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J Bacteriol. Mar 2012; 194(6): 1625–1626.
PMCID: PMC3294860

Genome Sequence of Staphylococcus aureus Strain 11819-97, an ST80-IV European Community-Acquired Methicillin-Resistant Isolate

Abstract

The European methicillin-resistant Staphylococcus aureus (MRSA) clone ST80-IV has historically dominated community-associated infections in major parts of Europe and is a lineage strongly linked to skin and soft tissue infections. Here, we report the genome sequence of an ST80-IV representative, 11819-97, isolated from a skin infection in Denmark in 1997.

GENOME ANNOUNCEMENT

Historically, community-associated methicillin-resistant Staphy-lococcus aureus (CA-MRSA) infections have been dominated by five lineages: ST1-IV (USA400), ST8-IV (USA300), ST30-IV (Pacific/Oceania), ST59-IV/V (USA1000, Taiwan), and ST80-IV (European CA-MRSA), each being geographically restricted (2). These CA-MRSA lineages have generally been characterized by carriage of mecA in a staphylococcal cassette chromosome mec element (SCCmec) type IV and the Panton-Valentine leukocidin (PVL). ST80-IV was first identified in the early 1990s and today is found throughout Europe, the Middle East, and Northern Africa (1, 3, 6, 8, 9). In Denmark, ST80-IV isolates accounted for ~40% of all CA-MRSA cases from 1999 to 2006, causing mostly skin and soft tissue infections (5, 6). Interestingly, ST80 isolates have almost exclusively been found as MRSA and characterized as being resistant to fusidic acid (fusB). Here, a Danish clinical MRSA isolate, 11819-97, collected from a skin abscess, was selected as a representative for the major phylogenetic group in Denmark.

The genome sequence was acquired using 319 Mb of paired-end (450-bp spacing) and 498 Mb of mate pair (4.5-kb spacing) sequencing data from the Illumina GAIIx platform (Illumina, San Diego, CA) with 100-bp reads. Roche Genome Sequencer FLX (Roche Diagnostics, Basel, Switzerland) sequences, 347 Mb of sequence data, 400-bp reads, with a contig N50 of 33 kb, were used to assist in plasmid assembly. Sequence data were assembled using CLC bio's Genomics Workbench 4.7 (CLC bio, Aarhus, Denmark) and Velvet 1.1 (10). Eighty-five contigs (>500 bp, contig N50 of 66 kb) were generated from the paired-end data, and with the addition of mate-pair data, the Velvet assembler generated 13 contigs (>500 bp, contig N50 of 990 kb). Gaps were closed using Sanger sequencing, and optical mapping (OpGen, Maryland) was used to verify accurate assembly. The genome was annotated using the IGS Annotation Engine.

The genome consisted of a 2,846,546-bp circular chromosome with a GC content of 32.9%, containing 2,643 coding sequences (CDS), 59 tRNAs, and 16 rRNA features. Approximately 72% of all CDS were assigned to clusters of orthologous groups (COG). Additionally a 22.3-kb partially sequenced plasmid, p11819-97, contained 23 CDS.

Initial analysis identified a novel SCCmec type IV cassette with an integrated partial plasmid (p18810-P03) in the J2 region, similar to SCCmec III (4). The chromosome encompassed three prophages, [var phi]Sa2, [var phi]Sa3, and an S. aureus [var phi]37-like prophage, by PHAST analysis (11). [var phi]Sa2 contained the lukS and lukF genes encoding the PVL, whereas [var phi]Sa3 contained two human innate immune modulatory genes (sak and scn). Two genomic islands, GIα and GIβ, were also present, with GIβ carrying lukD and lukE. Analysis showed the representative CC80 genome to be distinct from other sequenced lineages and to contain several novel gene clusters. The fusidic acid resistance gene (fusB) was carried on a plasmid dissimilar to the previously described fusB-carrying plasmid pUB101 (7). Further analysis will provide insight into the genetic background for the success of this community-associated lineage and community-associated lineages in general.

Nucleotide sequence accession numbers.

The sequences of the chromosome of S. aureus 11819-97 and p11819-97 plasmid draft have been deposited in GenBank under accession numbers CP003194 and CP003193, respectively.

ACKNOWLEDGMENTS

We thank Elvira Chapka for excellent technical assistance and Michelle Giglio at the University of Maryland, School of Medicine, for assistance with the annotation.

Statens Serum Institut provided funding for the genome sequencing.

REFERENCES

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