Whole genome sequencing
WGS was performed for all identified ESBL-E isolates. Total genomic DNA was extracted using the MagNA Pure 96 platform (Roche Applied Science, Mannheim, Germany). Genomic DNA was fragmented by shearing to a size of ~ 350 bp. Libraries were prepared using the NEBNext® DNA Library Prep kit (New England Biolabs, Ipswich, MA, USA) and subjected to 150 bp paired-end sequencing creating > 100 × coverage using Illumina technology (Novogene, HongKong, China). De novo genomic assemblies were generated using CLC Genomics Workbench v21 (Qiagen, Hilden Germany) using default parameters. Antimicrobial resistance (AMR) genes were detected and identified using the web-based Comprehensive Antibiotic Resistance Database (CARD) interface (https://card.mcmaster.ca/) restricted to perfect and strict hits . Conventional multi locus sequence types (MLST) and core-genome MLST cluster types were determined using each species’ corresponding scheme (https://cgmlst.org/ncs) in SeqSphere + v5 software (Ridom, Munster, Germany). The identity of all strains was verified by analyzing the genomic assemblies using the online TYGS platform (https://tygs.dsmz.de/) .