Genetic characterization of Flavobacterium columnare isolates from the Pacific Northwest, USA

Authors: ALEXANDRE SEBASTIAL, FERNANDA - University Of California, Davis; SHAHIN, KHALID - University Of California, Davis; Lafrentz, Benjamin; GRIFFIN, MATT - Mississippi State University; LOCH, THOMAS - Michigan State University; MUKKATIRA, KAVERAMMA - California Department Of Fish & Game; VEEK, TRESA - California Department Of Fish & Game; RICHEY, CHRISTINE - California Department Of Fish & Game; ADKISON, MARK - California Department Of Fish & Game; HOLT, RICHARD - Oregon State University; SOTO, ESTEBAN - University Of California, Davis

Submitted to: Diseases of Aquatic Organisms
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/16/2021
Publication Date: 5/6/2021
Citation: Alexandre Sebastial, F., Shahin, K., Lafrentz, B.R., Griffin, M.J., Loch, T.P., Mukkatira, K., Veek, T., Richey, C., Adkison, M., Holt, R.A., Soto, E. 2021. Genetic characterization of Flavobacterium columnare isolates from the Pacific Northwest, USA. Diseases of Aquatic Organisms. 144: 151-158. https://doi.org/10.3354/dao03588.
DOI: https://doi.org/10.3354/dao03588

Interpretive Summary: Columnaris disease is caused by the bacterium Flavobacterium columnare, which has substantial impacts on almost all fin fish aquaculture industries in the United States including catfish, rainbow trout, tilapia, sport fish, baitfish, and ornamental fish. Recent research has established the existence of four distinct genetic groups within the species F. columnare; however, very little is known about which genetic group(s) impact aquaculture in the US Pacific Northwest. In this research, 49 isolates of F. columnare that were recovered from infected fish in US Pacific Northwest were characterized using different molecular methods. Most isolates (83.7%) were assigned to genetic group 1 and these were comprised primarily of isolates from salmonid species. Six salmonid isolates (12.2%) were assigned to genetic group 3, and two isolates from ornamental fish were assigned to genetic group 2. This research demonstrates that genetic group 1 isolates are overly represented in salmonid aquaculture in the Pacific Northwest, which is consistent with this genetic group being predominantly associated with columnaris disease in salmonid fish. Of interest was the finding of genetic group 3 isolates in salmonids, which has only been reported once and suggests this genetic group may be more widespread and problematic in salmonid aquaculture than previously thought. In summary, the research demonstrates that although multiple genetic groups of F. columnare are found in the US Pacific Northwest, genetic group 1 is predominant and particularly prevalent among disease outbreaks in salmonid facilities. This work provides important baseline data for future research identifying management practices and strategies to control F. columnare infections in fish facilities in the US Pacific Northwest.

Technical Abstract: Flavobacterium columnare is the causative agent of columnaris disease. Previous work has demonstrated a high degree of genetic variability among F. columnare isolates, identifying four genetic groups (GGs), with some host associations. Herein, a total of 49 F. columnare isolates were characterized, the majority of which were collected from 15 different locations throughout the United States Pacific Northwest. Most isolates were collected from 2015-2018 and originated from disease outbreaks in salmonid hatcheries and rearing ponds, sturgeon hatcheries and ornamental fish. Other isolates were part of collections recovered from 1995-2018. Initial identification was confirmed by F. columnare species-specific qPCR. Study isolates were further characterized using a multiplex PCR that differentiates between the four currently recognized F. columnare GGs. Multiplex PCR results were supported by repetitive sequence mediated PCR fingerprinting and gyrB sequence analysis. Flavobacterium columnare GG1 was the most prevalent (83.7%, n=41/49), represented by isolates from salmonids (n=32), white sturgeon (n=2), channel catfish (n=1), ornamental goldfish (n=1), Koi (n=3) and two unknown hosts. Six/49 isolates (12.2%) were identified as GG3, which were cultured from rainbow (n=3) and steelhead trout (n=3). Two/49 isolates were identified as GG2 (4.1%) and were from ornamental fish. The biological significance of this genetic variability remains unclear, but it is thought this variation will have significant implications in fish health management. The results from this study provide baseline data for future work developing strategies to ameliorate columnaris related losses.