Discrimination of Klebsiella pneumoniae and Klebsiella oxytoca phylogenetic groups and other Klebsiella species by use of amplified fragment length polymorphism

Res Microbiol. Jan-Feb 2004;155(1):17-23. doi: 10.1016/j.resmic.2003.09.011.


Bacteria of the genus Klebsiella are opportunistic pathogens responsible for an increasing number of multiresistant infections in hospitals. The two clinically and epidemiologically most important species, Klebsiella pneumoniae and K. oxytoca, have recently been shown to be subdivided into three and two phylogenetic groups, respectively. The aim of this study was an in depth evaluation of the amplified fragment length polymorphism (AFLP) genetic characterization method for epidemiological and phylogenic analyzes of Klebsiella isolates. First, we investigated the variability of AFLP patterns for Klebsiella strains within and between different outbreaks. Second, by use of carefully characterized phylogenetically representative strains, we examined whether different Klebsiella species and phylogenetic groups can be discriminated using AFLP. Twenty-four strains originating from seven presumed outbreaks and 31 non-associated strains were investigated. The AFLP fingerprints of all epidemiologically associated strains showed three or fewer fragment differences, whereas unrelated strains differed by at least four fragments. Cluster analysis of the AFLP data revealed a very high concordance with the phylogenetic assignation of strains based on the gyrA sequence and ribotyping data. The species K. pneumoniae, K. oxytoca, K. terrigena and the possibly synonymous pair K. planticola/K. ornithinolytica each formed a separate cluster. Similarly, strains of the phylogenetic groups of K. pneumoniae and K. oxytoca fell into their corresponding clusters, with only two exceptions. This study provides a preliminary cut-off value for distinguishing epidemiologically non-related Klebsiella isolates based on AFLP data; it confirms the sharp delineation of the recently identified phylogenetic groups, and demonstrates that AFLP is suitable for identification of Klebsiella species and phylogenetic groups.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Proteins / genetics
  • Bacterial Typing Techniques / methods
  • Classification / methods*
  • Cluster Analysis
  • Cross Infection / epidemiology
  • Cross Infection / microbiology
  • DNA Fingerprinting / methods
  • DNA Gyrase / genetics
  • DNA, Bacterial / analysis
  • DNA, Bacterial / chemistry
  • DNA, Bacterial / isolation & purification
  • DNA, Ribosomal / analysis
  • DNA, Ribosomal / isolation & purification
  • Humans
  • Klebsiella / classification*
  • Klebsiella / genetics*
  • Klebsiella Infections / epidemiology
  • Klebsiella Infections / microbiology
  • Klebsiella oxytoca / classification
  • Klebsiella oxytoca / genetics
  • Klebsiella pneumoniae / classification
  • Klebsiella pneumoniae / genetics
  • Molecular Epidemiology / methods
  • Nucleic Acid Amplification Techniques / methods*
  • Phylogeny
  • Polymorphism, Restriction Fragment Length*
  • Ribotyping
  • Sequence Analysis, DNA


  • Bacterial Proteins
  • DNA, Bacterial
  • DNA, Ribosomal
  • DNA Gyrase