Search Results (131)

Background/Objectives: This study examines how seasonality, pollution, and sample type (water and sediment) influence the presence and distribution of antibiotic resistance genes (ARGs), with a focus on antibiotic resistance genes (ARGs) located on plasmids (the complete set of plasmid-derived sequences, including ARGs) in a tropical urban river. Methods: Samples were collected from three sites along a pollution gradient in the Virilla River, Costa Rica, during three seasonal campaigns (wet 2021, dry 2022, and wet 2022). ARGs in water and sediment were quantified by qPCR, and metagenomic sequencing was applied to analyze chromosomal and plasmid-associated resistance profiles in sediments. Tobit and linear regression models, along with multivariate ordination, were used to assess spatial and seasonal trends. Results: During the wet season of 2021, the abundance of antibiotic resistance genes (ARGs) such as sul-1, intI-1, and tetA in water samples decreased significantly, likely due to dilution, while intI-1 and tetQ increased in sediments, suggesting particle-bound accumulation. In the wet season 2022, intI-1 remained low in water, qnrS increased, and sediments showed significant increases in tetQ, tetA, and qnrS, along with decreases in sul-1 and sul-2. Metagenomic analysis revealed spatial differences in plasmid-associated ARGs, with the highest abundance at the most polluted site (Site 3). Bacterial taxa also showed spatial differences, with greater plasmidome diversity and a higher representation of potential pathogens in the most contaminated site. Conclusions: Seasonality and pollution gradients jointly shape ARG dynamics in this tropical river. Plasmid-mediated resistance responds rapidly to environmental change and is enriched at polluted sites, while sediments serve as long-term reservoirs. These findings support the use of plasmid-based monitoring for antimicrobial resistance surveillance in aquatic systems. Full article

Streptococcus iniae (S. iniae) is a globally significant aquatic pathogen responsible for severe economic losses in aquaculture. While the S. iniae infection often exhibits distinct seasonal patterns strongly correlated with water temperature, there is limited knowledge regarding the temperature-dependent immune evasion strategies of S. iniae. Our results demonstrated a striking temperature-dependent virulence phenotype, with significantly higher A. latus mortality rates observed at high temperature (HT, 33 °C) compared to low temperature (LT, 23 °C). Proteomic analysis revealed temperature-dependent upregulation of key virulence factors, including streptolysin S-related proteins (SagG, SagH), antioxidant-related proteins (SodA), and multiple capsular polysaccharide (cps) synthesis proteins (cpsD, cpsH, cpsL, cpsY). Flow cytometry analysis showed that HT infection significantly reduced the percentage of lymphocyte and myeloid cell populations in the head kidney leukocytes of A. latus, which was associated with elevated caspase-3/7 expression and increased apoptosis. In addition, HT infection significantly inhibited the release of reactive oxygen species (ROS) but not nitric oxide (NO) production. Using S. iniae cps-deficient mutant, Δcps, we demonstrated that the cps is essential for temperature-dependent phagocytosis resistance in S. iniae, as phagocytic activity against Δcps remained unchanged across temperatures, while NS-1 showed significantly reduced uptake at HT. These findings provide new insights into the immune evasion of S. iniae under thermal regulation, deepening our understanding of the thermal adaptation of aquatic bacterial pathogens. Full article

Korean rockfish, Sebastes schlegeli, a coastal species, is vulnerable to pollutants such as microplastics and bacteria. While interactions between microplastics and other pollutants have been studied, little is known about microplastic and bacteria interactions. This study examined the effects of combined exposure to polystyrene microplastics in the form of microbeads (MB; 0.2 µm, 5 and 50 beads/L) and Streptococcus iniae (1 × 10⁵ and 1 × 10⁷ CFU/mL) for five days on oxidative stress and apoptosis in Korean rockfish. We assessed the mRNA expression and activity of oxidative stress markers (SOD, CAT, H₂O₂, NO, CYP1A1, GST), plasma LPO levels, and caspase-3 expression in liver tissue. Co-exposure to high MB and S. iniae concentrations significantly elevated oxidative stress and apoptosis markers, suggesting enhanced toxicity. This may result from MB facilitating pathogen transport into the fish, indicating microplastics can act as vectors for bacterial infection in aquatic environments. Full article

