title: A very early-branching Staphylococcus aureus lineage lacking the carotenoid pigment staphyloxanthin.
abstract: Here we discuss the evolution of the northern Australian Staphylococcus aureus isolate MSHR1132 genome. MSHR1132 belongs to the divergent clonal complex 75 lineage. The average nucleotide divergence between orthologous genes in MSHR1132 and typical S. aureus is approximately sevenfold greater than the maximum divergence observed in this species to date. MSHR1132 has a small accessory genome, which includes the well-characterized genomic islands, νSAα and νSaβ, suggesting that these elements were acquired well before the expansion of the typical S. aureus population. Other mobile elements show mosaic structure (the prophage ϕSa3) or evidence of recent acquisition from a typical S. aureus lineage (SCCmec, ICE6013 and plasmid pMSHR1132). There are two differences in gene repertoire compared with typical S. aureus that may be significant clues as to the genetic basis underlying the successful emergence of S. aureus as a pathogen. First, MSHR1132 lacks the genes for production of staphyloxanthin, the carotenoid pigment that confers upon S. aureus its characteristic golden color and protects against oxidative stress. The lack of pigment was demonstrated in 126 of 126 CC75 isolates. Second, a mobile clustered regularly interspaced short palindromic repeat (CRISPR) element is inserted into orfX of MSHR1132. Although common in other staphylococcal species, these elements are very rare within S. aureus and may impact accessory genome acquisition. The CRISPR spacer sequences reveal a history of attempted invasion by known S. aureus mobile elements. There is a case for the creation of a new taxon to accommodate this and related isolates.
authors.affiliation: Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia.
authors.forename: Deborah C
authors.initials: DC
authors.lastname: Holt
authors.forename: Matthew T G
authors.initials: MT
authors.lastname: Holden
authors.forename: Steven Y C
authors.initials: SY
authors.lastname: Tong
authors.forename: Santiago
authors.initials: S
authors.lastname: Castillo-Ramirez
authors.forename: Louise
authors.initials: L
authors.lastname: Clarke
authors.forename: Michael A
authors.initials: MA
authors.lastname: Quail
authors.forename: Bart J
authors.initials: BJ
authors.lastname: Currie
authors.forename: Julian
authors.initials: J
authors.lastname: Parkhill
authors.forename: Stephen D
authors.initials: SD
authors.lastname: Bentley
authors.forename: Edward J
authors.initials: EJ
authors.lastname: Feil
authors.forename: Philip M
authors.initials: PM
authors.lastname: Giffard
mesh_terms: D001483:Base Sequence; D002876:Chromosomes, Bacterial; D019143:Evolution, Molecular; D016680:Genome, Bacterial; D020071:Interspersed Repetitive Sequences; D055029:Inverted Repeat Sequences / Q000235:genetics*; D008969:Molecular Sequence Data; D010802:Phylogeny; D012641:Selection, Genetic; D013211:Staphylococcus aureus / Q000145:classification* / Q000235:genetics*; D024341:Xanthophylls / Q000235:genetics*
chemical_list: D024341:Xanthophylls; C031841:staphyloxanthin