title: Genetic fingerprinting of Flavobacterium columnare isolates from cultured fish.
abstract: OBJECTIVE
  To evaluate the intraspecific diversity of the fish pathogen Flavobacterium columnare.
  
  
  RESULTS
  Genetic variability among Fl. columnare isolates was characterized using restriction fragment length polymorphism analysis of the 16S rDNA gene, intergenic spacer region (ISR) sequencing, and amplified fragment length polymorphism (AFLP) fingerprinting. Thirty Fl. columnare cultures isolated from different fish species and geographical origins as well as reference strains were included in the study. Fifteen isolates belonged to genomovar I while eleven were ascribed to genomovar II. Analysis of the ISR sequence confirmed the genetic differences between both genomovars but revealed a higher diversity among genomovar I isolates. The maximum resolution was provided by AFLP fingerprinting, as up to 22 AFLP profiles could be defined within the species.
  
  
  CONCLUSIONS
  We confirmed the division of Fl. columnare isolates from cultured fish into different genogroups. We showed that both genomovars I and II are present in channel catfish from the US. We described a unique genetic group represented by four Fl. columnare isolates from tilapia in Brazil which appears to be related to both genomovars. We were able to further subdivide the species by analysing the ISR. Finally, the use of AFLP allowed us to fingerprint the species at clone level without losing the higher genetic hierarchy of genomovar division.
  
  
  CONCLUSIONS
  This paper reports on an extensive assessment of the use of molecular tools for the study of the epidemiology of the fish pathogen Fl. columnare.
authors.affiliation: Department of Fisheries and Allied Aquacultures, Auburn University, Auburn, AL 36849, USA. ariascr@acesag.auburn.edu
authors.forename: C R
authors.initials: CR
authors.lastname: Arias
authors.forename: T L
authors.initials: TL
authors.lastname: Welker
authors.forename: C A
authors.initials: CA
authors.lastname: Shoemaker
authors.forename: J W
authors.initials: JW
authors.lastname: Abernathy
authors.forename: P H
authors.initials: PH
authors.lastname: Klesius
mesh_terms: D000818:Animals; D002397:Catfishes / Q000382:microbiology; D023681:Cichlids / Q000382:microbiology; D016172:DNA Fingerprinting / Q000379:methods; D004269:DNA, Bacterial / Q000235:genetics; D021901:DNA, Intergenic / Q000235:genetics; D004275:DNA, Ribosomal / Q000235:genetics; D005399:Fishes / Q000382:microbiology*; D005417:Flavobacterium / Q000235:genetics* / Q000302:isolation & purification; D005838:Genotype; D010802:Phylogeny; D011110:Polymorphism, Genetic / Q000235:genetics*; D012150:Polymorphism, Restriction Fragment Length
chemical_list: D004269:DNA, Bacterial; D021901:DNA, Intergenic; D004275:DNA, Ribosomal