Comparison of whole genome sequences of Streptococcus equi subsp. equi from an outbreak in Texas with isolates from within the region, Kentucky, USA, and other countries.

•Mutations can occur in S. equi isolates within an individual host during an outbreak.•Whole genome sequencing improves understanding of S. equi molecular epidemiology.•Culture of guttural pouch lavage fluid can be inadequate to find long-term carriers.•Cases of strangles caused by live vaccines may not be attributed to the vaccine.