Genome specialization and decay of the strangles pathogen, Streptococcus equi, is driven by persistent infection

Abstract

Strangles, the most frequently diagnosed infectious disease of horses worldwide, is caused by Streptococcus equi. Despite its prevalence, the global diversity and mechanisms underlying the evolution of S. equi as a host-restricted pathogen remain poorly understood. Here, we define the global population structure of this important pathogen and reveal a population replacement in the late 19th or early 20th Century. Our data reveal a dynamic genome that continues to mutate and decay, but also to amplify and acquire genes despite the organism having lost its natural competence and become host-restricted. The lifestyle of S. equi within the horse is defined by short-term acute disease, strangles, followed by long-term infection. Population analysis reveals evidence of convergent evolution in isolates from post-acute disease samples as a result of niche adaptation to persistent infection within a host. Mutations that lead to metabolic streamlining and the loss of virulence determinants are more frequently found in persistent isolates, suggesting that the pathogenic potential of S. equi reduces as a consequence of long-term residency within the horse post-acute disease. An example of this is the deletion of the equibactin siderophore locus that is associated with iron acquisition, which occurs exclusively in persistent isolates, and renders S. equi significantly less able to cause acute disease in the natural host. We identify several loci that may similarly be required for the full virulence of S. equi, directing future research toward the development of new vaccines against this host-restricted pathogen.

Comparison of nasopharyngeal and guttural pouch specimens to determine the optimal sampling site to detect Streptococcus equi subsp equi carriers by DNA amplification

“…This volume is considerably less than the 1 ml that was centrifuged for DNA extraction and this could have affected the culture results for those samples (23) that were positive on DNA amplification and culture negative. An important incidental finding is that the culture data shows a massive die-off occurred in the guttural pouch in the interval between acute phase strangles and convalescence and is consistent with recent studies in the UK showing S. equi undergoes genetic decay in the guttural pouch including loss of genes necessary for virulence and infectivity [23, 24]. This study found flocked swab sampling of the nasopharynx to be a poor method for testing with the eqbE LAMP PCR to detect S. equi in outwardly healthy convalescent horses.…”

Strangles in horses can be caused by vaccination with Pinnacle I. N.

“…The genomes of SeCF32 together with high and low capsule variants of Pinnacle share 126 single nucleotide polymorphisms (SNPs) with SeCF32 relative to the core reference genome of S. equi strain 4047 (Se4047), in agreement with the known origins of this vaccine [5]. A further 68 unique mutations were identified that were present in both of the Pinnacle phenotypes, but absent from SeCF32 and 222 other isolates of S. equi [5].…”

“…Following determination of raw sequencing reads, SNPs were identified compared to the reference genome Se4047 (NC 012471) [7] on the MiSeq instrument using GATK unified genotyper. SNPs in Se142 and Se136 were also compared to SeCF32 (ERR059719), Pinnacle H+ (ERR064582) and Pinnacle H− (ERR064583) [5].…”

“…A further 68 unique mutations were identified that were present in both of the Pinnacle phenotypes, but absent from SeCF32 and 222 other isolates of S. equi [5]. As a consequence of its derivation through treatment with NTG, Pinnacle-specific mutations were significantly enriched for C → T and G → A, but deficient in A → G and T → C transitions [6] when compared to DNA sequence data from 223 other strains of S. equi, including SeCF32 [5]. It is not known which of the 68 mutations in Pinnacle contribute to the attenuation of this strain.…”

“…It is not known which of the 68 mutations in Pinnacle contribute to the attenuation of this strain. One of the mutations is predicted to lead to the truncation of SEQ 1295, a putative membrane protein, whilst 41 mutations are predicted to lead to non-synonymous changes in the amino acid sequences of the encoded proteins [5]. However, very few of these mutations may contribute to the attenuation of the vaccine strain, raising questions regarding its potential to revert to virulence.…”