Surveillance, genetic diversity, and virulence characterisation of Francisella halioticida in blue mussels from the United Kingdom and Ireland.

Francisella halioticida is a recently recognized pathogen affecting molluscs. In Europe, its presence has been documented within mussel populations in both France and England. At present, data concerning its genetic variability in mussels remain scarce. Between 2024 and 2025, a comprehensive monitoring programme was implemented to assess F. halioticida prevalence in southern England, alongside analyses of archived samples from Scotland and Ireland. The findings indicated a low prevalence of the pathogen within the surveyed populations, primarily associated with mild or localized infections. Phylogenetic analyses based on multi-locus sequence analysis showed genetic variability of F. halioticida in mussels across surveyed locations and years, however a distinct F. halioticida cluster from mussels separated from F. halioticida infecting scallops and abalone was identified. A F. halioticida metagenome assembled genome was obtained from an infected mussel from southern England, with 3666 predicted ORFs, and a ~14.2 kb region containing a putative Francisella Pathogenicity Island, including genes associated with Type VI secretion system components (TssK, DotU, IglE, and IglH), together with several hypothetical proteins, and flanked by IS3 family transposases. Additional virulence-associated genes were detected, including transcriptional and global regulators, oxidative stress and detoxification genes, and metallopeptidases. These findings improve understanding of the occurrence, diversity, and genomic features of F. halioticida in wild mussel populations, highlighting the need for expanded surveillance and higher-resolution genomic data to better understand its epidemiology and pathogenic potential. This improved resolution enhances risk assessment, enables early detection of emerging lineages, and supports more targeted monitoring strategies for wild mussel populations.