Whole genome sequencing analysis of Salmonella enterica serovar Agona strains isolated from broilers and human cases

Whole genome sequence (WGS) analysis was carried out for Salmonella enterica serovar Agona strains isolated from broilers and human cases. WGS analysis was done using Miseq (Illumina) and read data were exported into fastq files. The fastq files were analyzed using CLC Genomics Workbench (CLC bio), and mapping to a reference genome (S. Agona strain SL483, GenBank Accession Number CP001138) and single nucleotide polymorphisms were detected. SNPs in the core genes of S. Agona (Zhou et al. PLoS Genetics 2013;9:e1003471) were collected from the detected SNPs. When the collected SNPs were analyzed by maximum likelihoood method, tested strains were clearly divided into two clusters. One of which included all broiler-derived strains and some of human-derived strains, indicating that one of route of S. Agona infection to human would be broilers.