Easy dna kittm

Two isolates of three bacterial species with resistance mechanisms of interest to the EURL-AR network were selected: Salmonella enterica (S. enterica), Escherichia coli (E. coli) and Campylobacter coli (C. coli). An overview of the strains and their details are found in Table 1.
Genomic DNA (gDNA) was extracted from the six GPT2020 isolates using an Invitrogen Easy-DNA KitTM (Invitrogen, Carlsbad, CA, USA). The gDNA of each strain was dried and supplemented with DNA stabilizing agent (DNAstable Plus, Biomatrica, https://www.biomatrica.com/download/hp-dnastable-plus-handbook/).
The GPT2020 strains were sequenced using the Sequel system (Pacific Bioscience, CA, USA) to obtain a closed reference genome and analysed using the bioinformatics tools to confirm the MLST and sequence type (ST) genes using the pipeline MLST v 2.0.4 [11 (link)] available from Center for Genomic Epidemiology http://www.genomicepidemiology.org/

Genomic DNA was extracted from 102 pig and wild boar isolates using an Invitrogen Easy-DNA Kit^TM (Invitrogen, Carlsbad, CA, United States) and DNA concentrations were determined using the Qubit dsDNA BR assay kit (Invitrogen). The genomic DNA was prepared for Illumina pair-end sequencing using the Illumina (Illumina, Inc., San Diego, CA, United States) Nextera XT^® Guide 150319425031942 following the protocol revision C¹. A sample of the pooled Nextera XT Libraries was loaded onto an Illumina HiSeq reagent cartridge using HiSeq Reagent Kit v2. The libraries were sequenced using an Illumina HiSeq platform.
Raw sequence data have been submitted to the European Nucleotide Archive² under study accession no.: PRJEB18803. The raw reads were de novo assembled using the assembly pipeline (version 1.0) available from the Center for Genomic Epidemiology (CGE)³, which is based on the Velvet algorithm for de novo short reads assembly (Zerbino and Birney, 2008 (link)). A complete list of genomic sequence data is available in the Supplementary Table S1.

The E. coli EC1945 isolate genome was sequenced at EURL-AR, DTU, Lyngby, Denmark, under the scope of the EFSA confirmatory testing [36 (link)]. Genomic DNA was extracted using an Invitrogen Easy-DNA KitTM (Invitrogen, Carlsbad, CA, United States), and the DNA concentrations were determined using the Qubit dsDNA BR assay kit (Invitrogen). Genomic DNA was prepared for Illumina pair-end sequencing using the Illumina (Illumina, Inc., San Diego, CA, USA) Nextera XT^® Guide following the protocol revision C1. A sample of the pooled Nextera XT Libraries was loaded onto an Illumina MiSeq reagent cartridge using MiSeq Reagent Kit v3. The libraries were sequenced using an Illumina MiSeq platform (Illumina). The raw reads were de novo assembled using the assembler pipeline (version 1.4) available from the Center for Genomic Epidemiology (CGE) (https://www.genomicepidemiology.org/) (accessed on 25 April 2022).
The Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under the accession JAUTEE000000000.