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Fishes
Special Issues
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: 15 February 2026 | Viewed by 208

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 100 words) can be sent to the Editorial Office for announcement on this website.

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 (1 paper)

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Research

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
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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