1. Present address: School of Applied Sciences, Faculty of Computing, Engineering and Science, University of South Wales, Pontypridd, CF37 4BD, UK
2. Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff, CF10 3AX, UK
3. Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry CV4 7AL, UK
4. Department of Chemistry and Warwick Integrative Synthetic Biology Centre, University of Warwick, CV4 7AL, UK
5. Present address: Pathogen Genomics Unit, Public Health Wales Microbiology Cardiff, University Hospital of Wales, Cardiff, CF14 4XW, UK
6. Present address: The Centre for Bacterial Cell Biology, Biosciences Institute, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4AX, UK
7. Department of Pediatrics, University of Michigan Medical School, Ann Arbor, Michigan, USA
8. Present address: Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
9. Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
10. Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia