Phenotypical and Genomic Characterization of the Mollusk Pathogen <i>Francisella halioticida</i>

The emergence and dissemination of aquatic pathogens pose significant risks to farmed species. Francisella halioticida, initially reported in abalones and Yesso scallops, was recently isolated from mussels in France, with some isolates showing high virulence. This study aimed to characterize and compare several F. halioticida isolates from mussels using phenotypic and genotypic approaches. Phenotypic analysis was performed using growth curves, biochemical profiles (API strips), and morphology assessed by electron microscopy. Genetic analysis has been performed through whole-genome comparison using classification methods and virulence markers seeking. Phenotypic analyses highlighted similarities among FR22 isolates and notable differences with FR21 and AG1. Notably, AG1 displayed distinct features. Antibiotic resistance profiling revealed the species' capacity to withstand multiple antimicrobial agents with various modes of action. Complete, circular genomes were assembled and compared using targeted and untargeted approaches. These analyses confirmed the affiliation of FR22 isolates with the F. halioticida species, while FR21 and AG1 taxonomy need to be further investigated. Virulence factor screening revealed the presence of secretion system components (types I, IV, and VI) in all isolates. A novel variant of the Francisella Pathogenicity Island (FPI) was described, shared by all virulent isolates. However, this FPI was absent in the low virulence isolate FR22b. In conclusion, this study discriminates against F. halioticida isolates and proposes new hypotheses on their virulence, contributing to improved detection tools and expanding our understanding of this emerging aquatic pathogen.