Pulsed-field gel electrophoresis and multi locus sequence typing for characterizing genotype variability of Yersinia ruckeri isolated from farmed fish in France.

Ségolène Calvez,Catherine Fournel,Diane-Gaëlle Douet,Patrick Daniel

doi:10.1186/s13567-015-0200-5

Ségolène Calvez, Catherine Fournel + Show 2 more

Open Access

https://doi.org/10.1186/s13567-015-0200-5

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Abstract

Yersinia ruckeri is a pathogen that has an impact on aquaculture worldwide. The disease caused by this bacterial species, yersiniosis or redmouth disease, generates substantial economic losses due to the associated mortality and veterinary costs. For predicting outbreaks and improving control strategies, it is important to characterize the population structure of the bacteria. The phenotypic and genetic homogeneities described previously indicate a clonal population structure as observed in other fish bacteria. In this study, the pulsed-field gel electrophoresis (PFGE) and multi locus sequence typing (MLST) methods were used to describe a population of isolates from outbreaks on French fish farms. For the PFGE analysis, two enzymes (NotI and AscI) were used separately and together. Results from combining the enzymes showed the great homogeneity of the outbreak population with a similarity > 80.0% but a high variability within the cluster (cut-off value = 80.0%) with a total of 43 pulsotypes described and an index of diversity = 0.93. The dominant pulsotypes described with NotI (PtN4 and PtN7) have already been described in other European countries (Finland, Germany, Denmark, Spain and Italy). The MLST approach showed two dominant sequence types (ST31 and ST36), an epidemic structure of the French Y. ruckeri population and a preferentially clonal evolution for rainbow trout isolates. Our results point to multiple types of selection pressure on the Y. ruckeri population attributable to geographical origin, ecological niche specialization and movements of farmed fish.

Highlights

A range of bacterial species affect aquaculture worldwide and are responsible for important economic losses as well as a substantial use of antibiotics on fish farms
Pulsed field gel electrophoresis pulsed-field gel electrophoresis (PFGE) was performed on all 127 clinical isolates and the eight reference strains
It was considered appropriate to interpret the PFGE patterns observed for each restriction enzyme using the Tenover criteria for genetic analysis, more than ten bands having been obtained for the restriction profiles [25] (Figures 1, 2 and 3)

Summary

Introduction

A range of bacterial species affect aquaculture worldwide and are responsible for important economic losses as well as a substantial use of antibiotics on fish farms. Since 1956, with the first isolation and identification of Y. ruckeri on a rainbow trout farm in the USA [2,3], the bacterial species has been isolated in many parts of the world: North and South America, Europe [4], Australia [5], and South Africa [6]. Y. ruckeri is a member of the Enterobacteriaceae family and is easy to identify by culture-based methods or molecular techniques such as PCR [7]. This pathogen was well described with a classification based on the O-antigens (heat-stable antigens) dividing the Y. ruckeri species into five (O1, O2, O5, O6 and O7) [8] or four (O1, O2, O3 and O4) [9] serogroups. To improve our understanding of the dissemination and evolution of this species, it is necessary to analyze the population structure and evaluate its phenotypic and genetic variability

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