Search Results (16)

Columnaris disease is a highly contagious infection that affects nearly all freshwater fish species worldwide. Grass carp, one of the most economically significant freshwater fish species in China, is particularly susceptible to the disease, leading to large-scale mortality. Flavobacterium columnare and F. covae are the primary pathogens causing columnaris disease in Chinese grass carp aquaculture. Herein, we compare mortality rates, replication rates of typical columnaris symptoms, histopathological changes, and bacterial content in the tissues of grass carp following infection using four challenge models. The mortality rate in grass carp challenged via intraperitoneal injection was 86.7%. All fish infected via intramuscular and intradermal injections died, while immersion resulted in lower mortality. Gill corrosion rates were 67%, 53%, and 87%, respectively, in the intramuscular injection, intradermal injection, and immersion groups. Correspondingly, skin ulceration rates were 75%, 91%, and 63%. However, surface symptoms in the intraperitoneal injection group were milder. Histopathological analysis revealed similar lesions in grass carp subjected to immersion, intramuscular, and intradermal infection, which differed from carp infected via intraperitoneal injection. The trends in bacterial loads in the gills and skin were similar, although the absolute bacterial content varied between tissues. Bacterial loads in the immersion and intraperitoneal injection groups were lower than those in the other groups. Based on these findings, we determined that the optimal model for simulating columnaris disease in grass carp is the intradermal injection of F. covae in 10–12 cm fish. The infection model generated via intradermal injection resembles natural F. covae infection and can serve as a good tool for evaluating the protective effect of anti-F. covae infection vaccines in grass carp. Full article

Due to the recent taxonomic reclassification of the species Flavobacterium columnare into four new species—Flavobacterium columnare, Flavobacterium davisii, Flavobacterium covae, and Flavobacterium oreochromis—it is necessary to re-evaluate isolates of previous outbreaks to better understand the epidemiology related to this bacterial group. Therefore, the aim of this study was to determine the taxonomic profile of Brazilian isolates of Flavobacterium spp. associated with columnaris disease using available diagnostic methods. Fifty isolates from different outbreaks (17 clinical cases) occurring in five different Brazilian states previously identified as F. columnare were selected and identified by multiplex PCR and MALDI-ToF methods. In addition, at least one isolate from each clinical case was analyzed by 16S rRNA gene sequencing. After inclusion of the MSPs (main spectra profiles), the isolates were identifiable, and when compared with the multiplex PCR results, they showed almost perfect agreement (94.2% Kappa = 0.85). Only F. davisii, F. covae, and F. oreochromis were found among the Brazilian isolates, with these species causing disease in neotropical fish hosts not previously reported (e.g., Siluriformes, Serrasalmidae, and Bryconidae), while F. columnare was not detected. This study provides evidence of Flavobacterium species associated with columnaris disease circulating in various aquaculture facilities across different regions of Brazil. This information is crucial for developing control programs and advancing epidemiologic studies on columnaris disease in Brazilian aquaculture. Full article

Humulus lupulus L. (hop) is a crucial crop within the brewing industry and a rich source of bioactive compounds. Traditionally concentrated in northeast regions of Europe, hop cultivation has expanded towards southern territories such as Italy over recent decades. Managing phytosanitary threats in Mediterranean climates poses challenges due to limited knowledge and registered agrochemicals. In pursuit of eco-friendly alternatives for disease management, we isolated 262 endophytic fungal strains from wild hop roots, stems, leaves, and flowers. Through phylogenetic analyses, we identified 51 operational taxonomic units. Dominant species such as Ilyonectria macrodidyma, Penicillium sp., Diaporthe columnaris, Plectosphaerella cucumerina, and Fusarium oxysporum were exclusive to roots. In contrast, Alternaria spp. and Epicoccum spp. were prevalent in other tissues, and Botrytis cinerea was exclusively detected in female flowers. We tested seven isolates—Epicoccum sp., Aureobasidium pullulans, Plectosphaerella cucumerina, Stemphylium vesicarium, Periconia byssoides, Talaromyces wortmannii, and Nigrospora sphaerica—against the four phytopathogenic fungi Alternaria sp., Fusarium oxysporum, Botrytis cinerea, and Sclerotinia sclerotiorum. All endophytes exhibited antagonistic effects against at least one pathogen, with Plectosphaerella cucumerina showing the strongest inhibition against Alternaria sp. This study marks the first exploration of endophytic fungi from various hop tissues. All isolated strains were ex situ conserved for future bioactivity assessments and biotechnological applications. Original data with a key relevance for the environmentally friendly management of plant diseases are provided. Full article

