S. equi genomics
Analysis of the S. equi genome has transformed our understanding of strangles in horses, facilitating the development of effective diagnostic tests and a prototype vaccine, Strangvac. However, Strangvac confers protection for only 2 months and further research is required to improve the effectiveness of strangles vaccines. In this project we will build on our knowledge of S. equi by comparing the genome sequences of 1,681 isolates recovered from horses residing around the world. We will identify new genes that enable S. equi to cause disease, survive in persistently infected carriers and evade the equine immune response.  We hypothesise that evidence of Streptococcus equi genome diversity and adaptation to a persistent lifestyle identifies key targets with which to prevent strangles. We aim to: 1. Define the diversity of mobile genetic elements across the population of S. equi, identifying new putative virulence genes, which may influence clinical outcome. 2. Identify examples of genome deletions, amplifications and inversions that have the potential to assist S. equi to persist and evade host responses. 3. Identify genes with elevated mutation rates, which are more likely to encode proteins important to the evolution of S. equi and/or those targeted by the equine immune response, representing new vaccine candidates. Our specific objectives are to: 1. Identify and compare core and non-core regions of the S. equi genomes and the putative virulence genes encoded by them. 2. Exploit sequencing data to quantify sequence reads across the genome and identify deletion, amplification and inversion events. 3. Identify genes with elevated mutation rate in isolates recovered from acute and persistently infected horses, and those showing evidence of adaptive change during S. equi emergence.