Whole Genome Sequencing of Bacterial Isolates

Libraries were created by using TruePrep™ DNA Library Prep Kit V2 for Illumina®. WGS was carried out using the Illumina HiSeq X Ten PE150 with 150-base paired-end reads Quality of FASTQ-formatted sequencing reads was controlled with a minimum quality Phred score of 30 (as a rolling average over 4 bases with a minimum individual base quality of 15) using Trimmomatic-0.36 software (Bolger et al., 2014 (link)). In silico serotyping was performed using SISTR (Yoshida C. E. et al., 2016 (link)). SISTR classified the isolates into the corresponding serotype based on the serovar antigen combinations and core-genome multilocus sequence typing (cgMLST). The cgMLST type utilized by SISTR was obtained from EnteroBase. As SISTR requires contigs as the input file, the reads were assembled using shovill coupled with SPAdes v3.13.1 (Bankevich et al., 2012 (link)). Genome sequences obtained in this study have been submitted as raw reads under bioproject number PRJNA639393.