Linear mixed models (LMMs) are commonly used in genome-wide association studies (GWASs) to evaluate population structures and relatedness. However, LMMs have been shown to be ineffective in controlling false positive errors for the analysis of resistance to Columnaris disease in Rainbow Trout. To solve this problem, we conducted a series of studies using generalized linear mixed-model association software such as GMMAT (v1.4.0) (generalized linear mixed-model association tests), SAIGE (v1.4.0) (Scalable and Accurate Implementation of Generalized mixed model), and Optim-GRAMMAR for scanning a total of 25,853 SNPs. Seven different SNPs (single-nucleotide polymorphisms) associated with the trait of resistance to Columnaris were detected by Optim-GRAMMAR, four SNPs were detected by GMMAT, and three SNPs were detected by SAIGE, and all of these SNPs can explain 8.87% of the genetic variance of the trait of resistance to Columnaris disease. The heritability of the trait of resistance to Columnaris re-evaluated by GMMAT was calibrated and was found to amount to a total of 0.71 other than 0.35, which was seriously underestimated in previous research. The identification of LOC110520307, LOC110520314, and LOC110520317 associated with the resistance to Columnaris disease will provide us more genes to improve the genetic breeding by molecular markers. Finally, we continued the haplotype and gene-based analysis and successfully identified some haplotypes and a gene (TTf-2) associated with resistance to Columnaris disease. Full article

Flavobacterium davisii is one of the causative agents of columnaris disease, significantly impacting Nile tilapia aquaculture. This study examines the invasion and immune evasion mechanisms of a highly virulent F. davisii strain through transcriptomic profiling of tilapia gills following acute immersion. We identified 8192 differentially expressed genes (DEGs) at 2 h, 6 h, and 12 h post-infection. They are enriched in pathways related to oxidative stress, immune suppression, tissue necrosis, and bacterial infection. Notably, early overexpression of rhamnose-binding lectin and mucin genes facilitated bacterial adhesion. Key immune genes, including those encoding major histocompatibility complex (MHC), immunoglobulins (Ig), Toll-like receptors (TLRs), and chemokines, were downregulated, indicating immune suppression. Conversely, immune evasion genes such as Fc receptor-like (FcRL) and programmed death-ligand 1 (PDL1) were upregulated, along with genes associated with reactive oxygen species (ROS) production, leading to increased tissue damage. Additionally, the upregulation of fibroblast growth factor and collagen genes suggested active tissue repair. In conclusion, F. davisii rapidly invades its host by enhancing adhesion to gill tissues, suppressing immune function, and inducing tissue damage. These findings enhance our understanding of F. davisii infection mechanisms and support the future breeding of disease-resistant tilapia and the development of sustainable control strategies. Full article

Aeromonas septicemia and columnaris disease are major bacterial diseases in grass carp; however, the drugs currently used to control these diseases pose environmental and health risks. This study aimed to screen for a probiotic Bacillus strain with antagonistic activity to prevent and control bacterial diseases in grass carp and to evaluate the antimicrobial activities, biosafety, and biocontrol effects of this strain. A Bacillus strain with antagonistic activity against Aeromonas hydrophila, obtained from grass carp intestines, was screened, and the isolate CYS06 was identified by analyzing the 16S rRNA and gyrA gene sequences. The antimicrobial spectrum of the strain CYS06 was determined, and the activities of amylase, cellulase, protease, and lipase of the strain CYS06 were determined. The whole genome of the strain CYS06 was sequenced using the nanopore sequencing technology platform, followed by the analysis of the antagonistic substance synthesis gene clusters and CAZy enzyme gene families. The biosafety of the strain CYS06 was evaluated via intraperitoneal injection into healthy grass carp. After the strain CYS06 was fed to the grass carp, its biological control effect on this fish was evaluated through artificial infection experiments. The strain CYS06 was identified as Bacillus velezensis, based on molecular identification, which shows broad antimicrobial activity against various fish pathogens. The strain CYS06 secretes amylase, cellulase, protease, and lipase. The genome size of the strain CYS06 is 3,914,159 bp, and it contains eight antagonistic substance synthesis gene clusters and many CAZy enzymes. The strain CYS06 exhibits high biological safety for grass carp, based on the challenge test. Feeding grass carp with the strain CYS06 for 4 weeks significantly enhanced the resistance of the fish to A. hydrophila. Strain CYS06 could inhibit the growth of Flavobacterium columnare under co-culture and reduce the amount of F. columnare adherence on the gills of grass carp, indicating that CYS06 has good potential for the prevention and control of columnaris disease. In conclusion, we isolated an antagonistic probiotic strain, CYS06, which exhibits a biological control effect on septicemia and columnaris disease caused by Aeromonas spp. and F. columnare in grass carp, respectively. This strain contains many antagonistic substance synthesis-related gene clusters and holds the potential to degrade various types of carbohydrates. As a biological control agent, the strain CYS06 exhibits significant potential for the prevention and control of bacterial diseases in grass carp. Full article

