First Complete Genome Sequences of Staphylococcus aureus subsp. aureus Rosenbach 1884 (DSM 20231T), Determined by PacBio Single-Molecule Real-Time Technology.

The first complete genome sequences of Staphylococcus aureus subsp. aureus Rosenbach 1884 strain DSM 20231(T), the type strain of the bacterium causing staphylococcal disease, were determined using PacBio RS II. The sequences represent the chromosome (2,755,072 bp long; G+C content, 32.86%) and a plasmid (27,490 bp long; G+C content, 30.69%).

GENOME ANNOUNCEMENT

Staphylococcus aureus is a Gram-positive, non-spore-forming, and nonmotile coccus. It is a human indigenous bacterium, and about 30% of healthy humans harbor it in their nasal passages (1). S. aureus is the major cause of staphylococcal disease. The emergence of antibiotic-resistant forms of pathogenic S. aureus is a worldwide problem in clinical medicine (2, 3). S. aureus has a genome size of approximately 2.8 Mb, with a G+C content of 32%. The chromosome contains pathogenicity islands and antibiotic resistance genes acquired through horizontal gene transfer of mobile genetic elements (MGEs) (4, 5). The MGEs occupy 15% to 20% of the chromosome (6, 7). During outbreaks, S. aureus genomes develop single nucleotide polymorphisms (SNPs) and small genetic rearrangements and acquire or lose MGEs containing resistance or virulence genes (8–10).

The type strain of S. aureus subsp. aureus Rosenbach 1884 (DSM 20231T) was first isolated in 1884 from human pleural fluid by Rosenbach (11). At present, >60 complete genome sequences of S. aureus are publicly available (http://www.ncbi.nlm.nih.gov/genome/genomes/154); however, the genome of the type strain of this species has not been completely sequenced (12). The type strain exhibits all of the relevant genotypic and phenotypic properties cited in the species circumscriptions; therefore, the complete genome sequence of the type strain is crucial for analyzing, comparing, and evaluating the characteristics of the species. Here, we report the first complete genome sequences of S. aureus subsp. aureus DSM 20231T determined by the single-molecule real-time (SMRT) technology (13).

Genomic DNA obtained from Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSMZ) was purified using the PowerClean DNA cleanup kit (Mo Bio Laboratories, Carlsbad, CA), followed by 20-kb library construction for P5-C3 chemistry without shearing. Eight SMRT cells of the libraries were sequenced using the PacBio RS II platform (Pacific Biosciences, Menlo Park, CA) with 180-min movies. The maximum and average subread lengths were 34,694 and 6,038 bp, respectively. De novo assembly was conducted by using the Hierarchical Genome Assembly Process 3 (HGAP3) workflow (14). Two circular contigs were obtained, one representing a chromosome (2,755,072 bp; average G +C content, 32.86%; maximum, 60%), and the other representing a plasmid (27,490 bp; G+C content, 30.69%). The chromosome included 29 sets of identical sequence pairs >1,000 bp in size (maximum, 3,063 bp) and several notable tandem repeats (e.g., 384 bp × 5 copies and 18 bp × 42 copies). The SMRT technology provides multikilobase extra-long reads and thereby can resolve these hard-to-sequence regions (15).

The complete genome sequences of the type strain of S. aureus subsp. aureus reported here can be used as the standard reference for the species and will accelerate the understanding of the pathogenomic characteristics of the species and their role in (antibiotic-resistant) staphylococcal disease.

Nucleotide sequence accession numbers.

The complete genome sequences of the S. aureus subsp. aureus DSM 20231T chromosome and plasmid were deposited in DDBJ/ENA/GenBank under the accession numbers CP011526 and CP011527, respectively.