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Flavobacterium psychrophilum, the causative agent of bacterial cold-water disease, is a devastating, worldwide distributed, fish pathogen causing significant economic loss in inland fish farms. Previous epidemiological studies showed that prevalent clonal complexes (CC) differ in fish species affected with disease such as rainbow trout, coho salmon and ayu, indicating significant associations between particular F. psychrophilum genotypes and host species. Yet, whether the population structure is driven by the trade of fish and eggs or by host-specific pathogenicity is uncertain. Notably, all F. psychrophilum isolates retrieved from ayu belong to Type-3 O antigen (O-Ag) whereas only very few strains retrieved from other fish species possess this O-Ag, suggesting a role in outbreaks affecting ayu. Thus, we investigated the links between genotype and pathogenicity by conducting comparative bath infection challenges in two fish hosts, ayu and rainbow trout, for a collection of isolates representing different MLST genotypes and O-Ag. Highly virulent strains in one host species exhibited low to no virulence in the other. F. psychrophilum strains associated with ayu and possessing Type-3 O-Ag demonstrated significant variability in pathogenicity in ayu, ranging from avirulent to highly virulent. Strikingly, F. psychrophilum strains retrieved from rainbow trout and possessing the Type-3 O-Ag were virulent for rainbow trout but not for ayu, indicating that Type-3 O-Ag alone is not sufficient for pathogenicity in ayu, nor does it prevent pathogenicity in rainbow trout. This study revealed that the association between a particular CC and host species partly depends on the pathogen's adaptation to specific host species. [ABSTRACT FROM AUTHOR]

Flavobacterium psychrophilum is the causative agent of Bacterial Cold Water Disease (BCWD)/ Rainbow Trout Fry Syndrome (RTFS) in rainbow trout Oncorhynchus mykiss. The disease is associated with significant mortality in trout farms and thereby responsible for severe economical losses in this part of the aquaculture industry. Vaccination of the very young life cycle stages is not successful due to the immature development of the adaptive immunity in yolksac larvae and early fry. This explains the extensive usage of antibiotics for control of BCWD/RTFS. Selective breeding of RTFS resistant fish may be a solution, and identification of markers associated with natural susceptibility/resistance to the disease may elevate breeding efforts towards more robust strains. We suggest a QTL (SNP Affx-88941461) for partial disease resistance on chromosome 25 (Omy25) based on our experimental F. psychrophilum challenges of outbred fish and subsequent GWAS analyses. The favourable SNP allele was designated Q, whereas q indicated the unfavourable allele. We validated this QTL in two subsequent challenge experiments by F. psychrophilum exposure of QQ, Qq and qq trout. In the first trial we produced trout carrying at least one favourable allele (QQ and Qq) associated with partial resistance by fertilizing trout eggs from non-selected (outbred) females with sperm from homozygous QQ males. In the second trial we also produced homozygous offspring by fertilizing trout eggs from QQ females with sperm from QQ males. The resistance profiles of these groups were then determined in the laboratory by triplicate or duplicate challenge experiments (common garden water bath exposure to F. psychrophilum), which showed a significantly higher survival in trout carrying the favourable allele. Field observations supplemented the laboratory studies. Under farm conditions QQ and Qq trout showed a higher survival rate compared to qq trout. In the present study chromosome 25 (Omy25) QTL was found associated with a partial resistance to F. psychrophilum. However, we recommend to include additional SNPs in future breeding studies because several QTL are associated with resistance.

We present the draft genome sequences of six Flavobacterium psychrophilum isolates recovered from diseased coho salmon ( Oncorhynchus kisutch ) cultured by two farms in Chile. This study provides the first detailed insights into the genomic characteristics of this fish pathogen recovered from a host with limited information and cultured in Chile., Competing Interests: The authors declare no conflict of interest.