The growth of aquaculture production in recent years has revealed multiple challenges, including the rise of antimicrobial resistance (AMR) in aquatic animal production, which is currently attracting significant attention from multiple one-health stakeholders. While antibiotics have played a major role in the treatment of bacterial infections for almost a century, a major consequence of their use is the increase in AMR, including the emergence of AMR in aquaculture. The AMR phenomenon creates a situation where antibiotic use in one system (e.g., aquaculture) may impact another system (e.g., terrestrial–human). Non-prudent use of antibiotics in aquaculture and animal farming increases the risk of AMR emergence, since bacteria harboring antibiotic resistance genes can cross between compartments such as wastewater or other effluents to aquatic environments, including intensive aquaculture. Transferable antimicrobial resistance gene (AMG) elements (plasmids, transposons, integrons, etc.) have already been detected in varying degrees from pathogenic bacteria that are often causing infections in farmed fish (Aeromonas, Vibrio, Streptococcus, Pseudomonas, Edwardsiella, etc.). This review of current veterinary approaches for the prevention and control of AMR emergence in aquaculture focuses on the feasibility of alternatives to antimicrobials and supplemental treatment applications during on-farm bacterial disease control and prevention. The use of vaccines, bacteriophages, biosurfactants, probiotics, bacteriocins, and antimicrobial peptides is discussed. Full article

Traditional hazard identification techniques for Vibrio parahaemolyticus often neglect the distinction between viable and nonviable bacteria in aquatic products, leading to overestimated disease risks and uncertainties in risk assessments. To address this limitation, we developed an automated PMA pretreatment instrument that integrates dark incubation and photo-crosslinking into a unified workflow, allowing customizable parameters such as incubation time, light exposure duration, and mixing speed while maintaining stable temperatures (<±1 °C fluctuation) to preserve bacterial DNA integrity. Leveraging this system, a duplex qPCR assay was optimized for simultaneous quantitative detection of V. parahaemolyticus and V. cholerae in aquatic products and environmental samples. The assay demonstrated robust performance with 90–110% amplification efficiencies across diverse matrices, achieving low limits of detection (LODs) of 10¹–10² CFU/mL in shrimp farming environment water and 10²–10³ CFU/g in shrimp (Litopenaeus vannamei) and oyster (Crassostrea gigas). Notably, it effectively discriminated viable bacteria from 10⁶ CFU/mL(g) nonviable cells and showed strong correlation with ISO-standard methods in real-world sample validation. This integrated platform offers a rapid, automated solution for accurate viable bacterial quantification, with significant implications for food safety, pathogen surveillance, and risk management in aquatic industries. Full article

In recent years, viral and bacterial diseases have posed serious challenges to the sustainable development of Macrobrachium rosenbergii (giant freshwater prawn) aquaculture, resulting in considerable economic losses across China. Among the bacterial pathogens, Aeromonas caviae has emerged as a notable opportunistic agent capable of causing large-scale mortality in various aquatic species. In this study, a highly virulent strain of A. caviae (designated GMRS4) was isolated from diseased M. rosenbergii exhibiting mass mortality in Yangzhou, Jiangsu Province. The isolate, a Gram-negative bacillus, was identified as the causative agent based on morphological, molecular, and histopathological analyses. Pathogenicity was confirmed through experimental infection, with the strain displaying marked virulence, evidenced by an LD₅₀ of 1.91 × 10⁶ CFU/mL at 96 h. Whole-genome sequencing of GMRS4 revealed 4078 coding sequences, including a suite of virulence-associated genes encoding extracellular enzymes (DNase, hemolysin, caseinase, and lecithinase) and toxins (serine protease, elastase, and flagellin). Antimicrobial susceptibility testing indicated resistance to several antibiotics, particularly those in the penicillin and sulfonamide classes, while maintaining sensitivity to quinolones. Genomic analysis further revealed multiple antibiotic resistance genes and virulence genes, offering insights into the pathogenic mechanisms and resistance profile of the strain. This study underscores the threat posed by A. caviae to freshwater prawn aquaculture and provides a genetic basis for developing targeted disease management strategies. Full article

