Next generation sequencing of Streptococcus equi subsp. equi isolated from horses imported into Japan

We have performed the genetic analysis based on the SeM gene on the isolates from imported horses quarantined at the Japanese border. However, it has been reported that the use of SeM typing as an epidemiological tool is hampered by its homoplasies and high mutation rates, even within individual horses.Whole-genome information could enable higher resolution among bacterial strains compared to the SeM gene analysis, and the core-genome multi-locus sequence typing was recently applied to reveal associations of S. equi with specific horse populations. In addition, information on pathogenic genes and antimicrobial resistance genes can be available from the whole-genome analysis, which is very useful to characterize the clinical isolates. We investigated the prevalence of both pathogenic and antimicrobial resistance genes in S. equi isolates from imported horses to show the genetic differences between S. equi isolates from asymptomatic carrier horses and those from horses with clinical signs.