Genetic analysis based on next generation sequencing of Streptococcus equi subsp. equi isolated from horses imported into Japan

Abstract

Strangles is a globally widespread, commonly diagnosed and important infectious disease of equids caused by Streptococcus equi subsp. equi. We performed whole genome sequencing of 19 S. equi isolates collected from imported horses at the Japanese border. Of these isolates, 15 isolates were obtained from clinical cases and 4 were from subclinical cases. The 19 isolates were grouped into 3 Bayesian analysis of population structure (BAPS) groups by the core genome single nucleotide polymorphism analysis corresponding to exporting country, SeM typing, or exporter of the horses. The 19 isolates possessed same pathogenic genes regardless of clinical status in imported horses and no antimicrobial resistance genes. The disease status of the horses may rather reflect the prior exposure of animals with sub-clinical infection to S. equi.

Keywords: Streptococcus equi; animal quarantine service; genetic analysis; next generation sequencing.

Fig. 1.

Phylogenetic tree based on 430 single nucleotide polymorphisms. The positions of the 19 Animal Quarantine Service strains isolated in quarantine are indicated by red circles, and the six Bayesian analysis of population structure (BAPS) clusters are shown outside of the phylogenetic tree. The name of the exporter listed in Supplementary Table 1 is shown after the colon in each strain. To enhance clarity and readability, the scale bar was removed from the phylogenetic tree by selecting the ‘Toggle scaling of the tree’ option in MEGA.