Heat shock proteins (HSPs), particularly HSP70, play a vital role in fish immune defense against pathogens. The administration of DnaK (bacterial homolog of HSP70) may be a strategy to potentiate the immune response and survival of aquatic organisms. This study evaluates the effect of cells overexpressing DnaK on mortality and immune-related gene expression in gnotobiotic sea bass larvae challenged with Vibrio anguillarum. Larvae were subjected to different treatments: NB (no bacteria), YS0 (E. coli with no plasmid), YS1 (E. coli expressing truncated DnaK), and YS2 (E. coli expressing DnaK), and then infected with V. anguillarum at 7 days post-hatching (dph). Mortality was monitored, and RT-qPCR was used to evaluate immune gene expression at 0, 18, 24, 36, and 120 hpc. While no significant variations were recorded in the non-challenged larvae, constant and sustained mortality was observed in challenged larvae from 60 to 120 hpc. However, lower mortality was observed in the larvae treated with DnaK. DnaK treatment promoted the expression of antimicrobial (hepcidin, transferrin) and chemotaxis genes (ccl4), which was further enhanced after a challenge with V. anguillarum, in conjunction with the modulation of il1β and il-8 at 120 hpc. These findings suggest that DnaK induces a potent innate immune response, improving survival against V. anguillarum and supporting its potential use as a disease-preventive strategy in aquaculture. Full article

Mycobacterium marinum is an opportunistic pathogen prevalent in aquatic environments, causing significant morbidity in fish, including Coho salmon (Oncorhynchus kisutch), a species increasingly cultured in Chinese salmonid aquaculture. This study investigated the immune response of Coho salmon to M. marinum infection and the bacterial proliferation dynamics in the liver and kidney. Transcriptome analysis revealed 5028 differentially expressed genes (DEGs) in the kidney and 3419 DEGs in the liver at 6 weeks post-infection. Gene Ontology and KEGG enrichment analysis highlighted pathways such as cytokine–cytokine receptor interaction, metabolic pathways, and Toll-like receptor signaling in the kidney, while the DEGs in the liver were enriched in metabolic pathways, immune system processes, and stress and defense responses. The temporal expression profiling of 15 immune-related genes, including acute-phase proteins (serum amyloid A-5 and hepcidin), cytokines (TNF-α, IL-1β, IL-17A), chemokines (CXCL13 and CCL19), pattern recognition receptors (Toll-like receptor 13), and other immune-related genes, showed significant upregulation against M. marinum infection, with stronger responses in the liver. Furthermore, it was found that there was a progressive proliferation of M. marinum in the infected liver and kidney from approximately 2.5 log₁₀ cfu/g at week 2 to about 6 log₁₀ cfu/g by 6 weeks, with a significantly higher load in the liver. These findings provide critical insights into the immune mechanisms of Coho salmon against M. marinum and the pathogen’s tissue-specific proliferation, offering a foundation for developing targeted control strategies against M. marinum in aquaculture. Full article

Aquaponics is an integrated method of aquatic animal and plant cultivation in a closed recycling system where the wastewater from aquatic animals is purified by microbes, which transform pollutants into nutrients for plants at the end of the chain. This technology allows to the efficiency of the area to be increased by a combination of cultivated plants and aquatic animals. Aquaponics produces environmentally friendly products by reducing fertilizer use and wastewater volume, increasing the extent of reuse by up to >90%. A promising way to increase efficiency in aquaponics is to use bacterial preparations (probiotics). This will allow control of the development of pathogens in the growing system, improving water quality and the growth rate of aquatic organisms. This paper overviews the experience of using probiotic preparations in aquaponic systems. It is shown that probiotics are able to increase the survival rate of aquatic organisms, improve the hydrochemical regime in recirculating aquaculture systems, and mitigate the risk of pathogenic contamination. There are a number of problems in aquaponics that prevent it from becoming more widespread and achieving maximum productivity, including problems with optimal pH and temperature, problems with nutrient and oxygen depletion, as well as diseases caused by phytopathogens and fish pathogens. The probiotics used do not take into account the biological needs of all components of the aquaponic system. The development of probiotic preparations from soil bacteria of the genus Bacillus will allow us to create a new class of probiotics specifically for aquaponics. Such preparations will work in a wide pH range, which will allow us to achieve maximum productivity for all components of aquaponics: animals, plants and bacteria. Full article

