Comparative genomics of crucian carp-isolated Flavobacterium psychrophilum: toward the foundations of overwintering mortality syndrome

TL;DR

This study analyzes the genome of a Flavobacterium psychrophilum strain from crucian carp, revealing genetic traits linked to its ability to cause disease in this species and adapt to aquaculture environments.

Contribution

The study provides the first genomic analysis of F. psychrophilum isolated from a cyprinid host, highlighting host-specific virulence factors and evolutionary insights.

Findings

The NJ01 strain has a 2.85 Mb genome with unique genetic elements linked to host specificity and environmental adaptation.

NJ01 encodes virulence factors like adhesion proteins and secreted enzymes that may aid in infecting crucian carp.

Phylogenomic analysis places NJ01 in a distinct lineage, suggesting evolutionary divergence from other F. psychrophilum strains.

Abstract

Flavobacterium psychrophilum is a Gram-negative bacterium that acts as a primary etiological agent of bacterial cold-water disease (BCWD) in salmonid fish. In the past 5 years, this pathogen has also been isolated from multiple freshwater fish species in China, including crucian carp (Carassius auratus gibelio), grass carp (Ctenopharyngodon idellus) and silver carp (Hypophthalmichthys molitrix), and identified as the causal agent of overwintering mortality syndrome. We report the whole-genome sequencing and analysis of F. psychrophilum strain NJ01, the first isolate from crucian carp, a cyprinid host. The NJ01 genome consists of a circular chromosome of approximately 2.85 Mb with a GC content of 32.5%, encoding about 2,300 predicted proteins. Comparative genomic analysis with reference strains revealed that NJ01 retains the core genomic features of F. psychrophilum while harboring unique genetic elements that may contribute to host specificity and environmental adaptation. NJ01 also harbors genes associated with antibiotic resistance and stress response, suggesting adaptation to aquaculture conditions. Phylogenomic analysis placed NJ01 within a distinct lineage, consistent with CH46 strains isolated from rainbow trout in china. Notably, NJ01 encodes a unique combination of virulence-associated factors such as adhesion proteins, secreted enzymes, and membrane transporters, which may facilitate infection in crucian carp. This study provides novel insights into the genomic basis of F. psychrophilum pathogenicity in a cyprinid host. The distinct virulence gene repertoire of NJ01 highlights potential host-specific pathogenic strategies and broadens current understanding of F. psychrophilum evolution. These findings may support the development of targeted measures for managing emerging F. psychrophilum infections in carp aquaculture.

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