Publications 2021

‘Sputum Proteomics in non-Tuberculous Mycobacterial Lung Disease’
Rebecca Hull, Jeffrey T.J. Huang, Alun K. Barton, Holly R. Keir, Huw Ellis, William Cookson, Miriam Moffatt, Michael Loebinger, James D. Chalmers
Chest Journal, (November 2021)

‘Integrated patient network and genomic plasmid analysis reveal a regional, multi-species outbreak of carbapenemase-producing Enterobacterales carrying both blaIMP and mcr-9 genes’
Adhiratha Boonyasiri, Ashleigh C. Myall, Yu Wan, (Boonyasiri, Myall and Wan are joint first authors) Frances Bolt, Alice Ledda,  Siddharth Mookerjee,Andrea Y. Weiße, Jane F. Turton, Hala Abbas, Ruta Prakapaite, Akshay Sabnis, Alireza Abdolrasouli, Kenny Malpartida-Cardenas, Luca Miglietta, Hugo Donaldson, Mark Gilchrist, Katie L. Hopkins, Matthew J Ellington, Jonathan A. Otter, Gerald Larouy-Maumus, Andrew M. Edwards, Jesus Rodriguez-Manzano, Xavier Didelot, Mauricio Barahona, Alison H. Holmes, Elita Jauneikaite, Frances Davies
MedRxiv preprint 2021

‘Storytelling as a research tool used to explore insights and as an intervention in public health: A systematic narrative review’
Becky McCall, Laura Shallcross, Michael Wilson, Chris Fuller and Andrew Hayward.
Int J Public Health, 66, Article 1604262  (November 2021).        

‘A new family of “megaphages” abundant in the marine environment’
Slawomir Michniewski, Branko Rihtman, Ryan Cook, Michael A. Jones, William H. Wilson, David J. Scanlan & Andrew Millard
ISME Communications 1, 58 (2021),

‘INfrastructure for a PHAge REference Database: Identification of Large-Scale Biases in the Current Collection of Cultured Phage Genomes’
Ryan Cook, Nathan Brown, Tamsin Redgwell, Branko Rihtman, Megan Barnes, Martha Clokie, Dov J. Stekel, Jon Hobman, Michael A. Jones, and Andrew Millard
Phage preprint (2021)

‘Predicting hospital-onset COVID-19 infections using dynamic networks of patient contacts: an observational study’
Ashleigh C Myall, James Richard Price, Robert L Peach, Mohamed Abbas, Siddharth Mookerjee, Nina Zhu, Isa Ahmad, Damien Keng Yen Ming, Farzan Ramzan, Daniel Teixeira, Christophe Graf, Andrea Y Wiesse, Stephan Harbarth, Alison Holmes, Mauricio Barahona
MedRxiv preprint (2021),

‘Informing antimicrobial management in the context of COVID-19: understanding the longitudinal dynamics of C-reactive protein and procalcitonin’
Damien K Ming, Ashleigh Myall, Bernard Hernandez, Andrea Y. Weiße, Robert L. Peach, Mauricio Barahona, Timothy M. Rawson & Alison H. Holmes
BMC Infectious Diseases, Article number: 932 (2021)

‘Network memory in the movement of hospital patients carrying antimicrobial-resistant bacteria’
Ashleigh Myall, Robert Peach, Andrea Weiße, Siddharth Mookerjee, Frances Davies, Alison Holmes and Mauricio Barahona
Applied Network Science 6, 34 (2021)

‘Development and Delivery of a Real-time Hospital-onset COVID-19 Surveillance System Using Network Analysis’
James Price, Siddharth Mookerjee, Eleonora Dyakova, Ashleigh Myall, Wendy Leung, Andrea Y Weiße, Yeeshika Shersing, Eimear Therese Brannigan, Tracey Galletly, David Muir, Paul Randell, Frances Davies, Frances Bolt, Mauricio Barahona, Jonathan Otter and Alison H Holmes
Clinical Infectious Diseases 72(1), 82–89 (2021)

‘Characterising contact in disease outbreaks via a network model of spatial-temporal proximity’
Ashleigh Myall, Robert Peach, Yu Wan, Siddharth Mookerjee, Elita Jauneikaite, Frankie Bolt, James Price, Frances Davies, Andrea Weiße, Alison Holmes and Mauricio Barahona.
medRxiv preprint (2021)

‘Proteomics identifies a type 1 IFN, prothrombotic hyperinflammatory circulating COVID-19 neutrophil signature distinct from non-COVID-19 ARDS’
Leila Rayes, Manuel Alejandro Sanchez-Garcia, Tyler Morrison, Andrew JM Howden, Emily R Watta, Simone Arienti, Pranvera Sadiku, Patricia Coelho, Ananda S Mirchandani, David Hope, Sarah K Clark, Jo Singleton, Shonna Johnston, Robert Grecian, Azin Poon, Sarah McNamara, Isla Harper, Max Head Fourman, Alejandro J Brenes, Shalini Pathak, Amy Lloyd, Gio Rodriguez Blanco, Alex Von Kriegsheim, Bart Ghesquiere, Wesley Vermaelen, Camilla T Cologna, Kevin Dhaliwal, Nik Hirani, David Dockrell, Moira KB Whyte, David M Griffith, Doreen A Cantrell and Sarah R Walmsley.
Wellcome Open Research 2021, 6.38

‘INfrastructure for a PHAge REference Database: Identification of large-scale biases in the current collection of phage genomes’
Ryan Cook, Nathan Brown, Tamsin Redgwell, Branko Rihtman, Megan Barnes, Martha Clokie, Dov J. Stekel, Jon Hobman, Michael A. Jones and Andrew Millard
bioRxiv (1 May 2021)

‘Hybrid assembly of an agricultural slurry virome reveals a diverse and stable community with the potential to alter the metabolism and virulence of veterinary pathogens’
Ryan Cook, Steve Hooton, Urmi Trivedi, Liz King, Christine E.R. Dodd Jon L. Hobman, Dov J. Stekel, Michael A. Jones and Andrew D. Millard
Microbiome (20 March 2021)

‘Genomic network analysis of environmental and livestock F-type plasmid populations’
William Matlock, Kevin Chau, Manal AbuOun, Emma Stubberfield, Leanne Barker, James Kavanagh, Hayleah Pickford, Daniel Gilson, Richard P. Smith, H. Soon Gweon, Sarah J. Hoosdally, Jeremy Swann, Robert Sebra, Mark J. Bailey, Timothy E. A. Peto, Derrick W. Crook, Muna F. Anjum, Daniel S. Read, A. Sarah Walker, Nicole Stoesser, Liam P. Shaw & REHAB consortium
The ISME Journal (1 March 2021)

‘Flanker: a tool for comparative genomics of gene flanking regions’
William Matlock, Samuel Lipworth, Bede Constantinides, Timothy E.A. Peto, A. Sarah Walker, Derrick Crook, Susan Hopkins, Liam P. Shaw and Nicole Stoesser
bioRxiv (22 February 2021)