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.

Comparative genome-scale modelling of Staphylococcus aureus strains identifies strain-specific metabolic capabilities linked to pathogenicity

“…1A). The most distantly related strain was the Australian S. aureus isolate MSHR1132 belonging to the clonal complex 75 lineage (17). Next, a representative set of 64 S. aureus Fig.…”

“…Biosynthesis genes for the staphyloxanthin pigment (encoded for by crtMNPQ) were found in all but one of the strains. This strain (MSHR1132) was specifically sequenced because of its lack of the yellow pigment (17).…”

Pathways and roles of wall teichoic acid glycosylation in Staphylococcus aureus

“…In particular tarM seems to be an ancient feature of S. aureus because the very early branching S. aureus clonal complex (CC) 75, sequence type (ST) 1850 strain MSHR1132 bears both, tarS and tarM in its genome (Holt et al, 2011) (Table 2) (Eugster et al, 2011), phage resistance (Tran et al, 1999) L. monocytogenes serotype 4b…”

MLST revisited: the gene-by-gene approach to bacterial genomics

“…3a). Furthermore, an allele-based rMLST analysis of 669 S. aureus isolates identified 229 unique rSTs based on 51 rps loci (two para logous loci, rpsN and rpmG, were excluded for the purposes of this analysis) and resolved the isolates into lineages that corresponded to previously described clonal complexes 83,90 , also indicating genealogical relationships among the clonal complexes (FIG. 3b).…”