The global population diversity of Streptococcus equi highlights transmission across international boundaries

Abstract

The genomes of 499 strains of S. equi, which were isolated between 1955 and 2015 from horses across the world, were sequenced to study the phylogenetic relationships of strains of different geographical and temporal origins. Phylogenetic trees were reconstructed based on single nucleotide polymorphisms in the core genome and the genetic diversity of isolates was examined relative to the country of origin. The molecular epidemiology of outbreaks, where information was available, was investigated in greater depth to enable the identification of outbreak sources. Sequencing strains from an outbreak at a rehoming centre in Norfolk, UK, in early 2015 identified that a breakdown in biosecurity measures in the isolation yard was responsible for recent cases of disease. This information enabled rapid remedial actions to be implemented, which minimised further cases and facilitated the resolution of the outbreak. The sequences of isolates recovered from an outbreak of strangles at a rehoming centre in Lincolnshire, UK, during 2007/8 provided evidence that this outbreak was triggered by persistently infected carrier animals, most likely from a previous spate of disease on this site. Following the outbreak, the identification and treatment of persistently infected horses enabled the eradication of S. equi from these premises. The transmission of four strains of S. equi linked to the import of horses from Europe led to multiple outbreaks of strangles in Dubai. Our data highlight potential benefits of preexport screening for the effective identification and treatment of carrier animals. Certain groups of S. equi were restricted to particular outbreaks or countries, for example isolates in Australia and New Zealand were related. However, the populations of S. equi recovered from several European countries (Ireland, Sweden, Belgium, France, the Netherlands, Spain, Italy and the UK) and Dubai were virtually indistinguishable. Our data highlight that the international movement of horses facilitates cross-border transmission of S. equi. International transmission is most likely to occur through a failure of pre-import health checks and quarantine procedures to identify outwardly healthy persistently infected animals. Pre-movement screening can identify persistently infected horses and prevent outbreaks of strangles. However,