Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Metagenomics NGS for identification of prosthetic joint infection pathogens

ABSTRACT: metagenomics NGS for identification of prosthetic joint infection pathogens

PROVIDER: PRJEB36849 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Application mNGS for identification of prosthetic joint infection pathogens

Project description:Application of next generation sequencing (NGS) for identification of prosthetic joint infection pathogens: a diagnostic evaluation study

| PRJEB35719 | ENA

In situ Staphylococcus aureus gene expression in a human prosthetic joint infection

Project description:Little is known about regulation of gene activity of the major pathogen Staphylococcus aureus during actual human infection. Here we characterize the transcriptome using deep RNA sequencing and the metabolome using NMR of S. aureus infected joint fluid derived from an acute human prosthetic joint infection, and compare them with the genome, transcriptome and metabolome of an isolate obtained from the sample grown in vitro (LB medium). The transcriptome indicated that the bacterial infection sustained on a versatile human-cell-based diet consisting of amino acids, glycans and nucleosides, since significant upregulation of genes involved in the catabolic degradation pathways of these compounds were observed in situ. This is consistent with metabolite analysis of the infected joint fluid and of S. aureus culture supernatants where the concentration of most amino acids and some amino sugars were found to be higher in the joint fluid, whereas the concentration of glucose was higher in culture supernatant. Furthermore, presumably because of oxygen limitations in the joint fluid, transcriptomic evidence for fermentation was observed, consistent with the presence of fermentation products (ethanol) in situ. Moreover, many, but not all, of the known virulence factor genes were upregulated in situ as well as the nine genes encoding the iron uptaking siderophore synthesis system.

2015-10-01 | GSE62091 | GEO

Identification of Prosthetic Joint Infection Pathogens Using a Shotgun Metagenomics Approach.

Project description: Not available

| S-EPMC6186856 | biostudies-literature

ONT MinION sequencing of prosthetic joint infection sonication fluids

Project description:ONT MinION sequencing of prosthetic joint infection sonication fluids

| PRJEB23460 | ENA

metagenomics NGS study

Project description:metagenomics NGS study

| PRJEB42456 | ENA

Comparative meta-omics for identifying pathogens associated with prosthetic joint infection.

Project description: Not available

| S-EPMC8660779 | biostudies-literature

Corynebacterium prosthetic joint infection.

Project description: Not available

| S-EPMC3347109 | biostudies-other

Shotgun metagenomics from positive blood culture bottles inoculated with prosthetic joint tissues positive for S. aureus

Project description:Typing and prediction of antibiotic resistance and virulence determinants in S. aureus using shotgun-metagenomics data from prosthetic joint tissue on blood culture bottles

| PRJEB43858 | ENA

Can metagenomic next-generation sequencing identify the pathogens responsible for culture-negative prosthetic joint infection?

Project description: Not available

| S-EPMC7106575 | biostudies-literature

Direct Detection and Identification of Prosthetic Joint Infection Pathogens in Synovial Fluid by Metagenomic Shotgun Sequencing.

Project description: Not available

| S-EPMC6113468 | biostudies-literature