Publications

Exploring uncatalogued genetic variation in antimicrobial resistance gene families in Escherichia coli: an observational analysis

Lipworth S. et al, (2024), The Lancet Microbe, 5, 100913 - 100913

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 Medicine, 22

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

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

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

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

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.

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

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

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

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

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

Lipworth S. et al, (2023)

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

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

Pouwels KB. et al, (2023)

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

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

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

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

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

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

Gu Q. et al, (2023)

Performance of self-collected saliva samples for SARS-CoV-2 mass testing in community settings

Kay O. et al, (2023), JOURNAL OF CLINICAL VIROLOGY PLUS, 3

Health record hiccups—5,526 real-world time series with change points labelled by crowdsourced visual inspection

Quan TP. et al, (2022), GigaScience, 12

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)

Assessment of an institutional guideline for vancomycin dosing and identification of predictive factors associated with dose and drug trough levels

Gu Q. et al, (2022), Journal of Infection, 85, 382 - 389

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

(2022), European Respiratory Journal, 60, 2200239 - 2200239

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

Pritchard E. et al, (2022)

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

Symptoms and Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Positivity in the General Population in the United Kingdom

Vihta KD. et al, (2022), Clinical Infectious Diseases, 75, e329 - e337

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

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

A data compendium associating the genomes of 12,289 Mycobacterium tuberculosis isolates with quantitative resistance phenotypes to 13 antibiotics

(2022), PLOS Biology, 20, e3001721 - e3001721

Genome-wide association studies of global Mycobacterium tuberculosis resistance to 13 antimicrobials in 10,228 genomes identify new resistance mechanisms

(2022), PLOS Biology, 20, e3001755 - e3001755

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

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

A data compendium associating the genomes of 12,289 Mycobacterium tuberculosis isolates with quantitative resistance phenotypes to 13 antibiotics.

The CRyPTIC Consortium None., (2022), PLoS biology, 20

M. tuberculosis microvariation is common and is associated with transmission: Analysis of three years prospective universal sequencing in England

Wyllie D. et al, (2022), Journal of Infection, 85, 31 - 39

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

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

Antibiotic Review Kit for Hospitals (ARK-Hospital): a stepped wedge cluster randomised controlled trial

Llewelyn MJ. et al, (2022)

Mycobacterium tuberculosis transmission in Birmingham, UK, 2009–19: An observational study

Walker TM. et al, (2022), The Lancet Regional Health - Europe, 17, 100361 - 100361

A crowd of BashTheBug volunteers reproducibly and accurately measure the minimum inhibitory concentrations of 13 antitubercular drugs from photographs of 96-well broth microdilution plates

Fowler PW. et al, (2022), eLife, 11

Antibody responses and correlates of protection in the general population after two doses of the ChAdOx1 or BNT162b2 vaccines

Wei J. et al, (2022), Nature Medicine, 28, 1072 - 1082

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

Sanderson N. et al, (2022)

Feasibility and acceptability of daily testing at school as an alternative to self-isolation following close contact with a confirmed case of COVID-19: a qualitative analysis.

Denford S. et al, (2022), BMC public health, 22

The 2021 WHO catalogue of Mycobacterium tuberculosis complex mutations associated with drug resistance: a genotypic analysis

Walker TM. et al, (2022), The Lancet Microbe, 3, e265 - e273

Assessment of a vancomycin dosing guideline and identification of predictive factors associated with dose and drug trough levels

Gu Q. et al, (2022)

Nanopore sequencing for Mycobacterium tuberculosis drug susceptibility testing and outbreak investigation

Hall MB. et al, (2022)

Impact of antibiotic use on patient-level risk of death in 36 million hospital admissions in England

Budgell EP. et al, (2022), Journal of Infection, 84, 311 - 320

Effect of Covid-19 Vaccination on Transmission of Alpha and Delta Variants

Eyre DW. et al, (2022), New England Journal of Medicine, 386, 744 - 756

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infectivity by Viral Load, S Gene Variants and Demographic Factors, and the Utility of Lateral Flow Devices to Prevent Transmission

Lee LYW. et al, (2022), Clinical Infectious Diseases, 74, 407 - 415

Monitoring populations at increased risk for SARS-CoV-2 infection in the community using population-level demographic and behavioural surveillance

Pritchard E. et al, (2022), The Lancet Regional Health - Europe, 13, 100282 - 100282

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

Yoon CH. et al, (2022)

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

Jackson N. et al, (2022)

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

Vihta K-D. et al, (2022)

Rapid turnaround multiplex sequencing of SARS-CoV-2: comparing tiling amplicon protocol performance

Constantinides B. et al, (2022)

The mobilome associated with Gram-negative bloodstream infections: A large-scale observational hybrid sequencing based study

Lipworth S. et al, (2022)

Tracking the Emergence of SARS-CoV-2 Alpha Variant in the United Kingdom

Walker AS. et al, (2021), New England Journal of Medicine, 385, 2582 - 2585

Ten Years of Population-Level Genomic Escherichia coli and Klebsiella pneumoniae Serotype Surveillance Informs Vaccine Development for Invasive Infections

Lipworth S. et al, (2021), Clinical Infectious Diseases, 73, 2276 - 2282

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Publications