Staphylococcus aureus small colony variant (JKD6229) vs. parent strain (JKD6210)
Ontology highlight
ABSTRACT:
ORGANISM(S): Staphylococcus aureus
PROVIDER: GSE20957 | GEO | 2010/08/13
SECONDARY ACCESSION(S): PRJNA124447
REPOSITORIES: GEO
Similar Datasets
Project description:Transcriptional profiling of the small colony variant (SCV) S. aureus isolate (JKD6229) compared to the parent isolate with a normal phenotype (JKD6210). Both isolates were from a patient with persistent S. aureus infection, and the SCV strain arose during failed antibiotic therapy. Two condition experiment JKD6229 vs JKD6210. 4 biological replicates, one replicate per slide.
2010-08-13 | E-GEOD-20957 | biostudies-arrayexpress
Project description:Respiration deficient S. aureus small colony variants (SCVs) frequently cause persistent infections, which necessitates they acquire iron, yet how SCVs obtain iron remains unknown. To address this, we created a stable hemB mutant in S. aureus USA300 strain LAC. The hemB SCV utilized exogenously supplied heme but was attenuated for growth under conditions of iron starvation. RNA-seq showed that both WT S. aureus and the hemB mutant sense and respond to iron starvation.
2022-09-06 | GSE184082 | GEO
Project 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
2014-12-02 | GSE63750 | GEO
Project description:WalKR is an essential two component regulatory system in S. aureus, thought to control cell wall metabolism. Using genome sequencing of 5 paired clinical isolates of vancomycin-susceptible and vancomycin-intermediate S. aureus we found frequent, but unique, mutations in this locus. To investigate the contribution of these mutations to vancomycin resistance allelic replacement WalK (G223D) and WalR (K208R) mutants were generated and compared to the parent strains. Mutations in walk and walR led to increased vancomycin resistance, reduced biofilms formation and attenuation of virulence, demonstrating that minor genetic changes in this locus can lead to significant changes in bacterial resistance and virulence. Microarray transcriptional comparisons were performed to investigate the regulatory effects of the WalK (G223D) and WalR (K208R) mutations, and demonstrated that while changes in genes affecting cell wall metabolism were detected, more dramatic changes were found in regulation of cellular metabolism. Transcriptional profiling of laboratory derived S. aureus walKR mutants compared to the parent isolates. TPS3130 has a single point mutation in walK, and TPS3190 has a single point mutation in walR. Two condition experiment TPS3130 vs JKD6009 and TPS3190 vs JKD6004. 3 biological replicates per isolate pair, one replicate per slide.
2012-05-31 | E-GEOD-29157 | biostudies-arrayexpress
Project description:Staphylococcus aureus thymidine-dependent small-colony variants (TD-SCVs) are frequently isolated from patients with chronic S. aureus infections after long-term treatment with trimethoprim-sulfamethoxazole (TMP-SMX). In TD-SCVs, mutations of thymidylate synthase (thyA, TS), essential for DNA synthesis, occur. However, it has never been shown, that TMP-SMX is responsible for the induction and selection of TD-SCVs. Short-term exposure of TMP-SMX induced the TD-SCV phenotype morphologically as shown in transmission electron-microscopy and on the transcriptional level by qRT-PCR in wild-type S. aureus, while selection of TD-SCVs with thyA mutations occurred only rarely after long-term exposure. In reversion experiments with clinical TD-SCVs, all revertants revealed compensating mutations at the initially identified mutation site. Whole DNA microarray analysis of a thyA deletion mutant (M-bM-^HM-^FthyA), which exhibited the typical TD-SCV phenotype, identified tremendous alterations compared to the wild-type. Important virulence regulators such as agr, arlRS, sarA and major virulence determinants including hla, hlb, sspA, sspB and geh were down-regulated, while genes associated with the colonization capacity like fnbA, fnbB, spa, clfB, sdrC and sdrD were up-regulated. The expression of genes involved in pyrimidine and purine metabolism as well as in nucleotide interconversion changed significantly. The M-bM-^HM-^FthyA-mutant was attenuated in virulence in both, a Caenorhabditis elegans killing model and an acute murine pneumonia model. Furthermore, competition experiments in vitro and in vivo (using a chronic pneumonia mouse model) revealed a survival and growth advantage of the M-bM-^HM-^FthyA-mutant under low thymidine conditions and TMP-SMX exposure. In conclusion, our results clearly show for the first time that TMP-SMX induces the TD-SCV phenotype after short-term exposure in S. aureus and that long-term exposure selects thyA mutations providing an advantage for TD-SCVs under specified conditions. Thus, our results help to understand the dynamic processes of induction and selection of S. aureus TD-SCVs during TMP-SMX exposure. 18 independent samples were analysed; for each isolate and time point 3 replicates were performed
2013-05-29 | E-GEOD-47406 | biostudies-arrayexpress
