Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A comprehensive microarray analysis of Enterococcus faecium in response to vancomycin in combination with the essential oil components carvacrol and cuminaldehyde

ABSTRACT: This study aims to determine the global gene expression in vancomycin resistant Enterococcus faecium (VRE) in response to a novel essential oil-vancomycin combination, and the individual components (vancomycin, carvacrol and cuminaldehyde) to help determine the mechanism of action of this antimicrobial formulation. This formulation increases the susceptibility of VRE to vancomycin and the array provides data on the synergistic mechanism of action. Five conditions (1. Control; 2. Carvacrol, 1.98 mM; 3. Cuminaldehyde, 4.20 mM; 4. Vancomycin, 0.031 mg/l; 5. Combination, 1.98 mM Carvacrol, 4.2 mM Cuminaldehyde, 0.031 mg/l vancomycin) all with 1% DMSO were tested in triplicate with a 60 minute exposure time before extraction.

ORGANISM(S): Enterococcus faecium

SUBMITTER: Laura Smith

PROVIDER: E-MTAB-8072 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Switching on antibiotic resistance in Staphylococcus aureus M-bM-^@M-^S Contribution of WalK and VraS histidine kinases in the development of vancomycin and daptomycin resistance

Project description:Staphylococcus aureus is a notorious bacterial pathogen that causes a broad range of human diseases, and isolates that are resistant to several antibiotic classes including last resort antibiotics like vancomycin and daptomycin complicate the situation. We characterized S. aureus VC40, a strain that shows full resistance to vancomycin (MIC of 64 M-BM-5g/ml) and daptomycin (MIC of 4 M-BM-5g/ml) as well as a decreased susceptibility to further cell wall active agents. Genome sequencing revealed mutations in genes encoding the histidine kinases WalK and VraS that control cell envelope related processes and gene expression profiling indicated the induction of the respective regulons in strain VC40. Reconstitution of the mutations in walK or vraS into the susceptible S. aureus NCTC 8325 background resulted in a considerably increased resistance to vancomycin and daptomycin with MICs surpassing the clinical breakpoints for these antibiotics, thereby generating vancomycin-intermediate S. aureus (VISA) strains. As observed for S. aureus VC40, the walKwalk and vraS mutations also led to an increased expression of the respective regulons in the NCTC 8325 background. Phenotypic studies showed that S. aureus VC40 as well as the walKwalk and vraS mutants of strain NCTC 8325 were characterized by a significantly thickened cell wall, a decreased growth rate, a reduced autolytic activity and an increased resistance to lysostaphin-induced lysis. These results demonstrate that the WalK and VraS histidine kinases act as major switches which allow S. aureus to rapidly develop vancomycin resistance up to the VISA level via mutation of one single gene locus and concomitantly contribute to cross-resistance to other antibiotics including the last resort antibiotic daptomycin. Microarray was used to evaluate alteration in the transcriptome of mutS mutant and compared to the parental strain VC40

2014-08-18 | E-GEOD-46887 | biostudies-arrayexpress

Expression Data from E. faecalis V583 under exposure to 10ug/ml vancomycin

Project description:The vancomycin resistant strain V583 was exposed to therapeutical dose of vancomycin in order to understand the cell response to the antibiotic besides the induction of the vanB genes E. faecalis V583 cells were collected at 10 minutes and 30 min after vancomycin addition and without vancomycin, for RNA extraction and hybridization on Affymetrix microarrays. The cells were collected when at 0.4. For each condition were made replicates.

2014-01-01 | E-GEOD-52263 | biostudies-arrayexpress

Proteome profile of Methicillin-Resistant Staphylococcus aureus Membrane-Derived Vesicles grown in presence of sub-MIC dosage of Vancomycin

Project description:Methicillin-resistant Staphylococcus aureus (MRSA) has evolved numerous antimicrobial resistance mechanisms and is identified as a serious public health threat by the World Health Organization and U.S. Centers for Disease Control and Prevention. The glycopeptide vancomycin (VAN) remains a cornerstone of therapy for severe MRSA infections despite increasing reports of therapeutic failure in hospitalized patients with bacteremia or pneumonia. Here we examined the effectiveness of MVs-derived methicillin-resistant SA (MRSA) to counteract vancomycin (VAN). We found that supplementation of a typical MIC assay using bacteriologic and tissue-mimicking media with purified MVs attenuated MRSA susceptibility to VAN but no other examined cell-wall targeting antibiotics. In addition, the purified MVs protected MRSA challenged with sub-therapeutic dosage of VAN against the host’s innate immune system. Additionally, the proteome of MV peptides from VAN exposed MRSA was characterized to determine if protein expression was altered.

