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Fishes
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Infection and Detection of Bacterial Pathogens in Aquaculture
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Infection and Detection of Bacterial Pathogens in Aquaculture

A special issue of Fishes (ISSN 2410-3888). This special issue belongs to the section "Welfare, Health and Disease".

Deadline for manuscript submissions: closed (15 February 2026) | Viewed by 4639

Special Issue Editors

Dr. Asma M. Karami

E-Mail Website
Guest Editor
Department of Veterinary and Animal Sciences, University of Copenhagen, 1870 Copenhagen, Denmark
Interests: aquaculture; selective breeding; natural resistance; vibriosis
Dr. Raquel Rodríguez-Vázquez

E-Mail Website
Guest Editor
Department of Zoology, Genetics and Physical Anthropology, University of Santiago de Compostela, 15705 Santiago de Compostela, Spain
Interests: genetics; bioinformatic analysis; fish immunology; aquaculture; transcriptomics; proteomics; genomics

Special Issue Information

Dear Colleagues,

Aquaculture plays a vital role in global food security, but bacterial infections pose significant challenges, leading to substantial economic losses and threats to aquatic animal health. This Special Issue focuses on the latest advancements in the identification, pathogenesis, and control of bacterial pathogens in aquaculture systems. It explores innovative diagnostic techniques, including molecular and immunological methods, to enhance early detection and disease management. Additionally, the issue examines the impact of antibiotic resistance, the role of microbiota in disease prevention, and sustainable disease control strategies such as probiotics, vaccines, phage therapy and selective breeding. By bringing together cutting-edge research, this collection aims to support the development of effective interventions to safeguard aquaculture productivity and sustainability.

Dr. Asma M. Karami
Dr. Raquel Rodríguez-Vázquez
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 250 words) can be sent to the Editorial Office for assessment.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Fishes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • molecular diagnostics
  • fish health
  • innate immunity
  • sustainable disease management
  • emerging infectious diseases

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Further information on MDPI's Special Issue policies can be found here.

Published Papers (4 papers)

