Escherichia coli
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA260093 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1573600.fastq.gz | Fastqsanger.gz | |||
| SRR1573610.fastq.gz | Fastqsanger.gz | |||
| SRR1573620.fastq.gz | Fastqsanger.gz | |||
| SRR1573601.fastq.gz | Fastqsanger.gz | |||
| SRR1573611.fastq.gz | Fastqsanger.gz |
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Project description:In order to explore the differentially expressed genes of E. coli B2 after citric acid induced antibiotic tolerance, we artificially induced the antibiotic tolerance of E. coli O157: H7 and verified its phenotype.
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Project description:In order to explore the differentially expressed genes of E. coli O157: H7 after citric acid induced antibiotic tolerance, we artificially induced the antibiotic tolerance of E. coli O157: H7 and verified its phenotype.
2023-03-10 | GSE226409 | GEO
Project description:The rise of antimicrobial resistant pathogens calls for new antibacterial treatments, but potent new compounds are scarce. Development of new antibiotics is difficult, especially against Gram-negative bacteria, as here uptake is strongly hindered by the additional outer membrane. Most antimicrobial agents against Gram-negatives use the porin mediated pathway to cross the outer membrane, which limits the choice of an antibiotic, as it has to fit by size, charge and hydrophilicity. In E. coli, the major porins OmpF and OmpC are associated with antibiotic translocation and therefore also with unspecific antibiotic cross-resistance. In this regard, alternative uptake routes are of interest. We were interested in the uptake opportunities of the small, natural product antibiotic negamycin and thereby found new uptake pathways across the outer membrane of E. coli. Besides OmpF and OmpC, we investigated the role of the minor porins OmpN and ChiP in negamycin translocation. We detected an effect of OmpN and ChiP on negamycin susceptibility and confirmed passage by electrophysiological assays. The structure of OmpN was resolved in order to analyze the negamycin translocation mechanism by computational simulations. As abundancy of these minor porins was low in E. coli, their transcript levels were analyzed by RNA-Seq. Increased transcripts levels of ompN and chiP were observed upon negamycin treatment, hinting at a role in antibiotic uptake. These new, additional uptake pathways across the outer membrane of E. coli highlight the antibiotic potential of negamycin, especially as resistance development is low due to availability of multiple uptake routes at both the outer and inner membranes
2023-10-01 | GSE183363 | GEO
Project description:The intention of this study is to analyse the effect of antibiotics on the gene expression of Escherichia coli. Shaking-flask cultivations of Escherichia coli K12GFP-UTL2 were carried out with a medium containing nalidixic acid. Cultures with antibiotic-free medium, which were run in an identical way, served as reference. Samples were taken at different times during the cultivations, the RNA was isolated and hybridised on whole genome yeast microarrays. Keywords: Influence of toxins on gene expression in E. coli
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Project description:Sequencing reads of Escherichia coli K-12 control and antibiotic-treated cultures enriched (Cappable-Seq) and not enriched (Ultra directional) for the 5’ end of primary transcripts.
2023-01-21 | GSE215300 | GEO
Project description:Treatment failures of antibiotic therapy are of major concern and can be caused by a misalignment of the antibiotic susceptibility determined in vitro with the behaviour of the pathogen in the patient. The aim of this study was to investigate the transcriptomic response of the uropathogenic strain E. coli CFT073 to antibiotic treatment in blood stream infection (BSI) models in order to understand and avoid antibiotic therapy failures in urosepsis treatments. Blood stream infection models were established by growing E. coli CFT073 in pooled human blood with and without ciprofloxacin. The antibiotic challenge was introduced at mid-logarithmic phase of growth of the organism to depict a clinical scenario. The responses were quantified by comparing to the responses at a given time point without the challenge. Global gene expression profiling of these conditions was examined using commercial DNA microarrays. The organism’s metabolic genes appeared to be regulated differently in each medium, this indicated that the bacterial growth regulation were different between the models. Bacterial growth in human serum mainly involved regulations of amino acid synthesis/utilisation such as glycine, arginine, thiamine, regulations of fimbrial proteins and bacteriophage genes. When comparing the responses to antibiotic challenge, bacteria grown in the respective medium displayed specific responses to the antibiotic challenge which were not seen in the other media. The common functions of genes that responded to the ciprofloxacin challenge were SOS response, DNA repair, DNA replication, fimbrial genes and bacteriophage initiation. A subset of the bacteriophage genes showed similar responses between the three models. From genes that were differentially regulated, responses observed in the serum model appeared to have the highest fold changes. In this study we established new models to investigate blood stream infections. They have been used to identify previously unknown differences in the molecular response to antibiotic treatment by the uropathogenic E. coli CFT073 depending on the media. These unique responses will help to unravel the complexity of bloodstream infection and can help to improve the antibiotic therapy that is used.
