Molecular typing of isolates of the fish pathogen, Flavobacterium columnare, by single-strand conformation polymorphism analysis

FEMS Microbiol Lett. 2007 Apr;269(1):63-9. doi: 10.1111/j.1574-6968.2006.00605.x. Epub 2007 Jan 11.

Abstract

Flavobacterium columnare intraspecies diversity was revealed by analyzing the 16S rRNA gene and the 16S-23S internal spacer region (ISR). Standard restriction fragment length polymorphism (RFLP) of these sequences was compared with single-strand conformation polymorphism (SSCP). Diversity indexes showed that both 16S-SSCP and ISR-SSCP improved resolution (D>or=0.9) when compared with standard RFLP. ISR-SSCP offered a simpler banding pattern than 16S-SSCP while providing high discrimination between isolates. SSCP analysis of rRNA genes proved to be a simple, rapid, and cost-effective method for routine fingerprinting of F. columnare.

Publication types

  • Comparative Study
  • Evaluation Study
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Animals
  • Bacterial Typing Techniques*
  • DNA, Ribosomal Spacer / chemistry
  • DNA, Ribosomal Spacer / classification
  • Fishes / microbiology*
  • Flavobacterium / classification*
  • Flavobacterium / genetics
  • Flavobacterium / isolation & purification
  • Phylogeny
  • Polymorphism, Restriction Fragment Length
  • Polymorphism, Single-Stranded Conformational*
  • RNA, Ribosomal, 16S / chemistry
  • RNA, Ribosomal, 16S / classification
  • Sequence Analysis, DNA

Substances

  • DNA, Ribosomal Spacer
  • RNA, Ribosomal, 16S