Fish Pathogens: An Ongoing Challenge for Aquaculture

A special issue of Pathogens (ISSN 2076-0817).

Deadline for manuscript submissions: 30 September 2025 | Viewed by 2702

Special Issue Editors


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Guest Editor
Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Former American Base of Gournes, Heraklion 71500, Crete, Greece
Interests: fish diseases; phage therapy; microbiology; marine aquaculture; biotechnology; vaccine development
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Guest Editor
Laboratory of Applied Hydrobiology, Department of Animal Science, School of Animal Biosciences, Agricultural University of Athens, 11855 Athens, Greece
Interests: fish diseases; microbiology; parasitology; virology; control; prevention

Special Issue Information

Dear Colleagues,

The growing global demand for seafood, coupled with the limited capacity of the wild-caught sector to meet this demand, has led to continued growth of the aquaculture industry around the world. According to FAO data, global aquaculture production has already exceeded that of wild-caught fish, providing approximately half of global fish consumption. Fish pathogens pose significant challenges to the aquaculture industry. These pathogens refer to a series of microorganisms that can cause fish diseases during the aquaculture process, including bacteria, viruses, fungi, parasites, etc. They can seriously affect the growth, development, and yield of farmed fish, and even lead to mass fish mortality, affecting the sustainability of aquaculture practices and causing huge economic losses to the aquaculture industry. Insights into the molecular machinations of virulence factors employed by these pathogens will be pivotal in unraveling their pathogenicity and devising targeted therapeutic or preventive strategies. Moreover, a comprehensive understanding of the economic dimensions of fish diseases, encompassing both direct production losses and broader market impacts, will be crucial for informing sustainable aquaculture practices and policy interventions.

This Special Issue aims to collect the latest research on fish pathogens, elucidating their impacts, significance, and current research focuses. This call for submissions extends to researchers engaged in marine and freshwater aquaculture, recognizing the global significance of fish pathogens across diverse aquatic environments. Contributions elucidating the molecular intricacies of the host–pathogen interplay, deciphering virulence determinants, and assessing the economic ramifications of fish diseases are particularly encouraged. We eagerly anticipate the submission of your latest findings, poised to enrich our collective understanding of fish pathogens and pave the way for innovative solutions to safeguard the future of aquaculture.

Dr. Pantelis Katharios
Dr. Bitchava Konstantina
Guest Editors

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Keywords

  • aquaculture pathogens
  • host–pathogen interactions
  • virulence factors
  • economic burden of fish diseases

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Published Papers (3 papers)