Background: The marine bacterium Vibrio campbellii has been a model system for the study of bacterial quorum sensing and is increasingly recognized as a formidable aquatic animal pathogen. While genetically tractable, the study of this species in basic and applied research still relies upon laborious and time-consuming conjugation methods for plasmid DNA transformation. Methods: In this study, we developed an electroporation protocol using the most studied strain of this species, V. campbellii ATCC BAA-1116. An electroporation efficiency of up to 3 × 10⁴ CFU/μg DNA was demonstrated using derived parameters (10 kV/cm, 400 Ω, 25 μF), which took cell growth phase at harvest, plasmid DNA amount, and recovery conditions into account. The electroporation protocol was tested using several different plasmids and with additional strains of V. campbellii and sister species V. harveyi. Results: Interestingly, of the eight other V. campbellii strains tested, only three others, which also happened to be the three most recent environmental isolates with the fewest number of laboratory passages, were amenable to electroporation-mediated transformation. Conclusions: This electroporation protocol expands the tool set for studying V. campbellii and provides interesting insights into DNA transformation and uptake in this and related bacterial species. Full article

Aquatic products play a crucial role in meeting the increasing global demands for high-quality proteins. However, the occurrence of bacterial diseases results in significant economic losses worldwide. Aeromonas hydrophila (A. hydrophila) is the pathogen of several fish diseases. Antibiotics were widely used in combating bacterial diseases in aquaculture. The increasing occurrences of antibiotic resistance necessitate the restricted use of antibiotics. Consequently, developing drugs that avoid antibiotic resistance is important for the future of aquaculture. Quorum sensing (QS) is critical for bacterial pathogens in regulating bacterial virulence and is a promising target for developing anti-infective agents. Here, we found that turmeric oil with a MIC of 256 μg/mL could dose-dependently reduce the virulence phenotypes regulated by QS, ranging from 8 to 64 μg/mL, suggesting that sub-inhibitory concentrations of turmeric oil could inhibit bacterial virulence. Further qPCR findings demonstrated that turmeric oil could significantly inhibit the transcription of aerA, ahyI, and ahyR by a 54-fold, 36-fold, and 56-fold change reduction, respectively. Cell live/dead staining and animal study results showed that turmeric oil could inhibit the pathogenicity of A. hydrophila. Fish treated with turmeric oil showed a reduced mortality rate of 60%, whereas all fish in the positive control group died. Moreover, treatment with turmeric oil could alleviate the renal injury. Collectively, the results suggested that targeting bacterial virulence might be a useful approach to combating bacterial infections, and turmeric oil could serve as a potential agent for combating A. hydrophila infections. Full article

Bacterial diseases cause high mortality and considerable losses in aquaculture. The rapid expansion of intensive aquaculture has further increased the risk of large-scale outbreaks. However, the emergence of drug-resistant bacteria, food safety concerns, and environmental regulations have severely limited the availability of antimicrobial. Compared to traditional antibiotics, antimicrobial peptides (AMPs) offer broad spectrum activity, physicochemical stability, and lower resistance development. However, their low natural yield and high extraction costs along with the time-consuming and expensive nature of traditional drug discovery, pose a challenge. In this study, we applied a machine-learning macro-model to predict AMPs from three macrogenomes in the water column of South American white shrimp aquaculture ponds. The AMP content per megabase in the traditional earthen pond (TC1) was 1.8 times higher than in the biofloc pond (ZA1) and 63% higher than in the elevated pond (ZP11). A total of 1033 potential AMPs were predicted, including 6 anionic linear peptides, 616 cationic linear peptides, and 411 cationic cysteine-containing peptides. After screening based on structural, and physio-chemical properties, we selected 10 candidate peptides. Using a rapid high-throughput cell-free protein expression system, we identified nine peptides with antimicrobial activity against aquatic pathogens. Three were further validated through chemical synthesis. The three antimicrobial peptides (K-5, K-58, K-61) showed some inhibitory effects on all four pathogenic bacteria. The MIC of K-5 against Vibrio alginolyticus was 25 μM, the cell viability of the three peptides was higher than 70% at low concentrations (≤12.5 μM), and the hemolysis rate of K-5 and K-58 was lower than 5% at 200 μM. This study highlights the benefits of machine learning in AMP discovery, demonstrates the potential of cell-free protein synthesis systems for peptide screening, and provides an efficient method for high-throughput AMP identification for aquatic applications. Full article

