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Streptococcus zooepidemicus is a dominant pneumococcal pathogen in adult horses and comprises a wide diversity of strain genotypes. Minocycline has been used as a second-line drug for lower respiratory bacterial infection in the facilities of Japan Racing Association. The aim of this study was to reveal the relationship between genotypes of equine S. zooepidemicus and tetracycline resistance genes. Sixty-two strains of S. zooepidemicus were isolated from ill horses between 2000 and 2014, and 20 (32.3%) strains possessed one of tetracycline resistance genes, tet(M), tet(O), or tet(W). Nine of the 20 strains harboring the resistance genes were isolated in 2010–2014, of which eight had the tet(O). Interestingly, the presence of tet(O) was strongly correlated with high minimum inhibitory concentration of minocycline. Genetic diversities were widely observed in S. zooepidemicus by multilocus sequence typing, and the resistance genes were distributed across many genotypes. However, all five ST-62 strains had tet(O), and both of two ST-61 strains had tet(W), suggesting that certain genotypes are associated with particular resistance genes. These data could help us to understand the relationship between the genotypes and tetracycline resistance genes in equine S. zooepidemicus.Three tetracycline resistance genes, tet(M), tet(O), or tet(W), were detected in clinical Streptococcus zooepidemicus.The presence of tet(O) was strongly correlated with high minimum inhibitory concentration of minocycline, compared to those of tet(W).Certain genotypes (ST-62 and ST-61) might be associated with particular resistance genes.