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Appl Environ Microbiol. 2019 Jan 18. pii: AEM.02305-18. doi: 10.1128/AEM.02305-18. [Epub ahead of print]

Large-scale Analysis of Flavobacterium psychrophilum MLST Genotypes Recovered From North American Salmonids Indicates Both Newly Identified and Recurrent Clonal Complexes are Associated with Disease.

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Department of Fisheries and Wildlife, College of Agriculture and Natural Resources, Michigan State University, East Lansing, MI, 48824, USA.
National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, USDA, 11861 Leetown Rd, Kearneysville, WV, 25430, USA.
Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, East Lansing, MI, 48824, USA.
Paul G. Allen School for Global Animal Health, College of Veterinary Medicine, Pullman, WA, 991614, USA.
Department of Fisheries and Wildlife Resources and the Aquaculture Research Institute, College of Natural Resources, University of Idaho, Moscow, ID 83844, USA.
MaIAGE, Inra, Université Paris-Saclay, 78350, Jouy-en-Josas, France.
Utah Division of Wildlife Resources, Fisheries Experiment Station, Logan, UT, 84341, USA.
Division of Fisheries Management, Pennsylvania Fish and Boat Commission, Harrisburg, PA, 17106, USA.
Alaska Department of Fish and Game, Commercial Fisheries Division, Fish Pathology, Laboratory, 333 Raspberry Road, Anchorage, AK, 99518, USA.
Division of Fish and Wildlife, Indiana Department of Natural Resources, Indianapolis, IN, 46204, USA.
Wisconsin Veterinary Diagnostic Laboratory, University of Wisconsin-Madison, Madison, WI, 53706, USA.
Division of Fish, Wildlife, and Parks - Fisheries Management, Wisconsin Department of Natural Resources, Madison, WI, 53707, USA.
Fish and Wildlife Division, Minnesota Department of Natural Resources, St. Paul, MN, 55155, USA.
Department of Fisheries and Wildlife, College of Agriculture and Natural Resources, Michigan State University, East Lansing, MI, 48824, USA


Flavobacterium psychrophilum, 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 within F. 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 American F. psychrophilum isolates that were recovered from ten fish host species from twenty US states and one 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 F. psychrophilum CC identified was CC-ST10, within which 10 novel genotypes were discovered, most of which came from O. mykiss 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 F. psychrophilum 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.Importance Flavobacterium psychrophilum 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 F. psychrophilum isolates that were recovered from diseased fish across North America. Results highlighted multiple F. psychrophilum 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 towards guiding the development of future disease prevention techniques.


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