2021-11-03 | PXD024232 | Pride

Enterococcus faecalis OG1RF control vs. treatment with vancomycin

Project description:Transcriptional profiling to investigate the effect of drug treatment on the E. faecalis cells. For microarray analysis, E. faecalis OG1RF was grown in FMC medium supplemented with 10 mM glucose to an optical density at 600 nm (OD600) of 0.3 and the cultures were divided in 3 aliquots. One aliquot was collected by centrifugation and immediately frozen (untreated control cells). The other aliquots were treated for 30 or 60 min with 1.25 X the minimum inhibitory concentration (MIC) of vancomycin (10 M-NM-<g ml-1). After an exposure time of 30 or 60 minutes, each of these cultures was also centrifuged and the pellets frozen. RNA was then isolated from each pellet for microarray analysis. This process was repeated 3 additional times, for a total of four replicates of each condition. RNA was extracted from four replicate samples of each condition of interest (control cells grown to OD600 = 0.3 in FMC medium supplemented with 10mM glucose, then treated with vancomycin for 30 or 60 minutes) and labeled with Cy3. For each replicate, labeled RNA was hybridized to slides along with Cy5-labeled reference RNA, extracted from E. faecalis OG1RF cells grown in BHI medium to mid-log.

2013-03-19 | E-GEOD-45300 | biostudies-arrayexpress

Remodeling of the Streptococcus mutans proteome in response to LrgAB and external stresses

Project description:This project investigates the changes in proteome profiles that occurred in the same set of S. mutans wild-type and lrgAB mutant samples used in our recently published RNA-seq study. To this end, mass spectrometry-based label-free quantitative proteomics, a technology known to enable comprehensive identification and quantification of complete bacterial proteomes, was adapted to study changes in S. mutans intracellular protein levels in response to aeration, heat, and vancomycin stress. Furthermore, the degree of correlation between S. mutans protein abundance profiles and gene expression changes was determined. Further understanding of these combined “-omics” data at the cellular or molecular level will enhance our knowledge of Cid/Lrg-mediated cellular responses of S. mutans to adverse environments. Furthermore, these “-omics” data will serve as a valuable resource that can be mined to help clarify the role of the S. mutans stress response and physiological activity to its dynamic survival in the oral cavity.

2018-10-24 | PXD006735 | Pride

Effects of Gut Microbiota Manipulation by Antibiotics on Host Metabolism in Obese Humans: a Randomized Double-blind Placebo-controlled Trial

Project description:The gut microbiota has been implicated in obesity and cardiometabolic diseases, although evidence in humans is scarce. We investigated how gut microbiota manipulation by antibiotics (7-day administration of amoxicillin, vancomycin, or placebo) affects host metabolism in 57 obese, prediabetic men. Vancomycin, but not amoxicillin, decreased bacterial diversity and reduced Firmicutes involved in short-chain fatty acid and bile acid metabolism, concomitant with altered plasma and/or fecal metabolite concentrations. Adipose tissue gene expression of oxidative pathways was upregulated by antibiotics, whereas immune-related pathways were downregulated by vancomycin. Antibiotics did not affect tissue-specific insulin sensitivity, energy/substrate metabolism, postprandial hormones and metabolites, systemic inflammation, gut permeability, and adipocyte size. Importantly, energy harvest, adipocyte size, and whole-body insulin sensitivity were not altered at 8-week follow-up, despite a still considerably altered microbial composition, indicating that interference with adult microbiota by 7-day antibiotic treatment has no clinically relevant impact on metabolic health in obese humans. This randomized, placebo-controlled, double-blind study had a 3-armed parallel design. Overweight/obese participants were randomized to oral intake of amoxicillin, vancomycin or placebo for 7 consecutive days. After an overnight fast, subcutaneous adipose tissue biopsies were taken that were subjected to gene expression profiling by array.

2016-07-15 | E-GEOD-76003 | biostudies-arrayexpress

The functional small RNA interactome reveals targets for the vancomycin-responsive sRNA RsaOI in vancomycin tolerant Staphylococcus aureu

