Publications

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

Developing a novel approach to complex evolution of antimicrobial resistance via mobile genetic elements from a persistent environmental biofilm

Mathers A. et al, (2024)

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

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

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

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

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

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

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

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

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

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 Med, 22

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

Sanderson ND. et al, (2024)

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

Ribosome Phenotypes Enable Rapid Antibiotic Susceptibility Testing inEscherichia coli

Farrar A. et al, (2024)

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

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

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

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

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

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

Cane J. et al, (2023)

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

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

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

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)

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

Wei J. et al, (2023)

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)

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

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

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

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

Pouwels KB. et al, (2023)

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

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

A longitudinal study reveals persistence of antimicrobial resistance on livestock farms is not due to antimicrobial usage alone.

Smith RP. et al, (2023), Front Microbiol, 14

Exploring the extent of uncatalogued genetic variation in antimicrobial resistance gene families inEscherichia coli

Lipworth S. et al, (2023)

Microbial diversity and antimicrobial resistance in faecal samples from acute medical patients assessed through metagenomic sequencing.

Yokoyama M. et al, (2023), PLoS One, 18

Surgical source control and colistin therapy for the management of osteomyelitis due to Pseudomonas aeruginosa with difficult-to-treat resistance

Nageshwaran V. et al, (2023), JAC-ANTIMICROBIAL RESISTANCE, 5

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

Shiaelis N. et al, (2022), ACS nano

Correlates of protection against SARS-CoV-2 Omicron variant and anti-spike antibody responses after a third/booster vaccination or breakthrough infection in the UK general population

Wei J. et al, (2022)

Treatment of enteric fever (typhoid and paratyphoid fever) with cephalosporins

Kuehn R. et al, (2022), Cochrane Database of Systematic Reviews, 2022

Detecting changes in population trends in infection surveillance using community SARS-CoV-2 prevalence as an exemplar

Pritchard E. et al, (2022)

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

Perkmann T. et al, (2022), Journal of clinical pathology

Mortality risks associated with empirical antibiotic activity in Escherichia coli bacteraemia: an analysis of electronic health records

Yoon CH. et al, (2022), Journal of Antimicrobial Chemotherapy, 77, 2536 - 2545

Molecular epidemiology and antimicrobial resistance phenotype of paediatric bloodstream infections caused by Gram-negative bacteria

Lipworth S. et al, (2022), Communications Medicine, 2

Omicron-associated changes in SARS-CoV-2 symptoms in the United Kingdom

Vihta1 KD. et al, (2022), Clinical Infectious Diseases

SARS-CoV-2 antibody trajectories after a single COVID-19 vaccination with and without prior infection

Wei J. et al, (2022), Nature Communications, 13

Whole genome sequencing reveals hidden transmission of carbapenemase-producing Enterobacterales.

Marimuthu K. et al, (2022), Nature communications, 13

Evaluation of metagenomic, 16S rRNA gene and ultra-plexed PCR-based sequencing approaches for profiling antimicrobial resistance gene and bacterial taxonomic composition of polymicrobial samples

Chau KK. et al, (2022)

Prediction of Antibiotic Resistance Evolution by Growth Measurement of All Proximal Mutants of Beta-Lactamase.

Feng S. et al, (2022), Molecular biology and evolution, 39

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

Sanderson N. et al, (2022)

Hospital outbreak of carbapenem-resistant Enterobacterales associated with a bla OXA-48 plasmid carried mostly by Escherichia coli ST399.

Ledda A. et al, (2022), Microbial genomics, 8

Omicron-associated changes in SARS-CoV-2 symptoms in the United Kingdom

Vihta K-D. et al, (2022)

Deep Learning and Single Cell Phenotyping for Rapid Antimicrobial Susceptibility Testing

Zagajewski A. et al, (2022)

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

Chau KK. et al, (2022)

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Publications