title: Genomic Sequencing of both Escherichia coli and Enterococcus: recurrent urinary tract infections
design: DNA was isolated following the Qiagen genomic DNA handbook. The only alteration was the addition of 250U of mutanolysin to the enzymatic lysis step for all samples. Sample libraries were prepared using the PCR-free Oxford Nanopore Technologies (ONT) Ligation Sequencing Kit (SQK-NBD114.24) with the NEBNext Companion Module (E7180L) to manufacturers specifications. No additional DNA fragmentation or size selection was performed. Nanopore sequencing was performed on an Oxford Nanopore a MinION Mk1B sequencer or a GridION sequencer using R10.4.1 flow cells in one or more multiplexed shared-flow-cell runs. Run design utilized the 400bps sequencing mode with a minimum read length of 200bp.