Author

D. W. Eyre

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Microbiology· 10

Signature Assays, Organisms & Methods

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Organism:human· 6 Approach:statistical model· 5 Assay:whole-genome sequencing· 5 Research Focus:variant calling· 4 Research Focus:differential expression· 3 Assay:metagenomics· 3 Organism:C. elegans· 2 Approach:deep learning· 2

Frequent Co-Authors

D. W. Crook· 5 shared N. D. Sanderson· 4 shared T. L. Street· 4 shared A. S. Walker· 3 shared J. Swann· 3 shared K. Cole· 3 shared K. E. Dingle· 3 shared M. H. Wilcox· 3 shared

Activity by Year

2017-2022 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 28 mutual co-author links

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5 shared papersMicrobiology

D. W. Crook

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Author profile →

10 papers

Recent·Most cited

Penicillin Binding Protein Substitutions Co-occur with Fluoroquinolone Resistance in 'Epidemic Lineages of Multi Drug-Resistant Clostridioides difficile

K. E. Dingle, J. Freeman, X. Didelot, D. W. Eyre, J. Swann, W. Spittal, E. V. Clark, K. A. Jolley, A. S. Walker, M. H. Wilcox, D. W. Crook

The paper identifies amino acid substitutions in penicillin binding proteins (PBPs) PBP1 and PBP3 as a mechanism of cephalosporin resistance in C. difficile, which co-occurs with fluoroquinolone resistance in epidemic lineages.

bioRxiv · May 23, 2022 · PreprintMicrobiology

Benchmarking taxonomic classifiers with Illumina and Nanopore sequence data for clinical metagenomic diagnostic applications

K. N. Govender, D. W. Eyre

This paper benchmarks taxonomic classifiers for metagenomic sequencing data, finding that Bracken with a standard database achieves the highest species-level classification accuracy across Illumina and Nanopore platforms.

bioRxiv · Jan 11, 2022Microbiology

The Clostridioides difficile species problem: global phylogenomic analysis uncovers three ancient, toxigenic, genomospecies

D. R. Knight, K. Imwattana, B. Kullin, E. Guerrero-Araya, D. Paredes-Sabja, X. Didelot, K. E. Dingle, D. W. Eyre, C. Rodriguez, T. V. Riley

This study identifies three ancient, toxigenic genomospecies within C. difficile using global phylogenomic analysis, reshaping its taxonomy and understanding of toxin gene evolution.

bioRxiv · Sep 21, 2020Microbiology

Optimizing DNA extraction methods for Nanopore sequencing of Neisseria gonorrhoeae direct from urine samples

T. L. Street, L. Barker, N. D. Sanderson, J. Kavanagh, S. Hoosdally, K. Cole, R. Newnham, M. Selvaratnam, M. Andersson, M. Llewelyn, J. O'Grady, D. W. Crook, D. W. Eyre

This study optimizes DNA extraction methods for Nanopore sequencing of Neisseria gonorrhoeae directly from urine samples to enable culture-free whole-genome reconstruction.

Journal of Clinical Microbiology · Feb 24, 2020Peer-reviewedMicrobiology

High precision Neisseria gonorrhoeae variant and antimicrobial resistance calling from metagenomic Nanopore sequencing

N. D. Sanderson, J. Swann, L. Barker, J. Kavanagh, S. Hoosdally, D. Crook, the GonFast Investigators Group, T. L. Street, D. W. Eyre

This study develops a workflow for high-precision variant and antimicrobial resistance calling from metagenomic Nanopore sequencing of Neisseria gonorrhoeae.

bioRxiv · Feb 7, 2020Microbiology

RNA polymerase mutations cause cephalosporin resistance in clinical Neisseria gonorrhoeae isolates

S. G. Palace, Y. Wang, D. H. F. Rubin, M. Welsh, T. D. Mortimer, K. Cole, D. W. Eyre, S. G. Walker, Y. Grad

The paper identifies RNA polymerase mutations in Neisseria gonorrhoeae that confer ceftriaxone resistance independently of penA mutations.

bioRxiv · Aug 28, 2019Microbiology

Hash-based core genome multi-locus sequencing typing for Clostridium difficile

D. W. Eyre, T. E. Peto, D. W. Crook, A. S. Walker, M. H. Wilcox

This paper introduces hash-cgMLST, a method for rapid genome comparison in Clostridium difficile, showing it matches standard cgMLST performance but with faster processing.

bioRxiv · Jun 28, 2019Microbiology

A role for tetracycline selection in the evolution of Clostridium difficile PCR-ribotype 078

K. E. Dingle, X. Didelot, T. P. Quan, D. W. Eyre, N. Stoesser, C. A. Marwick, J. Coia, D. Brown, S. Buchanan, U. Z. Ijaz, C. Goswami, G. Douce, W. N. Fawley, M. H. Wilcox, T. E. Peto, , D. W. Crook

The paper investigates the evolutionary history of Clostridium difficile RT078, finding that tetracycline resistance genes, particularly tetM, were acquired independently in multiple clonal expansions, contributing to its increased prevalence.

bioRxiv · Feb 8, 2018Microbiology

Real-time analysis of nanopore-based metagenomic sequencing from orthopaedic device infection

N. D. Sanderson, T. L. Street, D. Foster, J. Swann, B. L. Atkins, A. J. Brent, M. A. McNally, S. Oakley, A. Taylor, T. E. A. Peto, D. Crook, D. W. Eyre

This paper compares metagenomic sequencing using Illumina MiSeq and Oxford Nanopore MinION platforms for diagnosing prosthetic joint infections, demonstrating a real-time analysis pipeline for rapid bacterial detection.

bioRxiv · Nov 17, 2017Microbiology

Molecular diagnosis of orthopaedic device infection direct from sonication fluid by metagenomic sequencing

T. L. Street, N. D. Sanderson, B. L. Atkins, A. J. Brent, K. Cole, D. Foster, M. A. McNally, S. Oakley, L. Peto, A. Taylor, T. E. A. Peto, D. W. Crook, D. W. Eyre

This study shows metagenomic sequencing of sonication fluid can accurately diagnose prosthetic joint infections with high sensitivity and specificity.

bioRxiv · Mar 18, 2017Microbiology