Publications 2022

‘Enterobacterales plasmid sharing amongst human bloodstream infections, livestock, wastewater, and waterway niches in Oxfordshire, UK’
Will Matlock, Samuel Lipworth, Kevin K. Chau, Manal Abu Oun, Leanne Barker, James Kavanagh, Monique Andersson, Sarah Oakley, Marcus Morgan, Derrick W. Crook, Daniel S. Read, Muna Anjum, Liam P. Shaw and Nicole Stoesser
bioRxiv (Dec 2022)

‘Sense of personal agency towards mitigating the threat of antibiotic resistance: a focus group study with parents of children under 5 years old, conducted mid-pandemic’
Becky McCall, Andrew Hayward, Michael Wilson, Gill Forbes and Laura Shallcross
F1000 Resesarch (Dec 2022)

‘Does environmental exposure to pharmaceutical and personal care product residues result in the selection of antimicrobial-resistant microorganisms, and is this important in terms of human health outcomes?’
Isobel C. Stanton, Holly J. Tipper, Kevin Chau, Uli Klumper, Jessica Subirats and Aimee K. Murray
Environmental Toxicology and Chemistry (Nov 2022)

‘Antimicrobial resistance in dairy slurry tanks: a critical point for measurement and control’
Michelle Baker, Alexander D Williams, Steven P.T. Hooton, Richard Helliwell, Elizabeth King, Thomas Dodsworth, Rosa Maria Baena-Nogueras, Andrew Warry, Catherine A. Ortori, Henry Todman, Charlotte J. Gray-Hammerton, Alexander, C.W. Pritchard , Ethan IlesRyan CookRichard D. EmesMichael A JonesTheodore KypraiosHelen WestDavid A BarrettStephen J RamsdenRachel L GomesChris HudsonAndrew D MillardSujatha RamanCarol MorrisChristine E R DoddJan-Ulrich KreftJon L Hobman and Dov J Stekel
Environment International (November 2022)

‘Functional and Sequence-Specific Screening Protocols for the Detection of Novel Antimicrobial Resistance Genes in Metagenomic DNA’
Supathep Tansirichayia, William Hutton and Adam P. Roberts
Metagenomics, Methods in Molecular Biology, pp 51-72 (October 2022)

‘Dipeptidyl peptidase-1 inhibition in patients hospitalised with COVID-19: a multicentre, double-blind, randomised, parallel-group, placebo-controlled trial’
Holly R Keir, Merete B Long, Hani Abo-Leyah, Yan Hui Giam, Thenmalar Vadiveloo, Thomas Pembridge, Rebecca C Hull, Lilia Delgado, Margaret Band, Fiona McLaren-Neil, Simon Adamson, Eva Lahnsteiner, Amy Gilmour, Chloe Hughes, Benjamin JM New, David Connell, Rebecca Dowey, Helena Turton, Hollian Richardson, Diane Cassidy, Jamie Cooper, Jay Suntharalingam, Lavanya Diwakar, Peter Russell, Jonathan Underwood, Alexander Hicks, Davinder PS Dosanjh, Beth Sage, Devesh Dhasmana, Mark Spears, AA Roger Thompson, Christopher Brightling, Andrew Smith, Manish Patel, Jacob George, Alison M Condliffe, Amelia Shoemark, Graeme MacLennan and James D Chalmers
The Lancet (Sep 2022)

‘Prediction of hospital-onset COVID-19 infections using dynamic networks of patient contact: an international retrospective cohort study’
Ashleigh Myall, James R Price, Robert L Peach, Mohamed Abbas, Sid Mookergee, Nina Zhu, Isa Ahmad, Damien Ming, Farzan Ramzan, Daneil Teixeira, Christophe Graf, Andrea Y Weisse, Stephan Harbarth Alison Holmes and Mauricio Barahona
Lancet Digit Health (August 2022)

‘Molecular epidemiology and antimicrobial resistance phenotype of paediatric bloodstream infections caused by Gram-negative bacteria’
Sam Lipworth, Karina-Doris Vihta, Tim Davies, Sarah Wright, Merline Tabirao, Kevin Chau, Alison Vaughan, James Kavanagh, Leanne Barker, Sophie George, Shelley Segal, Stephane Paulus, Lucinda Barrett, Sarah Oakley, Katie Jeffery, Lisa Butcher, Tim Peto, Derrick Crook, Sarah Walker, Seilesh Kadambari and Nicole Stoesser
Communications Medicine (August 2022) DOI: 10.1038/s43856-022-00161-0

‘Neutrophil proteomics identifies temporal changes and hallmarks of delayed recovery in COVID19’
Merete B Long, Andrew JM Howden, Holly R Keir, Christina M Rollings, Yan Hui Giam, Thomas Pembridge, Lilia Delgado, Hani Abo-Leyah, Amy F Lloyd, Gabriel Sollberger, Rebecca Hull, Amy Gilmour, Chloe Hughes, Benjamin JM New, Diane Cassidy, Amelia Shoemark, Hollian Richardson, Angus I Lamond, Doreen A Cantrell, James D Chalmers and Alejandro J Brenes
MedRxiv preprint (Aug 2022)

