Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Escherichia coli strain:ESBL

ABSTRACT: Escherichia coli strain:ESBL Genome sequencing and assembly

PROVIDER: PRJNA641983 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR12117959_1.fastq.gz	Fastqsanger.gz
	SRR12117959_2.fastq.gz	Fastqsanger.gz
	SRR12117960_1.fastq.gz	Fastqsanger.gz
	SRR12117960_2.fastq.gz	Fastqsanger.gz
	SRR12117961_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 30

Similar Datasets

Escherichia coli strain:ESBL

Project description:Escherichia coli strain:ESBL Genome sequencing

| PRJNA661170 | ENA

Escherichia coli strain:ESBL-5

Project description:Escherichia coli strain:ESBL-5 Genome sequencing

| PRJNA1327120 | ENA

Escherichia coli strain:ESBL-3

Project description:Escherichia coli strain:ESBL-3 Genome sequencing

| PRJNA1327117 | ENA

Escherichia coli strain:ESBL-6

Project description:Escherichia coli strain:ESBL-6 Genome sequencing

| PRJNA1327587 | ENA

Comprehensive Assessment of Initial Adaptation of ESBL Positive ST131 E. coli to Carbapenem Exposure

Project description:Background: It remains unclear how high-risk Escherichia coli lineages, like sequence type (ST) 131, initially adapt to carbapenem exposure in its progression to becoming carbapenem resistant. Methods: Carbapenem mutation frequency was measured in multiple subclades of extended-spectrum β-lactamase (ESBL) positive ST131 clinical isolates using a fluctuation assay followed by whole genome sequencing (WGS) characterization. Genomic, transcriptomic, and porin analyses of ST131 C2/H30Rx isolate, MB1860, under prolonged, increasing carbapenem exposure was performed using two distinct experimental evolutionary platforms to measure fast vs. slow adaptation. Results: All thirteen ESBL positive ST131 strains selected from a diverse (n=184) ST131 bacteremia cohort had detectable ertapenem (ETP) mutational frequencies with a statistically positive correlation between initial ESBL gene copy number and mutation frequency (r = 0.87, P<1e-5). WGS analysis of mutants showed initial response to ETP exposure resulted in significant increases in ESBL gene copy numbers or mutations in outer membrane porin (Omp) encoding genes in the absence of ESBL gene amplification with subclade specific adaptations. In both experimental evolutionary platforms, MB1860 responded to initial ETP exposure by increasing blaCTX-M-15 copy numbers via modular, insertion sequence 26 (IS26) mediated pseudocompound transposons (PCTns). Transposase activity driven by PCTn upregulation was a conserved expression signal in both experimental evolutionary platforms. Stable mutations in Omp encoding genes were detected only after prolonged increasing carbapenem exposure consistent with clinical observations. Conclusions: ESBL gene amplification is a conserved response to initial carbapenem exposure, especially within the high-risk ST131 C2 subclade. Targeting such amplification could assist with mitigating carbapenem resistance development.

2024-08-04 | GSE273456 | GEO

High-throughput Solexa sequencing of total RNA from Escherichia coli wild type and ∆fnr strain (PK4854)

Project description:Investigation of whole genome gene expression level changes in a Escherichia coli MG1655 K-12 ∆fnr mutant, compared to the wild-type strain. The mutations engineered into this strain produce a strain lacking the FNR protein.

2013-06-20 | GSE41190 | GEO

The RegR virulence regulon of rabbit specific enteropathogenic Escherichia coli strain E22

Project description:To investigate the regulatory targets of the RegR virulence regulon of rabbit specific enteropathogenic Escherichia coli strain E22

2012-12-25 | GSE41093 | GEO

Psychological Evaluation According Colonic Colonization by Escherichia Coli of Patients After Colorectal Surgery

Project description:The purpose of this study is to determine whether the presence of pathogenic Escherichia coli in colon is associated with psychiatric disorders.

| 2230352 | ecrin-mdr-crc

Expression data from an Avian pathogenic Escherichia coli strain

Project description:Avian pathogenic Escherichia coli strains frequently cause extra-intestinal infections and are responsible for significant economic losses in the poultry industry worldwide. APEC isolates are closely related to human extraintestinal pathogenic E.coli strains and may also act as pathogens for humans. In this work, three type VI secretion systems were deleted to analyze which pathogenicity characteristics would change in the mutants, compared to wild type strain (SEPT 362).

2010-09-10 | GSE21893 | GEO

PatE in transcriptional activation of acid-resistance pathways of enterohemorrhagic Escherichia coli strain EDL933

Project description:An experiment to identify the downstream targets of PatE, a prophage encoded AraC-like transcriptional regulator, in transcriptional activation of acid-resistance pathways of enterohemorrhagic Escherichia coli strain EDL933 using deletion and complementation strains (Delta3 and Delta3_1, respectively).

2012-03-30 | GSE36922 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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