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ARS Home » Southeast Area » Auburn, Alabama » Aquatic Animal Health Research » Research » Publications at this Location » Publication #420223

Research Project: Integrated Research to Improve Aquatic Animal Health in Warmwater Aquaculture

Location: Aquatic Animal Health Research

Title: Comparative genomic analysis of Flavobacterium species causing columnaris disease of freshwater fish in Thailand: insights into virulence and resistance mechanisms

Author
item NGUYEN, DUNG HO MY - Chulalongkorn University
item CHOKMANGMEEPISARN, PUTITA - Chulalongkorn University
item KHIANCHAIKHAN, KAMOLWAN - Chulalongkorn University
item MORISHITA, MANAMI - Chulalongkorn University
item UCHUWITTAYAKUL, ANURAK - Kasetsart University
item Lafrentz, Benjamin
item RODKHUM, CHANNARONG - Chulalongkorn University

Submitted to: BMC Veterinary Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/9/2025
Publication Date: N/A
Citation: N/A

Interpretive Summary: A comprehensive genomic analysis of F. oreochromis, F. covae, and F. davisii, the causative agents of columnaris disease in freshwater fish in Thailand, was undertaken, marking the first report to highlight significant genetic variability in virulence, antimicrobial resistance, genomic islands, prophages, insertion elements, and CRISPR systems among these species. These findings underscored the genetic diversity, pathogenicity, survival mechanisms, and adaptive strategies exhibited by these species in response to environmental pressures. Understanding these variations may contribute to the development of effective control strategies for the impact of these pathogens on aquaculture, aquatic ecosystems and human health risks.

Technical Abstract: Columnaris disease, a prevalent disease among freshwater fish, is primarily caused by F. oreochromis, F. covae, and F. davisii 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 (CRISPR). A collective of 212 putative virulence genes were predicted across three species. Flavobacterium oreochromis showed the highest number of unique virulence genes, followed by F. davisii, and F. covae. Moreover, 195 genes were predicted as antibiotic resistance genes, with F. oreochromis and F. covae showing an abundance of unique genes associated with resistance to quinolone, fluoroquinolone, and tetracycline antibiotics. MIC testing revealed resistance to quinolone, fluoroquinolones and tetracycline in several isolates of F. oreochromis, F. covae, marking the first report of resistance in these species. A tetracycline resistance gene (tetA_2) was found in only one F. covae isolate and exhibited phenotypic resistance to this drug. Moreover, F. oreochromis and F. covae exhibited notable resistance to quinolones, with mutations observed in the resistance-determining regions (QRDRs) of gyrA, including Ser83Phe, Val, Ala, and Asp87Tyr, the latter representing a novel mutation point 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 quinolone-resistant (QR) phenotype.