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Flavobacterial diseases in fish are caused by multiple bacterial species within the family Flavobacteriaceae and are responsible for devastating losses in wild and farmed fish stocks ...around the world. In addition to directly imposing negative economic and ecological effects, flavobacterial disease outbreaks are also notoriously difficult to prevent and control despite nearly 100years of scientific research. The emergence of recent reports linking previously uncharacterized flavobacteria to systemic infections and mortality events in fish stocks of Europe, South America, Asia, Africa, and North America is also of major concern and has highlighted some of the difficulties surrounding the diagnosis and chemotherapeutic treatment of flavobacterial fish diseases. Herein, we provide a review of the literature that focuses on Flavobacterium and Chryseobacterium spp. and emphasizes those associated with fish.
Two strains (T16(T) and S12) of a Gram-reaction-negative, rod-shaped, yellow-pigmented bacterium were recovered from kidneys of feral spawning adult Chinook salmon (Oncorhynchus tshawytscha) and the ...gills of captive-reared Chinook salmon fingerlings suffering a mortality episode, respectively. Polyphasic characterization revealed that these strains possessed gliding motility, contained a flexirubin-type pigment, proteolysed multiple substrates (i.e. gelatin, casein and elastin), and had a mean DNA G+C content of 35.6 mol%. Sequencing of the 16S rRNA gene demonstrated that strains T16(T) and S12 were nearly identical to one another (>99% similarity) and were placed within the genus Flavobacterium, with Flavobacterium aquidurense CCUG 59847(T) (98.3%), Flavobaterium araucananum CCUG 61031(T) (98.2%) and Flavobacterium frigidimaris (AB183888, 98.1%) being their closest relatives. Subsequent phylogenetic analyses using neighbour-joining, maximum-parsimony and Bayesian methodologies demonstrated that strains T16(T) and S12 formed a well-supported clade within the genus Flavobacterium that was distinct from other Flavobacterium species. The major fatty acid constituents of strains T16(T) and S12 were iso-C15 : 0, C16 : 1ω6c and/or C16 : 1ω7c, iso-C17 : 0 3-OH, and iso-C15 : 0 3-OH according to fatty acid methyl ester analysis. The mean level of DNA-DNA relatedness between strain T16(T) and F. aquidurense CCUG 59847(T) and F. araucananum CCUG 61031(T) was 23 and 29%, respectively. Thus, the data accumulated in this study support the suggestion that strains T16(T) and S12 represent a novel species of the genus Flavobacterium, for which the name Flavobacterium spartansii sp. nov. is proposed. The type strain is T16(T) ( = LMG 27337(T) = ATCC BAA-2541(T)). Emended descriptions of F. aquidurense and F. araucananum are also proposed.
causes bacterial coldwater disease (BCWD) and is responsible for substantial losses in farm and hatchery-reared salmonids (Family
). Although
infects multiple economically important salmonids and is ...transmitted horizontally, the extent of knowledge regarding
shedding rates and duration is limited to rainbow trout (
). Concurrently, hundreds of
sequence types (STs) have been described using multilocus sequence typing (MLST), and evidence suggests that some variants have distinct phenotypes, including differences in host associations. Whether shedding dynamics differ among
variants and/or salmonids remains unknown. Thus, three
isolates (e.g., US19, US62, and US87) in three MLST STs (e.g., ST13, ST277, and ST275) with apparent host associations for coho salmon (
), Atlantic salmon (
), or rainbow trout were intramuscularly injected into each respective fish species. Shedding rates of live and dead fish were determined by quantifying
loads in water via quantitative PCR. Both live and dead Atlantic and coho salmon shed
, as did live and dead rainbow trout. Regardless of salmonid species, dead fish shed
at higher rates (e.g., up to ~10
-10
cells/fish/hour) compared to live fish (up to ~10
-10
cells/fish/hour) and for a longer duration (5-35 days vs 98 days); however, shedding dynamics varied by
variant and/or host species, a matter that may complicate BCWD management. Findings herein expand knowledge on
shedding dynamics across multiple salmonid species and can be used to inform future BCWD management strategies.IMPORTANCE
causes bacterial coldwater disease (BCWD) and rainbow trout fry syndrome, both of which cause substantial losses in farmed and hatchery-reared salmon and trout populations worldwide. This study provides insight into
shedding dynamics in rainbow trout (
) and, for the first time, coho salmon (
) and Atlantic salmon (
). Findings revealed that live and dead fish of all fish species shed the bacterium. However, dead fish shed
at higher rates than living fish, emphasizing the importance of removing dead fish in farms and hatcheries. Furthermore, shedding dynamics may differ according to
genetic variant and/or fish species, a matter that may complicate BCWD management. Overall, study results provide deeper insight into
shedding dynamics and will guide future BCWD management strategies.
