Publications

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

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

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)

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

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

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

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

Pouwels KB. et al, (2023)

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

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

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

Chau KK. et al, (2022)

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

Orlek A. et al, (2022)

The challenge of limited vaccine supplies: impact of prior infection on anti-spike IgG antibody trajectories after a single COVID-19 vaccination

Wei J. et al, (2021)

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, (2021)

Discordance between different bioinformatic methods for identifying resistance genes from short-read genomic data, with a focus onEscherichia coli

Davies TJ. et al, (2021)

SARS-CoV-2 anti-spike IgG antibody responses after second dose of ChAdOx1 or BNT162b2 and correlates of protection in the UK general population

Wei J. et al, (2021)

Symptoms and SARS-CoV-2 positivity in the general population in the UK

Vihta K-D. et al, (2021)

Anti-spike antibody response to natural SARS-CoV-2 infection in the general population

Wei J. et al, (2021)

Enhancing epidemiological investigation of nosocomial SARS-CoV-2 infection with whole genome sequencing: A retrospective cohort study across four hospitals in the UK

Lumley SF. et al, (2021)

The impact of SARS-CoV-2 vaccines on antibody responses in the general population in the United Kingdom

Wei J. et al, (2021)

Quantitative SARS-CoV-2 anti-spike responses to Pfizer-BioNTech and Oxford-AstraZeneca vaccines by previous infection status

Eyre DW. et al, (2021)

An observational cohort study on the incidence of SARS-CoV-2 infection and B.1.1.7 variant infection in healthcare workers by antibody and vaccination status

Lumley SF. et al, (2021)

Amplification-Free Detection of Viruses in Minutes using Single-Particle Imaging and Machine Learning

Shiaelis N. et al, (2021), Biophysical Journal, 120, 195a - 195a

Performance characteristics of five immunoassays for SARS-CoV-2: a head-to-head benchmark comparison

Ainsworth M. et al, (2020), The Lancet Infectious Diseases, 20, 1390 - 1400

Antibodies to SARS-CoV-2 are associated with protection against reinfection

Lumley SF. et al, (2020)

The unintended consequences of a surge in antibiotic resistance when removing wastewater drain biofilm

Kotay SM. et al, (2020)

Virus detection and identification in minutes using single-particle imaging and deep learning

Shiaelis N. et al, (2020)

A haemagglutination test for rapid detection of antibodies to SARS-CoV-2

Joly E. et al, (2020)

A haemagglutination test for rapid detection of antibodies to SARS-CoV-2

Townsend A. et al, (2020)

Genomic network analysis of an environmental and livestock IncF plasmid population

Matlock W. et al, (2020)

Differential occupational risks to healthcare workers from SARS-CoV-2: A prospective observational study

Eyre DW. et al, (2020)

Hospital outbreak of carbapenem-resistant Enterobacteriales associated with an OXA-48 plasmid carried mostly byEscherichia coliST399

Ledda A. et al, (2020)

SARS-CoV-2 RNA detected in blood samples from patients with COVID-19 is not associated with infectious virus

Andersson MI. et al, (2020)

Dynamics of mcr-1 prevalence and mcr-1-positive Escherichia coli after the cessation of colistin use as a feed additive for animals in China: a prospective cross-sectional and whole genome sequencing based molecular epidemiological study

Shen C. et al, (2020)

SARS-CoV-2 RNA detected in blood products from patients with COVID-19 is not associated with infectious virus.

Andersson MI. et al, (2020), Wellcome open research, 5

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Publications