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  • Third-generation cephalosporin resistance (3GC-R) in Escherichia coli is a rising problem in human and farmed-animal populations. We conducted whole-genome sequencing analysis of representative 3GC-R isolates previously collected from dairy farms in southwest England, and human urinary isolates collected from the same geographical area and time-period, and confirmed by PCR to carry acquired 3GC-R genes. This analysis identified blaCTX-M (131 isolates encoding CTX-M-1, -14, -15, -and 32 and the novel variant CTX-M-214), blaCMY-2 (6 isolates), and blaDHA-1 (1 isolate). A highly conserved plasmid was identified in 73 isolates, representing 27 E. coli sequence types. This novel ∼220-kb IncHI2 plasmid carrying blaCTX-M-32 was sequenced to closure and designated pMOO-32. 'This data is NERC-funded but not held by the EIDC. This data is archived in the European Nucleotide Archive'.

  • We do not fully understand how important types (species) of bacteria and packages of genetic material (genes) coding for antibiotic resistance move between humans, animals and the environment, or where, how and why antibiotic resistance emerges. This study looked in detail on a genetic level at bacteria in farm animals, human/animal sewage, sewage treatment works and rivers, to work out the complex network of transmission of important antibiotic-resistant bacteria and antibiotic resistance genes. The overarching aim was to use this information to work out how best to slow down the spread of antibiotic resistance between humans, livestock and the environment. Sampling occurred at three discrete time-points : January-April 2017, June-July 2017, October-November 2017. Research was funded through NERC grant NE/N019989/1. The environmental REsistome: confluence of Human and Animal Biota in antibiotic resistance spread (REHAB)

  • The two Bioprojects contain RNA-Seq transcriptome sequences (fastQ files) resulting from studies investigating gene expression in wild field voles (Microtus agrestis). RNA sequences are derived from studies investigating the immune response of voles in relation to sex and genotype. Accession numbers PRJEB23617 and PRJEB51626 This data is NERC-funded but not held by the EIDC. This data is archived in the European Nucleotide Archive (ENA) which is maintained by EMBL-EBI

  • This data is NERC-funded but not held by the EIDC. The data is archived in European Nucleotide Archive under primary accession reference PRJEB33721. This dataset is the DNA sequences from Illumina MiSeq sequencing of the bacterial 16S and fungal ITS2 genes in climate manipulated soils from the Climoor field experiment. Soil samples were collected in 2003 and 2017 after 4 and 18 years of manipulation, respectively. The experimental field site consists of three untreated control plots, three plots where the plant canopy air is artificially warmed during night time hours, and three plots where rainfall is excluded from the plots at least during the plants' growing season (March to September). The Climoor field experiment intends to answer questions regarding the effects of warming and drought on ecosystem processes and has been running since 1999. The microbial community data aims to understand how changes in soil hydrological and chemical properties have influenced the soil microbial composition and the implications of this for biogeochemical cycling. The data were collected as part of NERC project NEC05670 CWI-STU Fiona Seaton as part of the NERC Soils Training And Research Studentships Centre for Doctoral Training (STARS)

  • These data represent genomic datasets from LOFRESH project on 'Understanding the ecological relevance of eDNA in freshwater lotic ecosystems' These include metabarcoding datasets consisting of fastq files, forward and reverse reads, produced on an Illumina HiSeq platform. Metabarcoding datasets were produced using 18S, COI, 12S and rbcL multiplexed genetic markers. Also included is a metagenomic dataset consisting of fastq files, forward and reverse reads, produced on an Illumina HiSeq platform. Accession number of bioproject: PRJEB48362 This data is NERC-funded but not held by the EIDC. This data is archived in the European Nucleotide Archive (ENA) which is maintained by EMBL-EBI

  • Illumina short-read sequence data from targeted capture of 434 genes, including 150 chemosensory genes, in 104 individuals distributed across eight host races of the pea aphid. This data is NERC-funded but not held by the EIDC. This data is archived in the European Bioinformatics Institute SRA (Sequence Read Archive) with project accession reference PRJEB6325