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Microorganisms
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Infectious Diseases in Aquaculture
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Infectious Diseases in Aquaculture

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Veterinary Microbiology".

Deadline for manuscript submissions: 31 August 2025 | Viewed by 3743

Special Issue Editor

Dr. Cesar Marcial Escobedo-Bonilla

E-Mail Website
Guest Editor
Instituto Politecnico Nacional-CIIDIR Sinaloa, Blvd Juan de Dios Batiz Paredes 250, Colonia San Joachin, Guasave 81101, Sinaloa, Mexico
Interests: shrimp; viral diseases; pathology; evaluation of control methods

Special Issue Information

Dear Colleagues,

Aquaculture is an animal production industry. In 2023, its worth was USD 195 billion, producing 185 million tonnes of aquatic animals and 38 million tonnes of algae. This activity is threatened by infectious diseases precipitated by microbial agents such as viruses, bacteria, protozoa and fungi. Infectious disease starts when a pathogen enters a susceptible host, using the host’s cells and tissues to thrive and multiply, causing disease and often mortality. Depending on the pathogen’s requirement to multiply and survive at the expense of the host, they are considered either obligatory or opportunistic. Infectious diseases often cause massive mortalities and huge economic losses to aquaculture operations concerning crustaceans, mollusks, fish and other organisms. To reduce the impact of infectious diseases in aquaculture, various strategies should be developed and evaluated. These include rapid and sensitive diagnostic techniques, the modulation of the defense system of aquatic organisms, and an evaluation of experimental control methods. This Special Issue covers various aspects of infectious diseases such as novel diagnostic methods, emerging pathogens, and novel methods for disease control.

Dr. Cesar Marcial Escobedo-Bonilla
Guest Editor

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. 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

  • aquaculture
  • infectious diseases
  • pathogens
  • diagnostics
  • control methods

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Published Papers (4 papers)

