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Metagenome-assembled genome: ERR2245331_bin.177_CONCOCT_v1.1_MAG

Identifiers
BioSample: SAMEA14075689; SRA: ERS11678917
Organism
uncultured bacterium
cellular organisms; Bacteria; environmental samples
Attributes
collection date2015-01-01
broad-scale environmental contextMixed
local-scale environmental contextMixed
environmental mediumMixed
geographic locationNetherlands
investigation typemetagenome-assembled genome
isolation sourcemetagenome
project nameAntimicrobial resistance (AMR) in bacteria and associated morbidity and mortality is increasing. Use of antimicrobials for livestock selects for AMR that can subsequently be transferred to the human reservoir. This flow of AMR between reservoirs demands surveillance in livestock as well as in humans. As part of the EFFORT project (http://www.effort-against-amr.eu/), we have quantified and characterized the acquired resistance gene pools (resistomes) of 181 pig and 178 poultry farms from nine European countries, generating more than 5,000 Gigabases of DNA sequence, using shotgun metagenomics. The pig and poultry resistomes were very different in abundance and composition. There was a significant country effect on the resistomes, more so in pigs than poultry. We found higher AMR loads in pigs, while poultry resistomes were more diverse. We detected several newly described, critical AMR genes, including mcr-1 and optrA, which differed both between host species and countries. We found that the total AMR level, was associated with the overall country-specific antimicrobial usage in livestock and that countries with comparable usage patterns have similar resistomes.
sample nameERR2245331_bin.177_CONCOCT_v1.1_MAG
ENA-CHECKLISTERC000047
ENA-FIRST-PUBLIC2023-01-03
ENA-LAST-UPDATE2023-01-03
External IdSAMEA14075689
INSDC center aliasEBI
INSDC center nameEuropean Bioinformatics Institute
INSDC first public2023-01-03T00:32:50Z
INSDC last update2023-01-03T00:32:50Z
INSDC statuspublic
Submitter IdERR2245331_bin.177_CONCOCT_v1.1_MAG
assembly qualityMany fragments with little to no review of assembly other than reporting of standard assembly statistics
assembly softwaremetaSPAdes v3.14.1
binning parametersDefault
binning softwareCONCOCT v1.1
broker nameEMG broker account, EMBL-EBI
completeness score90.85
completeness softwareCheckM
contamination score0.74
geographic location (latitude)42.7339
geographic location (longitude)25.4858
metagenomic sourcemetagenome
sample derived fromSAMEA104467130
scientific_nameuncultured bacterium
sequencing methodIllumina HiSeq 2500
taxonomic identity markermulti-marker approach
Description

This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run ERR2245331 of study ERP024389.

BioProject
PRJEB50943 Large-scale analysis of novel cellular microbes
Retrieve all samples from this project

Submission
EBI; 2023-01-04
Accession:
SAMEA14075689
ID:
32557603

BioProject Nucleotide

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