Large-Scale Analysis of Flavobacterium psychrophilum Multilocus Sequence Typing Genotypes Recovered from North American Salmonids Indicates that both Newly Identified and Recurrent Clonal Complexes Are Associated with Disease

Abstract

Flavobacterium psychrophilum, the etiological agent of bacterial coldwater disease (BCWD) and rainbow trout fry syndrome (RTFS), causes significant economic losses in salmonid aquaculture, particularly in rainbow trout (Oncorhynchus mykiss). Prior studies have used multilocus sequence typing (MLST) to examine genetic heterogeneity withinF. psychrophilum. At present, however, its population structure in North America is incompletely understood, as only 107 isolates have been genotyped. Herein, MLST was used to investigate the genetic diversity of an additional 314 North AmericanF. psychrophilumisolates that were recovered from ten fish host species from 20 U.S. states and 1 Canadian province over nearly four decades. These isolates were placed into 66 sequence types (STs), 47 of which were novel, increasing the number of clonal complexes (CCs) in North America from 7 to 12. Newly identified CCs were diverse in terms of host association, distribution, and association with disease. The largestF. psychrophilumCC identified was CC-ST10, within which 10 novel genotypes were discovered, most of which came fromO. mykissexperiencing BCWD. This discovery, among others, provides evidence for the hypothesis that ST10 (i.e., the founding ST of CC-ST10) originated in North America. Furthermore, ST275 (in CC-ST10) was recovered from wild/feral adult steelhead and marks the first recovery of CC-ST10 from wild/feral fish in North America. Analyses also revealed that at the allele level, the diversification ofF. psychrophilumin North America is driven three times more frequently by recombination than random nucleic acid mutation, possibly indicating how new phenotypes emerge within this species.IMPORTANCEFlavobacterium psychrophilumis the causative agent of bacterial coldwater disease (BCWD) and rainbow trout fry syndrome (RTFS), both of which cause substantial losses in farmed fish populations worldwide. To better prevent and control BCWD and RTFS outbreaks, we sought to characterize the genetic diversity of several hundredF. psychrophilumisolates that were recovered from diseased fish across North America. Results highlighted multipleF. psychrophilumgenetic strains that appear to play an important role in disease events in North American aquaculture facilities and suggest that the practice of trading fish eggs has led to the continental and transcontinental spread of this bacterium. The knowledge generated herein will be invaluable toward guiding the development of future disease prevention techniques.

Phenotypic and Genetic Predictors of Pathogenicity and Virulence in Flavobacterium psychrophilum

“…In a large-scale epidemiological study done by Nilsen et al (2014) in countries around the Baltic Sea, the overwhelming majority of BCWD outbreaks in rainbow trout since the 1980s were attributed to a single clonal complex (CC), CC-ST10, comprising several closely related genotypes. Interestingly, CC-ST10 is also the predominant CC in several other European countries (Siekoula-Nguedia et al, 2012; Strepparava et al, 2013) as well as in Chile (Avendaño-Herrera et al, 2014) and in the United States (Van Vliet et al, 2016; Knupp et al, 2019) indicating a global distribution. Severe BCWD outbreaks have been associated with genotypes of CC-ST10 (Nilsen et al, 2014; Van Vliet et al, 2016) whereby virulence has been considered as a major contributor to its dominance in rainbow trout farms over both time and space.…”

“…The epidemiological data collected in the large scale F. psychrophilum MLST studies (Nilsen et al, 2014; Knupp et al, 2019) indicate that development of efficient control strategies against BCWD in rainbow trout should be directed toward genotypes of CC-ST10 or target specific virulence factors expressed by them. Targeting CC-ST10 using lytic bacteriophages isolated from the environment is theoretically an ideal approach, but so far, limited information is available regarding the phage-susceptibility of current virulent outbreak strains of F. psychrophilum in the Baltic Sea region.…”

Multiplex PCR for genotypingFlavobacterium columnare

“…LaFrentz et al () redesigned the primers developed by Ashrafi et al () to be able to amplify the six housekeeping genes of F. columnare isolates from all four genetic groups, which will facilitate such research. Similar research has been conducted with F. psychrophilum which has increased knowledge of molecular diversity, bacterial population structure, epidemiology and host associations (Avendano‐Herrera et al, ; Knupp et al, ; Nicolas et al, ; Siekoula‐Nguedia, Blanc, Duchaud, & Calvez, ; Strepparava, Nicolas, Wahli, Segner, & Petrini, ; Van Vliet, Wiens, Loch, Nicolas, & Faisal, ).…”

Twenty Years of Disk Diffusion Testing Indicate No Meaningful Loss of Antibiotic Susceptibility for Multiple Pathogens Isolated from Hatcheries Operated by the Idaho Department of Fish and Game

“…) and across North America (Knupp et al. ), and there are various aeromonad species that cause motile Aeromonas septicemia (Duman et al. ).…”