Insight into the genetic diversity and population structure of Flavobacterium psychrophilum in France Charlene Y.J. Siekoula-Nguedia 1, 2, 3 , Guillaume Blanc 2 , Eric Duchaud 4 & Segolene Calvez 1, 2, 3 1 INRA, UMR 1300 Biologie, Epidémiologie et Analyse de Risque, F-44307 Nantes, France 2 Oniris, Ecole Nationale Vétérinaire, Agroalimentaire et de l’Alimentation, UMR 1300 Biologie, Epidémiologie et Analyse de Risque, F-44307 Nantes, France 3 L’UNAM (Université Nantes, Angers, Le Mans), Nantes, F-44200 France 4 INRA, Virologie et Immunologie Moléculaires UR892, F-78350 Jouy-en-Josas, France Correspondence: segolene.calvez@oniris-nantes.fr Abstract Flavobacterium psychrophilum is the causative agent of bacterial cold water disease and rainbow trout fry syndrome in salmonid farming worldwide. These diseases are among the main hazards for French aquaculture [1]. In this study, a multilocus sequence typing (MLST) approach described previously [2] was used to evaluate the genetic diversity of this bacterium, and gain insight into its population structure. MLST analysis concerned a set of 66 isolates, recently collected from rainbow trout during clinical episodes in French farms located in the main geographical areas of production. Sequences of 7 housekeeping genes (trpB, gyrB, dnaK, tuf, fumC, murG and atpA) were investigated and a total of 5808 bp of the sequence were analyzed for each isolate. The analysis showed 81 SNPs (1.4% of total length) and low levels of both gene (H = 0.4313) and nucleotide diversity (π x 100 = 0.31 %). MLST identified numerous allele types (ATs) for each locus and sequence types (STs) resulting from the combination of these ATs (Tab. 1). A total of 15 STs were retrieved, 14 of which have never been described. eBURST analysis was used to infer evolutionary pattern between STs and to discriminate the 15 STs in one clonal complex of 4 genetically related STs and 11 singletons, as presented in Fig. 1. ST2 and the clonal complex (as ST2 is its primary founder) were previously described [2]. Phenomena responsible for genetic diversity have been sought and we found that the diversity was largely due to recombination, as demonstrated by a pairwise homoplasy index (PHI) significantly different from zero (p<0.05). Standardized association index (I A S ) that investigates the random association of genes in a population was also used to infer recombination among the F. psychrophilum isolates. For the entire sample, I A S was 0.6088 (p<0.05) and for the set of one single representative of each ST, I A S was 0.4761. Those two values showed statistically significant linkage disequilibrium (p<0.05), indicating a possible clonal structure of the population. When we divided all STs in clusters of closely related ones for a phylogenetic analysis [3], the linkage disequilibrium disappeared, indicating an epidemic type of the population structure.