Genome sequence of Staphylococcus aureus strain Newman and comparative analysis of staphylococcal genomes: polymorphism and evolution of two major pathogenicity islands

Abstract

Strains of Staphylococcus aureus, an important human pathogen, display up to 20% variability in their genome sequence, and most sequence information is available for human clinical isolates that have not been subjected to genetic analysis of virulence attributes. S. aureus strain Newman, which was also isolated from a human infection, displays robust virulence properties in animal models of disease and has already been extensively analyzed for its molecular traits of staphylococcal pathogenesis. We report here the complete genome sequence of S. aureus Newman, which carries four integrated prophages, as well as two large pathogenicity islands. In agreement with the view that S. aureus Newman prophages contribute important properties to pathogenesis, fewer virulence factors are found outside of the prophages than for the highly virulent strain MW2. The absence of drug resistance genes reflects the general antibiotic-susceptible phenotype of S. aureus Newman. Phylogenetic analyses reveal clonal relationships between the staphylococcal strains Newman, COL, NCTC8325, and USA300 and a greater evolutionary distance to strains MRSA252, MW2, MSSA476, N315, Mu50, JH1, JH9, and RF122. However, polymorphism analysis of two large pathogenicity islands distributed among these strains shows that the two islands were acquired independently from the evolutionary pathway of the chromosomal backbones of staphylococcal genomes. Prophages and pathogenicity islands play central roles in S. aureus virulence and evolution.

FIG. 1.

Circular display of S. aureus strain Newman chromosome. Green bars inside the first (outer) scale circle indicate the positions of genomic islands. The second circle shows open reading frames oriented in the forward direction, whereas the third circle indicates those oriented in the reverse direction. The fourth and fifth circles show genes for rRNAs and transfer RNAs, respectively. The sixth circle represents G+C content values. Purple indicates domains with G+C contents higher than 50%. The seventh circle shows G+C skew, in which purple indicates positive values.

FIG. 2.

Homology alignment of whole genomes between strains Newman and MW2 (A) and strains Newman and N315 (B). Gaps are highlighted with circles in green (unique elements to Newman), purple (unique to MW2 or N315), or yellow (the same elements but with differences). The νSaβ in panel A and νSaα in panel B are homologous each other, but only the pathogenicity island names are indicated in parentheses.

FIG. 3.

Comparison of major pathogenicity islands νSaα (A) and νSaβ (B) in Newman with other S. aureus strains. Arrows represent open reading frames and their orientations. The two islands for strain Newman are shown on the top of each panel, whereas each type of νSaα and νSaβ is shown with representative strains below that for Newman: νSaα of N315, MW2, MRSA252, and RF122 are shown as types I through IV (A), whereas νSaβ of N315, MW2, and MRSA252 are shown as types I through III (B), respectively. Refer to Fig. 4 for the classes of the islands carried by other strains. Note that HsdS sequences for strains are polymorphic and that a common type of the pathogenicity island always harbors identical HsdS sequences regardless of the strains. Another pathogenicity island, SaPIbov (8), is inserted downstream of guaA gene in type IV νSaα of strain RF122, and only the insertion position is indicated.

FIG. 4.

Tree view showing the phylogenic relationships among 12 S. aureus strains calculated based on the sequence diversity of seven housekeeping genes and the classification of the genomic islands (Fig. 3) νSaα (A) and νSaβ (B) using ellipses. The genomic island classification is based on its structural differences and HsdS sequences (1): when the HsdS sequences in either νSaα or νSaβ island from different strains are identical, the islands are categorized into a common class, whose genetic content is strongly associated with the HsdS allotype in the island, as shown in Fig. 3. If strains harbor a common class of νSaα (A) or νSaβ (Β), their names are covered by an ellipse with a unique color. Both HsdS in νSaα and νSaβ of RF122 are truncated, although νSaβ of the strain is classified into type II. The scale indicates the relative distance on the phylogenic tree view.