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PROVIDER: PRJNA1078256 | ENA |
REPOSITORIES: ENA
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Project description:Multiple infection sources for enterohemorrhagic Escherichia coli O157:H7 are known, including food of animal origin and produce. The ecology of this pathogen outside its human host is largely unknown. One third of its annotated genes still are hypothetical. To identify genetic determinants expressed under environmental factors, we applied strand-specific RNA-sequencing of strain E. coli EDL933 under 11 different biotic and abiotic conditions: LB medium at pH4, pH7, pH9, or at 15°C; LB with nitrite or trimethoprim-sulfamethoxazole; LB-agar surface, M9 minimal medium, spinach leaf juice, surface of living radish sprouts, and cattle feces. Of 5379 annotated genes, only 144 are transcriptionally completely inactive under all conditions. Of 1,771 hypothetical genes, 1,672 exhibit significant transcriptional signals under at least one condition. The pathogenicity island LEE showed highest transcriptional activity in LB medium, minimal medium, and after treatment with antibiotics. Unique sets of genes, including many hypothetical genes, are highly up regulated on radish sprouts, cattle feces, or in the presence of antibiotics. For instance, azoR is biotechnologically important, but its environmental function has been elusive. This gene is highly active on radish sprouts. Further, we observed induction of the shiga-toxin carrying phages by antibiotics and confirmed active biofilm related genes on radish sprouts, in cattle feces, and on agar plates. Thus, environmental transcriptomics uncovers hitherto unknown gene functions and regulatory patterns of Escherichia coli O157:H7.
2014-07-20 | GSE48199 | GEO
Project description:Comparative genomic hybridization between Escherichia coli strains to determine core and pan genome content of clinical and environmental isolates Two color experiment, Escherichia coli Sakai (reference), clinical and environmental Escherichia coli strains (testers): At least two replicates including a single dye swap for each reference-tester comparison
2012-08-30 | E-GEOD-39667 | biostudies-arrayexpress
Project description:Multiple infection sources for enterohemorrhagic Escherichia coli O157:H7 are known, including food of animal origin and produce. The ecology of this pathogen outside its human host is largely unknown. One third of its annotated genes still are hypothetical. To identify genetic determinants expressed under environmental factors, we applied strand-specific RNA-sequencing of strain E. coli EDL933 under 11 different biotic and abiotic conditions: LB medium at pH4, pH7, pH9, or at 15°C; LB with nitrite or trimethoprim-sulfamethoxazole; LB-agar surface, M9 minimal medium, spinach leaf juice, surface of living radish sprouts, and cattle feces. Of 5379 annotated genes, only 144 are transcriptionally completely inactive under all conditions. Of 1,771 hypothetical genes, 1,672 exhibit significant transcriptional signals under at least one condition. The pathogenicity island LEE showed highest transcriptional activity in LB medium, minimal medium, and after treatment with antibiotics. Unique sets of genes, including many hypothetical genes, are highly up regulated on radish sprouts, cattle feces, or in the presence of antibiotics. For instance, azoR is biotechnologically important, but its environmental function has been elusive. This gene is highly active on radish sprouts. Further, we observed induction of the shiga-toxin carrying phages by antibiotics and confirmed active biofilm related genes on radish sprouts, in cattle feces, and on agar plates. Thus, environmental transcriptomics uncovers hitherto unknown gene functions and regulatory patterns of Escherichia coli O157:H7. Eleven different conditions were sequenced on the SOLiD system. Of two of the condtions, spinach medium and LB-nitrite, technical replicates were sequenced. Of LB medium and radish sprouts, biological replicates were sequenced on an Illumina MiSeq.
