1. Morand, S., McIntyre, K. M. & Baylis, M. Domesticated animals and human infectious diseases of zoonotic origins: domestication time matters. Infect. Genet. Evol. 24, 76–81 (2014).

2. Woolhouse, M. E., Haydon, D. T. & Antia, R. Emerging pathogens: the epidemiology and evolution of species jumps. Trends Ecol. Evol. 20, 238–244 (2005).

3. Lowy, F. D. Staphylococcus aureus infections. N. Engl. J. Med. 339, 520–532 (1998).

4. Chambers, H. F. & Deleo, F. R. Waves of resistance: Staphylococcus aureus in the antibiotic era. Nat. Rev. Microbiol. 7, 629–641 (2009).

5. Peton, V. & Le Loir, Y. Staphylococcus aureus in veterinary medicine. Infect. Genet. Evol. 21, 602–615 (2014).

6. Bradley, A. J., Leach, K. A., Breen, J. E., Green, L. E. & Green, M. J. Survey of the incidence and aetiology of mastitis on dairy farms in England and Wales. Vet. Rec. 160, 253–257 (2007).

7. McNamee, P. T. & Smyth, J. A. Bacterial chondronecrosis with osteomyelitis (‘femoral head necrosis’) of broiler chickens: a review. Avian Pathol. 29, 477–495 (2000).

8. Van Duijkeren, E. et al. Methicillin-resistant Staphylococcus aureus in pigs with exudative epidermitis. Emerg. Infect. Dis. 13, 1408–1410 (2007).

9. Viana, D. et al. A single natural nucleotide mutation alters bacterial pathogen host tropism. Nat. Genet. 47, 361–366 (2015).

10. Feil, E. J. et al. How clonal is Staphylococcus aureus? J. Bacteriol. 185, 3307–3316 (2003).

11. Shepheard, M. A. et al. Historical zoonoses and other changes in host tropism of Staphylococcus aureus, identified by phylogenetic analysis of a population dataset. PLoS ONE 8, e62369 (2013).

12. Weinert, L. A. et al. Molecular dating of human-to-bovid host jumps by Staphylococcus aureus reveals an association with the spread of domestication. Biol. Lett. 8, 829–832 (2012).

13. Price, L. B. et al. Staphylococcus aureus CC398: host adaptation and emergence of methicillin resistance in livestock. mBio 3, e00305-11 (2012).

14. Fitzgerald, J. R. Livestock-associated Staphylococcus aureus: origin, evolution and public health threat. Trends Microbiol. 20, 192–198 (2012).

15. Holden, M. T. et al. A genomic portrait of the emergence, evolution, and global spread of a methicillin-resistant Staphylococcus aureus pandemic. Genome Res. 23, 653–664 (2013).

16. McAdam, P. R. et al. Molecular tracing of the emergence, adaptation, and transmission of hospital-associated methicillin-resistant Staphylococcus aureus. Proc. Natl Acad. Sci. USA 109, 9107–9112 (2012).

17. Spoor, L. E. et al. Livestock origin for a human pandemic clone of community-associated methicillin-resistant Staphylococcus aureus. mBio 4, e00356-13 (2013).

18. Lowder, B. V. et al. Recent human-to-poultry host jump, adaptation, and pandemic spread of Staphylococcus aureus. Proc. Natl Acad. Sci. USA 106, 19545–19550 (2009).

19. Viana, D. et al. Adaptation of Staphylococcus aureus to ruminant and equine hosts involves SaPI-carried variants of von Willebrand factor-binding protein. Mol. Microbiol. 77, 1583–1594 (2010).

20. Guinane, C. M. et al. Evolutionary genomics of Staphylococcus aureus reveals insights into the origin and molecular basis of ruminant host adaptation. Genome Biol. Evol. 2, 454–466 (2010).

21. Koymans, K. J., Vrieling, M., Gorham, R. D.Jr & van Strijp, J. A. Staphylococcal immune evasion proteins: structure, function, and host adaptation. Curr. Top. Microbiol. Immunol. 409, 441–489 (2017).

