Genetic variability of Flavobacterium psychrophilum, a pathogen of salmonids, in France

Genetic variability of Flavobacterium psychrophilum, a pathogen of salmonids, in France: an underestimated genetic diversity.

In Flavobacterium psychrophilum isolated from rainbow trout in France, the level of genetic variability was much lower for clinical isolates than for isolates from asymptomatic carriers. Recombination is a major determinant of this diversity, and an epidemic-like population structure has been demonstrated. For this study, two methods of typing similar levels of discrimination were used (MLST and PFGE).

National and/or international background/ issues/ problems

The Flavobacterium psychrophilum bacterium is a major pathogen of salmonids in the world, causing significant mortalities and thus economic losses for farmers. The recurrence of clinical cases in farms, particularly in rainbow trout in France, raises the question of the spread and transmission of this agent. In order to answer this question, work has focused on the genetic variability of F. psychrophilum in France using a PFGE (Pulsed Field Gel Electrophoresis) and MLST (Multi Locus Sequence Typing)(1) approach. 


The study of the genetic variability of 66 rainbow trout isolates collected during the clinical phase of the disease highlighted the presence of 15 different type sequences (ST), 14 of which had never been described. The eBURST analysis of these isolates showed the existence of a unique clonal complex of 8 STs (STs 2, 89, 91, 92, 93, 95, 97 and 98) with a common ancestor, ST2. The 7 other STs described correspond to typical sequences outside the clonal complex. ST2 is also the most represented with 47% of the isolates corresponding to this typical sequence. Calculations of different indices relating to diversity analysis make it possible to highlight the role of recombination in the genetic variability observed and, above all, to define the population structure studied as epidemic-type (2). The presence of a majority ST, which corresponds to the common ancestor, on French territory seems to highlight the role of commercial exchanges in the diffusion of this agent in fish farms.

At a finer geographical scale (a watershed) and on isolates from asymptomatic carrier fish (spleen or gill isolates), PFGE analysis reveals a higher diversity, confirmed by MLST on a selection of isolates. This diversity can probably be explained by the presence of environmental isolates showing either moderate virulence, less adaptation to the trout host, or less competitiveness with other genetic types. The genetic diversity of F. psychrophilum at the production sites located in the study catchment area, which is greater downstream than upstream, seems to indicate diffusion through the hydraulic network, in addition to that due to trade.

Perspectives/eventual impact

A better understanding of the genetic variability and spread of the pathogen will allow better management of the disease by implementing appropriate control strategies.


INRA, Molecular Virology and Immunology UR892, F-78350 Jouy-en-Josas, France LD40, Laboratoire d'analyse, F-40000 Mont de Marsan, France

GDSAA, Groupe de Défense Sanitaire Aquacole Aquitain, F-40000 Mont de Marsan, France



Siekoula-Nguedia, C., Blanc, G., Duchaud, E., Calvez, S., 2012, Genetic diversity of Flavobacterium psychrophilum isolated from rainbow trout in France: Predominance of a clonal complex. Veterinary Microbiology, Available online 20 July 2012, ISSN 0378-1135, 10.1016/j.vetmic.2012.07.022.

Siekoula-Nguedia, C., 2012. Etude de la variabilité génétique de Flavobacterium psychrophilum, pathogène de salmonidés. Thèse de l'Université de Nantes.



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Modification date : 11 September 2023 | Publication date : 27 June 2017 | Redactor : AC