SeM sequencing is an important tool to confirm the persistence of one strain and its derivatives of Streptococcus equi infection in horses.
A clinically severe strangles outbreak in 41 Icelandic horses was followed for over 13 months. Nasal and/or guttural pouch lavages were obtained on eleven separate occasions. Ten horses with repeated culture positive samples from either nasal or guttural pouch lavages for S. equi were included herein.
56 samples, 27 of which were culture positive, from ten persistent carriers were analyzed for S. equi by q-PCR (Båverud et al. 2007). All samples positive for the SeeI gene were cultured to obtain isolates of S. equi. Amplification of parts of the gene encoding the M-protein seM was performed either on isolated colony material, or, if no colonies could be isolated, directly on the DNA sample, with a nested amplification approach (Anzai et al. 2005). The seM sequence could be determined for six of the 29 samples solely qPCR positive. On comparison with the PubMLST seM database the outbreak was due seM type 72.
After three months isolates from two horses had seM gene sequences with one silent base change. After six months S. equi with truncated seM genes were found in two horses; one variant in a single horse once, and in the other horse a variant that persisted and later identified in two additional horses. Non-mucoid S. equi colonies were found in two horses after three months and thereafter, but were not correlated to the seM gene truncation.
This study shows that after acute strangles outbreaks many horses persistently PCR positive for S. equi are also intermittently culture positive. SeM sequencing can be performed directly on DNA extracts from clinical samples to identify spread of infection strain derivates despite absence of clinical signs of disease.