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Research

17 pages, 2295 KiB  
Article
Characterization of Microbiome Diversity in the Digestive Tract of Penaeus vannamei Fed with Probiotics and Challenged with Vibrio parahaemolyticus Acute Hepatopancreatic Necrosis Disease
by Lucio Galaviz-Silva, Abraham O. Rodríguez de la Fuente, Ricardo Gomez-Flores, José C. Ibarra-Gámez, Itza Eloisa Luna-Cruz, Joel H. Elizondo-Luevano, Ricardo Sánchez-Díaz and Zinnia J. Molina Garza
Pathogens 2025, 14(4), 320; https://doi.org/10.3390/pathogens14040320 - 27 Mar 2025
Viewed by 405
Abstract
The microbiome of the shrimp’s digestive tract shows differences between healthy and acute hepatopancreatic necrosis disease (AHPND)-affected shrimp. The present study aimed to evaluate the impact of probiotic consumption on the microbial community in experimentally AHPND-infected shrimp. Effective probiotics (EPs) Vibrio alginolyticus (Va32A), [...] Read more.
The microbiome of the shrimp’s digestive tract shows differences between healthy and acute hepatopancreatic necrosis disease (AHPND)-affected shrimp. The present study aimed to evaluate the impact of probiotic consumption on the microbial community in experimentally AHPND-infected shrimp. Effective probiotics (EPs) Vibrio alginolyticus (Va32A), V. campbellii (VcHA), and Bacillus pumilus (BPY100) and non-effective probiotics (NEPs) B. pumilus (Bp43, and BpY119), were employed in bioassays with Penaeus vannamei and challenged with AHPND-causing V. parahaemolyticus (VpAHPND). Stomach (Sto), intestine (Int), and hepatopancreas (Hep) were analyzed by metabarcoding (16S rRNA gene) to characterize the microbiome and biomarkers. Hep-VcHA showed the highest alpha diversity (Shannon index = 5.88; 166 ASVs), whereas the lowest was for Hep-Bp43 (2.33; 7 ASVs). Proteobacteria, Actinobacteria, Bacteroidetes, and Saccharibacteria were the most abundant phyla. The relative abundance of Vibrio sp. was the highest in the Hep and Int of Bp43, BPY119 and the positive control, followed by Rhodobacteraceae in the EP group. Principle coordinate analysis (PCoA) showed a cluster grouped negative (Sto and Hep) control with almost all organs in the EP group causing 28.79% of the variation. The core microbiome of EP was mainly represented by Rhodobacteraceae, Caldilineaceae, Celeribacter indicus, Illumatobacter, Microbacterium, Ruegeria atlantica, Saccharibacteria sp., Shimia biformata, and Thalassobius mediterraneus, whose relative abundance was enriched by probiotics, which may explain their protective roles against VpAHPND, whereas the low survival in the NEP group was associated with a higher diversity of Vibrio spp. Our results present an ecosystem-friendly alternative based on beneficial microorganisms to prevent and control AHPND and probably other bacterial diseases in shrimp farming. Full article
(This article belongs to the Special Issue Fish Pathogens: An Ongoing Challenge for Aquaculture)
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15 pages, 2282 KiB  
Article
Development and Characterization of Fluorescent Protein-Tagged Vibrio harveyi Strains as a Versatile Tool for Studying Infection Dynamics and Strain Interactions
by Charalampos Chalmoukis, Stavros Droubogiannis, Vassiliki A. Michalopoulou, Adriana Triga, Panagiotis F. Sarris and Pantelis Katharios
Pathogens 2025, 14(3), 247; https://doi.org/10.3390/pathogens14030247 - 3 Mar 2025
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Abstract
Fluorescent protein-tagged bacterial strains are widely used tools for studying host-pathogen interactions and microbial dynamics. In this study, we developed and characterized Vibrio harveyi strains genetically modified to express green fluorescent protein (GFP) and red fluorescent protein (RFP). These strains were constructed using [...] Read more.
Fluorescent protein-tagged bacterial strains are widely used tools for studying host-pathogen interactions and microbial dynamics. In this study, we developed and characterized Vibrio harveyi strains genetically modified to express green fluorescent protein (GFP) and red fluorescent protein (RFP). These strains were constructed using triparental mating and evaluated for phenotypic, genomic, and virulence attributes. Genomic analyses revealed strain-specific variations, including mutations in key regulatory and metabolic genes, such as luxO and transketolase. While plasmid acquisition imposed metabolic costs, resulting in altered growth and antibiotic sensitivities in certain transconjugants, others demonstrated robust phenotypic stability. Virulence assays using gilthead seabream larvae revealed that most tagged strains retained moderate pathogenicity, with visualization of co-infections highlighting the potential for studying strain-specific interactions. Furthermore, fluorescent microscopy confirmed the successful colonization and localization of tagged bacteria within host tissues. These findings underscore the utility of GFP- and RFP-tagged Vibrio harveyi as versatile tools for infection dynamics, offering a foundation for future research on strain interactions and pathogen-host relationships. Full article
(This article belongs to the Special Issue Fish Pathogens: An Ongoing Challenge for Aquaculture)
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17 pages, 1752 KiB  
Article
Identification and Phylogenetic Analysis of Flavobacterium spp. Associated with Aquaculture Fish Diseased from Brazil
by Peter Charrie Janampa-Sarmiento, Henrique Lopes Costa, Júlio César Câmara Rosa, Guilherme Campos Tavares and Henrique César Pereira Figueiredo
Pathogens 2025, 14(3), 219; https://doi.org/10.3390/pathogens14030219 - 22 Feb 2025
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Abstract
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 [...] Read more.
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
(This article belongs to the Special Issue Fish Pathogens: An Ongoing Challenge for Aquaculture)
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