{"database":"ENA","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Fastqsanger.gz":["ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR207/005/SRR2079245/SRR2079245_subreads.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR168/005/SRR1686735/SRR1686735.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR207/006/SRR2079246/SRR2079246_subreads.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR168/004/SRR1686734/SRR1686734.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR168/006/SRR1686736/SRR1686736.fastq.gz"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"omics_type":["Genomics"],"center_name":["416, Microbiology, University of Adelaide"],"full_dataset_link":["https://www.ebi.ac.uk/ena/browser/view/PRJNA268968"],"scientific_name":["Staphylococcus aureus"],"long_description":["We have observed that for a number of S. aureus strains as they switch to a SCV lifestyle there is the formation of an extracellular matrix. We focused our analysis on one strain, WCH-SK2. For bacterial survival in the host, the combination of low nutrients and the prolonged timeframe forms a stress that selects for a specific cell-type from the population. In this context, we used steady-state growth conditions with low nutrients and a controlled low growth rate, for a prolonged time and with methylglyoxal. These conditions induced S. aureus WCH-SK2 into a stable SCV cell-type, they did not revert after sub-culturing. Methods: Transcriptomic profiles of wild-type (WT) and SCV were generated in continuous culture in the presence of stress (high and low level of methylglyoxal). Results: Analysis revealed these cells possessed a metabolic and surface profile that was different from previously described SCVs or biofilm cells. The extracellular matrix was protein and extracellular DNA but not polysaccharide. The SCV cells induced expression of certain surface proteins (such as Ebh) and lantibiotic synthesis while down-regulating factors that stimulates immune response (leucocidin, capsule, carotenoid). We also studied further their genetic characteristics. They possessed an increased viability in the presence of antibiotics compared to their non-SCV form. Their stability implied there had been genetic changes, we determined the whole genome sequence of WCH-SK2 and its stable SCV forms at a single base resolution, employing Single Molecular Real-Time (SMRT) sequencing that also enables the methylome to be determined. The genetic features of this isolate have been identified the SCCmec type, the pathogenicity and genetic islands and virulence factors. The comparison has identified a set of genetic changes that occurred in the stable SCV form most notably to the global regulator MgrA and the phosphoserine phosphatase RsbU (part of the regulatory pathway of the sigma factor SigB). There was a shift in the methylation across the genome. Conclusions: Our data reveal a cell heterogeneity within a S. aureus population and using conditions that resemble long-term survival in the host has identified a previously unnoticed S. aureus cell-type, with a distinctive metabolic and molecular profile. The results from this study represent a unique identification of a suite of epigenetic, genetic and transcriptional factors that are implicated in the switch in S. aureus to its persistent SCV form Overall design: Total RNA of WT (batch culture) and SCV formed in high level of methylglyoxal (0.031%) at day 55 and SCV formed at low level of methylglyoxal (0.0078%) at day 30 of continuous culture. DNA genomic of WT and stable SCV formed in high level of methylglyoxal (0.031%)"],"tag":["pathogen:priority","pathogen:bacterium","xref:PubMed:25385795","pathogen"],"classification":["bacteria"],"repository":["ENA"],"description_synonyms":["small, Salmonella-containing vacuole, MGC130048, dTAF[[II]]230, TAF[[II]]250, d230, SGCG_HUMAN, 35 kDa dystrophin-associated glycoprotein, postnatal development, Sprain, SG-gamma, TAF200, A4, l(3)84Ab, dTAFII250, growth and development, BG:DS00004.13, bacterium-containing vacuole, TAFII-250, TAF250/230, EfW1, Cell, TYPE, SGCG, strain, dTAF230, DAGA4, development, dmTAF[[II]]230, TAFII250, reduced, dmTAF1, Taf230, p230, Strain, 35DAG, TAF[[II]]250/230, TFIID, sarcoglycan, cultivar, LGMD2C., tiny, MAM, gamma-SG, Sprains, SCG3, Staphlococcus pyogenes citreus, TAF250, Taf[[II]]250, gamma sarcoglycan, Taf200, Staphylococcus aureus subsp. anaerobius, dTAF[[II]]250, TAF[[II]]230, TFIID TAF250, DMDA1, growth pattern, underdeveloped, cel, Staphilococcus aureus, cell, non-developmental growth, postnatal growth, hypoplasia, Taf1p, Micrococcus aureus, TAF[II]250, pathogen-occupied vacuole, CG17603, gamma (35kDa dystrophin-associated glycoprotein), TAF[[II]], ecotype, Streptococcus aureus, dTAF250, DmelCG17603, DMDA, Micrococcus pyogenes, Staphylococcus pyogenes aureus, Taf250, SR3-5, 35kD dystrophin-associated glycoprotein, SCARMD2, gamma-sarcoglycan, Strains, Staphylococus aureus, TAF, growth, Strains and Sprains, TAF230, TAF1"],"name_synonyms":["Staphylococus aureus, Micrococcus aureus, Micrococcus pyogenes, Staphylococcus pyogenes aureus, Staphylococcus aureus subsp. anaerobius, Streptococcus aureus., Staphlococcus pyogenes citreus, Staphilococcus aureus"],"additional_accession":[]},"is_claimable":false,"name":"Staphylococcus aureus","description":"Prolonged growth of a clinical S. aureus strain selects for a stable SCV and Full genomic characterization of the development in a clinical Staphylococcus aureus strain of a stable Small Colony Variant cell-type","dates":{"last_updated":"2025-09-24","first_public":"2014-12-03"},"accession":"PRJNA268968","cross_references":{"GEO":["GSE63750"],"taxon":["1280"],"PubMed":["25385795"]}}