Draft Genome Sequences of Three
            <i>Flavobacterium psychrophilum</i>
            Strains Isolated from Coldwater Disease Outbreaks at Three Production Hatcheries

Neiger, Regg D.; Thomas, M. G.; Das, Sankar; Barnes, Michael E.; Fletcher, Brian; Snekvik, Kevin; Thompson, Jim; Scaria, Joy

doi:10.1128/genomea.00035-16

Cited by 8 publications

(4 citation statements)

References 9 publications

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“…Similar SSI values also indicate no overt effects on the immune response (Hadidi et al 2008;Wiens et al 2014) resulting from spheres or rods in the tanks. The relatively low SSI values reported in this study, compared with those in Barnes et al (2014) and Parker and Barnes (2015), are surprising because fish in all of the tanks showed symptoms of bacterial coldwater disease (Neiger et al 2016), and the causative agent of the disease, Flavobacterium psychrophilum, was isolated. It is possible that relative spleen sizes were low because the trout had ample time to recover after the bacterial coldwater disease infection before being sampled at the end of the study.…”

Section: Discussioncontrasting

confidence: 71%

“…() and Parker and Barnes (), are surprising because fish in all of the tanks showed symptoms of bacterial coldwater disease (Neiger et al. ), and the causative agent of the disease, Flavobacterium psychrophilum , was isolated. It is possible that relative spleen sizes were low because the trout had ample time to recover after the bacterial coldwater disease infection before being sampled at the end of the study.…”

Section: Discussionmentioning

confidence: 99%

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An Evaluation of Vertically Suspended Environmental Enrichment Structures during Rainbow Trout Rearing

2018

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Environmental enrichment is the addition of substrate or structural complexity to typically sterile culture environments, but the effects of enrichment on fish rearing performance are relatively unknown. This 127‐d study examined the growth and condition of juvenile Rainbow Trout Oncorhynchus mykiss reared in near‐fully covered circular tanks (1.8 m diameter) with three novel environmental treatments: (1) eight vertically suspended nylon strings with seven colored (6.4 cm diameter) plastic spheres (high density), (2) five vertically suspended strings with seven colored plastic spheres (low density), and (3) a mixture of five vertically suspended colored plastic spheres and nine vertically suspended aluminum rods. Near‐fully covered tanks without enrichment were used as a control. Weight gain, feed conversion ratio, individual fish length, and fish weight were significantly improved in environmentally enriched tanks compared with those features in the unenriched control. Among all of the treatments, the tanks of fish with high‐density spheres had significantly higher ending tank weights (i.e., total weight of fish in tank) and weight gain, both of which were nearly 65% and 75% greater, respectively, than in the control tanks. However, high density spheres also interfered with the self‐cleaning nature of the circular tanks. No significant differences in splenosomatic indices, viscerosomatic indices, hepatosomatic indices, and relative fin lengths were observed among the three enrichment treatments. Based on the results of this study, the use of either low‐density spheres or a mix of rods and spheres is recommended during the rearing of juvenile Rainbow Trout in circular tanks.

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Section: Discussioncontrasting

confidence: 71%

Section: Discussionmentioning

confidence: 99%

An Evaluation of Vertically Suspended Environmental Enrichment Structures during Rainbow Trout Rearing

2018

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“…Since the publication of the first F. psychrophilum complete genome (Duchaud et al, 2007 ) sequences from only a limited number of additional isolates have been published (Wiens et al, 2014 ; Wu et al, 2015 ; Castillo et al, 2016 ; Neiger et al, 2016 ; Shimizu et al, 2016 ; Rochat et al, 2017a ) and a global comparative genomics analysis of the species is missing. Here, we report the draft genome sequencing of 30 additional isolates selected on the basis of their origins and MLST profiles.…”

Section: Introductionmentioning

confidence: 99%

Genomic Diversity and Evolution of the Fish Pathogen Flavobacterium psychrophilum

et al. 2018

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Flavobacterium psychrophilum, the etiological agent of rainbow trout fry syndrome and bacterial cold-water disease in salmonid fish, is currently one of the main bacterial pathogens hampering the productivity of salmonid farming worldwide. In this study, the genomic diversity of the F. psychrophilum species is analyzed using a set of 41 genomes, including 30 newly sequenced isolates. These were selected on the basis of available MLST data with the two-fold objective of maximizing the coverage of the species diversity and of allowing a focus on the main clonal complex (CC-ST10) infecting farmed rainbow trout (Oncorhynchus mykiss) worldwide. The results reveal a bacterial species harboring a limited genomic diversity both in terms of nucleotide diversity, with ~0.3% nucleotide divergence inside CDSs in pairwise genome comparisons, and in terms of gene repertoire, with the core genome accounting for ~80% of the genes in each genome. The pan-genome seems nevertheless “open” according to the scaling exponent of a power-law fitted on the rate of new gene discovery when genomes are added one-by-one. Recombination is a key component of the evolutionary process of the species as seen in the high level of apparent homoplasy in the core genome. Using a Hidden Markov Model to delineate recombination tracts in pairs of closely related genomes, the average recombination tract length was estimated to ~4.0 Kbp and the typical ratio of the contributions of recombination and mutations to nucleotide-level differentiation (r/m) was estimated to ~13. Within CC-ST10, evolutionary distances computed on non-recombined regions and comparisons between 22 isolates sampled up to 27 years apart suggest a most recent common ancestor in the second half of the nineteenth century in North America with subsequent diversification and transmission of this clonal complex coinciding with the worldwide expansion of rainbow trout farming. With the goal to promote the development of tools for the genetic manipulation of F. psychrophilum, a particular attention was also paid to plasmids. Their extraction and sequencing to completion revealed plasmid diversity that remained hidden to classical plasmid profiling due to size similarities.

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“…Cleghorn Springs State Fish Hatchery in Rapid City, South Dakota has an endemic strain of Flavobacterium psychrophilum and regular outbreaks of BCWD [15]. BCWDinduced mortality of Shasta strain rainbow trout at the hatchery has ranged from 1% to nearly 70% [16,17].…”

Section: Introductionmentioning

confidence: 99%

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2023

HAAF

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Flavobacterium psychrophilum, the causative agent of Bacterial Cold-Water Disease (BCWD) is prevalent in salmonid hatcheries worldwide. This study evaluated the potential impact of a commercially available probiotic (BiOWiSH MultiBio 3PS) on BCWD-induced mortality in Shasta strain rainbow trout Oncorhynchus mykiss. The experiment consisted of three consecutive trials. The first trial began at initial feeding and lasted for 31 days. The second trial began on day 32 and lasted for 29 days and the third trial began on day 62 and lasted for 61 days. Tanks of fish received either Bio-Oregon trout feed (control) or Bio-Oregon trout feed top-coated with the BiOWiSH probiotic at 0.5g per kg of feed. Percent mortality was not significantly different between the two treatments in each trial. Feed conversion ratios were not significantly different between the treatments in the first and third trial. However, feed conversion ratio was significantly lower in the control compared to the probiotic treatment in the second trial, at 0.84 and 0.90, respectively. Further studies should be performed with feeds that contain alternative protein sources or at different concentrations of probiotic.

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Draft Genome Sequences of Three Flavobacterium psychrophilum Strains Isolated from Coldwater Disease Outbreaks at Three Production Hatcheries

Cited by 8 publications

References 9 publications

An Evaluation of Vertically Suspended Environmental Enrichment Structures during Rainbow Trout Rearing

An Evaluation of Vertically Suspended Environmental Enrichment Structures during Rainbow Trout Rearing

Genomic Diversity and Evolution of the Fish Pathogen Flavobacterium psychrophilum

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