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Research

30 pages, 1515 KB  
Article
Genomic Diversity and Taxonomy of Aeromonas spp. in Aquarium Fish: Potential Role of Ornamental Fish as Hidden Carriers
by Muhammed Duman, Nihed Ajmi, Hector Carmona-Salido, Görkem Tasci, Artun Yıbar, Soner Altun, Jesús L. Romalde and Izzet Burcin Saticioglu
Fishes 2026, 11(2), 74; https://doi.org/10.3390/fishes11020074 - 23 Jan 2026
Viewed by 678
Abstract
Aquarium fish are increasingly being recognized as reservoirs of zoonotic pathogens, with Aeromonas species posing a notable risk because of their environmental resilience and opportunistic pathogenicity. This study presents the most comprehensive genome-based investigation to date of Aeromonas diversity in aquarium fish, aiming [...] Read more.
Aquarium fish are increasingly being recognized as reservoirs of zoonotic pathogens, with Aeromonas species posing a notable risk because of their environmental resilience and opportunistic pathogenicity. This study presents the most comprehensive genome-based investigation to date of Aeromonas diversity in aquarium fish, aiming to characterize their taxonomic distribution, population structure, and genomic features. A total of 64 Aeromonas isolates were collected from various aquarium fish species. Wholegenome sequencing was conducted on all isolates to facilitate comparative genomic analyses. Key approaches included multilocus sequence typing (MLST), pairwise Digital DNA-DNA hybridization (dDDH), and the construction of a phylogenomic tree for species-level classification. Furthermore, a population structure analysis was performed to explore genomic diversity and evolutionary trends among the isolates. The results identified 14 distinct Aeromonas species, with A. veronii, A. caviae, and A. hydrophila being the most common. Importantly, several isolates exhibited taxonomic ambiguity, indicating the possible presence of new species or subspecies lineages. Furthermore, antimicrobial resistance gene profiles and virulence factor distributions varied significantly across clades, indicating genomic plasticity. This study highlights the underappreciated genomic complexity of Aeromonas populations in aquarium environments and raises concerns about the public health implications of pathogen reservoirs in ornamental fish. Full article
(This article belongs to the Special Issue Infection and Detection of Bacterial Pathogens in Aquaculture)
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17 pages, 3912 KB  
Article
Comparative Proteomic Profiling of a Virulent Wild-Type Nocardia seriolae and Its Attenuated Vaccine Strain
by Yao Yao, Weimei He, Li Wu, Lei Huang, Chengying Li, Yingying Tao, Xiaoyi Pan, Jianhong Shu, Yulong He, Jiayun Yao and Huapeng Feng
Fishes 2026, 11(1), 42; https://doi.org/10.3390/fishes11010042 - 9 Jan 2026
Viewed by 481
Abstract
Nocardia seriolae (N. seriolae) is a significant bacterial pathogen in global aquaculture, causing substantial economic losses. Live-attenuated vaccines represent a promising control strategy, but their molecular mechanisms remain poorly understood. This study employed a quantitative proteomic approach to compare the proteomic [...] Read more.
Nocardia seriolae (N. seriolae) is a significant bacterial pathogen in global aquaculture, causing substantial economic losses. Live-attenuated vaccines represent a promising control strategy, but their molecular mechanisms remain poorly understood. This study employed a quantitative proteomic approach to compare the proteomic profiles of a virulent wild-type strain (F1) and an attenuated vaccine strain (F110) of N. seriolae. Using a data-independent acquisition (DIA)-based LC-MS/MS analysis, we identified 4516 proteins, with 540 showing significant differential expression (311 upregulated, 229 downregulated). Bioinformatic analysis revealed that upregulated proteins in F110 were primarily involved in metabolic processes, including phosphatidate cytidylyltransferase and various enzymes related to amino acid and nucleotide metabolism. Conversely, downregulated proteins were enriched in virulence-associated functions, including HtpX and MFS transporter permease. These findings suggest that attenuation involves a complex reprogramming of metabolic pathways coupled with a reduction in key virulence factors, providing insights into the potential molecular basis of vaccine development and potential targets for novel therapeutic strategies. Full article
(This article belongs to the Special Issue Infection and Detection of Bacterial Pathogens in Aquaculture)
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14 pages, 2893 KB  
Article
Morphological and Histological Changes of Experimental Pseudomonas fluorescens Infection in Zebrafish (Danio rerio)
by Mariela González-Renteria, María del Carmen Monroy-Dosta, Miguel Angel Ramos-López, Juan Campos-Guillén, Jesús Dámaso Bustamante-González, Leticia González-Núñez, Alejandro Ávalos-Rodríguez, Eber Addí Quintana-Obregón and Martha Alicia Perera-García
Fishes 2025, 10(11), 551; https://doi.org/10.3390/fishes10110551 - 1 Nov 2025
Viewed by 1217
Abstract
Pseudomonas fluorescens is a bacterium that has been identified as a significant pathogen in fish from the aquaculture industry. However, the clinical signs and changes caused by the disease have not been studied well yet. This study aimed to determine the survival, morphological, [...] Read more.
Pseudomonas fluorescens is a bacterium that has been identified as a significant pathogen in fish from the aquaculture industry. However, the clinical signs and changes caused by the disease have not been studied well yet. This study aimed to determine the survival, morphological, and histopathological changes in zebrafish (Danio rerio) in an experiment involving 180 fish (0.250 ± 0.05 g). The organisms were inoculated intraperitoneally at four bacterial concentrations 1.5 × 106, 1.5 × 107, 1.5 × 108, and 1.5 × 109 CFU mL−1 with respective control groups. Results showed that cumulative mortality at 96 h post infection (hpi) was 0% (1.5 × 106 CFU mL−1), 0% (1.5 × 107 CFU mL−1), 6.66% (1.5 × 108 CFU mL−1), and 33.33% (1.5 × 109 CFU mL−1). The survival curves were not statistically different (p = 1.000). Corresponding to differences between clinical signs and concentrations for 24 hpi (p = 0.7576) there were no significant differences, for 48 hpi statistical differences were obtained (p = 0.0008), while for 72 hpi (p = 0.8922) and 96 hpi (p = 0.333) they were not observed. The predominant clinical signs were anorexia, lethargy, erratic swimming, and peritoneal haemorrhage. The acute septicemic clinical form was determined. Histological analyses showed that the gills, liver, and spleen were infected and had severe pathological alterations. These findings indicate that the zebrafish is susceptible to P. fluorescens infection. Full article
(This article belongs to the Special Issue Infection and Detection of Bacterial Pathogens in Aquaculture)
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16 pages, 1811 KB  
Article
Nanopore-Based Metagenomic Approaches for Detection of Bacterial Pathogens in Recirculating Aquaculture Systems
by Diego Valenzuela-Miranda, María Morales-Rivera, Jorge Mancilla-Schutz, Alberto Sandoval, Valentina Valenzuela-Muñoz and Cristian Gallardo-Escárate
Fishes 2025, 10(10), 496; https://doi.org/10.3390/fishes10100496 - 2 Oct 2025
Cited by 2 | Viewed by 1805
Abstract
The microbial community in a recirculating aquaculture system (RAS) is pivotal in fish health, contributing significantly to the productive performance during the growing-out phase. Classical and molecular methods using PCR for species-specific amplifications have traditionally been used for bacterial community surveillance. Unfortunately, these [...] Read more.
The microbial community in a recirculating aquaculture system (RAS) is pivotal in fish health, contributing significantly to the productive performance during the growing-out phase. Classical and molecular methods using PCR for species-specific amplifications have traditionally been used for bacterial community surveillance. Unfortunately, these approaches mask the real bacterial diversity and abundance, population dynamics, and prevalence of pathogenic bacteria. In this study, we explored the use of Oxford Nanopore Technology to characterize the microbiota and functional metagenomics in a commercial freshwater RAS. Intestine samples from Atlantic salmon (Salmo salar (85 ± 5.7 g)) and water samples from the inlet/outlet water, settling tank, and biofilters were collected. The full-length 16S rRNA gene was sequenced to reconstruct the microbial community, and bioinformatic tools were applied to estimate the functional potential in the RAS and fish microbiota. The analysis showed that bacteria involved in denitrification processes were found in water samples, as well as metabolic pathways related to hydrogen sulfide metabolism. Observations suggested that fish classified as sick exhibited decreased microbial diversity compared with fish without clinical symptomatology (p < 0.05). Proteobacteria were predominant in ill fish, and pathogens of the genera Aeromonas, Aliivibrio, and Vibrio were detected in all intestinal samples. Notably, Aliivibrio wodanis was detected in fish showing abnormal clinical conditions. Healthy salmon showed higher contributions of pathways related to amino acid metabolism and short-chain fatty acid fermentation (p < 0.05), which may indicate more favorable fish conditions. These findings suggest the utility of nanopore sequencing methods in assessing the microbial community in RASs for salmon aquaculture. Full article
(This article belongs to the Special Issue Infection and Detection of Bacterial Pathogens in Aquaculture)
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