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Microorganisms
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Pathogen Infections in Aquatic Animals—Advanced Detection Technologies, Precision Identification, and...
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Pathogen Infections in Aquatic Animals—Advanced Detection Technologies, Precision Identification, and Pathogenic Mechanisms

A Special Issue of Microorganisms (ISSN 2076-2607) belonging to the section "Veterinary Microbiology".

Deadline for manuscript submissions: 31 December 2026 | Viewed by 4536

Editors

Dr. Lu-Sheng Xin

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Guest Editor
School of Public Health, Jining Medical University, Jining, China
Interests: aquatic pathogen; pathogen detection; omics technology; bacteriostasis; seafood safety; bio-safety
Dr. Changming Bai

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Guest Editor
Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
Interests: pathogenicity, epidemiology and control measures of marine mollusk diseases; mollusk herpesviruses; strain differentiation and evolution
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Pathogen infections in aquatic animals involve the invasion and proliferation of various microorganisms, including bacteria, viruses, fungi, and parasites, which thrive in aquatic environments and cause diseases in fish, crustaceans, mollusks, and other aquatic organisms. These pathogens often pose significant threats to global aquaculture industries, leading to substantial economic losses and ecological imbalances.

This Special Issue aims to gather cutting-edge original research and comprehensive reviews on the intricate challenges posed by microbial pathogens in aquaculture and natural aquatic ecosystems. It will directly align with the journal’s aims and scope, as the exploration of pathogen isolation and identification, the development of robust detection methods, and the elucidation of pathogenic mechanisms are central to advancing our understanding of aquatic animal health and disease management. By bringing together diverse research in these critical areas, this Special Issue will contribute to the development of novel strategies for disease prevention, control, and treatment, thereby promoting sustainable aquaculture and safeguarding aquatic ecosystems. Its scope will be sufficiently focused to enable the compilation of a cohesive collection of high-quality articles yet broad enough to encourage contributions from a variety of disciplines.

Research areas may include (but are not limited to) the following:

  1. The isolation and identification of novel and emerging pathogens affecting aquatic animals.
  2. The development and validation of advanced diagnostic tools and rapid detection methods for aquatic animal pathogens (e.g., PCR-based assays, CRISPR-based diagnostics, biosensors, and immunological methods).
  3. The molecular mechanisms of pathogenicity, host–pathogen interactions, and immune responses in aquatic animals.
  4. Studies on pathogen virulence factors and their roles in disease progression.
  5. The epidemiology, transmission dynamics, and risk assessment of aquatic animal diseases.
  6. The development of effective vaccines, probiotics, prebiotics, and other prophylactic or therapeutic strategies to combat aquatic animal infections.
  7. Antimicrobial resistance in aquatic pathogens and strategies for its mitigation.
  8. The ecological impacts of pathogen outbreaks on wild aquatic populations and ecosystems.
  9. Genomic and proteomic approaches to understanding aquatic animal diseases.
  10. Innovative approaches to disease surveillance and ensuring biosecurity in aquaculture.

We look forward to receiving your contributions.

Dr. Lu-Sheng Xin
Dr. Changming Bai
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-anonymized peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms 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 2700 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

  • aquatic pathogen
  • pathogen detection
  • omics technology
  • bacteriostasis
  • seafood safety
  • bio-safety

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Published Papers (3 papers)

