CFIAFB20130200_Salmonella enterica
To extract genomic DNA from bacterial strains, a single colony was suspended in one mL of brain heart infusion (BHI) broth and incubated overnight at 37C. DNA was isolated from 400 L of broth cultures using the Promega Maxwell 16 Cell DNA purification kit as recommended by the manufacturer (Promega, WI, USA).  DNA was quantified with the Qubit dsDNA HS Assay Kit (Invitrogen, Eugene, USA) using the Qubit 3.0 Fluorometer following the manufacturers instructions. The sequencing library was constructed from 400 ng of gDNA using a Rapid Barcoding Sequencing Kit (SQK-RBK004, Oxford Nanopore Technologies, UK ) according to manufacturers instructions. Nanopore sequencing was performed using a FLO-MIN106D (R9.4.1) flow cell on a MinION Mk1B device (Oxford Nanopore Technologies). Raw electrical signals were collected using MinKNOW software and subsequently basecalled with a superaccurate model.