Contributed equally to this work with:
Current address: Warwick Medical School, University of Warwick, Coventry, United Kingdom
Environmental Research Institute, University College Cork, Cork, Ireland
Current address: Department of Microbiology, University College Cork, Cork, Ireland
Current address: Statens Serum Institut, Department of Microbiology and Infection Control, Copenhagen, Denmark
National Salmonella Reference Laboratory, Bacteriology Department, Galway University Hospital, Galway, Ireland
University College Dublin Centre for Food Safety, School of Public Health, Physiotherapy and Population Science, Dublin, Ireland
Scottish Salmonella, Shigella and Clostridium difficile Reference Laboratory, Microbiology Department, Stobhill Hospital, Glasgow, United Kingdom
Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Canada
Institut Pasteur, Microbial Evolutionary Genomics Unit, Paris, France
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