WGS of E. coli: CF sputum
Bacterial isolates from frozen cultures were streaked on tryptic soy (TSY) broth agar plates and grown for single colonies overnight at 37C. Single colonies were used to inoculate 2 ml overnight liquid cultures in TSY broth with shaking. Genomic DNA was extracted from 1 ml of overnight culture using the Promega Wizard Genomic DNA Purification Kit according to the manufacturers protocol. Illumina sequencing libraries were prepared using the Nextera XT DNA Library Prep Kit and sequenced on the Illumina MiSeq V3 (2x300 bp reads) or HiSeq V2 (2x250 bp reads) sequencers.