BugMat and FindNeighbour: command line and server applications for investigating bacterial relatedness

by Oriol Mazariegos-Canellas, Trien Do, Tim Peto, David W. Eyre, Anthony Underwood, Derrick Crook, David H. Wyllie
Published 2017-11-01

Detection of mixed infection from bacterial whole genome sequence data allows assessment of its role in Clostridium difficile transmission.

by David W Eyre, Madeleine L Cule, David Griffiths, Derrick W Crook, Tim E A Peto, A Sarah Walker, Daniel J Wilson
Published 2013-01-01

Probabilistic transmission models incorporating sequencing data for healthcare-associated Clostridioides difficile outperform heuristic rules and identify strain-specific differenc...

by David W Eyre, Mirjam Laager, A Sarah Walker, Ben S Cooper, Daniel J Wilson, CDC Modeling Infectious Diseases in Healthcare Program (MInD-Healthcare)
Published 2021-01-01

Human and Porcine Transmission of Clostridioides difficile Ribotype 078, Europe

by Geraldine Moloney, David W. Eyre, Micheál Mac Aogáin, Máire C. McElroy, Alison Vaughan, Tim E.A. Peto, Derrick W. Crook, Thomas R. Rogers
Published 2021-09-01

RNA polymerase mutations cause cephalosporin resistance in clinical Neisseria gonorrhoeae isolates

by Samantha G Palace, Yi Wang, Daniel HF Rubin, Michael A Welsh, Tatum D Mortimer, Kevin Cole, David W Eyre, Suzanne Walker, Yonatan H Grad
Published 2020-02-01

Asymptomatic Clostridium difficile colonisation and onward transmission.

by David W Eyre, David Griffiths, Alison Vaughan, Tanya Golubchik, Milind Acharya, Lily O'Connor, Derrick W Crook, A Sarah Walker, Tim E A Peto
Published 2013-01-01

Major genetic discontinuity and novel toxigenic species in Clostridioides difficile taxonomy

by Daniel R Knight, Korakrit Imwattana, Brian Kullin, Enzo Guerrero-Araya, Daniel Paredes-Sabja, Xavier Didelot, Kate E Dingle, David W Eyre, César Rodríguez, Thomas V Riley
Published 2021-06-01

Development and validation of early warning score systems for COVID‐19 patients

by Alexey Youssef, Samaneh Kouchaki, Farah Shamout, Jacob Armstrong, Rasheed El‐Bouri, Thomas Taylor, Drew Birrenkott, Baptiste Vasey, Andrew Soltan, Tingting Zhu, David A. Clifton, David W. Eyre
Published 2021-10-01

Clostridium difficile trehalose metabolism variants are common and not associated with adverse patient outcomes when variably present in the same lineageResearch in context

by David W. Eyre, Xavier Didelot, Anthony M. Buckley, Jane Freeman, Ines B. Moura, Derrick W. Crook, Tim E.A. Peto, A. Sarah Walker, Mark H. Wilcox, Kate E. Dingle
Published 2019-05-01

Short-term genome stability of serial Clostridium difficile ribotype 027 isolates in an experimental gut model and recurrent human disease.

by David W Eyre, A Sarah Walker, Jane Freeman, Simon D Baines, Warren N Fawley, Caroline H Chilton, David Griffiths, Alison Vaughan, Derrick W Crook, Tim E A Peto, Mark H Wilcox
Published 2013-01-01

Real-time analysis of nanopore-based metagenomic sequencing from infected orthopaedic devices

by Nicholas D Sanderson, Teresa L Street, Dona Foster, Jeremy Swann, Bridget L Atkins, Andrew J Brent, Martin A McNally, Sarah Oakley, Adrian Taylor, Tim E A Peto, Derrick W Crook, David W Eyre
Published 2018-09-01

Characterisation of Clostridium difficile hospital ward-based transmission using extensive epidemiological data and molecular typing.

by A Sarah Walker, David W Eyre, David H Wyllie, Kate E Dingle, Rosalind M Harding, Lily O'Connor, David Griffiths, Ali Vaughan, John Finney, Mark H Wilcox, Derrick W Crook, Tim E A Peto
Published 2012-02-01

A Role for Tetracycline Selection in Recent Evolution of Agriculture-Associated Clostridium difficile PCR Ribotype 078

by Kate E. Dingle, Xavier Didelot, T. Phuong Quan, David W. Eyre, Nicole Stoesser, Charis A. Marwick, John Coia, Derek Brown, Sarah Buchanan, Umer Z. Ijaz, Cosmika Goswami, Gill Douce, Warren N. Fawley, Mark H. Wilcox, Timothy E. A. Peto, A. Sarah Walker, Derrick W. Crook
Published 2019-03-01

Ct threshold values, a proxy for viral load in community SARS-CoV-2 cases, demonstrate wide variation across populations and over time

by A Sarah Walker, Emma Pritchard, Thomas House, Julie V Robotham, Paul J Birrell, Iain Bell, John I Bell, John N Newton, Jeremy Farrar, Ian Diamond, Ruth Studley, Jodie Hay, Karina-Doris Vihta, Timothy EA Peto, Nicole Stoesser, Philippa C Matthews, David W Eyre, Koen B Pouwels, COVID-19 Infection Survey team
Published 2021-07-01

Stringent thresholds in SARS-CoV-2 IgG assays lead to under-detection of mild infections

by David W. Eyre, Sheila F. Lumley, Denise O’Donnell, Nicole E. Stoesser, Philippa C. Matthews, Alison Howarth, Stephanie B. Hatch, Brian D. Marsden, Stuart Cox, Tim James, Richard J. Cornall, David I. Stuart, Gavin Screaton, Daniel Ebner, Derrick W. Crook, Christopher P. Conlon, Katie Jeffery, Timothy M. Walker, Timothy E. A. Peto
Published 2021-02-01