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Research

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24 pages, 16435 KB  
Article
Establishment of One-Pot ERA-CRISPR/Cas12a-Based Rapid Visual Assays and a TaqMan Quantitative PCR Assay for Lactococcus garvieae
by Haoyu Wang, Heng Sun, Feiming Chen, Zhiyuan Huang, Yu Chen, Xiaofeng Chen, Dogbey Rejoice Abla, Zhi Zhang, Huajian Lin, Liqun Wang and Yucong Huang
Microorganisms 2026, 14(4), 830; https://doi.org/10.3390/microorganisms14040830 - 5 Apr 2026
Viewed by 953
Abstract
Lactococcus garvieae is a major bacterial pathogen responsible for lactococcosis outbreaks in aquaculture, resulting in substantial economic losses worldwide. Accurate identification of L. garvieae remains challenging because of its genetic similarity to other Lactococcus species and the limited field applicability of many existing [...] Read more.
Lactococcus garvieae is a major bacterial pathogen responsible for lactococcosis outbreaks in aquaculture, resulting in substantial economic losses worldwide. Accurate identification of L. garvieae remains challenging because of its genetic similarity to other Lactococcus species and the limited field applicability of many existing molecular diagnostic methods. Therefore, there is an urgent need for a rapid, highly specific, and field-deployable analytical method that enables accurate identification of L. garvieae outside conventional laboratory settings. In this study, a one-pot analytical strategy integrating enzymatic recombinase amplification (ERA) with CRISPR/Cas12a detection was developed, enabling fluorescence or lateral flow dipstick (LFD) readouts within a single closed reaction tube. The one-pot ERA-CRISPR/Cas12a assays achieved a detection limit of 10 copies/reaction. When combined with a rapid DNA release protocol, qualitative detection could be completed within 50 min without the need for sophisticated instrumentation. In parallel, a TaqMan quantitative PCR assay was established as an analytical benchmark, exhibiting a detection limit of 20 copies/reaction with high linearity and good reproducibility. Clinical evaluation using 136 diseased fish samples demonstrated full concordance between the one-pot ERA-CRISPR/Cas12a and qPCR assays, with both methods achieving a positive detection rate of 23.5% (32/136). In addition, the ERA-CRISPR/Cas12a platform was successfully validated under simulated field conditions using a portable reaction device. This study presents a rapid and field-deployable CRISPR-based platform for the early detection and epidemiological surveillance of lactococcosis. Full article
(This article belongs to the Special Issue Pathogen Infections in Aquatic Animals—Advanced Detection Technologies, Precision Identification, and Pathogenic Mechanisms)
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21 pages, 2879 KB  
Article
Overcoming Target Drift: Development and Validation of a One-Step TaqMan qPCR Assay for Epidemiological Surveillance of Carpione rhabdovirus Circulating in Southern China
by Yucong Huang, Zhiyuan Huang, Haoyu Wang, Xiaojuan Li, Xin Liu, Huajian Lin, Zhi Zhang, Xiaofeng Chen, Jichang Jian and Heng Sun
Microorganisms 2026, 14(1), 126; https://doi.org/10.3390/microorganisms14010126 - 7 Jan 2026
Cited by 1 | Viewed by 900
Abstract
Carpione rhabdovirus (CAPRV) is an emerging virus within the family Rhabdoviridae, posing potential threats to aquaculture species such as golden pompano (Trachinotus anak). However, since the 21st century, and for CAPRV strains isolated from marine fish, only a single CAPRV2023 [...] Read more.
Carpione rhabdovirus (CAPRV) is an emerging virus within the family Rhabdoviridae, posing potential threats to aquaculture species such as golden pompano (Trachinotus anak). However, since the 21st century, and for CAPRV strains isolated from marine fish, only a single CAPRV2023 sequence has previously been available in public databases, with no additional sequences reported. Because the virus undergoes genetic variation, relying on this single sequence likely introduced mismatches or off-target risks in earlier detection assay designs. Notably, the previously developed two-step N-targeting detection assay was designed based solely on that single CAPRV2023 sequence. Consequently, this study involved determining and analyzing the N gene sequences from CAPRV isolates gathered from 2023 to 2025, with the aim of pinpointing conserved regions for assay development, and sequence comparisons subsequently verified the existence of mismatches in the primer–probe binding sites of the previous assay. Since quantitative assays in aquatic virology often define copy numbers utilizing either plasmid DNA templates or RNA templates produced via in vitro transcription, which may lead to variations in amplification kinetics and sensitivity, this study compared both standards to ensure reliable quantification across different nucleic acid types. Based on these findings, a one-step TaqMan quantitative PCR (qPCR) assay was developed and validated using dual nucleic acid standards, namely plasmid DNA and in vitro–transcribed RNA. Compared with conventional two-step qPCR, the one-step format combines cDNA synthesis and subsequent DNA amplification in a single sealed tube, thereby effectively preventing cross-contamination, simplifying the workflow, and improving detection efficiency. The assay exhibited strong linearity (R2 > 0.99) and consistent amplification efficiencies between 90% and 110%, demonstrating excellent quantitative performance. The detection limits were 2 copies per reaction for plasmid DNA and 20 copies for in vitro–transcribed RNA templates. No cross-reactivity was observed with other aquatic pathogens, and the assay showed strong repeatability and reproducibility (coefficients of variation below 2.0%), providing a sensitive and reliable tool for epidemiological surveillance and the analysis of CAPRV distribution in marine aquaculture systems of southern China. Full article
(This article belongs to the Special Issue Pathogen Infections in Aquatic Animals—Advanced Detection Technologies, Precision Identification, and Pathogenic Mechanisms)
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Review

