WGS of E.coli: stool
Whole genome sequencing was performed for the phenotypically confirmed ESBL producing E. coli isolates. Genomic DNA was extracted using the QIAamp DNA Mini Kit (Qiagen, Hilden, Germany) or STARMag 96X4 Universal Cartridge Kit (Seegene Inc, Walnut Creek, CA, USA). Genomic libraries were prepared using the Illumina DNA Prep (Illumina). Isolates were sequenced on the NextSeq 2000 system (Illumina) using 2 x 149 bp paired-end reads chemistry.