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Fishes
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Microbial Pathogens, Disease Control and Veterinary Drug Use in Aquaculture
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Microbial Pathogens, Disease Control and Veterinary Drug Use 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: 20 May 2026 | Viewed by 5864

Special Issue Editors

Dr. Haipeng Cao

E-Mail Website
Guest Editor
College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China
Interests: aquatic animal diseases; drug metabolism; molecular immunity
Dr. Yibin Yang

E-Mail
Guest Editor
Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China
Interests: bacterial diseases; intestinal inflammation; fish
Special Issues, Collections and Topics in MDPI journals
Dr. Yali Wang

E-Mail Website
Guest Editor Assistant
College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China
Interests: aquatic animal diseases; drug metabolism; molecular immunity

Special Issue Information

Dear Colleagues,

Aquaculture is one of the world’s fastest growing food production sectors. However, infectious diseases heavily limit the sustainable development of this industry. Thus, knowledge about microbial pathogens, disease control, and veterinary drug use in aquaculture is vital for the reduction of infectious disease outbreaks.

The Special Issue is focused on sharing research relating to all aspects of microbial pathogens, diseases control, and veterinary drug use in aquaculture, to contribute to aquatic animal health and improve healthy aquaculture.

We are pleased to invite you to collaborate with original research articles (basic and applied) or reviews in this Special Issue.

Dr. Haipeng Cao
Dr. Yibin Yang
Guest Editors

Dr. Yali Wang
Guest Editor Assistant

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

  • diseases
  • pathogens
  • control
  • aquaculture

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Published Papers (6 papers)