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Project description:When the survivors of antibiotic treatment (persisters) are repeatedly regrown and retreated with the same antibiotic for several cycles, the new population will soon adapt to the treatment condition and become tolerant to the drug. Here, we did evolution experiments on Escherichia coli populations by treating it with daily high concentration of different antibiotics (ampicillin, ciprofloxacin and apramycin) approximating clinical dosage, during the rapid growth-exponential phase. After a few cycles, we observed that the evolved populations exhibit extremely high tolerance to the drug, which are achieved by single point mutations in one of several genes. Interestingly, treatment with different antibiotics led to the selection of different mutants despite the shared persistence phenotype. Here, we applied spectral counting-based quantitative proteomics to study the proteome profile of the evolved E. coli populations from different cyclic antibiotic treatments.
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Project description:Mapping the occupancy of ArcA throughout the genome of Escherchia coli MG1655 K-12 using an affinity purified antibody under anaerobic and aerobic growth conditions. As a control, we also performed ChIP-chip onArcA in a ∆arcA mutant strain of Escherchia coli MG1655 K-12. Described in the manuscript The response regulator ArcA uses a diverse binding site architechture to globally regulate carbon oxidation in E. coli
2013-10-17 | GSE46413 | GEO
Project description:Human Peptidoglycan Recognition Proteins (PGRPs) kill bacteria, likely by over-activating stress responses in bacteria. To gain insight into the mechanism of PGRP killing of Escherichia coli and bacterial defense against PGRP killing, gene expression in E. coli treated with a control protein (bovine serum albumin, BSA), human recombinant PGRP (PGLYRP4), gentamicin (aminoglycoside antibiotic), and CCCP (membrane potential decoupler) were compared. Each treatment induced unique and somewhat overlapping pattern of gene expression. PGRP highly increased expression of genes for oxidative and disulfide stress, detoxification and efflux of Cu, As, and Zn, repair of damaged proteins and DNA, methionine and histidine synthesis, energy generation, and Fe-S clusters repair. PGRP also caused marked decrease in the expression of genes for Fe uptake and motility. Gene expression microarray in E. coli exposed to a human bactericidal innate immunity protein, PGRP, showed induction of oxidative stress response and defense genes, with different expression pattern than E. coli exposed to an aminoglycoside antibiotic and a membrane potential decoupler.
2014-07-25 | GSE44211 | GEO
Project description:Comparison of the whole genome gene expression level of an amoxicillin resistant E. coli strain with the wildtype it was derived from. The process of amoxicillin adaptation of E. coli MG1655 wildtype cells is further descibed in van der Horst, M, J.M. Schuurmans, M. C. Smid, B. B. Koenders, and B. H. ter Kuile (2011) in Microb. Drug Resist. 17:141-147. Resistance to amoxicillin was induced in E. coli by growth in the presence of stepwise increasing antibiotic concentrations. To investigate consequences of the aquisition of amoxicillin resistance the transcriptomic profile of sensitive and resistant cells was compared in the absence and presence of sub-inhibitory (0.25xMIC) amoxicillin concentrations was compared.
2013-05-27 | GSE47221 | GEO