Characterisation of S. equi strains by whole genome sequencing isolated from 2016 to 2019 in France

Albertine Léon (1, 2) , Sophie Castagnet (1, 2) , H. Wilson (3) , Jean-Christophe J.-C. Giard (2) , Andrew Waller (4, 5)

1 LABÉO - LABÉO, Pôle d’analyses et de recherche de Normandie
2 U2RM - Unité de Recherche Risques Microbiens
3 CAM - University of Cambridge [UK]
4 Intervacc AB
5 Department of Biomedical Sciences and Veterinary Public Health

Background: The prevalence of strangles, one of the most frequently diagnosed infectious diseases of horses worldwide, remains underestimated in France, despite causing economic losses to the equine industry. Streptococcus equi subsp equi (S. equi) is the causative agent and its persistence in guttural pouches of sub-clinical carriers plays an important role in the spread of the disease. Objectives: The aim of this study was to use whole genome sequencing to understand the genetic relationships of S. equi isolates recovered in France from 2016 to 2019 and compare them with international data. Study design: Longitudinal field study. Methods: The French Network for epidemio-surveillance of equine diseases (RESPE), collected 55 isolates from 23 horses implicated in 13 different outbreaks. DNAs from 18 of these strains were extracted, purified and whole genome sequenced according to Illumina recommendations. Genomes were analysed using Pathogenwatch and visualised in Microreact. Results: All isolates were classified as ST-179, recognised as “classic” S. equi. Genomes clustered into BAPS2 (Bayesian Analysis of Population Structure) but fell into two groups. Sequences in the first group, from different outbreaks (two in 2016 and one in 2017), differed from only some SNPs across the core genome and their closest relatives were previously recovered from horses in the United Arab Emirates. The second group were most closely related to other strains from France, Belgium, Spain, Sweden and the United Kingdom. Main limitations: Not all available isolates have been sequenced to date and the history of the horses from which these isolates were derived requires further investigation. Conclusions: Genomic analyses are undergoing to understand the differences between isolates from horses with acute strangles and sub-clinical carriers, by highlighting differences in genes involved in virulence, resistance, persistence or evasion of the immune system.

Domaines: Médecine vétérinaire et santé animale

Albertine Léon, Sophie Castagnet, H. Wilson, Jean-Christophe J.-C. Giard, Andrew Waller. Characterisation of S. equi strains by whole genome sequencing isolated from 2016 to 2019 in France. 11th International Equine Infectious Diseases, Sep 2021, Online, France. pp.22-22, ⟨10.1111/evj.20_13495⟩. ⟨hal-03362571⟩