Publications

Survey of healthcare-associated sink infrastructure, and sink trap antibiotic residues and biochemistry, in twenty-nine UK hospitals

Journal article

Rodger G. et al, (2025), Journal of Hospital Infection, 159, 140 - 147

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)

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)

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

Preprint

Vo H-AT. et al, (2025)

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

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

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)

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

Erratum: Towards quantifying plasmid similarity.

Journal article

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

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)

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

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)

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

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

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

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

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

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

Journal article

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

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)

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

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

Estimating the effect of antimicrobial resistance genes on minimum inhibitory concentration inEscherichia coli

Preprint

Lipworth S. et al, (2024)

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

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

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)

Global genomic epidemiology ofblaGES-5carbapenemase-associated integrons

Preprint

Matlock W. 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

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

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

Preprint

Rodger G. et al, (2024)

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)

E. coliphylogeny drives co-amoxiclav resistance through variable expression ofblaTEM-1

Preprint

Matlock W. 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

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

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

Preprint

Tan CCS. et al, (2023)

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

Infection Inspection: Using the power of citizen science to help with image-based prediction of antibiotic resistance inEscherichia coli

Preprint

Farrar A. et al, (2023)

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

OA-225 Optimising second line anchor drug options for children with HIV in Africa: 96 week results of the CHAPAS-4 randomised trial

Conference paper

Lugemwa A. et al, (2023), Abstracts of Oral Presentations, A8.1 - A8

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

A validated cloud-based genomic platform for co-ordinated, expedient global analysis of SARS-CoV-2 genomic epidemiology

Preprint

Amoako D. et al, (2023)

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

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