Illumina sequencing of Citrobacter freundii isolate cultured from Sheep faeces sample
All DNA extracts were sequenced using the Illumina HiSeq 4000, generating 150 bp paired-end reads. Libraries were constructed using the NEBNext Ultra DNA Sample Prep Master Mix Kit (NEB) with minor modifications and a custom automated protocol on a Biomek FX (Beckman Coulter). Ligation of adapters was performed using Illumina Multiplex Adapters, and ligated libraries were size-selected using Agencourt Ampure magnetic beads (Beckman Coulter). Each library was PCR-enriched with custom primers (index primer plus dual index PCR primer). Enrichment and adapter extension of each preparation was obtained using 9 l of a size-selected library in a 50 l PCR. Reactions were then purified with Agencourt Ampure XP beads (Beckman Coulter) on a Biomek NXp after 10 cycles of amplification (as per Illumina recommendations). Final size distributions of libraries were determined using a TapeStation system as above and quantified by Qubit fluorometry.