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33 pages, 8476 KB  
Review
Progress of Rapid Detection Technology for Aquatic Microorganisms: A Comprehensive Review
by Qin Liu, Zhuangzhuang Qiu, Mengli Yao, Boyan Jiao, Yu Zhou, Chenghua Li, Haipeng Liu and Lusheng Xin
Microorganisms 2026, 14(4), 939; https://doi.org/10.3390/microorganisms14040939 - 21 Apr 2026
Cited by 3 | Viewed by 2059
Abstract
Microbial contamination in aquatic environments poses severe threats to aquaculture sustainability, ecological balance and public health. Traditional culture-based detection methods, while standardized, are time-consuming and labor-intensive, often failing to meet the urgent need for rapid on-site monitoring required to prevent disease outbreaks and [...] Read more.
Microbial contamination in aquatic environments poses severe threats to aquaculture sustainability, ecological balance and public health. Traditional culture-based detection methods, while standardized, are time-consuming and labor-intensive, often failing to meet the urgent need for rapid on-site monitoring required to prevent disease outbreaks and manage water quality effectively. By integrating latest research advances (2020–2025), this study reviews advances in rapid detection technologies for aquatic microorganisms, including the evolution of nucleic acid amplification strategies, with a focused comparison of the analytical sensitivity and field deployability of quantitative polymerase chain reaction (qPCR) and mainstream isothermal amplification techniques (loop-mediated isothermal amplification, LAMP; recombinase polymerase amplification, RPA). Furthermore, this study reports on the emergence of Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-associated protein (Cas) systems as next-generation diagnostic tools, highlighting their integration with microfluidic Lab-on-a-Chip (LOC) platforms to achieve attomolar sensitivity. We also consider the application of portable nanopore sequencing for real-time pathogen identification and the growing role of Artificial Intelligence (AI) in analyzing complex diagnostic datasets. Advanced molecular methods have achieved significant reductions in time consumption—from days to less than one hour—while challenges regarding sample preparation and environmental matrix inhibition remain. The future of aquatic monitoring lies in integrated, automated systems that combine the specificity of CRISPR-Cas diagnostics with the connectivity of IoT-enabled biosensors. Comparative analysis indicates that isothermal amplification methods (LAMP, RPA) coupled with CRISPR-Cas systems offer the optimal balance of sensitivity, speed, and field deployability for point-of-care aquaculture diagnostics, while qPCR/dPCR remain indispensable for quantitative regulatory applications. We propose a structured technology selection framework to guide researchers and practitioners in choosing appropriate detection modalities based on specific sensitivity, cost, throughput, and deployment requirements. Full article
(This article belongs to the Special Issue Pathogen Infections in Aquatic Animals—Advanced Detection Technologies, Precision Identification, and Pathogenic Mechanisms)
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