Complete Genome Sequence of Staphylococcus aureus T0131, an ST239-MRSA-SCCmec Type III Clone Isolated in China

Abstract

We report here the complete genome sequence of Staphylococcus aureus T0131, which is a multiresistant clinical isolate recovered in China and the first sequenced epidemic ST239-MRSA-SCCmec type III strain obtained in Asia. Comparison with two published genomes of ST239 reveals the polymorphism among strains of this type from different continents.

GENOME ANNOUNCEMENT

Staphylococcus aureus is a ubiquitous bacterial pathogen and a leading cause of morbidity and mortality worldwide. The epidemiology of infections is influenced by rapid and widespread emergence of multidrug-resistant methicillin-resistant S. aureus (MRSA). ST239-MRSA-SCCmec type III is considered to be an epidemic strain of hospital-associated MRSA and is prevalent all over the world (2, 8, 10). S. aureus strain T0131, an ST239-MRSA-SCCmecIII isolate, was recovered from an 87-year-old patient in 2006.

Whole-genome sequencing of S. aureus strain T0131 was performed with a combined strategy of 454 sequencing (11) and Solexa sequencing technology (1). A genomic library containing 8-kb inserts was constructed and 368,922 paired-end reads were generated using the GS FLX system, giving 27.3-fold coverage of the genome. Then, 94.0% of the reads were assembled into 10 scaffolds totaling 2.9 Mbp using Newbler version 2.3 (454 Life Sciences, Branford, CT). A total of 9,132,826 reads (2.1-kb library) were generated to reach a depth of 313-fold coverage with an Illumina Solexa Genome Analyzer IIx and mapped to the scaffolds using the Burrows-Wheeler alignment (BWA) tool (9). Gap closure was performed by sequencing PCR products using an ABI 3730 capillary sequencer. Prediction and annotation were performed as described previously (4).

The complete genome of S. aureus strain T0131 contains a single circular chromosome of 2,913,900 bp, with a GC content of 32.8% and no extrachromosomal elements. In all, 2,711 protein-encoding genes, 54 tRNA-encoding genes, 6 rRNA operons, and an SCCmecIII were detected. Analyzing the seven housekeeping genes using the MLST database (http://www.mlst.net) confirmed T0131 as a member of the ST239 complex. Over 76% of genes were assigned to specific Clusters of Orthologous Groups (COG) functional groups, and 52% were assigned an enzyme classification number.

Comparison with the other two published genomes of S. aureus ST239 strains, JKD6008 (SCCmecIII, NCBI GenBank accession number CP002120) and TW20 (SCCmercury, EMBL accession number FN433596), revealed that T0131 and JKD6008 share the highest average nucleotide identity, at 99.95%, and JKD6008 and TW20 share the lowest, at 99.89%. TW20 has two plasmids which are absent in the SCCmecIII strains. T0131 shares 2,603 orthologous coding sequences (CDSs) with JKD6008 and 2,573 CDSs with TW20. T0131 has 85 specific genes compared with the other two genomes, and 65 of them form five pathogenic islands. It is worth noting that two copies of exfoliative toxin-encoding genes are present in two of the five pathogenic islands (13). T0131 possesses 21 copies of IS256 found in JKD6008, as well as three sets of Tn554 and a Tn552 found in TW20. It also has 25 other types of IS elements and four sets of transposons. A locus containing a lantibiotic synthesis gene cluster (3) and a restriction modification system (12) was found in T0131 and TW20 but was absent in JKD008. JKD6008 harbors an integrated pSK1-like plasmid which is absent in the other two (6, 7). Strains JKD6008, TW20, and T0131 were isolated in New Zealand (6), England (5), and China, respectively, and the result indicated that the polymorphisms among ST239 strains are of different continental origins.

Nucleotide sequence accession number.

The complete genome sequence has been deposited in NCBI GenBank under accession number CP002643.