Pathogenic infections can reshape the intestinal microbiota of aquatic animals, thereby impacting their health status. In this study, we aimed to investigate whether Vibrio parahaemolyticus infection induces dysbiosis in the intestinal bacterial community of Penaeus vannamei and to assess the associated ecological risks. Our findings revealed the deterministic processes in intestinal bacterial community assembly during bacterial infections, indicating that host selection, i.e., host immune response post-infection, has a significant influence on intestinal microbes. More importantly, we found that bacterial infection reshaped the intestinal community by reducing the relative abundance of probiotic Ruegeria species (e.g., R. atlantica, R. lacuscaerulensis, R. conchae, R. profundi, R. arenilitoris, R. pomeroyi) and increasing the relative abundance of Vibrio species (V. harveyi, V. sinaloensis, V. coralliilyticus, and V. brasiliensis). Significant negative correlations were observed between the relative abundance of these Ruegeria species and the relative abundance of Vibrio species. Moreover, the control P. vannamei contained a substantially higher number of keystone species belonging to Ruegeria in the bacterial community network, whereas bacterial infection individuals had few or no keystone species belonging to Ruegeria, with keystone species belonging to Vibrio becoming more prominent. Thus, the significant increase in Vibrio species abundance in the P. vannamei intestine following bacterial infection was associated with the marked reduction in Ruegeria species. Our findings will provide valuable insights into the complex interactions among bacterial infection, intestinal microbiota, and host health, and they provide guidance for the development of probiotics in promoting the healthy culture of P. vannamei. Full article

The Gram-negative genus Aeromonas contains diverse bacterial species that are prevalent in aquatic environments. This present study describes three novel Aeromonas strains: A. ichthyocola sp. nov. A-5^T and A. mytilicola subsp. aquatica subsp. nov. A-8^T isolated from rainbow trout (Oncorhynchus mykiss), and A. mytilicola sp. nov. A-7^T isolated from mussels (Mytilus galloprovincialis), respectively. Genomic analyses revealed that strains A-5^T and A-7^T shared the highest 16S rRNA gene sequence similarity with A. rivipollensis P2G1^T (99.7% and 99.8%, respectively), while strain A-8^T exhibited 99.7% identity with A. media RM^T. Together with morphological, physiological, and biochemical data, genome-based analyses provided additional evidence for species differentiation. Digital DNA–DNA hybridization (dDDH; 56.8−65.9%) and average nucleotide identity (ANI; 94.2–95.7%) values fell below the species delineation thresholds, confirming that these isolates represent distinct taxa. Pathogenicity assays using greater wax moth (Galleria mellonella) larvae demonstrated strain-specific virulence profiles. Further genomic analyses identified biosynthetic gene clusters for nonribosomal peptides (NRPs) and ribosomally synthesized and post-translationally modified peptides (RiPPs), which often have roles in secondary metabolite production. Ecological analyses, based on genomic comparisons and metagenomic database searches, revealed the adaptability of the strains to diverse habitats, including freshwater, wastewater, and activated sludge. Based on the genetic and phenotypic data, the novel taxa Aeromonas ichthyocola sp. nov. A-5ᵀ (LMG 33534ᵀ = DSM 117488ᵀ), Aeromonas mytilicola sp. nov. A-7ᵀ (LMG 33536ᵀ = DSM 117490ᵀ), and Aeromonas mytilicola subsp. aquatica subsp. nov. A-8ᵀ (LMG 33537ᵀ = DSM 117493ᵀ) are proposed. Full article

Aeromonas veronii, Aeromonas hydrophila, Plesiomonas shigelloides, and Citrobacter freundii are opportunistic pathogens that are widely distributed in aquatic environments and fish populations, causing fish diseases under stressful conditions. In this study, bacteria were isolated from a group of diseased common carp, Cyprinus carpio, with symptoms of hemorrhaging along the body surface, abdominal distention, and flatulence in the intestine. According to the results of biochemical characteristics and 16S rRNA sequencing analyses, the isolates were identified as A. veronii, A. hydrophila, P. shigelloides, and C. freundii. The virulence genes from these four representative bacterial strains were amplified. The experimentally co-infected fish showed similar symptoms to those observed in the naturally infected common carp. The LD₅₀ of C. freundii, P. shigelloides, A. veronii, A. hydrophila, and the mixture group were 1.95 × 10⁴, 4.74 × 10⁴, 5.12 × 10⁴, 1.53 × 10⁵, and 5.41 × 10⁴ CFU, respectively. The antibiotic resistance results showed that P. shigelloides, A. veronii, and A. hydrophila were most sensitive to ceftizoxime, florfenicol, enrofloxacin, and norfloxacin. C. freundii was most sensitive to ceftizoxime and gentamicin. Full article