Metagenome-assembled genome: ERR2244943_bin.41_metaWRAP_v1.1_MAG
This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run ERR2244943 of study ERP024389.
ENA first public
2022-01-19
ENA last update
2022-01-19
External Id
SAMEA12362719
INSDC center alias
EMG
INSDC center name
EMG
INSDC first public
2022-01-19T00:26:23Z
INSDC last update
2022-01-19T00:26:23Z
INSDC status
public
Submitter Id
ERR2244943_bin.41_metaWRAP_v1.1_MAG
assembly quality
Many fragments with little to no review of assembly other than reporting of standard assembly statistics
assembly software
metaSPAdes v3.14.1
binning parameters
MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters.
binning software
metaWRAP v1.1
broker name
EMG broker account, EMBL-EBI
collection date
2015-01-01
completeness score
98.87
completeness software
CheckM
contamination score
0.84
environment (biome)
Chicken digestive system
environment (feature)
Digestive tube
environment (material)
Fecal
geographic location (country and/or sea)
Netherlands
geographic location (latitude)
42.7339
geographic location (longitude)
25.4858
investigation type
metagenome-assembled genome
isolation source
chicken gut metagenome
metagenomic source
chicken gut metagenome
project name
Antimicrobial 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 derived from
SAMEA104467130
sample name
ERR2244943_bin.41_metaWRAP_v1.1_MAG
sequencing method
Illumina HiSeq 2500
taxonomic identity marker
multi-marker approach