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Research

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13 pages, 17540 KB  
Article
First Report of Elizabethkingia miricola Isolated from Low-Salinity-Cultured River Puffer (Takifugu obscurus) in South Korea
by Ki-Taek Cho, Dong-Hoon Lee, Beom-Hee Lee and Bo-Seong Kim
Fishes 2026, 11(4), 214; https://doi.org/10.3390/fishes11040214 - 2 Apr 2026
Viewed by 384
Abstract
This study reports the first isolation of Elizabethkingia miricola from cultured river puffer (Takifugu obscurus) in South Korea under low-salinity aquaculture conditions. A total of 5000 juvenile T. obscurus were reared for 20 months in a recirculating aquaculture system with salinity [...] Read more.
This study reports the first isolation of Elizabethkingia miricola from cultured river puffer (Takifugu obscurus) in South Korea under low-salinity aquaculture conditions. A total of 5000 juvenile T. obscurus were reared for 20 months in a recirculating aquaculture system with salinity maintained at 3–5 ppt. During the rearing period, fish exhibited a cumulative mortality rate of 58.17%, presenting clinical signs such as lethargy, fin rot, hepatic hemorrhage, and white nodules in the spleen and kidney. Biochemical and molecular analyses identified E. miricola in the internal organs of diseased fish. All isolates exhibited multidrug resistance and showed 98.8–99.8% 16S rRNA gene sequence similarity to E. miricola, forming a distinct phylogenetic cluster. Additionally, several virulence-associated genes (fabG, fabV, wecB, ureB, aceA, acyl) were detected in the isolates. Histopathological examination revealed granulomatous lesions in multiple organs, including the gill, heart, kidney, and spleen. This study represents the first report of E. miricola isolated from cultured river puffer in South Korea and suggests its potential association with disease in this species, as well as its possible zoonotic relevance. These findings highlight the importance of disease monitoring and pathogen surveillance in low-salinity aquaculture systems. Full article
(This article belongs to the Special Issue Microbial Pathogens, Disease Control and Veterinary Drug Use in Aquaculture)
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15 pages, 6570 KB  
Article
Development and Validation of a Multienzyme Isothermal Rapid Amplification Combined with Lateral-Flow Dipstick (MIRA-LFD) Assay for Trypanosoma Strains Circulating in Large Yellow Croaker (Larimichthys crocea)
by You Zuo, Bichai Liao, Luoxuan Lin, Tong Wu, Jiahao Yuan, Qianxi Xue, Haiyun Wei, Shuming Liu, Guangliang Huang, Xinhua Chen and Pan Qin
Fishes 2026, 11(2), 107; https://doi.org/10.3390/fishes11020107 - 10 Feb 2026
Viewed by 525
Abstract
Trypanosomiasis, caused by flagellated protozoa of the genus Trypanosoma, has recently emerged as a major threat to aquaculture in China, particularly in farmed large yellow croaker (Larimichthys crocea). Outbreaks lead to high mortality rates and severe economic losses. Conventional diagnostic [...] Read more.
Trypanosomiasis, caused by flagellated protozoa of the genus Trypanosoma, has recently emerged as a major threat to aquaculture in China, particularly in farmed large yellow croaker (Larimichthys crocea). Outbreaks lead to high mortality rates and severe economic losses. Conventional diagnostic tools, such as blood-smear microscopy and molecular assays including polymerase chain reaction or quantitative polymerase chain reaction (qPCR), are often limited by low sensitivity during early infection or by their dependence on sophisticated instruments and trained personnel, restricting their utility in field conditions. To address these challenges, a multienzyme isothermal rapid amplification (MIRA) assay coupled with a lateral-flow dipstick (LFD) was developed for the rapid detection of trypanosoma strains circulating in L. crocea targeting the 18S ribosomal ribonucleic acid gene. After optimizing primer-probe sets, the assay performance was evaluated using plasmid standards and a panel of common aquaculture pathogens. The MRA-LFD assay consistently detected plasmid DNA at concentrations as low as 0.01 fg/µL (≈2.1 copies/µL) and demonstrated no cross-reactivity with other pathogens. Using clinical DNA samples positive for Trypanosoma, the detection limit was 100 fg µL−1. Validation with 150 tissue samples from fish with and without clinical symptoms demonstrated high diagnostic consistency (94%) with qPCR results, confirming the reliability of the assay. This MIRA-LFD platform provides a sensitive, specific and portable diagnostic tool for early detection of Trypanosoma infections in large yellow croaker, offering valuable support for surveillance and disease management in aquaculture. Full article
(This article belongs to the Special Issue Microbial Pathogens, Disease Control and Veterinary Drug Use in Aquaculture)
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16 pages, 2908 KB  
Article
Isolation and Identification of Metanophrys sinensis from Shrimps (Litopenaeus vannamei) and Screening of Chinese Herbal Medicines for Its Control
by Mingfeng Ge, Yifan Xu, Juan Feng, Zheng Liang, Hao Cui, Xinxin Jiang, Jianping Wang, Shengwei Xu and Rongrong Ma
Fishes 2025, 10(12), 604; https://doi.org/10.3390/fishes10120604 - 25 Nov 2025
Viewed by 818
Abstract
The parasitic disease scuticociliatosis poses significant economic losses to shrimp culture. In this study, an unidentified species of ciliates was discovered in Litopenaeus vannamei. Morphological and molecular analyses were conducted to identify the parasite species, while a reinfection experiment was performed to [...] Read more.
The parasitic disease scuticociliatosis poses significant economic losses to shrimp culture. In this study, an unidentified species of ciliates was discovered in Litopenaeus vannamei. Morphological and molecular analyses were conducted to identify the parasite species, while a reinfection experiment was performed to assess its virulence towards L. vannamei. Simultaneously, Chinese herbal medicine was assessed for potential prevention and control of this pathogen. The results revealed that the SSU rDNA (93.87%), LSU rDNA (98.20%), and ITS1-5.8S-ITS2 rDNA (87.10%) genes exhibited high homology with Metanophrys sinensis, suggesting its classification within the genus Metanophry sp. The reinfection experiment demonstrated median lethal dosages of 6638 individuals/mL at 24 h and 4658 individuals/mL at 48 h for this ciliate on the host L.vannamei. In terms of drug control, we conducted a screening of 23 Chinese herbal extracts through in vivo injection trials and observed that Mume fructus extract exhibits potent biocidal activity. Specifically, the M. fructus extract solution with a final concentration of 5 mg/mL (0.5% v/v) eliminated all ciliates within 3 h. In conclusion, this study identified the ciliate parasite as Metanophrys sinensis and demonstrated its virulence to Litopenaeus vannamei. Mume fructus extract was found to effectively control the parasite, offering potential for managing scuticociliatosis in shrimp culture. Full article
(This article belongs to the Special Issue Microbial Pathogens, Disease Control and Veterinary Drug Use in Aquaculture)
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17 pages, 1594 KB  
Article
Isolation, Identification, and Virulence Properties of Enterobacter bugandensis Pathogen from Big-Belly Seahorse Hippocampus abdominalis
by Haibin Ye, Chenhao Teng, Yueqi Yang, Yiyao Liu, Li Li, Ying Fan, Youhong Wang, Jing Diao, Lingling Yu, Chunlei Gai and Haipeng Cao
Fishes 2025, 10(8), 411; https://doi.org/10.3390/fishes10080411 - 14 Aug 2025
Viewed by 1340
Abstract
Nowadays, members of the genus Enterobacter have been documented as human and aquaculture pathogens. To date, no reports have described Enterobacter bugandensis infecting Hippocampus abdominalis. In the present study, an isolate of E. bugandensis, designated H4, was identified as a causative pathogen [...] Read more.
Nowadays, members of the genus Enterobacter have been documented as human and aquaculture pathogens. To date, no reports have described Enterobacter bugandensis infecting Hippocampus abdominalis. In the present study, an isolate of E. bugandensis, designated H4, was identified as a causative pathogen in cultured H. abdominalis following Koch’s postulate, and its virulence properties were further described. The isolate’s genome consisted of a single circular chromosome and harbored several virulence and resistance genes, including, but not limited to, csgG, acrB, hcp, gndA, galF, rpoS, fur, rcsB, and phoP involved in adherence, antimicrobial activity, effector delivery systems, immune modulation, and regulation, as well as baeR, blaACT-49, ramA, hns, ftsI, acrA, gyrA, fabI, crp, oqxB, parE, gyrB, phoP, rpoB, tuf, ptsI, and fosA2 functioning against aminoglycoside, cephamycin, disinfecting agent and antiseptic, fluoroquinolone, macrolide, peptide, and other antimicrobials. Additionally, the isolate exhibited multiple resistance to cephalosporins, penicillins, and tetracyclines and demonstrated a median lethal dose (LD50) of 4.47 × 105 CFU/mL in H. abdominalis. To our knowledge, this is the first study to describe E. bugandensis infecting H. abdominalis. These findings highlight the zoonotic potential of E. bugandensis and underscore the need for targeted health management in seahorse farming. Full article
(This article belongs to the Special Issue Microbial Pathogens, Disease Control and Veterinary Drug Use in Aquaculture)
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17 pages, 8541 KB  
Article
Characterization of Immune Response Against Mycobacterium marinum Infection in Coho Salmon (Oncorhynchus kisutch)
by Le Li, Danlei Xu, Xiaoqing Yu, Chunlei Gai, Haibin Ye and Jing Diao
Fishes 2025, 10(6), 268; https://doi.org/10.3390/fishes10060268 - 3 Jun 2025
Cited by 1 | Viewed by 1017
Abstract
Mycobacterium marinum is an opportunistic pathogen prevalent in aquatic environments, causing significant morbidity in fish, including Coho salmon (Oncorhynchus kisutch), a species increasingly cultured in Chinese salmonid aquaculture. This study investigated the immune response of Coho salmon to M. marinum infection [...] Read more.
Mycobacterium marinum is an opportunistic pathogen prevalent in aquatic environments, causing significant morbidity in fish, including Coho salmon (Oncorhynchus kisutch), a species increasingly cultured in Chinese salmonid aquaculture. This study investigated the immune response of Coho salmon to M. marinum infection and the bacterial proliferation dynamics in the liver and kidney. Transcriptome analysis revealed 5028 differentially expressed genes (DEGs) in the kidney and 3419 DEGs in the liver at 6 weeks post-infection. Gene Ontology and KEGG enrichment analysis highlighted pathways such as cytokine–cytokine receptor interaction, metabolic pathways, and Toll-like receptor signaling in the kidney, while the DEGs in the liver were enriched in metabolic pathways, immune system processes, and stress and defense responses. The temporal expression profiling of 15 immune-related genes, including acute-phase proteins (serum amyloid A-5 and hepcidin), cytokines (TNF-α, IL-1β, IL-17A), chemokines (CXCL13 and CCL19), pattern recognition receptors (Toll-like receptor 13), and other immune-related genes, showed significant upregulation against M. marinum infection, with stronger responses in the liver. Furthermore, it was found that there was a progressive proliferation of M. marinum in the infected liver and kidney from approximately 2.5 log10 cfu/g at week 2 to about 6 log10 cfu/g by 6 weeks, with a significantly higher load in the liver. These findings provide critical insights into the immune mechanisms of Coho salmon against M. marinum and the pathogen’s tissue-specific proliferation, offering a foundation for developing targeted control strategies against M. marinum in aquaculture. Full article
(This article belongs to the Special Issue Microbial Pathogens, Disease Control and Veterinary Drug Use in Aquaculture)
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Review

