Complete genomes of two clinical Staphylococcus aureus strains: evidence for the rapid evolution of virulence and drug resistance

Abstract

Staphylococcus aureus is an important nosocomial and community-acquired pathogen. Its genetic plasticity has facilitated the evolution of many virulent and drug-resistant strains, presenting a major and constantly changing clinical challenge. We sequenced the approximately 2.8-Mbp genomes of two disease-causing S. aureus strains isolated from distinct clinical settings: a recent hospital-acquired representative of the epidemic methicillin-resistant S. aureus EMRSA-16 clone (MRSA252), a clinically important and globally prevalent lineage; and a representative of an invasive community-acquired methicillin-susceptible S. aureus clone (MSSA476). A comparative-genomics approach was used to explore the mechanisms of evolution of clinically important S. aureus genomes and to identify regions affecting virulence and drug resistance. The genome sequences of MRSA252 and MSSA476 have a well conserved core region but differ markedly in their accessory genetic elements. MRSA252 is the most genetically diverse S. aureus strain sequenced to date: approximately 6% of the genome is novel compared with other published genomes, and it contains several unique genetic elements. MSSA476 is methicillin-susceptible, but it contains a novel Staphylococcal chromosomal cassette (SCC) mec-like element (designated SCC(476)), which is integrated at the same site on the chromosome as SCCmec elements in MRSA strains but encodes a putative fusidic acid resistance protein. The crucial role that accessory elements play in the rapid evolution of S. aureus is clearly illustrated by comparing the MSSA476 genome with that of an extremely closely related MRSA community-acquired strain; the differential distribution of large mobile elements carrying virulence and drug-resistance determinants may be responsible for the clinically important phenotypic differences in these strains.

Fig. 1.

Schematic circular diagrams of the MRSA252 and MSSA476 chromosomes. Where appropriate, categories are shown as pairs of concentric circles representing both coding strands. The outer colored segments on the gray outer ring represent genomic islands and horizontally acquired DNA (see figure for key). Inside the gray outer ring, the rings from outside to inside represent scale in Mbp, annotated CDS (colored according to predicted function), tRNA and rRNA (green), additional DNA compared to the other S. aureus strain described here (MSSA476 or MRSA252 where appropriate; red), additional DNA compared to other sequenced S. aureus strains [N315 (5), Mu50 (5), and MW2 (6); blue], percentage of G + C content, and G + C deviation (>0%, olive; <0%, purple). Color coding for CDSs is as follows: 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 plus insertion sequence elements; gray, miscellaneous.

Fig. 2.

Comparison of SCC elements. Shown are the schematic diagrams of S. aureus type II SCCmec of MRSA252 (first schematic), non-mec SCC₄₇₆ of MSSA476 (second schematic), the type IV SCCmec of MW2 (third schematic), and the non-mec SCC₁₂₂₆₃ from S. hominis (fourth schematic). Genes are marked in the direction of transcription as arrows. Genes with similarity in all elements are marked in the same color; genes with no similarity are white. Conserved regions in the SCC elements are joined by light blue shading. Genes within the S. hominis SCC₁₂₂₆₃ element that are similar to genes downstream of the SCC elements in the community-acquired strains MSSA476 and MW2 and within the MRSA252 SCCmec are shaded in gray. The black arrows in the MRSA252 SCCmec element indicate the additional CDS in comparison to the type II SCCmec elements of N315 and Mu50. The colored boxes at the end of the SCC elements mark the left and right attachment sites (blue, attL; green, attR). Inverted complementary repeats at the boundaries of the elements are marked by red arrows.

Fig. 3.

Phylogenetic diversity of the sequenced S. aureus strains. The split decomposition tree was constructed by using concatenated sequences of the seven loci used in MLST for a selection of STs from the staphylococcal MLST database. The graph was constructed by using splitstree Version 3.1 (34). Distances were estimated by using hamming (uncorrected) distances. The positions of all seven strains for which complete genome sequences are available are shown.