title: Metagenome-assembled genome: ERP122455_co1_30
organism: uncultured Staphylococcaceae bacterium
description: This sample represents a Third Party Annotation (TPA) Metagenome-assembled genome assembled from the metagenomic runs ERR5295732,ERR5295859 of study ERP122455.
attributes.tag: ENA first public
attributes.value: 2024-12-11
attributes.tag: INSDC center name
attributes.value: CMR
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: ERP122455_co1_30
attributes.tag: assembly quality
attributes.value: Many fragments with little to no review of assembly other than reporting of standard assembly statistics
attributes.tag: assembly software
attributes.value: metaSPAdes;3.15.4;default
attributes.tag: binning parameters
attributes.value: coverage and kmer
attributes.tag: binning software
attributes.value: MetaBAT2;2.15;default
attributes.tag: broad-scale environmental context
attributes.value: engineered
attributes.tag: collection date
attributes.value: 2017-06-07
attributes.tag: completeness score
attributes.value: 87.7
attributes.tag: completeness software
attributes.value: CheckM2;1.0.2;default
attributes.tag: contamination score
attributes.value: 2.75
attributes.tag: environmental medium
attributes.value: engineered
attributes.tag: geographic location (country and/or sea)
attributes.value: United Kingdom
attributes.tag: geographic location (latitude)
attributes.value: 52.83877326
attributes.tag: geographic location (longitude)
attributes.value: -1.24955258
attributes.tag: investigation type
attributes.value: metagenome-assembled genome
attributes.tag: isolation_source
attributes.value: metagenome
attributes.tag: local environmental context
attributes.value: metagenome
attributes.tag: metagenomic source
attributes.value: metagenome
attributes.tag: project name
attributes.value: Our vision is to establish a strategic research programme in antimicrobial resistance (AMR) in waste from agricultural farm environments. Our aim is to quantify and mitigate the risks of emergence of resistant pathogens and AMR gene reservoirs associated with mixing antimicrobials with waste matter in these environments.The project is focussed on the University of Nottingham's (UoN) dairy and arable farm, which is typical of high performance UK dairy production, with ~200 high yielding cows. Slurry is stored in a 3M L slurry tank and subsequently spread on surrounding fields. We hypothesise that conditions in the slurry tank environment drive the evolution and acquisition of antimicrobial resistance, and the slurry acts as a reservoir for AMR that is regularly distributed into the environmentThe project consists of six integrated Research Questions:RQ1: What are the levels and nature of antimicrobial and virulence genes present in the slurry tank, their prevalence, carriage, and bacterial hosts?RQ2: What are the chemical agents in the tank? What is their persistence?RQ3: To what extent is resistance maintained after slurry application to soil?RQ4: How can we elicit culturally embedded ways in which scientists and stakeholders know AMR risks? How can we use narrative and visual methods of engaging across these ways of knowing to develop resources for deliberation on AMR risk management?RQ5: To what extent can we reduce resistance profiles through changes in slurry tank composition?RQ6: Can we quantify the risk of emergence of AMR pathogens and what factors are predicted to control this risk best?
attributes.tag: sample derived from
attributes.value: SAMEA8023930
attributes.tag: sample name
attributes.value: ERP122455_co1_30
attributes.tag: scientific_name
attributes.value: uncultured Staphylococcaceae bacterium
attributes.tag: sequencing method
attributes.value: Illumina NovaSeq 6000
attributes.tag: taxonomic identity marker
attributes.value: multi-marker approach