Long term dynamics of a Streptococcus equi ssp equi outbreak, assessed by qPCR and culture and seM sequencing in silent carriers of strangles.

The aim of the study was to use culture, qPCR and seM sequencing to map Streptococcus equi subspec. equi (S.equi) isolates in long term carrier animals. A strangles outbreak affecting 41 Icelandic horses was followed to determine strangles free status using nasal and/or guttural pouch lavages collected serially on eleven separate occasions over 13 months. Ten persistent carriers, of which eight had repeated culture positive samples for S. equi, were selected for the study. Of 115 samples collected, 61 were S. equi positive on qPCR; from which 32 were also culture positive. Amplification of parts of the gene encoding the M-protein seM was performed on isolated colony material (n = 32) or, where only PCR product was obtained, directly on the DNA sample (n = 29) with a nested amplification approach. The seM sequence could be determined for six of the 29 samples that were solely qPCR positive. The outbreak was due to a S. equi strain of seM type 72. Three months after initial sampling isolates from two horses had seM gene sequences with one amino acid 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 that was later identified in two additional horses. Non- mucoid S. equi colonies were found in two horses. Importantly, after acute strangles outbreaks many horses not only remain persistently qPCR positive for S. equi but are also intermittently culture positive.