In the present study, chitosan-based bivalent nanovaccines of S. iniae and F. covae were administered by immersion vaccination at 30 and 40 days after hatching (DAH), and the third vaccination was orally administered by feeding at 50 DAH. ELISA revealed that the levels of total IgM and specific IgM to S. iniae and F. covae were significantly elevated in all vaccinated groups at 10, 20, and 30 days after vaccination (DAV). A qRT-PCR analysis of immune-related genes revealed significantly higher IgT expression in the vaccinated groups compared to the control group, as revealed by 44–100-fold changes in the vaccinated groups compared to the control (p < 0.001) at every tested time point after vaccination. All vaccinated groups expressed IgM, MHCIIα, and TCRα at significantly higher levels than the control group at 10 and/or 20 DAV (p < 0.05). In the S. iniae challenge tests, the survival of vaccinated groups ranged from 62.15 ± 2.11 to 75.70 ± 3.36%, which significantly differed from that of the control group (44.44 ± 1.92%). Similarly, all vaccinated groups showed higher survival rates of 68.89 ± 3.85 to 77.78 ± 5.09% during F. covae challenge than the control groups (50.00 ± 3.33%) (p < 0.05). Full article

Aquaculture farms in Arkansas, USA routinely battle columnaris disease caused by Flavobacterium covae. Columnaris is prevalent during stressful events such as feed training and when fish are stocked at high densities in holding vats before sale. Kaolin clay was effective in laboratory trials as a treatment for columnaris in catfish. As a result, fish farmers are interested in applying kaolin products but were hesitant as they feared that the high doses of kaolin clay in vats might negatively affect the gills and overall health of fish. Therefore, we evaluated potential clay concentrations that might be used to prophylactically treat fish in vats. The effects of low to excessively high doses (0, 1, 2, 4, or 8 g/L) of kaolin clay (AkuaPro^TM, Imerys, GA, USA) were evaluated using a 72 h bioassay conducted in static tanks using Micropterus salmoides, Pomoxis nigromaculatus, Lepomis macrochirus, Ictalurus punctatus, Notemigonus crysoleucas, and Pimephales promelas. Results of these trials revealed a 100% survival rate across all six fish species exposed to kaolin clay at concentrations of up to 8 g/L for 48 h (followed by a 24 h recovery period in clean water) with no adverse effects to eyes, skin, gastrointestinal tract, or liver histology noted at any treatment. In addition, Micropterus salmoides analyzed for heavy metals due to exposure to the clay indicated that concentrations did not differ from control fish. Full article

Two prevalent bacterial diseases in catfish aquaculture are enteric septicemia of catfish and columnaris disease caused by Edwardsiella ictaluri and Flavobacterium covae, respectively. Chronic and recurring outbreaks of these bacterial pathogens result in significant economic losses for producers annually. Determining if these pathogens can persist within sediments of commercial ponds is paramount. Experimental persistence trials (PT) were conducted to evaluate the persistence of E. ictaluri and F. covae in pond sediments. Twelve test chambers containing 120 g of sterilized sediment from four commercial catfish ponds were inoculated with either E. ictaluri (S97-773) or F. covae (ALG-00-530) and filled with 8 L of disinfected water. At 1, 2, 4-, 6-, 8-, and 15-days post-inoculation, 1 g of sediment was removed, and colony-forming units (CFU) were enumerated on selective media using 6 × 6 drop plate methods. E. ictaluri population peaked on Day 3 at 6.4 ± 0.5 log₁₀ CFU g⁻¹. Correlation analysis revealed no correlation between the sediment physicochemical parameters and E. ictaluri log₁₀ CFU g⁻¹. However, no viable F. covae colonies were recovered after two PT attempts. Future studies to improve understanding of E. ictaluri pathogenesis and persistence, and potential F. covae persistence in pond bottom sediments are needed. Full article

