E. et al, (2023)

When should factorial designs be used for late-phase randomised controlled trials?

Conference paper

White IR. et al, (2023), Clinical trials (London, England)

Swab pooling enables rapid expansion of high-throughput capacity for SARS-CoV-2 community testing.

Journal article

Fagg J. et al, (2023), Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology, 167

Cycle Threshold Values as Indication of Increasing SARS-CoV-2 New Variants, England, 2020-2022.

Journal article

Harrison RE. et al, (2023), Emerging infectious diseases, 29, 2024 - 2031

Lineage replacement and evolution captured by 3 years of the United Kingdom Coronavirus (COVID-19) Infection Survey.

Journal article

Lythgoe KA. et al, (2023), Proceedings. Biological sciences, 290

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

Preprint

Rodger G. et al, (2023)

Evaluation of sequence hybridization for respiratory viruses using the Twist Bioscience Respiratory Virus Research panel and the OneCodex Respiratory Virus sequence analysis workflow

Journal article

Kapel N. et al, (2023), Microbial Genomics, 9

A second update on mapping the human genetic architecture of COVID-19.

Journal article

COVID-19 Host Genetics Initiative None., (2023), Nature, 621, E7 - E26

[A global core outcome measurement set for snakebite clinical trials].

Conference paper

Abouyannis M. et al, (2023), Medecine tropicale et sante internationale, 3

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

Journal article

Eyre DW. et al, (2023), The Lancet Infectious Diseases, 23, 922 - 932

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

Preprint

Wei J. et al, (2023)

Compensatory mutations are associated with increasedin vitrogrowth in resistant clinical samples ofMycobacterium tuberculosis

Preprint

Brunner V. and Fowler PW., (2023)

Temporal trends and clinical characteristics of acute hepatitis with unknown aetiology and human adenovirus infections in Oxfordshire from 2016 to 2022

Preprint

Tan CCS. et al, (2023)

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).

Journal article

Russell NJ. et al, (2023), PLoS medicine, 20

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

Journal article

Riddell A. et al, (2023), Antibiotics, 12, 923 - 923

Protection against SARS-CoV-2 Omicron BA.4/5 variant following booster vaccination or breakthrough infection in the UK

Journal article

Wei J. et al, (2023), Nature Communications, 14

Justifying the More Restrictive Alternative: Ethical Justifications for One Health AMR Policies Rely on Empirical Evidence

Journal article

Johnson T. and Matlock W., (2023), Public Health Ethics, 16, 22 - 34

High-resolution characterization of short-term temporal variability in the taxonomic and resistome composition of wastewater influent.

Journal article

Chau KK. et al, (2023), Microbial genomics, 9

Reply: Epidemiological cut-off values for a 96-well broth microdilution plate for high-throughput research antibiotic susceptibility testing ofM. tuberculosis

Journal article

(2023), European Respiratory Journal, 61, 2300426 - 2300426

Rise in alanine aminotransferase after HCV treatment is a highly sensitive screen for treatment failure.

Journal article

Flower B. et al, (2023), Clinical liver disease, 21, 138 - 142

Bedaquiline and clofazimine resistance in Mycobacterium tuberculosis: an in-vitro and in-silico data analysis

Journal article

Sonnenkalb L. et al, (2023), The Lancet Microbe, 4, e358 - e368

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.

Journal article

Aranega-Bou P. et al, (2023), medRxiv

Risk of new-onset Long Covid following reinfection with SARS-CoV-2: community-based cohort study

Preprint

Bosworth ML. et al, (2023)

Penicillin Binding Protein Substitutions Cooccur with Fluoroquinolone Resistance in Epidemic Lineages of Multidrug-Resistant Clostridioides difficile

Journal article

Dingle KE. et al, (2023), mBio

Microbial Persistence, Replacement and Local Antimicrobial Therapy in Recurrent Bone and Joint Infection.

Journal article

Young BC. et al, (2023), Antibiotics (Basel, Switzerland), 12

Employment outcomes of people with Long Covid symptoms: community-based cohort study

Preprint

Ayoubkhani D. et al, (2023)

The quality of vital signs measurements and value preferences in electronic medical records varies by hospital, specialty, and patient demographics

Journal article

Jackson N. et al, (2023), Scientific Reports, 13

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

Preprint

Pouwels KB. et al, (2023)

Inclusion of minor alleles improves catalogue-based prediction of fluoroquinolone resistance inMycobacterium tuberculosis

Journal article

Brankin AE. and Fowler PW., (2023), JAC-Antimicrobial Resistance, 5

Enterobacterales plasmid sharing amongst human bloodstream infections, livestock, wastewater, and waterway niches in Oxfordshire, UK.

Journal article

Matlock W. et al, (2023), eLife, 12

Evaluation of Nanopore sequencing for Mycobacterium tuberculosis drug susceptibility testing and outbreak investigation: a genomic analysis.

Journal article

Hall MB. et al, (2023), The Lancet. Microbe, 4, e84 - e92

Standard of care for viral haemorrhagic fevers (VHFs): a systematic review of clinical management guidelines for high-priority VHFs

Journal article

Rigby I. et al, (2023), The Lancet Infectious Diseases

Genomic Sequencing from Sputum for Tuberculosis Disease Diagnosis, Lineage Determination, and Drug Susceptibility Prediction.

Journal article

Nilgiriwala K. et al, (2023), Journal of clinical microbiology

Antibiotic review kit for hospitals (ARK-Hospital): a stepped-wedge cluster-randomised controlled trial

Journal article

Llewelyn MJ. et al, (2023), The Lancet Infectious Diseases, 23, 207 - 221

High number of SARS-CoV-2 persistent infections uncovered through genetic analysis of samples from a large community-based surveillance study

Preprint

Ghafari M. et al, (2023)

Impact of sub-optimal HIV viral control on activated T-cells: an earnest sub study.

Journal article

Arrigoni FIF. et al, (2023), AIDS

Pharmacokinetics and pharmacodynamics of azithromycin in severe malaria bacterial co-infection in African children (TABS-PKPD): a protocol for a Phase II randomised controlled trial

Preprint

Olupot-Olupot P. et al, (2023)

Virus Detection and Identification in Minutes Using Single-Particle Imaging and Deep Learning

Journal article

Shiaelis N. et al, (2023), ACS Nano, 17, 697 - 710

Efficacy of ultra-short, response-guided sofosbuvir and daclatasvir therapy for hepatitis C in a single-arm mechanistic pilot study

Journal article

Flower B. et al, (2023), eLife, 12

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