WGS of human uropathogenic E. coli
Total DNA was extracted from E. coli using the Qiagen DNeasy Blood and Tissue Kit. DNA was checked for quality and quantity using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific, Wilmington, DE, USA) and Qubit 2.0 fluorometer (Life Technologies, USA), respectively. Sequencing libraries were prepared with the NextEra XT library preparation kit (Illumina Inc., San Diego, CA, USA). All isolates underwent short-read sequencing on the Illumina MiSeq platform.