Progressive evolution of Streptococcus equi from Streptococcus equi subsp. zooepidemicus and adaption to equine hosts.

This study uses large-scale genomic analysis to trace the evolutionary history of Streptococcus equi, a bacterium causing a highly contagious and debilitating horse disease known as strangles. Comparing it to its ancestral form, researchers uncover the genetic changes that allowed S. equi to adapt to equine hosts and continue to evolve globally.

Research Methodology and Data Collection

• The researchers employed whole-genome sequencing—a process to determine the complete DNA sequence of an organism’s genome—at a single time. They recovered 1,201 whole-genome sequences of S. equi from both clinical samples and public databases. Furthermore, 74 diverse samples of the ancestral bacterium were sequenced for comparative analysis.
• A dated Bayesian phylogeny was constructed—an evolutionary tree outlining the timeline and lineage relationships of the bacteria. Ancestral state reconstructions were used to derive the order and timing of gene gain and loss events.

Findings and Key Results

• A novel S. equi lineage was identified branching from donkeys on Chinese farms nearly 300 years ago. This lineage diverged after S. equi emerged from its ancestral form but before the global spread.
• The ancestral state reconstruction revealed S. equi acquired certain virulence factors—molecules produced by bacteria mainly contributing to their effectiveness (virulence)—after this divergence.
• The equibactin locus—a genomic segment key to the bacterium’s virulence—was found in both S. equi lineages but not in the ancestral bacterium, strengthening its role in the bacterium’s emergence.
• Further, a new population sweep starting in the early 2000s was detected. Now, this clade represents more than 80% of the identified UK cases since 2016.
• Several sub-lineages have also demonstrated increased fitness, with some acquiring a new prophage—a viral genome inserted and replicated as part of the bacterial DNA—with additional toxin genes.

Conclusions and Implications

• The researchers provide strong evidence supporting the critical role of the equibactin locus in shaping S. equi’s evolution into a pathogen exclusive to equids or horse-like animals. However, other virulence factors were fixed much later, during the global population sweep in the early 1900s.
• There were second signs of a population sweep in the UK and evidence of gene acquisitions implying S. equi continues to adapt. Hence, continued surveillance and research are necessary to assess potential risks to the equine industry.