Identification of four distinct phylogenetic groups in Flavobacterium columnare with fish host associations

Authors: Lafrentz, Benjamin; Garcia, Julio; Waldbieser, Geoffrey - Geoff; Evenhuis, Jason; LOCH, THOMAS - Michigan State University; LILES, MARK - Auburn University; WONG, FONG - Merck Research Laboratories; CHANG, SIOW - Merck Research Laboratories

Submitted to: Frontiers in Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/27/2018
Publication Date: 3/13/2018
Citation: Lafrentz, B.R., Garcia, J.C., Waldbieser, G.C., Evenhuis, J., Loch, T.P., Liles, M.R., Wong, F.S., Chang, S.F. 2018. Identification of four distinct phylogenetic groups in Flavobacterium columnare with fish host associations. Frontiers in Microbiology. 9:452. https://doi.org/10.3389/fmicb.2018.00452.
DOI: https://doi.org/10.3389/fmicb.2018.00452

Interpretive Summary: Columnaris disease is caused by the bacterium Flavobacterium columnare, which is very well known by most aquaculture producers. This disease 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. A 2015 survey of the Alabama catfish industry alone indicated that approximately 1.5 million pounds of fish were lost due to this disease and the incidence in the rainbow trout industry is on the rise. While there has been some success in controlling and preventing columnaris using antibiotics, chemicals, and vaccines, losses in aquaculture operations due to this disease remain substantial. Previous research has shown that there is a large degree of genetic diversity among F. columnare strains recovered from columnaris disease cases. However, little has been done to quantify or characterize this diversity in a systematic fashion. Using high resolution genetic methods, this research analyzed numerous strains of F. columnare collected from disease cases from geographically distant regions, different fish species, and different years. The research established the existence of four distinct genetic groups within the species F. columnare. Additionally, the research indicated biological relevance to the identified genetic diversity, with some genetic groups isolated preferentially from columnaris disease cases in specific fish species. This research has shown that there are four key bacterial players in columnaris disease and it is important to understand which of these players are predominant in each aquaculture industry impacted by this disease. An increased understanding of which genetic groups are most prevalent in different regions and/or aquaculture industries will allow for the development of improved targeted control and treatment measures for columnaris disease.

Technical Abstract: Columnaris disease, caused by the Gram-negative bacterium Flavobacterium columnare, is one of the most prevalent fish diseases worldwide. An exceptionally high level of genetic diversity among isolates of F. columnare has long been recognized, whereby six established genomovars have been described to date. However, little has been done to quantify or characterize this diversity further in a systematic fashion. The objective of this research was to perform phylogenetic analyses of 16S rRNA and housekeeping gene sequences to decipher the genetic diversity of F. columnare. Fifty isolates and/or genomes of F. columnare, originating from diverse years, geographic locations, fish hosts, and representative of the six genomovars were analyzed in this study. A multilocus phylogenetic analysis (MLPA) of the 16S rRNA and six housekeeping genes supported four distinct F. columnare genetic groups. There were associations between genomovar and genetic group, but these relationships were imperfect indicating that genomovar assignment does not accurately reflect F. columnare genetic diversity. To expand the dataset, an additional ninety 16S rRNA gene sequences were retrieved from GenBank and a phylogenetic analysis of this larger dataset also supported the establishment of four genetic groups. Examination of isolate historical data indicated biological relevance to the identified genetic diversity, with some genetic groups isolated preferentially from specific fish species or families. It is proposed that F. columnare isolates be assigned to the four genetic groups defined in this study rather than genomovar in order to facilitate a standard nomenclature across the scientific community. An increased understanding of which genetic groups are most prevalent in different regions and/or aquaculture industries may allow for the development of improved targeted control and treatment measures for columnaris disease.