Phylogeography and population structure of the biologically invasive phytopathogen Erwinia amylovora inferred using minisatellites

• Published in: Environmental microbiology 2014-07, Vol.16 (7), p.2112-2125
• Main Authors: Bühlmann, Andreas, Dreo, Tanja, Rezzonico, Fabio, Pothier, Joël F, Smits, Theo H. M, Ravnikar, Maja, Frey, Jürg E, Duffy, Brion
• Format: Article
• Language: English
• Subjects: Animal, plant and microbial ecology; Applied ecology; bacteria; Bacterial Typing Techniques; Bacteriology; Bayes Theorem; Biological and medical sciences; Biological evolution; Conservation, protection and management of environment and wildlife; epidemiological studies; Epidemiology; Erwinia amylovora; Erwinia amylovora - classification; Erwinia amylovora - genetics; Erwinia amylovora - pathogenicity; Europe; fruit trees; Fundamental and applied biological sciences. Psychology; General aspects; Genetic Markers; Genetics of eukaryotes. Biological and molecular evolution; genome; Genome, Bacterial; genomics; Haplotypes; Microbial ecology; Microbiology; Middle East; Minisatellite Repeats; Miscellaneous; Molecular Epidemiology; Parks, reserves, wildlife conservation. Endangered species: population survey and restocking; Phylogeography; Plant Diseases - microbiology; plant diseases and disorders; plant pathogens; pome fruits; population structure; Punicaceae - microbiology; quarantine; United States; Virulence
• ISSN: 1462-2912; 1462-2920
• DOI: 10.1111/1462-2920.12289

Erwinia amylovora causes a major disease of pome fruit trees worldwide, and is regulated as a quarantine organism in many countries. While some diversity of isolates has been observed, molecular epidemiology of this bacterium is hindered by a lack of simple molecular typing techniques with sufficiently high resolution. We report a molecular typing system of E. amylovora based on variable number of tandem repeats (VNTR) analysis. Repeats in the E. amylovora genome were identified with comparative genomic tools, and VNTR markers were developed and validated. A Multiple‐Locus VNTR Analysis (MLVA) was applied to E. amylovora isolates from bacterial collections representing global and regional distribution of the pathogen. Based on six repeats, MLVA allowed the distinction of 227 haplotypes among a collection of 833 isolates of worldwide origin. Three geographically separated groups were recognized among global isolates using Bayesian clustering methods. Analysis of regional outbreaks confirmed presence of diverse haplotypes but also high representation of certain haplotypes during outbreaks. MLVA analysis is a practical method for epidemiological studies of E. amylovora, identifying previously unresolved population structure within outbreaks. Knowledge of such structure can increase our understanding on how plant diseases emerge and spread over a given geographical region.