2024-09-19
ENA first public
ERC000050
ENA-CHECKLIST
EMBL Heidelberg
INSDC center name
public
INSDC status
ERS21057287
SRA accession
spire_mag_00407788
Submitter Id
Many fragments with little to no review of assembly other than reporting of standard assembly statistics
assembly quality
megahit 1.2.9
assembly software
default
binning parameters
metabat 2.12.1
binning software
human digestive system
broad-scale environmental context
EBI-EMG
broker name
missing: third party data
collection date
93.54
%
completeness score
checkm2 0.1.3
completeness software
0.42
%
contamination score
This sample represents a Third Party Annotation (TPA) binned metagenome assembled from the metagenomic run SRR8695477 of study SRP187836.
description
stool
environmental medium
Italy
geographic location (country and/or sea)
44.29000000
DD
geographic location (latitude)
11.21000000
DD
geographic location (longitude)
metagenome-assembled genome
investigation type
human gut metagenome
isolation_source
human gut
local environmental context
human gut metagenome
metagenomic source
Phocaeicola vulgatus
organism
The rate of infection by antibiotic-resistant bacteria (ARB) is continuously raising worldwide, particularly because of the selective pressure resulting from the increasing usage of broad-spectrum antibiotics. This burden of ARB is of particular relevance for hematological patients, who undergo frequent antimicrobial prophylaxis and treatments. The prolonged exposure to health care settings may indeed favor the progressive accumulation of antimicrobial resistance genes in the gut microbiome of patients. Consequently, opportunistic ARB can accumulate in intestinal niches, where they can take advantage of the chemotherapy-induced damage to the gut epithelium and the overlapping neutropenia, spreading through the gut wall and causing life-threatening systemic infections.</p><p>The gut microbiome of pediatric patients undergoing allo-hematopoietic stem cell transplantation (HSCT) has recently been considered as a potential reservoir of antimicrobial resistance, with important implications in terms of patient mortality rate. By means of shotgun metagenomics, here we explored the dynamics of the gut resistome – i.e. the pattern of antibiotic resistance genes provided by the gut microbiome – in eight pediatric patients undergoing HSCT, half of whom developed acute Graft-versus-Host Disease (aGvHD).
project name
SAMN11081381
sample derived from
Phocaeicola vulgatus
scientific_name
Illumina Genome Analyzer IIx
sequencing method
multi-marker approach
taxonomic identity marker
binned metagenome: spire_mag_00407788
title