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Research Project: Pathogen Characterization, Host Immune Response and Development of Strategies to Reduce Losses to Disease in Aquaculture

Location: Aquatic Animal Health Research

Title: Genomovars and genomes: Deciphering the genetic diversity of Flavobacterium columnare

item Lafrentz, Benjamin
item Garcia, Julio
item Waldbieser, Geoffrey - Geoff
item Evenhuis, Jason
item LOCH, THOMAS - Michigan State University
item LILES, MARK - Auburn University
item WONG, FONG - Merck Animal Health
item CHANG, SIOW - Merck Animal Health

Submitted to: American Fishery Society (Fish Health Section) Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: 3/20/2017
Publication Date: 3/30/2017
Citation: Lafrentz, B.R., Garcia, J.C., Waldbieser, G.C., Evenhuis, J., Loch, T.P., Liles, M.R., Wong, F.S., Chang, S.F. 2017. Genomovars and genomes: Deciphering the genetic diversity of Flavobacterium columnare. In: Annual Meeting of the Fish Health Section, American Fisheries Society, East Lansing, Michigan, April 2-3, 2017. p. 66.

Interpretive Summary:

Technical Abstract: Columnaris disease, caused by the Gram-negative bacterium Flavobacterium columnare, is one of the leading causes of disease losses to the catfish industry in the Southeast USA. An exceptionally high level of genetic diversity among isolates of F. columnare has long been recognized, yet very little has been done to quantify or characterize this diversity. The objective of this research was to define the genetic diversity by comparing the whole genome sequences of a collection of F. columnare isolates. Genomic DNA from thirteen isolates, representative of the five established genomovars of F. columnare, were sequenced using the Illumina HiSeq Platform. To determine phylogenetic relationships, housekeeping genes were analyzed by maximum likelihood and draft genome sequences were analyzed by Average Nucleotide Identity (ANI) to compare the genetic relatedness among isolates. Phylogenetic analysis of the 16S rRNA, gyrB, and nine concatenated housekeeping genes yielded four distinct clusters (genetic groups), one of which was comprised of a single isolate. There was an association between the three primary genetic groups and genomovar. Genetic groups 1, 2, and 3 were comprised of isolates assigned to genomovars I and I/II, genomovars II and II-B, and genomovar III, respectively. The cluster comprised of a single isolate (genetic group 4) was one in which genomovar assignment was not previously possible due to PCR failure. Sequences from additional isolates that were not previously typeable to genomovar were included into the 16S rRNA phylogenetic analysis and the results demonstrated that they all were included into the genetic group 4. The ANI values of isolates within a genetic group were > 99%, while comparison of genomes of isolates of different genetic groups were < 92%. The results from this research establish the existence of four phylogenetically distinct genetic groups within the species Flavobacterium columnare. Ongoing research is focused on identifying the genetic group(s) that are most prevalent the Southeast USA catfish industry. Understanding which genetic groups are most prevalent will allow for the development of better targeted control and treatment measures for columnaris disease.