characteristics.text: ERC000047
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2022-01-26T20:50:45Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2022-01-26T20:50:45Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA12362727
characteristics.characteristic: External Id
characteristics.text: EMG
characteristics.characteristic: INSDC center name
characteristics.text: 2022-01-26T20:50:45Z
characteristics.characteristic: INSDC first public
characteristics.text: 2022-01-26T20:50:45Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS9969525
characteristics.characteristic: SRA accession
characteristics.text: ERR2244943_bin.53_metaWRAP_v1.1_MAG
characteristics.characteristic: Submitter Id
characteristics.text: Many fragments with little to no review of assembly other than reporting of standard assembly statistics
characteristics.characteristic: assembly quality
characteristics.text: metaSPAdes v3.14.1
characteristics.characteristic: assembly software
characteristics.text: MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters.
characteristics.characteristic: binning parameters
characteristics.text: metaWRAP v1.1
characteristics.characteristic: binning software
characteristics.text: EBI-EMG
characteristics.characteristic: broker name
characteristics.text: 2015-01-01
characteristics.characteristic: collection date
characteristics.text: 62.72
characteristics.unit: %
characteristics.characteristic: completeness score
characteristics.text: CheckM
characteristics.characteristic: completeness software
characteristics.text: 1.01
characteristics.unit: %
characteristics.characteristic: contamination score
characteristics.text: This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run ERR2244943 of study ERP024389.
characteristics.characteristic: description
characteristics.text: Chicken digestive system
characteristics.characteristic: environment (biome)
characteristics.text: Digestive tube
characteristics.characteristic: environment (feature)
characteristics.text: Fecal
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0009523
characteristics.characteristic: environment (material)
characteristics.text: Netherlands
characteristics.characteristic: geographic location (country and/or sea)
characteristics.text: 42.7339
characteristics.unit: DD
characteristics.characteristic: geographic location (latitude)
characteristics.text: 25.4858
characteristics.unit: DD
characteristics.characteristic: geographic location (longitude)
characteristics.text: metagenome-assembled genome
characteristics.characteristic: investigation type
characteristics.text: chicken gut metagenome
characteristics.characteristic: isolation source
characteristics.text: chicken gut metagenome
characteristics.characteristic: metagenomic source
characteristics.text: uncultured Clostridia bacterium
characteristics.characteristic: organism
characteristics.text: 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.
characteristics.characteristic: project name
characteristics.text: SAMEA104467130
characteristics.characteristic: sample derived from
characteristics.text: uncultured Clostridia bacterium
characteristics.characteristic: scientific_name
characteristics.text: Illumina HiSeq 2500
characteristics.unit: %
characteristics.characteristic: sequencing method
characteristics.text: multi-marker approach
characteristics.characteristic: taxonomic identity marker
characteristics.text: Metagenome-assembled genome: ERR2244943_bin.53_metaWRAP_v1.1_MAG
characteristics.characteristic: title