Identification of Four Distinct Phylogenetic Groups in Flavobacterium columnare With Fish Host Associations

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 90 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.

Vertebrate mucus stimulates biofilm development and upregulates iron acquisition genes in Flavobacterium columnare

“…Among the genomovar I isolates, only 0901393 is highly virulent, while CDI‐A causes little to no disease (Declercq et al, ). More recent work has also sought to reclassify F. columnare isolates through genotypic analyses into four distinct categories (Lafrentz et al, ). We have thus far relied on the classically defined genomovar system (Kayansamruaj et al, ); however, we would be remiss if we did not point out that it is possible that our current classification of these isolates could differ under the new genetic grouping system.…”

Multiplex PCR for genotypingFlavobacterium columnare

“…Columnaris disease, caused by the Gram‐negative bacterium Flavobacterium columnare , is one of the leading causes of disease losses to many aquaculture industries worldwide. It has been suggested that the development of effective prevention and control measures may have been hampered by a lack of a complete understanding of the genetic diversity (LaFrentz et al, ). The genetic diversity of F. columnare was first realized over 30 years ago (Song, Fryer, & Rohovec, ), and since that time, different molecular techniques have been used to investigate diversity.…”

“…Recently, LaFrentz et al () performed a multilocus phylogenetic analysis of 50 F. columnare isolates and used the genotype determined by 16S‐RFLP (i.e. genomovar) as the basis for comparison of the derived phylogenies.…”

“…The results identified four distinct genetic groups and demonstrated that the 16S‐RFLP genotyping method does not completely reflect the diversity revealed by the analyses. Three of the four genetic groups contained isolates of different 16S‐RFLP genotypes, and the results also showed that the 16S‐RFLP genotyping method cannot differentiate between genetic groups 2 and 4 (LaFrentz et al, ). The authors suggested that isolates be assigned to the genetic groups identified in that study rather than to genomovar via 16S‐RFLP genotyping.…”

“…The authors suggested that isolates be assigned to the genetic groups identified in that study rather than to genomovar via 16S‐RFLP genotyping. However, the only way to assign an unknown isolate to genetic group is through sequencing of the 16S rRNA gene or other housekeeping genes (LaFrentz et al, ) and performing phylogenetic analyses with isolates of known genetic type. This can be time‐consuming, expensive, and not all laboratories can perform such analyses.…”