E coli O25:H4 ST131 strain 14142
The genomic DNA was prepared for Illumina pair-end sequencing using the Illumina Nextera XT DNA Library Prep Guide Document # 15031942 v05 May 2019 following the protocol  (Nextera XT DNA Library Prep Kit Reference Guide (15031942) (illumina.com)). The library was sequenced on an Illumina MiSeq using MiSeq Reagent Kit v2 and 500 cycles with a Standard Flow Cell. The raw data was demultiplexed using Illuminas bcl2fastq tool (Illumina, CA, USA), checked for quality using the FastQC tool (BaseSpace, Illumina, CA, USA) and then quality-trimmed (Q25) and adapter-trimmed (multiplexing and sequencing adapters) using the FastQ Toolkit (BaseSpace, Illumina, CA, USA).