Project description:Staphylococcus aureus thymidine-dependent small-colony variants (TD-SCVs) are frequently isolated from patients with chronic S. aureus infections after long-term treatment with trimethoprim-sulfamethoxazole (TMP-SMX). In TD-SCVs, mutations of thymidylate synthase (thyA, TS), essential for DNA synthesis, occur. However, it has never been shown, that TMP-SMX is responsible for the induction and selection of TD-SCVs. Short-term exposure of TMP-SMX induced the TD-SCV phenotype morphologically as shown in transmission electron-microscopy and on the transcriptional level by qRT-PCR in wild-type S. aureus, while selection of TD-SCVs with thyA mutations occurred only rarely after long-term exposure. In reversion experiments with clinical TD-SCVs, all revertants revealed compensating mutations at the initially identified mutation site. Whole DNA microarray analysis of a thyA deletion mutant (∆thyA), which exhibited the typical TD-SCV phenotype, identified tremendous alterations compared to the wild-type. Important virulence regulators such as agr, arlRS, sarA and major virulence determinants including hla, hlb, sspA, sspB and geh were down-regulated, while genes associated with the colonization capacity like fnbA, fnbB, spa, clfB, sdrC and sdrD were up-regulated. The expression of genes involved in pyrimidine and purine metabolism as well as in nucleotide interconversion changed significantly. The ∆thyA-mutant was attenuated in virulence in both, a Caenorhabditis elegans killing model and an acute murine pneumonia model. Furthermore, competition experiments in vitro and in vivo (using a chronic pneumonia mouse model) revealed a survival and growth advantage of the ∆thyA-mutant under low thymidine conditions and TMP-SMX exposure. In conclusion, our results clearly show for the first time that TMP-SMX induces the TD-SCV phenotype after short-term exposure in S. aureus and that long-term exposure selects thyA mutations providing an advantage for TD-SCVs under specified conditions. Thus, our results help to understand the dynamic processes of induction and selection of S. aureus TD-SCVs during TMP-SMX exposure.
2013-05-29 | GSE47406 | GEO
Project description:Vancomycin-intermediate Staphylococcus aureus (VISA) evolve in a strain-specific manner and acquire mutations that lead to alterations in cell wall metabolism that reduce susceptibility to vancomycin. We had earlier isolated several VISA mutant strains of the clinical hVISA strain MM66. This study is aimed at analyzing the metabolome of these mutants in comparison to the parent strain.
2016-01-12 | ST000309 | MetabolomicsWorkbench
Project description:WalKR is an essential two component regulatory system in S. aureus, thought to control cell wall metabolism. Using genome sequencing of 5 paired clinical isolates of vancomycin-susceptible and vancomycin-intermediate S. aureus we found frequent, but unique, mutations in this locus. To investigate the contribution of these mutations to vancomycin resistance allelic replacement WalK (G223D) and WalR (K208R) mutants were generated and compared to the parent strains. Mutations in walk and walR led to increased vancomycin resistance, reduced biofilms formation and attenuation of virulence, demonstrating that minor genetic changes in this locus can lead to significant changes in bacterial resistance and virulence. Microarray transcriptional comparisons were performed to investigate the regulatory effects of the WalK (G223D) and WalR (K208R) mutations, and demonstrated that while changes in genes affecting cell wall metabolism were detected, more dramatic changes were found in regulation of cellular metabolism.
2012-06-01 | GSE29157 | GEO
Project description:To determine if significant genomic changes are associated with the development of vancomycin intermediate Staphylococcus aureus, genomic DNA microarrays were performed to compare the initial vancomycin susceptible Staphylococcus aureus (VSSA) and a related vancomycin intermediate Staphylococcus aureus (VISA) isolate from five unique patients (five isolate pairs). Keywords: comparative genomic hybridization
2006-11-03 | GSE5047 | GEO
Project description:In this study we have profiled a clinical tobramycin resistant P. aeruginosa strain that exhibited a small colony variant (SCV) phenotype. Both, the resistance and the colony morphology phenotypes were lost upon passaging the isolate under rich medium conditions. Transcriptional and mutational profiling revealed that the SCV harbored activating mutations in the two two-component systems AmgRS and PmrAB. Introduction of these mutations singularly into the type strain PA14 conferred tobramycin and colistin resistance, respectively. However, their combined introduction had an additive effect on the tobramycin resistance phenotype. Activation of the AmgRS system slightly reduced the colony size of the PA14 wild-type, whereas the simultaneous overexpression of gacA, the response regulator of the GacSA two component system, further reduced colony size. In conclusion, we uncovered combinatorial influences of two-component systems on clinically relevant phenotypes, such as resistance and the expression of the SCV phenotype. Our results clearly demonstrate that combined activation of P. aeruginosa two-component systems exhibit pleiotropic effects with unforeseen consequences.
2017-08-22 | GSE99729 | GEO