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ABSTRACT:
PROVIDER: PRJEB52382 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR9627620.fastq.gz | Fastqsanger.gz | |||
| ERR9627621.fastq.gz | Fastqsanger.gz | |||
| ERR9627622.fastq.gz | Fastqsanger.gz | |||
| ERR9627623.fastq.gz | Fastqsanger.gz | |||
| ERR9627617.fastq.gz | Fastqsanger.gz |
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Project description:Protein aggregates occur in all living cells due to misfolding of proteins. In bacteria, protein aggregation is associated with cellular inactivity, which is related to dormancy and tolerance to stressful conditions, including the exposure to antibiotics. In Escherichia coli, the membrane toxin TisB is an important factor for dormancy and antibiotic tolerance upon DNA damage mediated by the fluoroquinolone antibiotic ciprofloxacin. Here, we show that TisB provokes protein aggregation in response to ciprofloxacin. The stress response and TisB-dependent protein aggregates are analyzed by LC-MS.
2024-10-04 | PXD049478 | Pride
Project description:Campylobacter jejuni is one of the most important zoonotic enteric bacterial pathogens able to colonize the gastrointestinal tract of various animals. The number of campylobacteriosis cases has increased worldwide and the particular concern has been the high level of fluoroquinolone resistance observed in C. jejuni isolates. In this study, we explored the effect of ciprofloxacin in Campylobacter jejuni by gene expression microarray analysis. The comparisons of transcriptional responses were performed in the absence and presence of ciprofloxacin with the wild-type strain 81-176 and its intermediate-resistant variant (P3). The resistant variant contained a single-nucleotide mutation causing amino acid change Asp-90-Asn in the gyrA gene instead of the most common Thr-86-Ile, causing a high-level resistance to ciprofloxacin. After the short-term exposure to a relatively high concentration of ciprofloxacin, the viability of C. jejuni 81-176 wild-type cells remained notably high when compared with other gram-negative bacteria. The general responses of short-term ciprofloxacin exposure were determined from both genetic backgrounds and resulted in the expression variation of genes participating in general cellular processes, e.g. , in carbon and amino-acid metabolism and protein transport. Ciprofloxacin effect for gene expression was measured from both genetic backgrounds after 1 hour exposure at the level of 0 and 8 µg/ml ciprofloxacin in MH-broth. For RNA isolation, 5 independent experiments with and without ciprofloxacin were performed, and 4 replicates of each total RNA was applied for the gene expression study.
2012-12-31 | E-GEOD-41822 | biostudies-arrayexpress
Project description:Campylobacter jejuni is one of the most important zoonotic enteric bacterial pathogens able to colonize the gastrointestinal tract of various animals. The number of campylobacteriosis cases has increased worldwide and the particular concern has been the high level of fluoroquinolone resistance observed in C. jejuni isolates. In this study, we explored the effect of ciprofloxacin in Campylobacter jejuni by gene expression microarray analysis. The comparisons of transcriptional responses were performed in the absence and presence of ciprofloxacin with the wild-type strain 81-176 and its intermediate-resistant variant (P3). The resistant variant contained a single-nucleotide mutation causing amino acid change Asp-90-Asn in the gyrA gene instead of the most common Thr-86-Ile, causing a high-level resistance to ciprofloxacin. After the short-term exposure to a relatively high concentration of ciprofloxacin, the viability of C. jejuni 81-176 wild-type cells remained notably high when compared with other gram-negative bacteria. The general responses of short-term ciprofloxacin exposure were determined from both genetic backgrounds and resulted in the expression variation of genes participating in general cellular processes, e.g. , in carbon and amino-acid metabolism and protein transport.
2012-12-31 | GSE41822 | GEO
Project description:Gene expression of P. aerruginosa changes after short-term exposure to ciprofloxacin at sub-inhibitory concentrations but the effect of long-term exposure which select for the most fitted subpopulations is not known. We used microarrays to investigate the changes in gene expression of P.aeruginosa PAO1 and mutator (Δ mutS) after long-term evolution (94 daily passages) in LB in the presence and absence of ciprofloxacin
2016-02-25 | GSE78255 | GEO
Project description:Enterococcus faecium has emerged as a major opportunistic pathogen for two decades, with the spread of hospital-adapted multidrug-resistant clones. Members of the intestinal microbiota, they are subjected to numerous bacterial stresses, including antibiotics at subinhibitory concentrations (SICs). Since fluoroquinolones are extensively prescribed, SICs are very likely to occur in vivo with potential effects on bacterial metabolism with subsequent modulation of opportunistic traits. The aim of the study was to evaluate globally the impact of subinhibitory concentrations (SICs) of ciprofloxacin on antimicrobial resistance and pathogenicity of E. faecium. Transcriptomic analysis was performed by RNA-seq (HiSeq 2500, Illumina) using the vanB-positive reference strain E. faecium Aus0004 in the absence or presence of ciprofloxacin SIC (0.38 mg/L, i.e. MIC 1/8). Several genetic and phenotypic tests were used for validation. In the presence of ciprofloxacin SIC, 196 genes were significantly induced whereas 286 were significantly repressed, meaning that 16.8% of the E. faecium genome was altered. Amongst upregulated genes, EFAU004_02294 (fold change of 14.3) encoded a protein (EfmQnr) homologue of Qnr proteins involved in quinolone resistance in Gram-negative bacilli. Its implication in intrinsic and adaptive FQ resistance in E. faecium was experimentally ascertained. Moreover, EFAU004_02292 coding for the collagen adhesin Acm was also induced by SIC of ciprofloxacin (fold change of 8.2), and higher adhesion capabilities were demonstrated phenotypically. Both Efmqnr and Acm determinants may play an important role in the transition from a commensal to a pathogenic state of E. faecium that resides in the gut of patients receiving a fluoroquinolone therapy.
