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

• Published in: Applied and environmental microbiology Vol. 85; no. 6; pp. 1 - 14
• Main Authors: Knupp, Christopher, Wiens, Gregory D, Faisal, Mohamed, Call, Douglas R, Cain, Kenneth D, Nicolas, Pierre, Van Vliet, Danielle, Yamashita, Coja, Ferguson, Jayde A, Meuninck, Dave, Hsu, Hui-Min, Baker, Bridget B, Shen, Ling, Loch, Thomas P
• Format: Journal Article
• Language: English
• Published: United States American Society for Microbiology 15.03.2019
• Subjects: Animals; Aquaculture; Aquaculture facilities; Canada - epidemiology; Computer Science; Disease control; Economic conditions; Economic impact; Eggs; Etiology; Fish; Fish diseases; Fish Diseases - epidemiology; Fish Diseases - microbiology; Fish eggs; Fish farms; Fish populations; Flavobacteriaceae Infections - epidemiology; Flavobacteriaceae Infections - microbiology; Flavobacteriaceae Infections - veterinary; Flavobacterium - classification; Flavobacterium - genetics; Flavobacterium - isolation & purification; Flavobacterium psychrophilum; Genetic diversity; Genotype; Genotypes; Heterogeneity; Life Sciences; Mathematics; Microbial Ecology; Multilocus Sequence Typing; Mutation; Nucleic acids; Oncorhynchus mykiss; Oncorhynchus mykiss - microbiology; Outbreaks; Phenotypes; Phylogeny; Population structure; Recombination; Salmon; Salmonids; Trout; Canada; North America; fish disease; genetic diversity; recombination; Flavobacteriaceae; MLST; bacterial coldwater disease; Flavobacterium psychrophilum; rainbow trout fry syndrome; mlst; flavobacteriaceae; flavobacterium psychrophilum
• ISSN: 0099-2240; 1098-5336
• DOI: 10.1128/AEM.02305-18

, 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 ( ). Prior studies have used multilocus sequence typing (MLST) to examine genetic heterogeneity within 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 American isolates 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 largest CC identified was CC-ST10, within which 10 novel genotypes were discovered, most of which came from experiencing 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 of in North America is driven three times more frequently by recombination than random nucleic acid mutation, possibly indicating how new phenotypes emerge within this species. is 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 hundred isolates that were recovered from diseased fish across North America. Results highlighted multiple genetic 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.