A Shiga Toxin-Encoding Prophage Recombination Event Confounds the Phylogenetic Relationship Between Two Isolates of Escherichia coli O157:H7 From the Same Patient by David R. Greig, David R. Greig, Claire Jenkins, Timothy J. Dallman, Timothy J. Dallman

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Analysis Shiga Toxin-Encoding Bacteriophage in a Rare Strain of Shiga Toxin-Producing Escherichia coli O157:H7 stx2a/stx2c by David R. Greig, David R. Greig, Amy F. W. Mikhail, Timothy J. Dallman, Timothy J. Dallman, Claire Jenkins

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Development and validation of a random forest algorithm for source attribution of animal and human Salmonella Typhimurium and monophasic variants of S. Typhimurium isolates in Engl... by Jaromir Guzinski, Yue Tang, Marie Anne Chattaway, Timothy J. Dallman, Liljana Petrovska

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FLORA: a novel method to predict protein function from structure in diverse superfamilies. by Oliver C Redfern, Benoît H Dessailly, Timothy J Dallman, Ian Sillitoe, Christine A Orengo

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Genomic surveillance detects Salmonella enterica serovar Paratyphi A harbouring blaCTX-M-15 from a traveller returning from Bangladesh. by Satheesh Nair, Martin Day, Gauri Godbole, Tranprit Saluja, Gemma C Langridge, Timothy J Dallman, Marie Chattaway

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Whole-Genome Sequencing for National Surveillance of Shigella flexneri by Marie A. Chattaway, David R. Greig, Amy Gentle, Hassan B. Hartman, Timothy J. Dallman, Claire Jenkins

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Inspection of chicken wings and legs for animal welfare monitoring using X-ray computed tomography, visual examination, and histopathology by Kacper Libera, Roozbeh Valadian, Patiharn Vararattanavech, Sri Nithya Dasari, Timothy J. Dallman, Erik Weerts, Len Lipman

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Highly Pathogenic Clone of Shiga Toxin–Producing Escherichia coli O157:H7, England and Wales by Lisa Byrne, Timothy J. Dallman, Natalie Adams, Amy F.W. Mikhail, Noel McCarthy, Claire Jenkins

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Re-analysis of an outbreak of Shiga toxin-producing Escherichia coli O157:H7 associated with raw drinking milk using Nanopore sequencing by David R. Greig, Vivienne Do Nascimento, David L. Gally, Saheer E. Gharbia, Timothy J. Dallman, Claire Jenkins

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Rapid geographical source attribution of Salmonella enterica serovar Enteritidis genomes using hierarchical machine learning by Sion C Bayliss, Rebecca K Locke, Claire Jenkins, Marie Anne Chattaway, Timothy J Dallman, Lauren A Cowley

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Prediction of Phenotypic Antimicrobial Resistance Profiles From Whole Genome Sequences of Non-typhoidal Salmonella enterica by Saskia Neuert, Saskia Neuert, Satheesh Nair, Martin R. Day, Michel Doumith, Philip M. Ashton, Kate C. Mellor, Kate C. Mellor, Claire Jenkins, Claire Jenkins, Katie L. Hopkins, Neil Woodford, Elizabeth de Pinna, Gauri Godbole, Gauri Godbole, Timothy J. Dallman, Timothy J. Dallman

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SGI-4 in Monophasic Salmonella Typhimurium ST34 Is a Novel ICE That Enhances Resistance to Copper by Priscilla Branchu, Oliver J. Charity, Matt Bawn, Gaetan Thilliez, Timothy J. Dallman, Liljana Petrovska, Robert A. Kingsley, Robert A. Kingsley

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Evaluating the use of multilocus variable number tandem repeat analysis of Shiga toxin-producing Escherichia coli O157 as a routine public health tool in England. by Lisa Byrne, Richard Elson, Timothy J Dallman, Neil Perry, Philip Ashton, John Wain, Goutam K Adak, Kathie A Grant, Claire Jenkins

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Evolutionary Context of Non–Sorbitol-Fermenting Shiga Toxin–Producing Escherichia coli O55:H7 by Kyle Schutz, Lauren A. Cowley, Sharif Shaaban, Anne Carroll, Eleanor McNamara, David L. Gally, Gauri Godbole, Claire Jenkins, Timothy J. Dallman

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Evolution of Salmonella enterica serotype Typhimurium driven by anthropogenic selection and niche adaptation. by Matt Bawn, Nabil-Fareed Alikhan, Gaëtan Thilliez, Mark Kirkwood, Nicole E Wheeler, Liljana Petrovska, Timothy J Dallman, Evelien M Adriaenssens, Neil Hall, Robert A Kingsley

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Linkage of Whole Genome Sequencing, Epidemiological, and Clinical Data to Understand the Genetic Diversity and Clinical Outcomes of Shigella flexneri among Men Who Have Sex with Me... by Holly D. Mitchell, Nicholas R. Thomson, Claire Jenkins, Timothy J. Dallman, Anaïs Painset, Peter Kirwan, Valerie Delpech, Amy F. W. Mikhail, Nigel Field, Gwenda Hughes

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Horizontal antimicrobial resistance transfer drives epidemics of multiple Shigella species by Kate S. Baker, Timothy J. Dallman, Nigel Field, Tristan Childs, Holly Mitchell, Martin Day, François-Xavier Weill, Sophie Lefèvre, Mathieu Tourdjman, Gwenda Hughes, Claire Jenkins, Nicholas Thomson

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Informal genomic surveillance of regional distribution of Salmonella Typhi genotypes and antimicrobial resistance via returning travellers. by Danielle J Ingle, Satheesh Nair, Hassan Hartman, Philip M Ashton, Zoe A Dyson, Martin Day, Joanne Freedman, Marie A Chattaway, Kathryn E Holt, Timothy J Dallman

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Genomic epidemiology of Shigella in the United Kingdom shows transmission of pathogen sublineages and determinants of antimicrobial resistance by Kate S. Baker, Timothy J. Dallman, Nigel Field, Tristan Childs, Holly Mitchell, Martin Day, François-Xavier Weill, Sophie Lefèvre, Mathieu Tourdjman, Gwenda Hughes, Claire Jenkins, Nicholas Thomson

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The Transformation of Reference Microbiology Methods and Surveillance for Salmonella With the Use of Whole Genome Sequencing in England and Wales by Marie Anne Chattaway, Timothy J. Dallman, Lesley Larkin, Satheesh Nair, Jacquelyn McCormick, Amy Mikhail, Hassan Hartman, Gauri Godbole, David Powell, Martin Day, Robert Smith, Kathie Grant

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