Columnaris disease, caused by the Gram-negative bacterium
, is one of the most prevalent fish diseases worldwide. An exceptionally high level of genetic diversity among isolates of
has long been ...recognized, whereby six established genomovars have been described to date. However, little has been done to quantify or characterize this diversity further in a systematic fashion. The objective of this research was to perform phylogenetic analyses of 16S rRNA and housekeeping gene sequences to decipher the genetic diversity of
. Fifty isolates and/or genomes of
, originating from diverse years, geographic locations, fish hosts, and representative of the six genomovars were analyzed in this study. A multilocus phylogenetic analysis (MLPA) of the 16S rRNA and six housekeeping genes supported four distinct
genetic groups. There were associations between genomovar and genetic group, but these relationships were imperfect indicating that genomovar assignment does not accurately reflect
genetic diversity. To expand the dataset, an additional 90 16S rRNA gene sequences were retrieved from GenBank and a phylogenetic analysis of this larger dataset also supported the establishment of four genetic groups. Examination of isolate historical data indicated biological relevance to the identified genetic diversity, with some genetic groups isolated preferentially from specific fish species or families. It is proposed that
isolates be assigned to the four genetic groups defined in this study rather than genomovar in order to facilitate a standard nomenclature across the scientific community. An increased understanding of which genetic groups are most prevalent in different regions and/or aquaculture industries may allow for the development of improved targeted control and treatment measures for columnaris disease.
Flavobacterium psychrophilum
, the etiological agent of bacterial coldwater disease and rainbow trout fry syndrome, causes considerable losses in salmonid aquaculture globally. Systemic
F. ...psychrophilum
infections in rainbow trout (
Oncorhynchus mykiss
) lead to a range of clinical signs, including ulcerative lesions in the skin and muscle and splenitis. Previous studies offered an integrative analysis of the skeletal muscle response to
F. psychrophilum
infection in rainbow trout. However, little is known about the molecular mechanism of immune response in the spleen, which is an important immune organ of rainbow trout. Here, we investigated the time-course splenic transcriptome profiles in uninfected rainbow trout (CK) and
F. psychrophilum
–infected rainbow trout at day 3 and day 7 (D3, D7) by RNA-seq analyses. Among the 7,170 differentially expressed genes (DEGs) in the three comparisons (D3 vs. CK, D7 vs. CK, D3 vs. D7), 1,286 DEGs showed consistent upregulation or downregulation at D3 and D7 and were associated with pattern recognition, acute-phase response, complement cascade, chemokine and cytokine signaling, and apoptosis. The Real time quantitative PCR (RT-qPCR) analysis of eight DEGs confirmed the accuracy of the RNA-Sequencing (RNA-seq) data. Our results reflected a general process from pathogen recognition to inflammatory cytokine generation and delineated a putative Toll-like receptor signaling pathway in rainbow trout spleen, following
F. psychrophilum
infection. Taken together, these results provide new insights into the molecular mechanism of the immune response to
F. psychrophilum
infection and are a valuable resource for future research on the prevention and control of bacterial coldwater disease during salmon culture.
This report of the BOOST2012 workshop presents the results of four working groups that studied key aspects of jet substructure. We discuss the potential of first-principle QCD calculations to yield a ...precise description of the substructure of jets and study the accuracy of state-of-the-art Monte Carlo tools. Limitations of the experiments’ ability to resolve substructure are evaluated, with a focus on the impact of additional (pile-up) proton proton collisions on jet substructure performance in future LHC operating scenarios. A final section summarizes the lessons learnt from jet substructure analyses in searches for new physics in the production of boosted top quarks.
We present the report of the hadronic working group of the BOOST2010 workshop held at the University of Oxford in June 2010. The first part contains a review of the potential of hadronic decays of ...highly boosted particles as an aid for discovery at the LHC and a discussion of the status of tools developed to meet the challenge of reconstructing and isolating these topologies. In the second part, we present new results comparing the performance of jet grooming techniques and top tagging algorithms on a common set of benchmark channels. We also study the sensitivity of jet substructure observables to the uncertainties in Monte Carlo predictions.
Infectious diseases are a leading cause of losses in the aquaculture industry and conservation programs globally. Simultaneously, infectious diseases pose a substantial risk to fish being ...hatchery-reared and released into natural habitats for conservation purposes, including the Great Lakes lake sturgeon (Acipenser fulvescens, i.e., GL-LST). Recently, an alloherpesvirus (lake sturgeon herpesvirus 2, i.e., LSHV-2) capable of inducing disease and/or mortality in adult and juvenile GL-LSTs was detected in two adult GL-LST populations. To begin developing disease prevention and/or control methods, in vitro experiments were designed to determine the susceptibility of LSHV-2 to disinfectants commonly used in hatchery and aquaculture facilities (Virkon®-Aquatic: potassium peroxymonosulfate; Ovadine®: polyvinylpyrrolidone iodine complex; and Perox-Aid®: hydrogen peroxide). Cultured LSHV-2 was exposed to each disinfectant at two concentrations (Virkon®-Aquatic: 0.5% and 1%; Ovadine®: 50 and 100 ppm; and Perox-Aid®: 500 and 1000 ppm) in duplicate for durations of 1, 10, and 30 min. Following exposure, the disinfectant was neutralized, and after a 14-day incubation period on a white sturgeon × lake sturgeon hybrid cell line (WSxLS), percent reduction was calculated by comparing the 50% tissue culture infectious doses (TCID50/mL) of the virus with and without disinfectant exposure. When exposed to Perox-Aid®, LSHV-2 percent reduction ranged from 58.7% to 99.5%. When exposed to Ovadine®, the percent reduction ranged from 99.4% to 100%. Lastly, the percent reduction when exposed to Virkon®-Aquatic was 100% for both concentrations and all timepoints. The results herein provide evidence that both Virkon®-Aquatic and Ovadine® are virucidal to LSHV-2 and may represent a means to reduce virus transmission risk under field settings.
