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Abstract
A Correction to this paper has been published: https://doi.org/10.1038/s41467-021-22238-5
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1 University of Bath, The Milner Centre for Evolution, Department of Biology and Biochemistry, Bath, UK (GRID:grid.7340.0) (ISNI:0000 0001 2162 1699)
2 University of Bath, The Milner Centre for Evolution, Department of Biology and Biochemistry, Bath, UK (GRID:grid.7340.0) (ISNI:0000 0001 2162 1699); MRC Cloud Infrastructure for Microbial Bioinformatics (CLIMB) Consortium, London, UK (GRID:grid.14105.31) (ISNI:0000000122478951)
3 University of Oslo, Department of Biostatistics, Oslo, Norway (GRID:grid.5510.1) (ISNI:0000 0004 1936 8921); University of Helsinki, Department of Mathematics and Statistics, Helsinki Institute for Information Technology, Helsinki, Finland (GRID:grid.7737.4) (ISNI:0000 0004 0410 2071)
4 University of Bath, The Milner Centre for Evolution, Department of Biology and Biochemistry, Bath, UK (GRID:grid.7340.0) (ISNI:0000 0001 2162 1699); University of Oslo, Department of Biostatistics, Oslo, Norway (GRID:grid.5510.1) (ISNI:0000 0004 1936 8921)
5 National Institute of Infectious Diseases, Antimicrobial Resistance Research Centre, Tokyo, Japan (GRID:grid.410795.e) (ISNI:0000 0001 2220 1880)
6 Uppsala University, Uppsala University, Department for medical biochemistry and microbiology, Uppsala, Sweden (GRID:grid.8993.b) (ISNI:0000 0004 1936 9457)
7 Institute of Life Science, Swansea University Medical School, Swansea, UK (GRID:grid.4827.9) (ISNI:0000 0001 0658 8800)
8 Environment Agency, National Laboratory Service, Starcross, UK (GRID:grid.2678.b) (ISNI:0000 0001 2338 6557)
9 University of Liverpool, Department of Epidemiology and Population Health, Institute of Infection & Global Health, Wirral, UK (GRID:grid.10025.36) (ISNI:0000 0004 1936 8470)
10 University of Oxford, Department of Zoology, Oxford, UK (GRID:grid.4991.5) (ISNI:0000 0004 1936 8948)
11 University of Oslo, Department of Biostatistics, Oslo, Norway (GRID:grid.5510.1) (ISNI:0000 0004 1936 8921); University of Helsinki, Department of Mathematics and Statistics, Helsinki Institute for Information Technology, Helsinki, Finland (GRID:grid.7737.4) (ISNI:0000 0004 0410 2071); Wellcome Sanger Institute, Parasites and Microbes, Cambridge, UK (GRID:grid.10306.34) (ISNI:0000 0004 0606 5382)
12 University of Bath, The Milner Centre for Evolution, Department of Biology and Biochemistry, Bath, UK (GRID:grid.7340.0) (ISNI:0000 0001 2162 1699); MRC Cloud Infrastructure for Microbial Bioinformatics (CLIMB) Consortium, London, UK (GRID:grid.14105.31) (ISNI:0000000122478951); University of Oxford, Department of Zoology, Oxford, UK (GRID:grid.4991.5) (ISNI:0000 0004 1936 8948)