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.

FIG. 1.

Circular diagram of the S. aureus MSHR1132 chromosome. Key for the circular diagram (outer to inner): Outer colored segments on the gray outer ring represent genomic islands and horizontally acquired DNA (see figure for key); scale (in Mb); annotated CDSs colored according to predicted function are shown on a pair of concentric circles, representing both coding strands; S. aureus reciprocal fasta matches shared with the S. aureus strains (blue): MRSA252, MSSA476, MW2, N315, Mu50, Mu3, COL, NCTC8325, USA3000 FPR3757, JH9, Newman, RF122, LGA251, TW20; Staphylococcus reciprocal fasta matches shared with the staphylococcal species (purple): S. epidermidis, S. saprophyticus, S. haemolyticus, S. carnosus, reciprocal fasta matches shared with Macrococcus caseolyti cus (green); CDS functions: dark blue, pathogenicity/adaptation; black, energy metabolism; red, information transfer; dark green, surface associated; cyan, degradation of large molecules; magenta, degradation of small molecules; yellow, central/intermediary metabolism; pale green, unknown; pale blue, regulators; orange, conserved hypothetical; brown, pseudogenes; pink, phage and IS elements; and gray, miscellaneous.

FIG. 2.

Nucleotide divergence plot of MRSA252 compared with USA300_FPR3757, MSHR1132 and S. epidermidis RP62a. (A) Plot of the nucleotide divergence against gene position between the genomes of MRSA252 and USA300_FPR3757 (purple), MSHR1132 (red) and S. epidermidis RP62a (green). (B) The divergence between MRSA252 and MSHR1132 is approximately seven times greater than that between MRSA252 and USA300_FPR3757 and slightly less than half the divergence between S. aureus and S. epidermidis.

FIG. 3.

Nucleotide divergence and genome content neighbor joining trees. The neighbor joining tree was generated from distances matrices based on (A) genome content and (B) nucleotide divergence between MRSA252, USA300_FPR3757, ED98, MSHR1132, and S. epidermidis RP62a.

FIG. 4.

Variation within the CC75 lineage. Analysis of six CC75 multilocus sequence types by neighbor joining, which resolves three groups.

FIG. 5.

CC75 isolates lack staphyloxanthin. The S. aureus clinical isolate SCC1007 (ST93) (Tong et al. 2009) (left) produces staphyloxanthin, whereas the CC75 isolate MSHR1132 (right) does not.

FIG. 6.

Structure of SCCmec and CRISPR/Cas region. Diagram of the structure of the region including SCCmec and CRISPR/Cas in MSHR1132, S. aureus 08BA02176 (ST398), S. epidermidis RP62a, and S. aureus MRSA252.

FIG. 7.

Structure of the MSHR1132 νSaα and νSaβ genomic islands The MSHR1132 genome contains novel νSaα and νSaβ genomic islands, which were assigned types V and IV, respectively.