Molecular epidemiology of Salmonella enterica subsp. enterica serovar Agona using whole genome sequence data.

The whole genome sequence (WGS) data were used for molecularepidemiology of Salmonella enterica subsp. enterica serovar Agonastrains. All WGS data were obtained using NextSeq500 or Miseq systems(Illumina). The WGS data were analyzed using CLC Genomics Workbench.Read data were mapped to a reference genome with the 'Non-specificmatch was ignored' option. Single nucleotide polymorphisms (SNPs) weredetected using a fixed ploidy variant detection method with the 'acoverage and count filter with minimum coverage was 30' option. TheSNPs detected were further selected using an in-house Ruby (ISO/IEC30170) script when a SNP was located in the core-genes of S. Agonastrains. All SNP sets were analyzed using BioNumerics software. TheseSNPs were checked by the phiw test for significant recombination usingSplits Tree Ver. 4.11.3.