Progressive evolution of Streptococcus equi from Streptococcus equi subsp. zooepidemicus and adaption to equine hosts

Abstract

Streptococcus equi subsp. equi causes the equine respiratory disease ‘strangles’,which is highly contagious, debilitating, and costly to the equine industry. S. equiemerged from the ancestral Streptococcus equi subsp. zooepidemicus and continuesto evolve and disseminate globally, causing disease and considerable economiclosses. Previous work has shown that there was a global population replacementaround the beginning of the twentieth century, obscuring the early genetic events inthis emergence. Here, we have used largescale genomic analysis of S. equi and itsancestor S. zooepidemicus to identify evolutionary events leading to the successfulexpansion of S. equi.1201 whole genome sequences of S. equi were recovered from clinical samples orfrom data available in public databases. Sixty-six whole genome sequencesrepresentative of the diversity of S. zooepidemicus were used to compare the genecontent and examine the evolutionary emergence of S. equi. A dated Bayesianphylogeny was constructed, and ancestral state reconstruction was used to determinethe order and timing of gene gain and loss events between the different species andbetween different S. equi lineages. Additionally a newly developed framework wasused to investigate the fitness of different S. equi lineages.We identified a novel S. equi lineage, comprising isolates from donkeys in Chinesefarms, which diverged nearly 300 years ago, after the emergence of S. equi from S.zooepidemicus, but before the global sweep. Ancestral state reconstructiondemonstrated that phage-encoded virulence factors slaA, seeL and seeM wereacquired by the global S. equi after the divergence of the basal donkey lineage. Weidentified the equibactin locus in both S. equi populations, but not S. zooepidemicus,reinforcing its role as a key S. equi virulence mechanism involved in its initialemergence. Evidence of a further population sweep beginning in the early 2000s wasdetected in the UK. This clade now accounts for more than 80% of identified UK casessince 2016. Several sub-lineages demonstrated increased fitness, within which weidentified the acquisition of a new, fifth prophage containing additional toxin genes.We definitively show that acquisition of the equibactin locus was a major determinant inS. equi becoming an equid-exclusive pathogen, but that other virulence factors werefixed by the population sweep at the beginning of the 20th century. Evidence of asecondary population sweep in the UK and acquisition of further advantageous genesimplies that S. equi is continuing to adapt and therefore continued investigations arerequired to determine further risks to the equine industry.