2.3 Whole Genome Sequencing Analysis
Genomic DNA of bacterial isolates was extracted using the DNeasy Blood & Tissue Kits (Qiagen, Germany) according to the manufacture’s instruction. Qubit® 3.0 fluorometer (Invitrogen, USA) was used to measure the DNA concentration. A total amount of 0.2 μg DNA was then used as input material for the DNA library preparations using NEB Next® UltraTM DNA Library Prep Kit for Illumina (NEB, USA), and subsequently sequenced using the 2 × 150 bp paired-end library on HiSeq 2500 sequencing system (Illumina). Following trimming and filtering by the NGS_QC Toolkit (v2.3.3), the raw reads were subjected to de novo assembly by SPAdes 3.6 (Bankevich et al., 2012). The subsequent annotation of the assembled genome was performed by Prokka version 1.12 (Seemann, 2014). Plasmid were identified using Plasmid Finder 2.1 (https://cge.cbs.dtu.dk/services/PlasmidFinder/). The antimicrobial resistance genes and chromosomal mutations were analyzed using ResFinder 3.2 (Zankari et al., 2012). CRISPR typing of the isolates was performed as previously described (Li, 2021).