Publications

Double testing with lateral flow antigen test devices for COVID-19: does a second test in quick succession add value?

Futschik ME. et al, (2024), Journal of Virological Methods, 329

Quantitative drug susceptibility testing for Mycobacterium tuberculosis using unassembled sequencing data and machine learning

(2024), PLOS Computational Biology, 20, e1012260 - e1012260

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

The impact of different antimicrobial exposures on the gut microbiome in the ARMORD observational study

Peto L. et al, (2024)

The impact of different antimicrobial exposures on the gut microbiome in the ARMORD observational study

Peto L. et al, (2024)

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

Rifampicin resistant Mycobacterium tuberculosis in Vietnam, 2020-2022.

Van Nguyen H. et al, (2024), Journal of clinical tuberculosis and other mycobacterial diseases, 35

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

Prediction of pyrazinamide resistance in Mycobacterium tuberculosis using structure-based machine-learning approaches

Carter JJ. et al, (2024), JAC-Antimicrobial Resistance, 6

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

Wei J. et al, (2024), Nature Communications, 15

MmpR5 protein truncation and bedaquiline resistance in Mycobacterium tuberculosis isolates from South Africa: a genomic analysis

Roberts LW. et al, (2024), The Lancet Microbe

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

Hostile: accurate decontamination of microbial host sequences.

Constantinides B. et al, (2023), Bioinformatics (Oxford, England), 39

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

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

A second update on mapping the human genetic architecture of COVID-19.

COVID-19 Host Genetics Initiative None., (2023), Nature, 621, E7 - E26

Evaluation of sequence hybridization for respiratory viruses using the Twist Bioscience Respiratory Virus Research panel and the OneCodex Respiratory Virus sequence analysis workflow.

Kapel N. et al, (2023), Microbial genomics, 9

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

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

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

Genomic Sequencing from Sputum for Tuberculosis Disease Diagnosis, Lineage Determination, and Drug Susceptibility Prediction.

Nilgiriwala K. et al, (2023), Journal of clinical microbiology

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

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

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

Modern Solutions for Ancient Pathogens: Direct Pathogen Sequencing for Diagnosis of Lepromatous Leprosy and Cerebral Coenurosis.

Young BC. et al, (2022), Open forum infectious diseases, 9

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

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

Antibody escape of SARS-CoV-2 Omicron BA.4 and BA.5 from vaccine and BA.1 serum

Tuekprakhon A. et al, (2022), Cell, 185, 2422 - 2433.e13

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

Catwalk: identifying closely related sequences in large microbial sequence databases.

Volk D. et al, (2022), Microbial genomics, 8

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

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

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

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

Potent cross-reactive antibodies following Omicron breakthrough in vaccinees

Nutalai R. et al, (2022), Cell, 185, 2116 - 2131.e18

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

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

Realising the Potential of Genomics for M. tuberculosis: A Silver Lining to the Pandemic?

Walker TM. and Crook DW., (2022), China CDC Weekly, 4, 437 - 439

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

Identifying Bacterial Airways Infection in Stable Severe Asthma Using Oxford Nanopore Sequencing Technologies

Jabeen MF. et al, (2022), Microbiology Spectrum, 10

An Observational Cohort Study on the Incidence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection and B.1.1.7 Variant Infection in Healthcare Workers by Antibody and Vaccination Status

Lumley SF. et al, (2022), Clinical Infectious Diseases, 74, 1208 - 1219

Clinical Metagenomic Sequencing for Species Identification and Antimicrobial Resistance Prediction in Orthopedic Device Infection.

Street TL. et al, (2022), Journal of clinical microbiology, 60

Systematic review of wastewater surveillance of antimicrobial resistance in human populations.

Chau KK. et al, (2022), Environ Int, 162

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

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

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Publications