strain T16
was isolated from a disease outbreak in hatchery-reared Chinook salmon (
) fingerlings. To gain insight into its genomic content, structure and virulence pathogenesis factors, comparative ...genome analyses were performed using genomes from environmental and virulent
strains.
shared low average nucleotide identity (ANI) to well-known fish-pathogenic flavobacteria (e.g.,
, and
), indicating that it is a new and emerging fish pathogen. The genome in T16
had a length of 5,359,952 bp, a GC-content 35.7%, and 4,422 predicted protein-coding sequences.
core genome analysis showed that the number of shared genes decreased with the addition of input genomes and converged at 1182 genes. At least 8 genomic islands and 5 prophages were predicted in T16
. At least 133 virulence factors associated with virulence in pathogenic bacteria were highly conserved in
T16
. Furthermore, genes linked to virulence in other bacterial species (e.g., those encoding for a type IX secretion system, collagenase and hemolysin) were found in the genome of
T16
and were conserved in most of the analyzed pathogenic
.
was resistant to ampicillin and penicillin, consistent with the presence of multiple genes encoding diverse lactamases and the penicillin-binding protein in the genome. To allow for future investigations into
virulence
, a transposon-based random mutagenesis strategy was attempted in
T16
using pHimarEm1. Four putative gliding motility deficient mutants were obtained and the insertion sites of pHimarEm1 in the genome of these mutants were characterized. In total, study results clarify some of the mechanisms by which emerging flavobacterial fish pathogens may cause disease and also provide direly needed tools to investigate their pathogenesis.
Flavobacterium psychrophilum, the etiological agent of bacterial coldwater disease (BCWD) and rainbow trout fry syndrome, causes great economic losses in salmonid aquaculture worldwide. Recent ...molecular studies have uncovered important epidemiological and ecological aspects of this pathogen; however, such data are lacking for F. psychrophilum populations affecting aquaculture in China. Herein, F. psychrophilum phenotype, genotype, and virulence were characterized for isolates recovered from epizootics in multiple salmonid aquaculture facilities across China. Thirty-one F. psychrophilum isolates, originating from four provinces and three host fish species, were predominantly homogeneous biochemically but represented 5 sequence types (STs) according to multilocus sequence typing (MLST) that belonged to clonal complex CC-ST10 or 3 newly recognized singleton STs. PCR-based serotyping classified 19 and 12 F. psychrophilum isolates into molecular serotypes 1 and 0, respectively, showing an obvious relationship with host species. Antimicrobial susceptibility analysis via broth microdilution revealed reduced susceptibility to enrofloxacin, flumequine, and oxolinic acid, moderate susceptibility to gentamicin, erythromycin, and florfenicol, and variable susceptibility to ampicillin and oxytetracycline.
challenge experiments confirmed the ability of two representative Chinese F. psychrophilum isolates to induce typical signs of BCWD and mortality in 1-year-old rainbow trout (Oncorhynchus mykiss). Findings collectively demonstrate (i) that BCWD outbreaks in China studied thus far are caused by F. psychrophilum lineages that are common on other continents (e.g., CC-ST10) and others that have not been reported elsewhere (e.g., ST355, ST356, ST357), (ii) that F. psychrophilum molecular serotypes distinguish isolates from different host fish species, even within STs, and (iii) reduced F. psychrophilum antimicrobial susceptibility against compounds used for BCWD control in China.
Flavobacterium psychrophilum causes substantial economic losses in salmonid aquaculture worldwide. Although this bacterium is also believed to be a disease source in China, published reports of its presence do not yet exist. Herein, F. psychrophilum was linked to multiple disease outbreaks in several salmonid aquaculture facilities within four Chinese provinces, and polyphasic characterization revealed that most isolates were genetically distinct from strains recovered on other continents. Analyses further revealed the predominating molecular serotypes, antimicrobial susceptibility profiles, and pathogenic potential of two representative recovered isolates. Collectively, the results presented here provide important data on the epidemiology and disease ecology of F. psychrophilum in China and pave the way for targeted prevention and control methods to be pursued in the future.
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