‘Complete Genome Sequence of Pseudomonas aeruginosa Bacteriophage vB_PaeP_PaCe’
Ryan Cook, Taylor Darby and Dwayne R. Roach
ASM Journals (July 2022)

‘Reconstruction of transmission chains of SARS-CoV-2 amidst multiple outbreaks in a geriatric acute-care hospital: a combined retrospective epidemiological and genomic study’
Mohamed Abbas, Anne Cori, Samuel Cordsey, Florian Laubscher, Tomas Robalo Nunes, Ashleigh Myall, Julien Salamun, Philippe Huber, Dina Zekry, Virginie Prendki, Anne Iten, Laure Vieux, Valerie Sauvan, Christophe E Graf and Septhan Harbarth
Elife (July 2022)

‘Molecular ecology and risk factors for third-generation cephalosporin-resistant Escherichia coli carriage by dogs living in urban and nearby rural settings’
Jordan Sealey, Ashley Hammond, Taylor, Oliver Mounsey, Virginia C Gould, Kristen K Reyher and Matthew B Avison
Journal of Antimicrobial Chemotherapy (July 2022) DOI:10.1093/jac/dkac208)

Enterobacterales-associated plasmid sharing amongst human bloodstream infections, livestock, wastewater, and waterway niches: a genomic surveillance study in Oxfordshire, UK’
William Matlock, Samuel Lipworth, Kevin K Chau, Manal Abu Oun, Leanne Barker, James Kavanagh, Monique Andersson, Sarah Oakley, Marcus Morgan, Derrick W. Crook, Daniel S. Read, Mua Anjum, Liam P. Shaw and Nicole Stoesser
bioRXiv (July 2022)

‘Hypoxia shapes the immune landscape in lung injury and promotes the persistence of inflammation’
Ananda S. Mirchandani, Stephen J. Jenkins, Calum C. Bain, Manuel A. Sanchez-Garcia, Hannah Lawson, Patricia Coelho, Fiona Murphy, David M.Griffith, Ailang Zhang, Tyler Morrison, Tony Ly, Simone Arienti, Pranvera Sadiku, Emily R. Watts, Rebecca S. Dickinson, Leila Reyes, George Cooper, Sarah Clark, David Lewis, Van Kelly, Christos Spanos, Kathryn M Musgrave, Liam Delaney, Isla Harper, Jonathan Scott, Nicholas J. Parkinson, Antony J. Rostron, J. Kenneth Baillie, Sara Clohisey, Clare Pridans, Lara Campana, Philip Starkey Lewis, A. John Simpson, David H. Dockrell, Jurgen Schwarze, Nikhil Hirani, Peter J. Ratcliffe, Christopher W. Pugh, Kamil Kranc, Stuart J. Forbes, Moira K.B Whyte and Sarah Walmsley
Nature Immunology (July 2022) 

‘Studies on enmetazobactam clarify mechanisms of widely used Beta-lactamase inhibitors’
Pauline A. Lang, Ritu Raj, Anthony Tumber, Christopher T. Lohans, Patrick Rabe, Carol V. Robinson, Jurgen Brem and  Christopher J. Schofield
PNAS (April 2022)

‘The mobilome associated with Gram-negative bloodstream infections: A large-scale observational hybrid sequencing based study’
Samuel Lipworth, William Matlock, Liam Shaw, Karina-Doris Vihta, Gilliam Rodger, Kevin Chau, Leanne Barker, Sophie George, James Kavanagh, Timothy Davies, Alison Vaughan, Monique Andersson, Katie Jeffery, Sarah Oakley, Marcus Morgan, Susan Hopkins, Timothy Peto, Derrick Crook, Sarah Walker and Nicole Stoesser
MedRXiv Preprint (April 2022)

‘Profiling systemic inflammation and neutrophil function in hospitalized patients with COVID19: results from PREDICT-COVID19’
Merete Long, Holly R Keir, Yan Hui Giam, Andrew J M Howden, Alejandro J Brenes, Christina Rollings, Thomas Pembridge, Lilia Delgado, Hani Abo-Leyah, Rebecca C Hull, Amy Gilmour, Chloe Hughes, Rebecca Dowey, Helena Turton, Benjamin J M New, David W Connell, Hollian Richardson, Roger Thompson, Alison M Condliffe, Angus I Lamond, Diane M Cassidy, Amelia Shoemark, Doreen A Cantrell and James D Chalmers
ERJ Open Research (May 2022) DOI: 10.1183/23120541.LSC-2022.130

‘Similarities and differences in molecular epidemiology of third-generation cephalosporin-resistant Escherichia coli carried by dogs living in urban and nearby rural settings and associated behavioural risk factors’
Jordan Sealey, Ashley Hammond, Oliver Mounsey, Virginia C. Gould, Kristen K. Reyher and Matthew B. Avison
bioRxiv preprint (April 2022) doi:

‘Using system dynamics modelling to assess the economic efficiency of innovations in the public sector – a systematic review’
Nidhee Jadeja, Nina J Zhu, Reda M Lebcir, Franco Sassi, Alison Holmes and Raheelah Ahmad
PloS One (February 2022)