Project description:Vancomycin tolerance in multidrug resistance Staphylococcus aureus is correlated with dysregulation of small RNAs although their contribution to antibiotic tolerance in poorly understood. RNA-RNA interactome profiling techniques are expanding our understanding of sRNA-mRNA interactions in bacteria; however, determining the function of these interactions for hundreds of sRNA-mRNA pairs is a major challenge. At steady-state, protein and mRNA abundances are often highly correlated and lower than expected protein abundance may indicate translational repression of an mRNA. We used label-free quantitative proteomics to examine changes in protein expression in vancomycin tolerant S. aureus strain in response to vancomycin treatment. We correlated the protein levels with gene transcript abundance and ribosome occupancy to identify sRNA-mRNA interactions that regulate mRNA translation. We used the machine learning technique self-organising maps (SOMS) to cluster genes with similar transcription and translation patterns and identified a cluster of mRNAs that appeared to be post-transcriptionally repressed. By integrating our clustering analysis with the sRNA-mRNA interactome data generated in vancomycin tolerant S. aureus by RNase III-CLASH, we identified a cluster of sRNAs that may be mediating translational repression. We have confirmed sRNA-dependant post-transcriptional repression of several mRNAs in this cluster. Two of these interactions are mediated by RsaOI, a sRNA that is highly upregulated by vancomycin, and these targets include HPr and the cell-wall autolysin Atl, with only Atl downregulated at the protein level upon vancomycin treatment. These findings suggest RsaOI coordinates carbon metabolism and cell wall turnover during vancomycin treatment

2024-03-18 | PXD049022 | Pride

Gene expression analysis of Vancomycin resistance in Stapyloccoccus aureus strains: 2275, 2279, 2276, 2277, 2278, and 2283.

Project description:Understanding novel mechanism bacteria ustilize in the clinics to become resistant to antibiotics is critical. The study aims to identify genes associated with Vancomycin resistance. Clinical isolates from a single patient with increasing resistance to vancomycin were grown in the presence and absence of vancomycin.Staphylococcus aureus strain 2275 is the reference for this series. S. aureus isolates from a single patient were grown in the presence and absence of vancomycin over a 2 hour time course. RNA samples were extracted at 30, 60 90 and 120 minutes post exposure to antibiotic. Samples were hybridized on aminosilane coated slides with 70-mer oligos comparing mock treated and treated cells to the first strain isolated in the lineage. Differnetial gene expression patterns were determined.

2011-04-08 | E-GEOD-26353 | biostudies-arrayexpress

A Single Amino-Acid Substitution of RNA Polymerase M-CM-^_ subunit Confers A Novel Class of VISA phenotype on hVISA Strain Mu3

Project description:hVISA clinical strain Mu3 spontaneously generates VISA at an extremely high frequency (1x10-6 or greater) within its cell population. The VISA-converted mutant strains generally grow slower than their parent hVISA strain, but they usually form colonies on vancomycin-containing agar plates after 48 hours of incubation on population analysis. However, we noticed a curious group of VISA mutants whose colony formation is much more delayed and observed as discrete colonies only after 96 hours incubation. They have extremely prolonged lag-phase and doubling-times, but recorded vancomycin MICs of 8 to 24 mg/L when determined after 48 to 96 hours of incubation. We established strain Mu3-6RS having vancomycin MIC of 12 mg/L (at 72h) as a representative of the M-bM-^@M-^Xslow VISAM-bM-^@M-^Y (sVISA) strains. Its cell wall was thickened, and autolytic activity was decreased as compared with those of the parent strain Mu3. Whole genome sequencing of Mu3-6RS revealed only one mutation, which substituted the 512th amino-acid sequence of RNA polymerase M-CM-^_-subunit from Arg of Mu3 to Proline. Its VISA phenotype was unstable, and the strain frequently reverted to hVISA with concomitant loss of small colony morphology, cell-wall thickness and reduced autolytic activity. Sequencing of rpoB genes of the reverted strains revealed mutations affecting the 512th codon replacing the Proline of Mu3-6RS to Leucine, Serine, or Histidine. This study proposes sVISA as a discrete class of VISA phenotype, which can serve as a temporary shelter for S. aureus to survive relatively high concentrations of vancomycin. The sVISA spontaneously returns to hVISA when the threat of vancomycin passes by. The rpoB(R512P) mutation may be regarded as a M-bM-^@M-^Xregulatory mutationM-bM-^@M-^Y switching on and off the reversible sVISA phenotype. 5 sample analysis using 60mer-oligo microarray, 3 rpoB mutant(R512P,R512L,R512S), 2 wild-type strain(Mu3, M-NM-^TIP)

2014-03-31 | E-GEOD-50826 | biostudies-arrayexpress

Gene expression analysis of Vancomycin resistance in Stapyloccoccus aureus strains: PA, C1 and T8.

Project description:The study aims to identify genes associated with Vancomycin resistance. Wild type and a mutant cells line were treated with antibiotic at multiple concentrations and RNA samples extracted over a two hour time course.Staphylococcus aureus strain PA is the reference for this series. Wild type and a mutant cells line were treated with antibiotic at multiple concentrations and RNA samples extracted over a two hour time course. Samples were hybridized on aminosilane coated slides with 70-mer oligos.

2011-04-08 | E-GEOD-26400 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data