Columnaris disease caused by Flavobacterium covae leads to substantial economic losses in commercially important fish species worldwide. The US channel catfish (Ictalurus punctatus) industry is particularly vulnerable to this disease. Therefore, there is an urgent need to develop a vaccine to reduce the economic losses caused by this disease. Secreted extracellular products (SEPs) are considered to be essential bacterial virulence factors that often provide immunogenicity and protection. The current study sought to identify the main SEPs of F. covae and to evaluate their potential to provide protection in channel catfish against columnaris disease. SDS-PAGE analysis of SEPs revealed five protein bands with molecular weights ranging from 13 to 99 kDa. Mass spectrometry analysis showed that these SEPs were hypothetical protein (AWN65_11950), zinc-dependent metalloprotease (AWN65_10205), DNA/RNA endonuclease G (AWN65_02330), outer membrane protein beta-barrel domain (AWN65_12620), and chondroitin-sulfate-ABC endolyase/exolyase (AWN65_08505). Catfish fingerlings were vaccinated with SEPs, SEPs emulsified with mineral oil adjuvant, or heat-inactivated SEPs, or they were sham-immunized through intraperitoneal (IP) injection. After 21 days, an F. covae challenge showed 58.77% and 46.17% survival in the catfish vaccinated with the SEPs and the SEPs emulsified with adjuvant compared to the sham-vaccinated control (100% mortality within 120 h post-infection). However, the heat-inactivated SEPs failed to provide significant protection (23.15% survival). In conclusion, although SEPs contain potentially important immunogenic proteins, further work is needed to optimize their use for long-lasting protection against columnaris disease in fish. These results are significant given the economic impact of columnaris disease on fish farming worldwide. Full article

Biotic and abiotic plant stress (e.g., frost, fungi, diseases) can significantly impact crop production. It is thus essential to detect such stress at an early stage before visual symptoms and damage become apparent. To this end, this paper proposes a novel deep learning method, called Spectral Convolution and Channel Attention Network (SC-CAN), which exploits the difference in spectral responses of healthy and stressed crops. The proposed SC-CAN method comprises two main modules: (i) a spectral convolution module, which consists of dilated causal convolutional layers stacked in a residual manner to capture the spectral features; (ii) a channel attention module, which consists of a global pooling layer and fully connected layers that compute inter-relationship between feature map channels before scaling them based on their importance level (attention score). Unlike standard convolution, which focuses on learning local features, the dilated convolution layers can learn both local and global features. These layers also have long receptive fields, making them suitable for capturing long dependency patterns in hyperspectral data. However, because not all feature maps produced by the dilated convolutional layers are important, we propose a channel attention module that weights the feature maps according to their importance level. We used SC-CAN to classify salt stress (i.e., abiotic stress) on four datasets (Chinese Spring (CS), Aegilops columnaris (co(CS)), Ae. speltoides auchery (sp(CS)), and Kharchia datasets) and Fusarium head blight disease (i.e., biotic stress) on Fusarium dataset. Reported experimental results show that the proposed method outperforms existing state-of-the-art techniques with an overall accuracy of 83.08%, 88.90%, 82.44%, 82.10%, and 82.78% on CS, co(CS), sp(CS), Kharchia, and Fusarium datasets, respectively. Full article

Vaccines are widely employed in aquaculture to prevent bacterial infections, but their use by the U.S. catfish industry is very limited. One of the main diseases affecting catfish aquaculture is columnaris disease, caused by the bacterial pathogen Flavobacterium columnare. In 2011, a modified-live vaccine against columnaris disease was developed by selecting mutants that were resistant to rifampin. The previous study has suggested that this vaccine is stable, safe, and effective, but the mechanisms that resulted in attenuation remained uncharacterized. To understand the molecular basis for attenuation, a comparative genomic analysis was conducted to identify specific point mutations. The PacBio RS long-read sequencing platform was used to obtain draft genomes of the mutant attenuated strain (Fc1723) and the parent virulent strain (FcB27). Sequence-based genome comparison identified 16 single nucleotide polymorphisms (SNP) unique to the mutant. Genes that contained mutations were involved in rifampin resistance, gliding motility, DNA transcription, toxin secretion, and extracellular protease synthesis. The results also found that the vaccine strain formed biofilm at a significantly lower rate than the parent strain. These observations suggested that the rifampin-resistant phenotype and the associated attenuation of the vaccine strain result from the altered activity of RNA polymerase (RpoB) and possible disrupted protein secretion systems. Full article

