Antimicrobial Resistance and Pathogen Surveillance in Aquaculture
A special issue of Pathogens (ISSN 2076-0817).
Deadline for manuscript submissions: 31 October 2026 | Viewed by 195
Special Issue Editors
Interests: pathogens; viruses; aquaculture; Rickettsiales; AMR
Special Issue Information
Dear Colleagues,
As global aquaculture continues to expand and intensify, new production technologies are enabling increasingly higher stocking densities with the aim of reducing costs and maximizing output. However, these conditions can elevate physiological stress and increase susceptibility to bacterial, fungal, and viral infections. Although vaccination represents an important preventive strategy, its limited availability and variable effectiveness against several aquaculture pathogens often restrict its impact on disease control. In this context, antimicrobials remain the primary tool for controlling infectious disease outbreaks in aquaculture. In regions with strong regulatory frameworks, their use is largely restricted to targeted metaphylactic interventions under veterinary oversight. By contrast, in less regulated settings, prophylactic and non-regulated use remains common, significantly contributing to the emergence and spread of antimicrobial resistance (AMR) in aquaculture environments.
Despite its growing importance, systematic AMR surveillance in aquaculture remains limited. Monitoring efforts frequently focus on detecting the presence or absence of pathogens, while overlooking whether these organisms harbor AMR determinants or mobilizable genetic elements that may facilitate their dissemination. Emerging evidence also suggests that understudied components of the aquatic microbiome—such as bacteriophages—may act as reservoirs or vectors of AMR, yet their roles remain largely unexplored.
This Special Issue aims to bring together cutting-edge research on AMR and pathogen surveillance in finfish, crustaceans, and mollusks.
We welcome studies on bacterial, viral, and fungal pathogens; characterization of AMR genes and mobilomes; innovative diagnostics; environmental surveillance; and novel frameworks for monitoring and mitigating AMR in aquaculture systems.
Dr. Roberto Cruz-Flores
Dr. Karla Camacho
Guest Editors
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Keywords
- antimicrobial resistance (AMR)
- pathogen surveillance
- aquaculture
- environmental surveillance
- bacterial infections
- viral infections
- fungal infections
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