Escherichia coli clinical isolates
Genomic DNA was extracted from the isolates using the Qiagen QIAamp DNA Mini Kit. Starting with 300-500ng of DNA, samples were sheared in a 96-well format using a Covaris LE220 focused ultrasonicator targeting 380 base pair inserts. The resulting sheared DNA was cleaned with Agencourt AMPure XP beads to remove sample impurities prior to library construction. End-repair, A-tailing, and ligation were performed as directed by KAPA Hyper Prep Kit (Kapa Biosystems, Wilm- ington, MA). Following ligation, the samples were subjected to an AMPure XP cleanup to remove excess adapters. Samples were then amplified by 5 cycles of PCR using the KAPA HiFi HotStart DNA Polymerase, followed by a final AMPure XP cleanup. Final libraries were quantified by fluorometric assay (Quant-it, Invitrogen) and the molecular weight distribution of library fragments was checked using the Agilent Bioanalyzer. Barcoded genome libraries were pooled and loaded on the Illumina NextSeq instrument, where cluster generation and paired-end 150bp read sequencing occurred sequentially.