2014-07-20 | E-GEOD-48199 | biostudies-arrayexpress
Project description:Comparative genomic hybridization between Escherichia coli strains to determine core and pan genome content of clinical and environmental isolates
2012-08-30 | GSE39667 | GEO
Project description:Global response to ciprofloxacin in low level quinolone resistant Escherichia coli: a shorter path to survival. Background: Bactericidal activity of quinolones in bacteria has been related to a combination of DNA fragmentation, ROS production and programmed dead cell systems. Subjacent molecular systems responsible for reduction of bactericidal effect in low-level quinolone resistance (LLQR) phenotypes remain to be clarified. To answer this question and to define new possible antimicrobial targets, the transcriptomic profile in isogenic Escherichia coli harbouring quinolone resistance mechanisms in the presence of ciprofloxacin was evaluated. Materials and methods: E. coli 25922 was used as background strain. Four LLQR isogenic strains were tested for transcriptomic assays: ATCC 25922 (wild-type), EC14 (coding for QnrS1), EC19 (marR deletion and coding for QnrS1) and EC24 (Ser83Leu substitution in GyrA and coding for QnrS1). Cells in exponential phase (DO600=0.4) were exposed to 1 mg/L of ciprofloxacin (breakpoint for reduced susceptibility according to CLSI) during 1 hour and, further, RNA was purified. Gene expression analysis was performed using AGILENT technology. Data obtained for each strain were always normalized to the wild-type E. coli ATCC 25922. Specific ROS modulation targets were validated by genetic and biochemical approach. Results: A radical differential response to ciprofloxacin in LLQR strains, either up or downregulation, was observed (proportional to the MIC values). Multiple genes implicated in ROS production (related to TCA cycle, aerobic respiration or detoxification systems) were upregulated (sdhC up to 63.5-folds) in LLQR mutants. SOS system components were downregulated (recA up to 30.7-folds). yihE, coding for a protective kinase of programmed cell death, was also upregulated (up to 5.2-folds). SdhC inhibition sensitized LLQR phenotypes (up to Log=2.3 after 24 hours). Conclusions: At clinical relevant concentration of ciprofloxacin, the pattern of genes expression of critical systems for bacterial survival and mutant development were significantly modified in LLQR phenotypes. This approach allowed validating ROS modulation as an interesting target in terms of bacterial sensitization.
2017-01-01 | GSE86341 | GEO
Project description:New and rapid antimicrobial susceptibility/resistance testing methods are required for bacteria from positive blood cultures. In the current study we developed and evaluated a targeted LC-MS/MS assay for the detection of beta-lactam, aminoglycoside and fluoroquinolone resistance mechanisms in blood cultures positive for E. coli or K. pneumoniae. Selected targets were the beta-lactamases SHV, TEM, OXA-1-like, CTX-M-1-like, CMY-2-like, chromosomal E. coli AmpC, OXA-48-like, NDM, VIM and KPC, the aminoglycoside modifying enzymes AAC(3)-Ia, AAC(3)-II, AAC(3)-IV, AAC(3)-VI, AAC(6’)-Ib, ANT(2”)-I and APH(3’)-VI, the 16S-RMTases ArmA, RmtB, RmtC and RmtF, the quinolone resistance mechanisms QnrA, QnrB, AAC(6’)-Ib-cr, the wildtype QRDR of GyrA, and for E. coli, the porins OmpC and OmpF. The developed assay was evaluated using 100 prospectively collected positive blood cultures, 100 negative blood cultures inoculated with isolates that were previously collected from blood cultures, and 48 isolates inoculated with isolates carrying genes of less prevalent resistance mechanisms.
2022-07-01 | PXD025365 | Pride
Project description:In this study, we carried out genome-scale CRISPRi modulation combining fluorescence-activated cell sorting (FACS) and next-generation sequencing (NGS) to identify genetic determinants for FFAs overproduction in Escherichia coli. The pcnBi (AP) strain that repressed the expression of pcnB produced 2992 mg l FFAs, which was 4.0-fold of the CF (A) strain. To analyze the underlying mechanism of FFAs overproduction, the engineered strain pcnBi and the control strain CF were applied to the transcriptomic and proteomic analyses.
2024-05-18 | PXD052390 |
Project description:We report identification and characterization of antibiotic persister mutants carrying characteristic mutations in the Escherichia coli rpoB gene
2021-01-26 | GSE165446 | GEO