Publications

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

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

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

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

Orlek A. et al, (2022)

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

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

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

Chau KK. et al, (2022)

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

Wei J. et al, (2022), Nat Commun, 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)

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

Sanderson N. 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

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

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

Lipworth S. et al, (2022), Commun Med (Lond), 2

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)

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

Panton–Valentine leucocidin is the key determinant of Staphylococcus aureus pyomyositis in a bacterial GWAS

Young BC. et al, (2019), eLife, 8

Reconciling the potentially irreconcilable? Genotypic and phenotypic amoxicillin-clavulanate resistance in Escherichia coli

Davies TJ. et al, (2019)

TETyper: a bioinformatic pipeline for classifying variation and genetic contexts of transposable elements from short-read whole-genome sequencing data

Sheppard A. et al, (2018)

Transmission patterns of hyper-endemic multi-drug resistant Klebsiella pneumoniae in a Cambodian neonatal unit: a longitudinal study with whole genome sequencing

Smit PW. et al, (2017)

Trends in Escherichia coli bloodstream infection, urinary tract infections and antibiotic susceptibilities in Oxfordshire, 1998-2016: an observational study

Vihta K-D. et al, (2017)

Bayesian Reconstruction of Transmission within Outbreaks using Genomic Variants

De Maio N. et al, (2017)

Epidemiology of paediatric gastrointestinal colonisation by extended spectrum cephalosporin-resistant Escherichia coli and Klebsiella pneumoniae isolates in north-west Cambodia

Aartsen JJV. et al, (2017)

Genomic epidemiology of globalKlebsiella pneumoniaecarbapenemase (KPC)-producingEscherichia coli

Stoesser N. et al, (2017)

High rates of human faecal carriage of mcr-1-positive multi-drug resistant isolates emerge in China in association with successful plasmid families

Zhong L-L. et al, (2017)

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Publications