In this study, we compared 142 Yersinia ruckeri isolates collected between 2013 and 2016 from 6 different regions in Turkey. A total of 18 different genogroups were found, though most of the isolates clustered into the same genogroup as serotype O1. As immunization of fish with inactivated Y. ruckeri by injection, immersion, or feeding provide minimal protection against Y. ruckeri infection in Turkey, many fish producers use antimicrobials unrestrictedly, resulting in antimicrobial resistance in aquatic pathogens. Accordingly, we investigated resistance to the antimicrobials most commonly used to treat yersiniosis. More than 80% of the Y. ruckeri isolates were susceptible to sulfamethoxazole-trimethoprim (SXT), florfenicol (FFC), and tetracycline, whereas none were susceptible to sulfamethoxazole. The most commonly used antimicrobials (SXT and FFC) can be effectively administered because the resistance levels to these drugs are the lowest among those reported for agents used to control enteric red mouth disease (12.6 and 14.7%, respectively). In conclusion, to the best of our knowledge, this study is the first characterization of the antimicrobial resistance genes floR, sulI, tetC, tetD, and tetE in Y. ruckeri isolates from aquaculture. Additionally, we detected the sulII gene but not the tetA, tetB, tetM, tetS, or sulIII genes.

Plesiomonas shigelloides is the only species in its genus and has zoonotic importance due to the serious implications resulting from the consumption of contaminated seafood. This is the first report on the genomic features of the whole-genome sequence (WGS) of P. shigelloides strain V78, recovered from diseased rainbow trout, Oncorhynchus mykiss. The genome of P. shigelloides V78 consists of 4,478,098 base pairs (bps), which encode 3730 proteins, and has a G + C content of 51.1%. The bioinformatics analysis of WGS of V78 confirmed the presence of 121 tRNA genes and 42 rRNA genes (15 genes for 5S rRNA, 13 genes for 16S rRNA, and 14 genes for 23S rRNA). Comprehensive genome analyses revealed that the strain encodes secondary metabolites, antimicrobial resistance, and virulence genes. The strain V78 has 31 known antibiotic resistance models, which encode many antimicrobial resistances. In addition, strain V78 has 42 different virulence genes, such as adhesion, a secretion system, and motility. The digital DNA–DNA hybridization value against P. shigelloides NCTC 10360 was 74.2%, while the average nucleotide identity value was 97.1%. Based on the scrutinized analysis of genomic data, strain V78 should be considered a novel subspecies of P. shigelloides, for which Plesiomonas shigelloides subsp. oncorhynchi is proposed, with V78^T as the type strain (=LMG 33380^T=DSM 117059^T).