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Updated: Mar 31, 2026

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A multilocus sequence analysis scheme for characterization of Flavobacterium columnare isolates.

Roghaieh Ashrafi1, Katja Pulkkinen2, Lotta-Riina Sundberg3

  • 1Centre of Excellence in Biological Interactions, Department of Biological and Environmental Science, University of Jyvaskyla, P.O. Box 35, Jyväskylän yliopisto, FI-40014, Finland. roghaieh.ashrafi@jyu.fi.

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Columnaris disease, caused by Flavobacterium columnare, impacts aquaculture globally. This study reveals Finnish F. columnare strains exhibit an epidemic population structure with clonal expansion, improving understanding of columnaris disease epidemiology.

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Area of Science:

  • Aquatic microbiology
  • Fish disease epidemiology
  • Bacterial population genetics

Background:

  • Columnaris disease, caused by Flavobacterium columnare, poses a significant threat to global aquaculture.
  • The molecular epidemiology and population structure of F. columnare remain inadequately understood.

Purpose of the Study:

  • To investigate the population structure and genetic diversity of F. columnare in Finland.
  • To analyze spatiotemporal changes in F. columnare genetic diversity.
  • To establish a framework for F. columnare discrimination and phylogenetic analysis.

Main Methods:

  • Multilocus sequence typing (MLST) and analysis (MLSA) using six housekeeping genes.
  • Sequencing of approximately 3,509 nucleotides from 83 F. columnare strains collected between 2003 and 2012.
  • Phylogenetic analysis and assessment of genetic diversity and recombination.

Main Results:

  • Eight sequence types and moderate genetic diversity (H=0.460) were identified.
  • Phylogenetic analysis revealed two distinct lineages and five clusters.
  • Recombination played a more significant role in generating diversity than mutation, with evidence of clonality.

Conclusions:

  • Finnish F. columnare strains display an epidemic population structure with clonal expansion of successful genotypes.
  • The study provides a robust methodology for F. columnare isolate analysis.
  • Enhanced understanding of the geographic distribution and epidemiology of columnaris disease is facilitated.