Salmonella enterica
Genomic DNA was extracted using the ZymoBIOMICS DNA/RNA Miniprep kit (Zymo Research, Irvine, CA) according to the manufacturers protocol.  Isolated DNA was quantified by Qubit (ThermoFisher Scientific, Waltham, MA).  DNA libraries were prepared using the Thermo Fisher IonXpress Plus Fragment Library Kit (ThermoFisher Scientific), according to the manufacturers protocol.  Library quantity was assessed with Qubit (ThermoFisher Scientific).  The DNA extracts were subjected to whole genome sequencing using the Thermo Fisher Ion S5 200 bp sequencing platform.  De novo genome assembly was performed using SPAdes