Comparison of nasopharyngeal and guttural pouch specimens to determine the optimal sampling site to detect Streptococcus equi subsp equi carriers by DNA amplification

Background: Streptococcus equi subsp equi (S. equi) is the cause of '' equine strangles '' which is a highly infectious upper respiratory disease. Detection of S. equi is influenced by site of specimen collection, method of sampling, and type of diagnostic test that is performed. We hypothesized i) that a loop-mediated isothermal amplification (LAMP) assay that targets the S. equi-specific eqbE gene would be more sensitive than a realtime PCR assay that targets the S. equi-specific seeI gene and ii) that LAMP of specimens obtained by guttural pouch lavage (GPL) would be more sensitive than LAMP of nasopharyngeal specimens to identify S. equi carriers. Methods: A nasopharyngeal flocked swab, nasopharyngeal wash, and GPL specimen was collected from 44 convalescent horses and the eqbE LAMP assay was performed. The seeI realtime PCR assay and aerobic culture were also performed on the GPL specimen. Logistic regression was performed to compare sampling sites and test methods (P-values <= 0.05 were considered significant). Results: One of 41 nasopharyngeal flocked swabs, 6/38 nasopharyngeal wash and 24/44 GPL specimens were positive by eqbE LAMP. 18/44 GPL specimens were positive by seeI PCR and S. equi was isolated from 4/44 of these specimens. Detection of S. equi DNA was 51 times more likely from the GPL samples than nasopharyngeal samples (OR 51.0, P < 0. 0001). When eqbE LAMP GPL samples were positive, it was eight times more likely that the guttural pouch had any abnormality on endoscopy (OR 8.2, P <= 0.005), almost 20 times more likely that mild empyema was found (OR 19.7, P <= 0.002), and eight times more likely that the SeeI PCR was positive for S. equi DNA (OR 8.1, P <= 0.006). Conclusion: This study demonstrates that guttural pouch lavage specimens should be used to detect S. equi and that the eqbE LAMP assay was comparable to the seeI PCR.