title: Evaluation of phenotypic and molecular typing techniques for determining diversity in Erwinia carotovora subspp. atroseptica.
abstract: A number of phenotypic and molecular fingerprinting techniques, including physiological profiling (Biolog), restriction fragment length polymorphism (RFLP), enterobacterial repetitive intergenic consensus (ERIC) and a phage typing system, were evaluated for their ability to differentiate between 60 strains of Erwinia carotovora ssp. atroseptica (Eca) from eight west European countries. These techniques were compared with other fingerprinting techniques, random amplified polymorphic DNA (RAPD) and Ouchterlony double diffusion (ODD), previously used to type this pathogen. Where possible, data were represented as dendrograms and groups/subgroups of strains identified. Simpson's index of diversity (Simpson's D) was used to compare groupings obtained with the different techniques which, with the exception of Biolog, gave values of 0.46 (RFLP), 0. 39 (ERIC), 0.83 (phage typing), 0.82 (RAPD) and 0.26 (ODD). Of the techniques tested, phage typing showed the highest level of diversity within Eca, and this technique will now form the basis of studies into the epidemiology of blackleg disease.
authors.affiliation: Scottish Crop Research Institute, Invergowrie, Dundee, UK. itoth@scri.sari.ac.uk
authors.forename: I K
authors.initials: IK
authors.lastname: Toth
authors.forename: Y
authors.initials: Y
authors.lastname: Bertheau
authors.forename: L J
authors.initials: LJ
authors.lastname: Hyman
authors.forename: L
authors.initials: L
authors.lastname: Laplaze
authors.forename: M M
authors.initials: MM
authors.lastname: López
authors.forename: J
authors.initials: J
authors.lastname: McNicol
authors.forename: F
authors.initials: F
authors.lastname: Niepold
authors.forename: P
authors.initials: P
authors.lastname: Persson
authors.forename: G P
authors.initials: GP
authors.lastname: Salmond
authors.forename: A
authors.initials: A
authors.lastname: Sletten
authors.forename: J M
authors.initials: JM
authors.lastname: van Der Wolf
authors.forename: M C
authors.initials: MC
authors.lastname: Pérombelon
mesh_terms: D015373:Bacterial Typing Techniques; D001434:Bacteriophage Typing; D014644:Genetic Variation; D015336:Molecular Probe Techniques; D016973:Pectobacterium carotovorum / Q000145:classification* / Q000235:genetics; D010641:Phenotype; D010802:Phylogeny; D012150:Polymorphism, Restriction Fragment Length; D019105:Random Amplified Polymorphic DNA Technique; D012703:Serotyping