title: A full genomic characterization of the development of a stable Small Colony Variant cell-type by a clinical Staphylococcus aureus strain.
abstract: A key to persistent and recurrent Staphylococcus aureus infections is its ability to adapt to diverse and toxic conditions. This ability includes a switch into a biofilm or to the quasi-dormant Small Colony Variant (SCV). The development and molecular attributes of SCVs have been difficult to study due to their rapid reversion to their parental cell-type. We recently described the unique induction of a matrix-embedded and stable SCV cell-type in a clinical S. aureus strain (WCH-SK2) by growing the cells with limiting conditions for a prolonged timeframe. Here we further study their characteristics. They possessed an increased viability in the presence of antibiotics compared to their non-SCV form. Their stability implied that there had been genetic changes; we therefore determined both the genome sequence of WCH-SK2 and its stable SCV form at a single base resolution, employing Single Molecular Real-Time (SMRT) sequencing that enabled the methylome to also be determined. The genetic features of WCH-SK2 have been identified; the SCCmec type, the pathogenicity and genetic islands and virulence factors. The genetic changes that had occurred in the stable SCV form were identified; most notably being in MgrA, a global regulator, and RsbU, a phosphoserine phosphatase within the regulatory pathway of the sigma factor SigB. There was a shift in the methylomes of the non-SCV and stable SCV forms. We have also shown a similar induction of this cell-type in other S. aureus strains and performed a genetic comparison to these and other S. aureus genomes. We additionally map RNAseq data to the WCH-SK2 genome in a transcriptomic analysis of the parental, SCV and stable SCV cells. The results from this study represent the 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.
authors.affiliation: Research Centre for Infectious Disease, Department of Molecular and Cellular Biology, The University of Adelaide, Adelaide, SA 5005, Australia.
authors.forename: Long M G
authors.initials: LMG
authors.lastname: Bui
authors.affiliation: Research Centre for Infectious Disease, Department of Molecular and Cellular Biology, The University of Adelaide, Adelaide, SA 5005, Australia. Electronic address: stephen.kidd@adelaide.edu.au.
authors.forename: Stephen P
authors.initials: SP
authors.lastname: Kidd
mesh_terms: D000900:Anti-Bacterial Agents / Q000494:pharmacology; D019175:DNA Methylation; D004251:DNA Transposable Elements; D024881:Drug Resistance, Bacterial; D057890:Epigenomics; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D056726:Genetic Association Studies; D014644:Genetic Variation; D016680:Genome, Bacterial; D023281:Genomics; D005838:Genotype; D006801:Humans; D008826:Microbial Sensitivity Tests; D050296:Microbial Viability / Q000187:drug effects; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA; D013203:Staphylococcal Infections / Q000382:microbiology*; D013211:Staphylococcus aureus / Q000187:drug effects / Q000235:genetics* / Q000254:growth & development*; D059467:Transcriptome
chemical_list: D000900:Anti-Bacterial Agents; D004251:DNA Transposable Elements
keywords: Methylome; Persister cells; Small Colony Variants; Staphylococcus aureus; Whole genome sequencing