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24 pages, 2260 KB  
Review
Utilization of Plant-Derived Essential Oils as Natural Alternatives for Controlling Fish Pathogens: A Critical Review of Their Use Against Aeromonas hydrophila
by Sasirekha Rajendran, Berta Maria Heinzmann, Juliana Cargnelutti and Bernardo Baldisserotto
Fishes 2026, 11(2), 120; https://doi.org/10.3390/fishes11020120 - 17 Feb 2026
Viewed by 961
Abstract
Aeromonas hydrophila infection is typically linked to outbreaks of diseases and its pathogenicity seems to be connected to environmental stress in hosts whose immune systems are compromised. Fish diseases have long been treated using synthetic antibiotics, but there are environmental and health concerns [...] Read more.
Aeromonas hydrophila infection is typically linked to outbreaks of diseases and its pathogenicity seems to be connected to environmental stress in hosts whose immune systems are compromised. Fish diseases have long been treated using synthetic antibiotics, but there are environmental and health concerns regarding their use due to the development of bacterial resistance. It has been suggested that essential oils (EOs), which are alternative antibacterial agents, could be applied in the aquaculture industry. Their biodegradability, affordability, efficiency, and quick metabolism minimize the likelihood of them building up in bodily tissues and provoking bacterial resistance. EOs can directly influence bacteria, altering the lipid composition and structure of bacterial cell membranes, enhancing their permeability, and disrupting their structure. In addition, they can boost fish immunity and increase resistance to contagious bacteria. EOs can be incorporated into fish diets as nutritional additives and/or applied in baths. This review discusses the in vitro and in vivo methodologies used to study the effects of EOs on A. hydrophila and the results obtained so far, as well as perspectives for new studies. Full article
(This article belongs to the Special Issue Microbial Pathogens, Disease Control and Veterinary Drug Use in Aquaculture)
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