Immersion vaccination with a biomimetic mucoadhesive nanovaccine has been shown to induce a strong mucosal immune response against columnaris disease, a serious bacterial disease in farmed red tilapia caused by Flavobacterium columnare. However, the induction of a systemic immune response by the vaccine is yet to be investigated. Here, we examine if a specific humoral immune response is stimulated in tilapia by a biomimetic-mucoadhesive nanovaccine against Flavobacterium columnare using an indirect-enzyme-linked immunosorbent assay (ELISA), serum bactericidal activity (SBA) and the expression of immune-related genes within the head-kidney and spleen, together with assessing the relative percent survival of vaccinated fish after experimentally infecting them with F. columnare. The anti-IgM antibody titer of fish at 14 and 21 days post-vaccination was significantly higher in chitosan complex nanoemulsion (CS-NE) vaccinated fish compared to fish vaccinated with the formalin-killed vaccine or control fish, supporting the serum bactericidal activity results at these time points. The cumulative mortality of the unvaccinated control fish was 87% after challenging fish with the pathogen, while the cumulative mortality of the CS-NE vaccinated group was 24%, which was significantly lower than the formalin-killed vaccinated and control fish. There was a significant upregulation of IgM, IgT, TNF α, and IL1-β genes in the spleen and kidney of vaccinated fish. Significant upregulation of IgM and IgT genes was observed in the spleen of CS-NE vaccinated fish. The study confirmed the charged-chitosan-based mucoadhesive nanovaccine to be an effective platform for immersion vaccination of tilapia, with fish generating a humoral systemic immune response against columnaris disease in vaccinated fish. Full article

Viruses of bacteria, bacteriophages, specifically infect their bacterial hosts with minimal effects on the surrounding microbiota. They have the potential to be used in the prevention and treatment of bacterial infections, including in the field of food production. In aquaculture settings, disease-causing bacteria are often transmitted through the water body, providing several applications for phage-based targeting of pathogens, in the rearing environment, and in the fish. We tested delivery of phages by different methods (via baths, in phage-coated material, and via oral delivery in feed) to prevent and treat Flavobacterium columnare infections in rainbow trout fry using three phages (FCOV-S1, FCOV-F2, and FCL-2) and their hosts (FCO-S1, FCO-F2, and B185, respectively). Bath treatments given before bacterial infection and at the onset of the disease symptoms were the most efficient way to prevent F. columnare infections in rainbow trout, possibly due to the external nature of the disease. In a flow-through system, the presence of phage-coated plastic sheets delayed the onset of the disease. The oral administration of phages first increased disease progression, although total mortality was lower at the end of the experiment. When analysed for shelf-life, phage titers remained highest when maintained in bacterial culture media and in sterile lake water. Our results show that successful phage therapy treatment in the aquaculture setting requires optimisation of phage delivery methods in vivo. Full article

Enteric septicemia of catfish, columnaris disease and streptococcosis, caused by Edwardsiella ictaluri, Flavobacterium columnare and Streptococcus iniae, respectively, are the most common bacterial diseases of economic significance to the pond-raised channel catfish Ictalurus punctatus industry. Certain management practices are used by catfish farmers to prevent large financial losses from these diseases such as the use of commercial antibiotics. In order to discover environmentally benign alternatives, using a rapid bioassay, we evaluated a crude extract from the roots of muscadine Vitis rotundifolia against these fish pathogenic bacteria and determined that the extract was most active against F. columnare. Subsequently, several isolated compounds from the root extract were isolated. Among these isolated compounds, (+)-hopeaphenol (2) and (+)-vitisin A (3) were found to be the most active (bacteriostatic activity only) against F. columnare, with 24-h 50% inhibition concentrations of 4.0 ± 0.7 and 7.7 ± 0.6 mg/L, respectively, and minimum inhibitory concentrations of 9.1 ± 0 mg/L for each compound which were approximately 25X less active than the drug control florfenicol. Efficacy testing of 2 and 3 is necessary to further evaluate the potential for these compounds to be used as antibacterial agents for managing columnaris disease. Full article