The Genome Sequence of a Type ST239 Methicillin-Resistant Staphylococcus aureus Isolate from a Malaysian Hospital
© The Author(s) 2014
Published: 15 June 2014
We report the genome sequence of a healthcare-associated MRSA type ST239 clone isolated from a patient with septicemia in Malaysia. This clone typifies the characteristics of ST239 lineage, including resistance to multiple antibiotics and antiseptics.
KeywordsStaphylococcus aureus MRSA Malaysia Genomics
Classification and features
Classification and general features of Staphylococcus aureus MRSA PR01
Species Staphylococcus aureus
Type strain MRSA PR01
Terminal electron receptor
Human respiratory tract, skin
Sample collection time
Genome sequencing information
Genome project history
One 350bp Illumina GAIIx genomic library
Illumina GAIIx, Sanger
CLCBio Genomics Workbench
Gene calling method
Glimmer and GeneMark
Genome Database release
Genbank Date of Release
January 11, 2014
Medical, Tree of life
Growth conditions and DNA isolation
MRSA PR01 was grown overnight under aerobic conditions in Tryptic Soy Broth at 37°C. DNA extraction was performed using MasterPure™ Gram Positive DNA Purification Kit (Epicentre, Madison, USA) as per manufacturer’s instructions. The concentration and purity of resultant DNA was assessed by UV spectrophotometry (Nanodrop, Thermo Scientific). 5 µg of genomic DNA (A260/280 = 1.88) was used for library preparation.
Genome sequencing and assembly
The genome sequence was obtained using 104 Mb of paired-end (300 bp spacing) data from the Illumina GAII x platform (Illumina, San Diego, CA) with 36-bp reads. Sequence data were assembled using CLCBio Genomics Workbench (CLC bio, Aarhus, Denmark). One hundred and ninety-five contigs (N50: 13,272 bp) were generated, and were overlaid with the reference sequence Mu50 using OSLay. Fourteen supercontigs were generated as a result. Gaps were closed using Sanger sequencing.
Nucleotide content and gene count levels of the MRSA PR01 genome
% of totala
Genome size (bp)
DNA G+C content (bp)
Genes assigned to COGs
Number of genes associated with the 25 general COG functional categories
RNA processing and modification
Replication, recombination and repair
Chromatin structure and dynamics
Cell cycle control, mitosis and meiosis
Signal transduction mechanisms
Cell wall/membrane biogenesis
Intracellular trafficking and secretion
Posttranslational modification, protein turnover, chaperones
Energy production and conversion
Carbohydrate transport and metabolism
Amino acid transport and metabolism
Nucleotide transport and metabolism
Coenzyme transport and metabolism
Lipid transport and metabolism
Inorganic ion transport and metabolism
Secondary metabolites biosynthesis, transport and catabolism
General function prediction only
Not in COGs
Initial analysis of the genome revealed several key features. This genome has a typical SCCmec type III cassette, containing cadmium resistance genes. SCCmec type III is a composite element that is comprised of SCCmec and SCCmercury. In the MRSA PR01 genome, like others, this region harbors ccrC, pI258 and Tn554 as well as the genes involved in cadmium resistance. The MRSA PR01 genome contains two pathogenicity islands, and several resistance features were identified such as the qacA gene, which confers resistance to antiseptics such as cationic biocides, quaternary ammonium salts, and diamidines via an export-mediated mechanism, and the norA gene which confers resistance to hydrophilic quinolones such as norfloxacin and ciprofloxacin. There were 9 regions defined as prophage regions by PHAST  with one complete prophage region.genes were identified in the genome. A total of 2,267 genes (72.66%) were assigned a putative function. The remaining genes were annotated as hypothetical proteins. The properties and the statistics of the genome are summarized in Table 3. The distribu-tion of genes into COGs and KEGG functional cate-gories is presented in Table 4.
This study is the first to report on the whole genome sequence of a Malaysian MRSA isolate. Preliminary analysis of the genome has highlighted the genetic determinants that are responsible for the organism to adapt easily to selective pressures. Further research is being conducted to provide insight on the adaptive power of this healthcare-associated strain to attain high resistance to antibiotics.
Nucleotide sequence accession numbers. This Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession ANPO00000000. The version described in this paper is the first version, ANPO01000000.
Description of Sulfurimonas hongkongensis sp. nov.
Sulfurimonas hongkongensis (hong.kong.en’sis. N.L. fem. adj. hongkongensis pertaining to Hong Kong, the city where the type strain was isolated).
Strain AST-10T is rod-shaped with size of 0.2–0.4 µm × 0.5–1.2 µm. It is an obligate anaerobe and oc-curs singly. The temperature range for growth is 15–35°C, optimum at 30°C. The pH range for growth is 6.5–8.5, optimum at 7.0–7.5. The salinity range for growth is 10–60 g L−1, and optimum at 30 g L−1. Strictly chemolithoautotrophic growth oc-curs with H2, HS- or S2O32− as an electron donor and with nitrate as an electron acceptor. Nitrate is reduced to N2, and reduced sulfur compounds are oxidized into S0 or SO42− (depending on molar ratio of S2O32−/NO3−). The major cellular fatty acids are C14:0, C16:0, 2-OH C16:0, C16:1, C18:0, and C18:1, with C16:0 2-OH as a unique fatty acid different from other spe-cies in the genus Sulfurimonas.
The type strain AST-10T = DSM 2096T = JCM 18418T, was isolated from coastal sediment at the Kai Tak Approach Channel connected to Victoria Harbour in Hong Kong, China. The GC content of the genome is 34.9%. The genome sequence has been deposited at DDBJ/EMBL/GenBank under accession number AUPZ00000000.
Dr. Lin Cai thanks The University of Hong Kong for the Postdoctoral Fellowship. This study was finan-cially supported by the Research Grants Council of Hong Kong (HKU7201/11E).
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