2017-02-04 | GSE94507 | GEO
Project description:Serratia marcescens, a member of the order Enterobacterales, is adept at colonizing healthcare environments and an important cause of invasive infections. Antibiotic resistance is a daunting problem in S. marcescens because in addition to plasmid-mediated mechanisms, most isolates have considerable intrinsic resistance to multiple antibiotic classes. To discover endogenous modifiers of antibiotic susceptibility in S. marcescens, a high-density transposon insertion library was subjected to sub-minimal inhibitory concentrations of two cephalosporins, cefoxitin and cefepime, as well as the fluoroquinolone ciprofloxacin. Comparisons of transposon insertion abundance before and after antibiotic exposure identified hundreds of potential modifiers of susceptibility to these agents. Using single gene deletions, we validated several candidate modifiers of cefoxitin susceptibility and chose ydgH, a gene of unknown function, for further characterization. In addition to cefoxitin, deletion of ydgH in S. marcescens resulted in decreased susceptibility to multiple 3rd generation cephalosporins, and in contrast, to increased susceptibility to both cationic and anionic detergents. YdgH is highly conserved throughout the Enterobacterales, and we observed similar phenotypes in Escherichia coli O157:H7 and Enterobacter cloacae mutants. YdgH is predicted to localize to the periplasm and we speculate that it may be involved there in cell envelope homeostasis. Collectively, our findings provide insight into chromosomal mediators of antibiotic resistance in S. marcescens and will serve as a resource for further investigations of this important pathogen.
2021-09-07 | GSE169651 | GEO
Project description:Gene expression of P. aerruginosa changes after short-term exposure to ciprofloxacin at sub-inhibitory concentrations but the effect of long-term exposure which select for the most fitted subpopulations is not known. We used microarrays to investigate the changes in gene expression of P.aeruginosa PAO1 and mutator (Î? mutS) after long-term evolution (94 daily passages) in LB in the presence and absence of ciprofloxacin Three different colonies from the ancestral populations of PAO1 and mutator (Î? mutS) as well as from the evolved populations (day 94) of each of the three lineages (A;B;C) in the presence or absence of ciprofloxacin at a concentration of 0.05 µg/ml were used for overnight cultures in LB and total RNA was extracted at OD600nm=1 and hybridized on P. aeruginosa Affymetrix chip.
2016-02-25 | E-GEOD-78255 | biostudies-arrayexpress
Project description:Clofazimine exposure in vitro selects efflux pump mutants and bedaquiline resistance
| PRJNA494324 | ENA
Project description:Fluoroquinolones (FQs) are one class of commonly used antimicrobials in clinical therapy of diseases caused by Campylobacter and other foodborne pathogens. The molecular mechanisms underlying the response of Campylobacter to FQ treatment is of interest because unlike other enteric bacteria, Campylobacter lacks many genes encoding components of DNA repair systems and SOS response. To understand how Campylobacter survive antibiotic treatment, DNA microarray was used to compare the gene expression profiles of C. jejuni 11168 in the presence and absence of ciprofloxacin. Our analysis identified 45 genes that showed ≥1.5-fold (p<0.05) changes in expression in the presence of ciprofloxacin. The up-regulated genes (13) are involved in cell membrane biosynthesis and DNA repair or have unknown functions, while the majority of the down-regulated genes (32) are involved in cellular process and energy metabolism. These findings suggest that C. jejuni modulates membrane biosynthesis, increases spontaneous mutation rates, and decreases metabolism in response to fluoroquinolone treatment. Keywords: 0.06 µg/ml (0.5X MIC) or 1.2 µg/ml (10X MIC) ciprofloxacin treated campylobacter VS. untreated campylobacter, the bacterial cells were treated for 0.5 hour
2008-06-09 | GSE10471 | GEO
Project description:Expression profiling of wild type E. coli K-12 strain MG1655 with exogenous glutathione (GSH) supplementation, sub-inhibitory ciprofloxacin concentration and GSH with inhibitory ciprofloxacin concentration. We used microarrays to detail the global gene expression program underlying ciprofloxacin exposure and glutathione mediated abrogation of ciprofloxacin's anti-bacterial action.
2018-01-29 | GSE93896 | GEO