Draft Genome Sequence of Staphylococcus aureus ST672, an Emerging Disease Clone from India

Abstract

We report the draft genome sequence of methicillin-resistant Staphylococcus aureus (MRSA) strain ST672, an emerging disease clone in India, from a septicemia patient. The genome size is about 2.82 Mb with 2,485 open reading frames (ORFs). The staphylococcal cassette chromosome mec (SCCmec) element (type V) and immune evasion cluster appear to be different from those of strain ST772 on preliminary examination.

GENOME ANNOUNCEMENT

Methicillin-resistant Staphylococcus aureus (MRSA) epidemiology has undergone tremendous changes since the advent of community-associated MRSA containing staphylococcal cassette chromosome mec (SCCmec) elements type IV and V in the 1990s (1, 2). Although these strains originated in the community, they have successfully invaded hospitals and are replacing traditionally hospital-associated MRSA with SCCmec element types I, II, and III (5).

The major clones of MRSA present in Indian hospitals and the community are ST22 EMRSA-15 (SCCmec type IV) and ST772 (SCCmec type V). In addition, there is a new and emerging clone, ST672, which we have characterized as carrying SCCmec type V, agr type I, and capsular polysaccharide type 8 and as Panton-Valentine leukocidin (PVL) negative by microarray (7). The allelic pattern for ST672 derived from the multilocus sequence type (MLST) database is 4-3-1-1-11-72-11 for the seven housekeeping genes. Coombs et al. from Australia have reported ST672 carrying SCCmec element IVa as well as V (3). Our collection includes three carrier methicillin-susceptible S. aureus (MSSA) isolates from nasal swabs of outpatients in a hospital, two disease MRSA isolates from blood and pus, and one MSSA isolate from an eye infection. The spa types of carrier isolates are t3840 and t3841, and all disease isolates have spa type t1309. Here we report the draft genome sequence of an S. aureus ST672 strain named GR1 (spa type t1309), isolated from the blood of a septicemia patient.

Genomic DNA from GR1 (ST672) was fragmented to 300 to 400 bp, and paired-end sequencing was performed on an Illumina HiSeq-1000 sequencer. About 11 million paired-end reads (75 nucleotides [nt] each) were obtained, of which ∼9.8 million reads (∼250-fold coverage) passed a quality filter with the following criteria: average read quality score of at least 35, minimum base quality of 30, and no undetermined base. We randomly sampled 20% of the reads to obtain a 50-fold coverage of the genome. Three such random read samples were obtained and assembled using Velvet (9).

The reads were assembled into 64, 73, and 71 contigs, respectively, for the three assemblies, covering ∼2.82 million base pairs. For quality assessment, we mapped all the raw reads back to the contigs. This analysis gave insert size distribution in the expected range and comparable to USA300 sequence reads (6). When aligned against fully sequenced S. aureus genomes using BLASTN (E value, <10⁻¹⁰⁰), we found ∼89 to 94% similarity.

GLIMMER predicted 2,485 open reading frames (ORFs) in at least two of three assemblies, of which 2,298 (92%) showed homology to ORFs in other fully sequenced S. aureus genomes (phmmer: E value, <10⁻¹⁰ and ≥40% global sequence identity) (4). We detected a truncated β-hemolysin (hlb) gene with a 43-kb β-hemolysin converting phage inserted within the split hlb. The phage carries staphylokinase (sak) and staphylococcal complement inhibitor (scn) in its immune evasion cluster. We identified the SCCmec type V element, which is different from that of ST772. Two virulence determinants, a kdp operon (virulence regulator during pathogenesis) and an arginine deiminase locus comprising arcC, arcD, arcB, arcA, and argR genes, not detected by microarray, were found in the genome sequence and later validated by PCR (8).

Nucleotide sequence accession numbers.

This whole-genome shotgun project has been deposited at GenBank under the accession number AJLX00000000. The version described in this paper is the first version. The raw Illumina sequencing reads have been deposited with the Short Read Archive and are available under the accession number SRX146853.