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

Abstract

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.

New Multilocus Variable-Number Tandem-Repeat Analysis (MLVA) Scheme for Fine-Scale Monitoring and Microevolution-Related Study of Ralstonia pseudosolanacearum Phylotype I Populations

“…It also illustrates that mutation dynamics of VNTR loci can be different depending on the loci and on the species studied (62,63). SMM is the predominant mutational model for some plant-pathogenic bacteria (24,27,64), but data remain scarce on the actual mutation model at play and the possible variations around this model within the Proteobacteria phylum.…”

“…citri [21][22][23]), evaluating the structure and evolution of pathogen populations (X. citri pv. citri [22] and Erwinia amylovora [24]), and global surveillance (Xanthomonas oryzae pv. oryzae and X. oryzae pv.…”

Origin of the Outbreak in France of Pseudomonas syringae pv. actinidiae Biovar 3, the Causal Agent of Bacterial Canker of Kiwifruit, Revealed by a Multilocus Variable-Number Tandem-Repeat Analysis

“…MLVA was used in an epidemiological survey to trace the routes of Haemophilus influenzae outbreaks (8) or Bacillus anthracis (2,9) outbreaks. MLVA was applied to monomorphic plant-pathogenic bacteria belonging to different genera and species such as Xylella fastidiosa (10), Xanthomonas citri (11), Ralstonia solanacearum (12), "Candidatus Liberibacter asiaticus" (13), Erwinia amylovora (14), and Xanthomonas arboricola pathovars (15). MLVA was first applied on Pseudomonas syringae by Gironde and Manceau (16) and provided new insights into host specificity of P. syringae pathogenic on brassicaceous and solanaceous plants.…”

A novel plasmid pEA68 of Erwinia amylovora and the description of a new family of plasmids

“…Plasmid peA29 had a variant in the small sequence repeat (Schnabel and Jones 1998) also called VnTr-A (Bühlmann et al 2014), which has been reported for peA29 in european strains of E. amylovora (Mann et al 2013;Smits et al 2010). The sequence of the second plasmid showed that it is a circular plasmid of 68,763 bp with a g+C content of 60.39 %, what can be an indication of its foreign origin, because the g+C content of the chromosome of E. amylovora is 53.60 % (Smits et al 2010).…”