22. Koop, G. et al. Identification of LukPQ, a novel, equid-adapted leukocidin of Staphylococcus aureus. Sci. Rep. 7, 40660 (2017).

23. Loffler, B. et al. Staphylococcus aureus panton-valentine leukocidin is a very potent cytotoxic factor for human neutrophils. PLoS Pathog. 6, e1000715 (2010).

24. Vrieling, M. et al. LukMF’ is the major secreted leukocidin of bovine Staphylococcus aureus and is produced in vivo during bovine mastitis. Sci. Rep. 6, 37759 (2016).

25. De Jong, N. W. M. et al. Identification of a staphylococcal complement inhibitor with broad host specificity in equid Staphylococcus aureus strains. J. Biol. Chem. 293, 4468–4477 (2018).

26. Wilson, G. J. et al. A novel core genome-encoded superantigen contributes to lethality of community-associated MRSA necrotizing pneumonia. PLoS Pathog. 7, e1002271 (2011).

27. Tong, S. Y. et al. Novel staphylococcal species that form part of a Staphylococcus aureus-related complex: the non-pigmented Staphylococcus argenteus sp. nov. and the non-human primate-associated Staphylococcus schweitzeri sp. nov. Int. J. Syst. Evol. Microbiol. 65, 15–22 (2015).

28. Thaipadungpanit, J. et al. Clinical and molecular epidemiology of Staphylococcus argenteus infections in Thailand. J. Clin. Microbiol. 53, 1005–1008 (2015).

29. Aanensen, D. M. et al. Whole-genome sequencing for routine pathogen surveillance in public health: a population snapshot of invasive Staphylococcus aureus in Europe. mBio 7, e00444-16 (2016).

30. Minin, V. N. & Suchard, M. A. Counting labeled transitions in continuous-time Markov models of evolution. J. Math. Biol. 56, 391–412 (2008).

31. De Maio, N., Wu, C. H., O’Reilly, K. M. & Wilson, D. New routes to phylogeography: a Bayesian structured coalescent approximation. PLoS Genet. 11, e1005421 (2015).

32. Sheppard, S. K. et al. Cryptic ecology among host generalist Campylobacter jejuni in domestic animals. Mol. Ecol. 23, 2442–2451 (2014).

33. Deringer, J. R., Ely, R. J., Monday, S. R., Stauffacher, C. V. & Bohach, G. A. Vβ-dependent stimulation of bovine and human T cells by host-specific staphylococcal enterotoxins. Infect. Immun. 65, 4048–4054 (1997).

34. Howden, B. P., Peleg, A. Y. & Stinear, T. P. The evolution of vancomycin intermediate Staphylococcus aureus (VISA) and heterogenous-VISA. Infect. Genet. Evol. 21, 575–582 (2014).

35. UK One Health Report: Antibiotics Use in Humans and Animals (Public Health England & Veterinary Medicines Directorate, 2015).

36. Ward, M. J. et al. Time-scaled evolutionary analysis of the transmission and antibiotic resistance dynamics of Staphylococcus aureus CC398. Appl. Environ. Microbiol. 80, 7275–7282 (2014).

37. Murray, S. et al. Recombination-mediated host adaptation by avian Staphylococcus aureus. Genome Biol. Evol. 9, 830–842 (2017).

38. Ward, M. J. et al. Identification of source and sink populations for the emergence and global spread of the East-Asia clone of community-associated MRSA. Genome Biol. 17, 160 (2016).

39. Argimon, S. et al. Microreact: visualizing and sharing data for genomic epidemiology and phylogeography. Microb. Genom. 2, e000093 (2016).

40. Zerbino, D. R. Using the Velvet de novo assembler for short-read sequencing technologies. Curr. Protoc. Bioinformatics 11, 11.5 (2010).

41. Zerbino, D. R. & Birney, E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18, 821–829 (2008).

42. Boetzer, M., Henkel, C. V., Jansen, H. J., Butler, D. & Pirovano, W. Scaffolding pre-assembled contigs using SSPACE. Bioinformatics 27, 578–579 (2011).