Epidemiology of Clostridium difficile in infants in Oxfordshire, UK: Risk factors for colonization and carriage, and genetic overlap with regional C. difficile infection strains.

by Nicole Stoesser, David W Eyre, T Phuong Quan, Heather Godwin, Gemma Pill, Emily Mbuvi, Alison Vaughan, David Griffiths, Jessica Martin, Warren Fawley, Kate E Dingle, Sarah Oakley, Kazimierz Wanelik, John M Finney, Melina Kachrimanidou, Catrin E Moore, Sherwood Gorbach, Thomas V Riley, Derrick W Crook, Tim E A Peto, Mark H Wilcox, A Sarah Walker, Modernising Medical Microbiology Informatics Group (MMMIG)
Published 2017-01-01

SARS-CoV-2 RNA detected in blood products from patients with COVID-19 is not associated with infectious virus [version 2; peer review: 2 approved]

by Monique I. Andersson, Carolina V. Arancibia-Carcamo, Kathryn Auckland, J. Kenneth Baillie, Eleanor Barnes, Tom Beneke, Sagida Bibi, Tim Brooks, Miles Carroll, Derrick Crook, Kate Dingle, Christina Dold, Louise O. Downs, Laura Dunn, David W. Eyre, Javier Gilbert Jaramillo, Heli Harvala, Sarah Hoosdally, Samreen Ijaz, Tim James, William James, Katie Jeffery, Anita Justice, Paul Klenerman, Julian C. Knight, Michael Knight, Xu Liu, Sheila F. Lumley, Philippa C. Matthews, Anna L. McNaughton, Alexander J. Mentzer, Juthathip Mongkolsapaya, Sarah Oakley, Marta S. Oliveira, Timothy Peto, Rutger J. Ploeg, Jeremy Ratcliff, Melanie J. Robbins, David J. Roberts, Justine Rudkin, Rebecca A. Russell, Gavin Screaton, Malcolm G. Semple, Donal Skelly, Peter Simmonds, Nicole Stoesser, Lance Turtle, Susan Wareing, Maria Zambon
Published 2020-10-01

Differential occupational risks to healthcare workers from SARS-CoV-2 observed during a prospective observational study

by David W Eyre, Sheila F Lumley, Denise O'Donnell, Mark Campbell, Elizabeth Sims, Elaine Lawson, Fiona Warren, Tim James, Stuart Cox, Alison Howarth, George Doherty, Stephanie B Hatch, James Kavanagh, Kevin K Chau, Philip W Fowler, Jeremy Swann, Denis Volk, Fan Yang-Turner, Nicole Stoesser, Philippa C Matthews, Maria Dudareva, Timothy Davies, Robert H Shaw, Leon Peto, Louise O Downs, Alexander Vogt, Ali Amini, Bernadette C Young, Philip George Drennan, Alexander J Mentzer, Donal T Skelly, Fredrik Karpe, Matt J Neville, Monique Andersson, Andrew J Brent, Nicola Jones, Lucas Martins Ferreira, Thomas Christott, Brian D Marsden, Sarah Hoosdally, Richard Cornall, Derrick W Crook, David I Stuart, Gavin Screaton, Oxford University Hospitals Staff Testing Group, Timothy EA Peto, Bruno Holthof, Anne-Marie O'Donnell, Daniel Ebner, Christopher P Conlon, Katie Jeffery, Timothy M Walker
Published 2020-08-01

Antibody testing for COVID-19: A report from the National COVID Scientific Advisory Panel [version 1; peer review: 2 approved]

by Emily R. Adams, Mark Ainsworth, Rekha Anand, Monique I. Andersson, Kathryn Auckland, J. Kenneth Baillie, Eleanor Barnes, Sally Beer, John I. Bell, Tamsin Berry, Sagida Bibi, Miles Carroll, Senthil K. Chinnakannan, Elizabeth Clutterbuck, Richard J. Cornall, Derrick W. Crook, Thushan de Silva, Wanwisa Dejnirattisai, Kate E. Dingle, Christina Dold, Alexis Espinosa, David W. Eyre, Helen Farmer, Maria Fernandez Mendoza, Dominique Georgiou, Sarah J. Hoosdally, Alastair Hunter, Katie Jefferey, Dominic F. Kelly, Paul Klenerman, Julian Knight, Clarice Knowles, Andrew J. Kwok, Ullrich Leuschner, Robert Levin, Chang Liu, César López-Camacho, Jose Martinez, Philippa C. Matthews, Hannah McGivern, Alexander J. Mentzer, Jonathan Milton, Juthathip Mongkolsapaya, Shona C. Moore, Marta S. Oliveira, Fiona Pereira, Elena Perez, Timothy Peto, Rutger J. Ploeg, Andrew Pollard, Tessa Prince, David J. Roberts, Justine K. Rudkin, Veronica Sanchez, Gavin R. Screaton, Malcolm G. Semple, Jose Slon-Campos, Donal T. Skelly, Elliot Nathan Smith, Alberto Sobrinodiaz, Julie Staves, David I. Stuart, Piyada Supasa, Tomas Surik, Hannah Thraves, Pat Tsang, Lance Turtle, A. Sarah Walker, Beibei Wang, Charlotte Washington, Nicholas Watkins, James Whitehouse, National COVID Testing Scientific Advisory Panel
Published 2020-06-01