Pathogen: clinical or host-associated sample from Escherichia albertii JL1480
Multiplex whole genome libraries were prepared using the Nextera XT DNA library preparation kit (Illumina, San Diego, CA) with dual indexing. Genomic library DNA was quantified by Qubit fluorometer dsDNA HS kit (Life Technologies Carlsbad, CA), and normalized to equivalent amplifying concentrations. The pooled libraries were sequenced on an Illumina Miseq Desktop Sequencer using Miseq Reagent Kit v2 for 500 cycles at the NGS Section of the VDL at Iowa State University (Ames, Iowa). 2x250 paired-end reads were produced following standard Illumina protocols. Raw reads of each sample were demultiplexed automatically on the MiSeq with the default settings.