Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Enterobacteriaceae

ABSTRACT: Metagenome Sequencing of Urine Samples for Antimicrobial Resistance in Enterobacteriaceae.

PROVIDER: PRJNA1171213 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR31065125_1.fastq.gz	Fastqsanger.gz
	SRR31065126_1.fastq.gz	Fastqsanger.gz
	SRR31065127_1.fastq.gz	Fastqsanger.gz
	SRR31065128_1.fastq.gz	Fastqsanger.gz
	SRR31065129_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 60

Similar Datasets

First dataset - bacterial proteome of carbapanemase-producing Escherichia coli and other Enterobacteriaceae under antibiotic pressure

Project description:Antibiotic resistance associated with the expression of the clinically significant carbapenemases, IMP, KPC, and NDM and OXA-48 in Enterobacteriaceae is emerging as a worldwide calamity to health care. In Australia, IMP-producing Enterobacteriaceae is the most prevalent carbapenemase-producing Enterobacteriaceae (CPE). Genomic characteristics of such carbapenemase-producing Enterobacteriaceae (CPE) are well described, but the corresponding proteome is poorly characterised. We have thus developed a method to analyse dynamic changes in the proteome of CPE under antibiotic pressure. Specifically, we have investigated the effect of meropenem at sub-lethal concentrations to develop a better understanding of how antibiotic pressure leads to resistance. Escherichia coli, producing either NDM, IMP or KPC type carbapenemase were included in this study, and their proteomes were analysed in growth conditions with or without meropenem.

2018-07-11 | PXD008019 | Pride

High-throughput transposon mutagenesis in the family Enterobacteriaceae reveals core essential genes and rapid turnover of essentiality

Project description:The Enterobacteriaceae are a scientifically and medically important clade of bacteria, containing the gut commensal and model organism Escherichia coli, as well as several major human pathogens including Salmonella enterica and Klebsiella pneumoniae. Essential gene sets have been determined for several members of the Enterobacteriaceae, and the E. coli Keio single-gene deletion library is often regarded as a gold standard for gene essentiality studies. However, it remains unclear how much essential genes vary between strains and species. To investigate this, we have assembled a collection of thirteen sequenced high-density transposon mutant libraries from five genera of the Enterobacteriaceae. We first benchmark a number of gene essentiality prediction approaches, investigate the effects of transposon density on essentiality prediction, and identify biases in transposon insertion sequencing data. Based on these investigations we develop a new classifier for gene essentiality. Using gene essentiality defined by this new classifier, we define a core essential genome in the Enterobacteriaceae of 201 universally essential genes, and reconstruct an ancestral essential gene set of 296 genes. Despite the presence of a large cohort of variably essential genes, we find an absence of evidence for genus-specific essential genes. A clear example of this sporadic essentiality is given by the set of genes regulating the σE extracytoplasmic stress response, which appears to have independently become essential multiple times in the Enterobacteriaceae. Finally, we compare our essential gene sets to the natural experiment of gene loss in obligate insect endosymbionts closely related to the Enterobacteriaceae. This isolates a remarkably small set of genes absolutely required for survival, and uncovers several instances of essential stress responses masked by redundancy in free-living bacteria.

2024-08-20 | GSE216013 | GEO

Enterobacteriaceae

Project description:Genome sequencing and assembly of Enterobacteriaceae with acquired resistance to polymyxin

| PRJNA275512 | ENA

A novel mobile genomic island: introducing ‘cephalosporinase morons’ in Enterobacteriaceae

Project description:The exchange of mobile genomic islands (MGIs) between microorganisms is often mediated by phages. As a consequence, not only phage genes are transferred, but also genes that have no particular function in the phage's lysogenic cycle. If they provide benefits to the phage's host, such genes are referred to as ‘morons’. The present study was aimed at characterizing a set of Enterobacter cloacae, Klebsiella pneumoniae and Escherichia coli isolates with exceptional antibiotic resistance phenotypes from patients in a neonatal ward. Unexpectedly, these analyses unveiled the existence of a novel family of closely related MGIs in Enterobacteriaceae. The respective MGI from E. cloacae was named MIR17-GI. Importantly, our observations show that MIR17-GI-like MGIs harbor genes associated with high-level resistance to cephalosporins. Further, we show that MIR17-GI-like islands are associated with integrated P4-like prophages. This implicates phages in the spread of cephalosporin resistance amongst Enterobacteriaceae. The discovery of a novel family of MGIs spreading ‘cephalosporinase morons’ is of high clinical relevance, because high-level cephalosporin resistance has serious implications for the treatment of patients with Enterobacteriaceal infections.

2018-08-21 | PXD007113 | Pride

Enterobacteriaceae

Project description:Enterobacteriaceae Genome sequencing

| PRJNA1026753 | ENA

Enterobacteriaceae

Project description:Enterobacteriaceae Genome sequencing

| PRJNA573827 | ENA

Enterobacteriaceae

Project description:Enterobacteriaceae Genome sequencing

| PRJNA1100992 | ENA

Enterobacteriaceae

Project description:Enterobacteriaceae Genome sequencing