title: Historical zoonoses and other changes in host tropism of Staphylococcus aureus, identified by phylogenetic analysis of a population dataset.
abstract: BACKGROUND
  Staphylococcus aureus exhibits tropisms to many distinct animal hosts. While spillover events can occur wherever there is an interface between host species, changes in host tropism only occur with the establishment of sustained transmission in the new host species, leading to clonal expansion. Although the genomic variation underpinning adaptation in S. aureus genotypes infecting bovids and poultry has been well characterized the frequency of switches from one host to another remains obscure. We sought to identify sustained switches in host tropism in the S. aureus population, both anthroponotic and zoonotic, and their distribution over the species phylogeny. METHODOLOGIES/RESULTS: We have used a sample of 3042 isolates, representing 696 distinct MLST genotypes, from a well-established database (www.mlst.net). Using an empirical parsimony approach (AdaptML) we have investigated the distribution of switches in host association between both human and non-human (henceforth referred to as animal) hosts. We reconstructed a credible description of past events in the form of a phylogenetic tree; the nodes and leaves of which are statistically associated with either human or animal habitats, estimated from extant host-association and the degree of sequence divergence between genotypes. We identified 15 likely historical switching events; 13 anthroponoses and two zoonoses. Importantly, we identified two human-associated clade candidates (CC25 and CC59) that have arisen from animal-associated ancestors; this demonstrates that a human-specific lineage can emerge from an animal host. We also highlight novel rabbit-associated genotypes arising from a human ancestor.
  
  
  CONCLUSIONS
  S. aureus is an organism with the capacity to switch into and adapt to novel hosts, even after long periods of isolation in a single host species. Based on this evidence, animal-adapted S. aureus lineages exhibiting resistance to antibiotics must be considered a major threat to public health, as they can adapt to the human population.
authors.affiliation: MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom. mas03@ic.ac.uk
authors.forename: Marcus A
authors.initials: MA
authors.lastname: Shepheard
authors.forename: Vicki M
authors.initials: VM
authors.lastname: Fleming
authors.forename: Thomas R
authors.initials: TR
authors.lastname: Connor
authors.forename: Jukka
authors.initials: J
authors.lastname: Corander
authors.forename: Edward J
authors.initials: EJ
authors.lastname: Feil
authors.forename: Christophe
authors.initials: C
authors.lastname: Fraser
authors.forename: William P
authors.initials: WP
authors.lastname: Hanage
mesh_terms: D000818:Animals; D019143:Evolution, Molecular; D054884:Host-Pathogen Interactions; D006801:Humans; D010802:Phylogeny; D011817:Rabbits; D013045:Species Specificity; D013211:Staphylococcus aureus / Q000502:physiology*; D018523:Tropism; D015047:Zoonoses / Q000635:transmission*