Genomic Evidence for the Evolution of Streptococcus equi: Host Restriction, Increased Virulence, and Genetic Exchange with Human Pathogens

Abstract

The continued evolution of bacterial pathogens has major implications for both human and animal disease, but the exchange of genetic material between host-restricted pathogens is rarely considered. Streptococcus equi subspecies equi (S. equi) is a host-restricted pathogen of horses that has evolved from the zoonotic pathogen Streptococcus equi subspecies zooepidemicus (S. zooepidemicus). These pathogens share approximately 80% genome sequence identity with the important human pathogen Streptococcus pyogenes. We sequenced and compared the genomes of S. equi 4047 and S. zooepidemicus H70 and screened S. equi and S. zooepidemicus strains from around the world to uncover evidence of the genetic events that have shaped the evolution of the S. equi genome and led to its emergence as a host-restricted pathogen. Our analysis provides evidence of functional loss due to mutation and deletion, coupled with pathogenic specialization through the acquisition of bacteriophage encoding a phospholipase A2 toxin, and four superantigens, and an integrative conjugative element carrying a novel iron acquisition system with similarity to the high pathogenicity island of Yersinia pestis. We also highlight that S. equi, S. zooepidemicus, and S. pyogenes share a common phage pool that enhances cross-species pathogen evolution. We conclude that the complex interplay of functional loss, pathogenic specialization, and genetic exchange between S. equi, S. zooepidemicus, and S. pyogenes continues to influence the evolution of these important streptococci.

Characterization of the haem-uptake system of the equine pathogen Streptococcus equi subsp. equi

“…a ligand-binding lipoprotein (SeHtsA), a permease (SeHtsB) and an ATPase (SeHtsC). The sequences of SeShp (residues 30-261) and SeHtsA (residues 21-294), determined in this study for strain TW, are identical to those determined for strain SEM1 (Nygaard et al, 2006b) and strain 4047 (Holden et al, 2009). The N-termini of Shp, SeShp and SzShp show most homology and are likely to possess the same immunoglobulin-like fold as that of Shp (Aranda et al, 2007;Holden et al, 2009;Nygaard et al, 2006b).…”

“…The sequences of SeShp (residues 30-261) and SeHtsA (residues 21-294), determined in this study for strain TW, are identical to those determined for strain SEM1 (Nygaard et al, 2006b) and strain 4047 (Holden et al, 2009). The N-termini of Shp, SeShp and SzShp show most homology and are likely to possess the same immunoglobulin-like fold as that of Shp (Aranda et al, 2007;Holden et al, 2009;Nygaard et al, 2006b). The HtsA proteins exhibit strong (40 %) identity with the staphylococcal IsdE protein which has been shown to possess a bi-lobed structure characteristic of class III periplasmic binding proteins (Grigg et al, 2007b).…”

“…equi possesses a number of factors which would result in erythrocyte lysis and release of Hb and haem (Harrington et al, 2002;Holden et al, 2009;Timoney, 2004). We showed that S. equi can utilize haem and Hb as iron sources.…”

“…The S. equi and S. zooepidemicus genomes (Holden et al, 2009) possess a highly homologous 10 gene cluster, the first five genes of which resemble the Hts haem-uptake system of S. pyogenes ( Fig. 1a; Bates et al, 2003;Lei et al, 2002).…”

“…These include numerous ligand-binding surface-associated and secreted proteins, several superantigens and the hyaluronic acid capsule (Harrington et al, 2002;Holden et al, 2009;Timoney, 2004). Recently, S. equi homologues of the S. pyogenes Shp (designated SeShp) and HtsA (designated SeHtsA) have been described.…”