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Publications

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

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

Peto L. et al, (2024)

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

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

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

Penicillin Binding Protein Substitutions Cooccur with Fluoroquinolone Resistance in Epidemic Lineages of Multidrug-Resistant Clostridioides difficile

Dingle KE. et al, (2023), mBio

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

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

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

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

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