Unwelcome neighbours: Tracking the transmission of Streptococcus equi in the United Kingdom horse population.

Background: Strangles (Streptococcus equi infection) remains endemic in the UK, with ~300 laboratory diagnoses annually. Sub-clinically infected long-term carriers are considered a key driver of endemicity. Analysing genomes of circulating strains could provide valuable transmission insights of this pathogen.

Objectives: To determine the population structure and diversity of UK S. equi isolates and to model transmission using epidemiological and whole genome sequencing data.

Study design: Retrospective cross-sectional epidemiological and genomic surveillance.

Methods: A dated phylogenetic tree derived from 511 S. equi isolates collected from UK horses between 2015 and 2022 was reconstructed. Bayesian Analysis of Population Structure (BAPS) identified clusters of related genomes, while iGRAPH identified clusters of sequences appropriate for transmission analysis, performed using Transphylo.

Results: BAPS identified nine groups, with 82% of strains clustering into two (McG-BAPS3, McG-BAPS5). A statistically significant association (p < 0.001) was found between the year of recovery and trends in the frequency of McG-BAPS groups, with McG-BAPS3 increasing and McG-BAPS5 decreasing in prevalence over the study period. Eight transmission clusters encompassing 64% of total sequences (n = 286/447) underwent analysis. Sixteen direct transmission pairs were identified; 10 were between horses from different UK regions. A transmission chain extending over a 6-month period was inferred from isolates from nine horses.

Main limitations: Bacterial strains from sub-clinically infected carrier horses may be underrepresented due to data collection via positive laboratory diagnoses. Furthermore, a low sampling proportion relative to overall UK cases provided only a snapshot of broader, unsampled transmission events.

Conclusions: The rapid change in S. equi population structure indicates acutely infected/recently convalesced short-term carrier horses play a more influential role in transmission than long-term carriers. Our work provides novel insights to our understanding of S. equi transmission dynamics. Transmission of genetically related strains across diverse regions suggests a real-time sequence-based surveillance system could inform interventions to minimise transmission.