title: Accurate identification of fastidious Gram-negative rods: integration of both conventional phenotypic methods and 16S rRNA gene analysis.
abstract: BACKGROUND
  Accurate identification of fastidious Gram-negative rods (GNR) by conventional phenotypic characteristics is a challenge for diagnostic microbiology. The aim of this study was to evaluate the use of molecular methods, e.g., 16S rRNA gene sequence analysis for identification of fastidious GNR in the clinical microbiology laboratory.
  
  
  RESULTS
  A total of 158 clinical isolates covering 20 genera and 50 species isolated from 1993 to 2010 were analyzed by comparing biochemical and 16S rRNA gene sequence analysis based identification. 16S rRNA gene homology analysis identified 148/158 (94%) of the isolates to species level, 9/158 (5%) to genus and 1/158 (1%) to family level. Compared to 16S rRNA gene sequencing as reference method, phenotypic identification correctly identified 64/158 (40%) isolates to species level, mainly Aggregatibacter aphrophilus, Cardiobacterium hominis, Eikenella corrodens, Pasteurella multocida, and 21/158 (13%) isolates correctly to genus level, notably Capnocytophaga sp.; 73/158 (47%) of the isolates were not identified or misidentified.
  
  
  CONCLUSIONS
  We herein propose an efficient strategy for accurate identification of fastidious GNR in the clinical microbiology laboratory by integrating both conventional phenotypic methods and 16S rRNA gene sequence analysis. We conclude that 16S rRNA gene sequencing is an effective means for identification of fastidious GNR, which are not readily identified by conventional phenotypic methods.
authors.affiliation: Institute of Medical Microbiology, University of Zurich, 8006 Zurich, Switzerland.
authors.forename: Maria G
authors.initials: MG
authors.lastname: de Melo Oliveira
authors.forename: Susanne
authors.initials: S
authors.lastname: Abels
authors.forename: Reinhard
authors.initials: R
authors.lastname: Zbinden
authors.forename: Guido V
authors.initials: GV
authors.lastname: Bloemberg
authors.forename: Andrea
authors.initials: A
authors.lastname: Zbinden
mesh_terms: D001431:Bacteriological Techniques / Q000379:methods*; D006090:Gram-Negative Bacteria / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification* / Q000502:physiology; D006801:Humans; D025202:Molecular Diagnostic Techniques / Q000379:methods*; D008969:Molecular Sequence Data; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA
chemical_list: D012336:RNA, Ribosomal, 16S