43. Nadalin, F., Vezzi, F. & Policriti, A. GapFiller: a de novo assembly approach to fill the gap within paired reads. BMC Bioinform. 13, S8 (2012).

44. Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).

45. Stamatakis, A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312–1313 (2014).

46. Drummond, A. J., Suchard, M. A., Xie, D. & Rambaut, A. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol. Biol. Evol. 29, 1969–1973 (2012).

47. Corander, J., Marttinen, P., Sirén, J. & Tang, J. Enhanced Bayesian modelling in BAPS software for learning genetic structures of populations. BMC Bioinform. 9, 539 (2008).

48. Marttinen, P. et al. Detection of recombination events in bacterial genomes from large population samples. Nucleic Acids Res. 40, e6 (2012).

49. Ayres, D. L. et al. BEAGLE: an application programming interface and high-performance computing library for statistical phylogenetics. Syst. Biol. 61, 170–173 (2012).

51. Aibar, S., Fontanillo, C., Droste, C. & De Las Rivas, J. Functional gene networks: R/Bioc package to generate and analyse gene networks derived from functional enrichment and clustering. Bioinformatics 31, 1686–1688 (2015).

52. Seemann, T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30, 2068–2069 (2014).

53. Camacho, C. et al. BLAST+: architecture and applications. BMC Bioinform. 10, 421 (2009).

50. Jones, P. et al. InterProScan 5: genome-scale protein function classification. Bioinformatics 30, 1236–1240 (2014).

54. Delcher, A. L., Phillippy, A., Carlton, J. & Salzberg, S. L. Fast algorithms for large-scale genome alignment and comparison. Nucleic Acids Res. 30, 2478–2483 (2002).

55. Contreras-Moreira, B. & Vinuesa, P. GET_HOMOLOGUES, a versatile software package for scalable and robust microbial pangenome analysis. Appl. Environ. Microbiol. 79, 7696–7701 (2013).

56. Rice, P., Longden, I. & Bleasby, A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 16, 276–277 (2000).

57. Wright, D. W., Angus, T., Enright, A. J. & Freeman, T. C. Visualisation of BioPAX networks using BioLayout Express3D. F1000Res 3, 246 (2014).

58. Paradis, E. Analysis of diversification: combining phylogenetic and taxonomic data. Proc. Biol. Sci. 270, 2499–2505 (2003).

59. David, S. et al. Evaluation of an optimal epidemiological typing scheme for Legionella pneumophila with whole-genome sequence data using validation guidelines. J. Clin. Microbiol. 54, 2135–2148 (2016).

60. Barker, D., Meade, A. & Pagel, M. Constrained models of evolution lead to improved prediction of functional linkage from correlated gain and loss of genes. Bioinformatics 23, 14–20 (2007).

61. Rambaut, A., Drummond, A. J., Xie, D., Baele, G. & Suchard, M. A. Posterior summarisation in Bayesian phylogenetics using Tracer 1.7. System. Biol. https://doi.org/10.1093/sysbio/syy032 (2018).

62. Edgar, R. C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792–1797 (2004).

63. Suyama, M., Torrents, D. & Bork, P. PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Res. 34, W609–W612 (2006).

64. Bruen, T. & Bruen, T. PhiPack: PHI Test and Other Tests of Recombination (McGill University, Montreal, 2005).

65. Huerta-Cepas, J., Serra, F. & Bork, P. ETE 3: reconstruction, analysis, and visualization of phylogenomic data. Mol. Biol. Evol. 33, 1635–1638 (2016).

66. Yang, Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24, 1586–1591 (2007).

67. Zhang, J., Nielsen, R. & Yang, Z. Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. Mol. Biol. Evol. 22, 2472–2479 (2005).

68. Maere, S., Heymans, K. & Kuiper, M. BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in biological networks. Bioinformatics 21, 3448–3449 (2005).