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Different methods were evaluated to extract DNA from pooled nematodes belonging to Anisakis, Contracaecum, Pseudoterranova and Hysterothylacium genera isolated from edible fish. Pooled DNA extraction is the first and compulsory step to allow the identification of a large number of samples through high-throughput DNA sequencing with drastic time and cost reductions.

Polyphasic analysis of four new Vibrio isolates originating from the haemolymph of diseased cultured oysters is described. The new isolates were closely related to Vibrio splendidus, having 98 % 16S rRNA gene sequence similarity. Phylogenetic analysis based on DNA gyrase subunit B (gyrB), RNA polymerase Quo factor (rpoD), replication origin-binding protein (rctB) and transmembrane regulatory protein (toxR) genes, fluorescent amplified fragment length polymorphism and DNA-DNA hybridization experiments clearly showed that the new isolates form a tight genomic group that is different from the currently known Vibrio species. It is proposed that these new isolates should be accommodated in a novel species, Vibrio gigantis sp. nov. Phenotypic features that differentiate V. gigantis from other known Vibrio species include arginine dihydrolase, gelatinase and beta-galactosidase activities, NO2 production, growth at 35 degrees C, and utilization of sucrose, melibiose, amygdalin, glycerol, galactose, starch and glycogen. The type strain is LGP 13(T) (=LMG 22741(T)=CIP 108656(T)).

For several years, strains phenotypically related to Vibrio splendidus have been associated with mortality outbreaks of molluscs. A former study on Crassostrea gigas demonstrated the genetic diversity of V splendidus strains associated with diseased animals. Another study suggested that different strains may act in an additive/synergistic way leading to higher C. gigas mortality rates. Here, a strain pair (31+32) was characterised at taxonomic and virulence levels. Using a polyphasic approach, these strains were confirmed to be V splendidus-related, without a clear discrimination between V. kanaloae and V. pomeroyi since hybridisation rates with both these strains were above 70%. Following experimental infection of C. gigas by injection in the adductor muscle or in the pallial cavity, the host alterations induced were described. After injection of strains 31 and/or 32, bacteria were localised at the periphery of the muscle and induced extensive lesions of the translucent part of the adductor muscle. Muscle alterations were of 3 kinds: (1) presence of isolated rounded muscular fibres containing non-homogenous granular material and surrounded by a translucent halo; (2) presence of non-homogenous granular material in the cytoplasm of entire muscle bands; (3) affection of wide muscle areas with extremely condensed muscle fibres. Infiltration associated with these lesions was notably absent in the vast majority of the individuals.

Infectious diseases are a limiting factor to the development and sustainability of aquaculture. For mollusc cultures, only prophylactic measures may be applied, their development usually facilitated by the reproduction of the disease under experimental conditions. To develop an experimental infection in Crassostrea gigas, Vibrio strains were isolated and their virulence was experimentally evaluated. Collaboration phenomena between some strains were observed in infection trial, leading to higher mortality rate when two strains are concomitantly inoculated. Two pathogenic strains, belonging to the polyphyletic group of Vibrio splendidus and named 31 and 32 illustrate this phenomenon. They induce extensive alterations of the adductor muscle in C. gigas. The issue of infection trials with these strains is influenced by intrinsic C. gigas factors. Eventually, strain 32 was used as target strain to select inhibitory strain, potentially usable as a probiotic., Les maladies infectieuses sont un frein au développement et à la pérennité des élevages aquacoles. Le développement de moyens de lutte est facilité par la reproduction de la maladie en structure expérimentale. Afin de développer une infection expérimentale chez Crassostrea gigas, des souches de Vibrio ont été isolées et leur virulence a été évaluée expérimentalement. Des phénomènes de collaboration entre certaines souches sont observés en infection expérimentale, se traduisant par un taux de mortalité supérieur lorsque deux souches sont inoculées ensemble. Deux souches pathogènes, appartenant au groupe polyphylétique de Vibrio splendidus et nommées 31 et 32 illustrent ce phénomène. Elles induisent des altérations du muscle adducteur de C. gigas. L'issue de l'infection expérimentale est influencée par des facteurs intrinsèques à C. gigas. Enfin, la souche 32 a été utilisée pour sélectionner une souche inhibitrice de sa croissance, potentiellement utilisable en tant que probiotique.

Polyphasic analysis of five new Vibrio isolates originating from the haernolymph of diseased cultured oysters is described. The new isolates were closely related to Vibrio splendidus, having 98 % 16S rRNA gene sequence similarity. gyrB phylogenetic analysis, fluorescent amplified-fragment length polymorphism (FAFLP) fingerprinting and DNA-DNA hybridization experiments clearly showed that the new isolates form a tight genomic group that is different from the currently known Vibrio species. It is proposed to accommodate these isolates in a novel species, Vibrio crassostreae sp. nov. (type strain LGP 7(T) =LMG 22240(T)=Clp 108327(T)). Phenotypic and chemotaxonomic features that differentiate V. crassostreae from other known Vibrio species include arginine dihydrolase, utilization and fermentation of various carbon sources, beta-galactosidase activity, NO2 production and the presence of the fatty acids 14: 0 iso and 16: 0 iso.

Nowadays, cupped oyster, Crassostrea gigas, production is the main shellfish production in France. Spats cultivated on most farms are usually collected in the wild, but hatchery spats are becoming more numerous, and represent around 10% of today's cultivated spats. During the summer period, when the temperatures are higher, high mortality rates have been regularly observed in cupped in oyster C. gigas (60 to 100%) spats since 1991, both in hatcheries-nurseries and in their natural habitat. Over the last five years, these episodes have become a big concern for all the professionals., La production d'huître creuse, Crassostrea gigas, est aujourd'hui la principale production française de coquillages. Le naissain mis en élevage dans les différents centres de production est généralement obtenu par captage naturel mais l'utilisation de naissain d'écloserie est en constante progression depuis quelques a1U1ées, et représente aujourd'hui près de 10% du naissain mis en élevage. En période estivale, à la faveur de températures élevées, de forts taux de mortalité de naissains d'huître creuse C. gigas (60 à 100%) sont rapportés régulièrement depuis 1991, dans les écloseries-nurseries ainsi qu'en milieu naturel. Au cours des cinq dernières a1U1ées, ces épisodes récurrents sont apparus commne un sujet préoccupant pour l'ensemble de la profession