untrimmed paired illumina sequences of HVKP2
approx. 109 CFU/mL from an overnight Mueller Hinton broth culture was added to DNAshield (Zymo Research) and DNA extraction and sequencing carried out by MicrobesNG (Birmingham, UK). At MicrobesNG, 10 to 50 L of the cell suspension were used for DNA extraction: cells were lysed with TE buffer containing lysozyme (final concentration 0.1 mg/mL) and RNase A (ITW Reagents) (final concentration 0.1 mg/mL), incubated for 25 min at 37C. Proteinase K (VWR Chemicals) (final concentration 0.1 mg/mL) and SDS (Sigma-Aldrich) (final concentration 0.5% v/v) were added and incubated for 5 min at 65C. Genomic DNA was purified using a minimum of 0.4x volume of SPRI beads and resuspended in EB buffer (Qiagen). DNA was quantified with a fluorescence assay (Quant-iT dsDNA HS kit, ThermoFisher Scientific) in an Eppendorf AF2200 plate reader (Eppendorf UK Ltd). Genomic DNA libraries were prepared using the Nextera XT Library Prep Kit (Illumina) following the manufacturers protocol with the following modifications: 2 ng of DNA were used as input, and PCR elongation time was increased to 1 min from 30 s. DNA quantification and library preparation were carried out on a Hamilton Microlab STAR automated liquid handling system (Hamilton Bonaduz). Libraries were sequenced with an Illumina sequencer (HiSeq 2500 or NovaSeq 6000) using a 250 bp paired end protocol