Nguyen Dung Ho My, Chokmangmeepisarn Putita, Khianchaikhan Kamolwan, Morishita Manami, Uchuwittayakul Anurak, LaFrentz Benjamin R, Rodkhum Channarong
Center of Excellence in Fish Infectious Diseases (CE FID), Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand.
Laboratory of Aquatic Animal Health Management, Department of Aquaculture, Faculty of Fisheries, Kasetsart University, Bangkok, 10900, Thailand.
BMC Vet Res. 2025 May 19;21(1):357. doi: 10.1186/s12917-025-04488-3.
Columnaris disease, a prevalent disease among farmed and wild freshwater fish, is caused by the Flavobacterium columnare group, which includes four distinct species: F. columnare, F. oreochromis, F. covae, and F. davisii. Among these, F. oreochromis, F. covae, and F. davisii are particularly prevalent in farmed freshwater fish in Thailand. In this study, a comparative genomic analysis of 22 isolates was conducted to elucidate virulence factors, antibiotic resistance genes (ARGs), genomic islands (GIs), phages, insertion elements (ISs), and clustered regularly interspaced short palindromic repeats (CRISPRs).
A total of 212 putative virulence genes were predicted across three species with F. oreochromis exhibiting the highest number of unique virulence genes, followed by F. davisii, and F. covae. Moreover, 195 genes were predicted as ARGs, with F. oreochromis and F. covae showing an abundance of unique genes associated with resistance to quinolone, fluoroquinolone, and tetracycline antibiotics. Antimicrobial susceptibility testing, assessed with epidemiological cut-off values (ECVs), revealed decreased susceptibility to quinolones, fluoroquinolones and tetracycline in several isolates of F. oreochromis and F. covae. F. oreochromis and F. covae exhibited notable decreased susceptibility to quinolones, with mutations observed in the quinolone resistance-determining regions (QRDRs) of gyrA, including Ser83Phe, Ser83Val, Ser83Ala, and Asp87Tyr, the latter representing a novel mutation among isolates from Thailand. As a result, these findings suggest that gyrA is major target for quinolone in F. oreochromis, F. covae, and F. davisii, while gyrB, parC, parE might be less important to the decreased phenotypic susceptibility to this class of antimicrobials. Moreover, a tetracycline resistance gene (tetA_2) was found in only one F. covae isolate, which exhibited decreased phenotypic susceptibility to this drug, marking the first report of decreased susceptibility in this species.
This study provides insights into the genetic and pathogenic diversity of Flavobacterium species, aiding in the development of strategies to manage columnaris disease in farmed freshwater fish in Thailand.
柱状病是养殖和野生淡水鱼中一种常见疾病，由柱状黄杆菌属引起，该属包括四个不同物种：柱状黄杆菌、奥氏黄杆菌、科氏黄杆菌和戴维斯黄杆菌。其中，奥氏黄杆菌、科氏黄杆菌和戴维斯黄杆菌在泰国养殖淡水鱼中尤为普遍。在本研究中，对22株分离株进行了比较基因组分析，以阐明毒力因子、抗生素抗性基因（ARG）、基因组岛（GI）、噬菌体、插入元件（IS）和规律成簇间隔短回文重复序列（CRISPR）。
在三个物种中总共预测到212个假定的毒力基因，其中奥氏黄杆菌的独特毒力基因数量最多，其次是戴维斯黄杆菌和科氏黄杆菌。此外，预测到195个基因是抗生素抗性基因，奥氏黄杆菌和科氏黄杆菌显示出大量与喹诺酮、氟喹诺酮和四环素类抗生素抗性相关独特基因。用流行病学临界值（ECV）评估的抗菌药物敏感性测试表明，奥氏黄杆菌和科氏黄杆菌的几个分离株对喹诺酮、氟喹诺酮和四环素的敏感性降低。奥氏黄杆菌和科氏黄杆菌对喹诺酮的敏感性显著降低，在gyrA的喹诺酮抗性决定区（QRDR）观察到突变，包括Ser83Phe、Ser83Val、Ser83Ala和Asp87Tyr，后者是泰国分离株中的一种新突变。因此，这些发现表明，gyrA是奥氏黄杆菌、科氏黄杆菌和戴维斯黄杆菌中喹诺酮的主要靶点，而gyrB、parC、parE对这类抗菌药物表型敏感性降低可能不太重要。此外，仅在一个科氏黄杆菌分离株中发现一个四环素抗性基因（tetA_2），该分离株对该药物的表型敏感性降低，这是该物种敏感性降低的首次报道。
本研究为黄杆菌属的遗传和致病多样性提供了见解，有助于制定泰国养殖淡水鱼柱状病的管理策略。
