ETEC strain carrying CS13
Library preparation was performed using the NEBNext Ultra DNA library prep kit for illumina (New England Biolabs) and standard illumina multiplexing adapters with minor modifications to manufacturers protocol. Libraries were PCR amplified (10 cycles) on a Tetrad (Bio-Rad) using in-house dual indexing primers previously described (11). Post-PCR purification performed using Agencourt Ampure XP (Beckman Coulter; ratio 1:0.75). Individual libraries were normalised using PicoGreen (Thermo Fisher). Individual libraries were normalised and pooled together accordingly. The size profile of the pooled library was analysed on the 4200 TapeStation. The pooled library was quantified using Qubit (Invitrogen) and diluted to ~10 nM for storage. The 10 nM library was denatured and further diluted prior to loading on the sequencer. Paired end sequencing was performed using a HiSeq2500, Rapid 250bp paired end platform (Illumina).