WGS of Escherichia coli: urine isolate
NEBNext UltraT DNA Library Prep Kit for Illumina, clustering, and sequencing reagents were used throughout the process following the manufacturer's recommendations. Briefly, the genomic DNA was fragmented by acoustic shearing with a Covaris LE220 instrument. Fragmented DNA was end repaired and adenylated. Adapters were ligated after adenylation of the 3'ends followed by enrichment by limited cycle PCR. DNA library were validated using D1000 ScreenTape on the Agilent 4200 TapeStation (Agilent Technologies, Palo Alto, CA, USA), and was quantified using Qubit 2.0 Fluorometer. The DNA library was also quantified by real time PCR (Applied Biosystems, Carlsbad, CA, USA), clustered a flowcell and loaded on the Illumina MiSeq instrument according to manufacturer's instructions.