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Research

24 pages, 11117 KiB  
Article
Host–Microbiota–Parasite Interactions in Grass Carp: Insights from Ichthyophthirius multifiliis Infection
by Fangxiang Li, Dongdong Jiang, Qing Wang, Ouqin Chang, Jiyuan Yin, Meiling Yu and Houjun Pan
Microorganisms 2025, 13(4), 872; https://doi.org/10.3390/microorganisms13040872 - 10 Apr 2025
Viewed by 397
Abstract
The ciliate parasite Ichthyophthirius multifiliis poses significant threats to grass carp (Ctenopharyngodon idellus) aquaculture. However, the limited understanding of host microbiota shifts and immune responses hinders effective control strategies. This study integrated analyses of host pathological indices, immune response and skin/gill/gut [...] Read more.
The ciliate parasite Ichthyophthirius multifiliis poses significant threats to grass carp (Ctenopharyngodon idellus) aquaculture. However, the limited understanding of host microbiota shifts and immune responses hinders effective control strategies. This study integrated analyses of host pathological indices, immune response and skin/gill/gut microbiota shifts after I. multifiliis infection. A histopathological examination identified gill and fin tissues embedded with I. multifiliis, accompanied by epithelial necrosis, and inflammatory cell infiltration. Biochemical profiling revealed marked elevations in aspartate aminotransferase (AST), alanine aminotransferase (ALT), urea (UREA), and creatinine (CREA) levels, indicating impaired hepatic and renal function. Quantitative RT-PCR analyses demonstrated the up-regulation of mucosal immune gene IgT and pro-inflammatory cytokine TNF-α while increasing the trend of systemic immune gene IgM. 16S rRNA sequencing revealed significant reductions in skin microbiota diversity. At the genus level, opportunistic pathogens Aeromonas and Vibrio proliferated in the intestine, whereas Flavobacterium and Candidatus Megaira increased in the skin and gills. Correlation analyses identified positive associations between Aeromonas/Vibrio abundance and host phenotype, contrasting with negative correlations observed for Sphingomonas, Acinetobacter, and Leifsonia. These findings demonstrate that I. multifiliis infection induces host microbiome dysbiosis and potentially opportunistic bacterial infections. This investigation advances our understanding of tripartite host–microbiota–parasite interactions and supports microbial community-based parasitosis control in fish culture. Full article
(This article belongs to the Special Issue Infectious Diseases in Aquaculture)
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20 pages, 9871 KiB  
Article
First Report and Pathogenicity Analysis of Photobacterium damselae subsp. piscicida in Cage-Cultured Black Rockfish (Sebastes schlegelii) Associated with Skin Ulcers
by Dandan Zhou, Binzhe Zhang, Yulie Qiu, Xuepeng Li and Jian Zhang
Microorganisms 2025, 13(2), 441; https://doi.org/10.3390/microorganisms13020441 - 17 Feb 2025
Viewed by 660
Abstract
Photobacterium damselae subsp. Piscicida (PDP), a marine bacterium, has been reported to infect a variety of economically important marine species worldwide. Understanding the occurrence and pathogenicity of PDP is crucial for effective disease control and ensuring the success of aquaculture operations. In late [...] Read more.
Photobacterium damselae subsp. Piscicida (PDP), a marine bacterium, has been reported to infect a variety of economically important marine species worldwide. Understanding the occurrence and pathogenicity of PDP is crucial for effective disease control and ensuring the success of aquaculture operations. In late August 2023, an epidemic outbreak of P. damselae subsp. piscicida DQ-SS1, accompanied by significant mortality, was recorded in cage-cultured black rockfish (Sebastes schlegelii) located on Daqin Island for the first time. Genomic analysis revealed that DQ-SS1 possesses 2 chromosomes, with a total size of 4,510,445 bp and 3923 predicted CDSs. Pathogenic genes analysis identified 573 and 314 genes related to pathogen–host interactions and virulence, respectively. Additionally, DQ-SS1 displayed susceptibility to 15 antimicrobials, was resistant to 11 antimicrobials, and was intermediately sensitive to four antibiotics. Meanwhile, the in vitro assay revealed that the extracellular products (ECP) of DQ-SS1 were lethal to macrophages and exhibited hemolysin, lipase, and amylase activities. Moreover, DQ-SS1 also demonstrated the ability to survive in fish serum and resist complement-mediated killing. The in vivo assay showed that the infected fish exhibited severe histopathological alterations, such as the infiltration of inflammatory cells, cellular degeneration and necrosis, and loose cell aggregation. Lastly, the in vivo infection assays revealed the LD50 of DQ-SS1 was 1.7 × 103 CFU/g. This is the first study to elucidate the pathogenicity and genomic characteristics of multidrug-resistant PDP in cage-cultured S. schlegelii, which contributes to the advancement of diagnostic and preventative strategies for this disease in marine-cultured fishes and provides information for an in-depth study of the pathogenic mechanism of PDP. Full article
(This article belongs to the Special Issue Infectious Diseases in Aquaculture)
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17 pages, 5546 KiB  
Article
The Isolation and Identification of Pseudoalteromonas sp. H27, a Bacterial Strain Pathogenic to Crassostrea gigas
by Heyang Qin, Junyi Jiang, Zhikai Jing, Jiayu Wang, Shuang Xu, Rongwei Chen, Bo Wang, Zhongming Huo and Lei Fang
Microorganisms 2025, 13(2), 296; https://doi.org/10.3390/microorganisms13020296 - 30 Jan 2025
Viewed by 936
Abstract
Bacterial infection is frequently observed in disease outbreaks of aquatic animals, making it of significance to isolate and identify the bacterial pathogens. In this study, diseased individuals of Crassostrea gigas were sampled from the nearshore area in Zhanjiang, Guangdong in May 2023. Culturable [...] Read more.
Bacterial infection is frequently observed in disease outbreaks of aquatic animals, making it of significance to isolate and identify the bacterial pathogens. In this study, diseased individuals of Crassostrea gigas were sampled from the nearshore area in Zhanjiang, Guangdong in May 2023. Culturable bacteria were isolated from the diseased tissue and a pathogenic strain labeled as H27 was screened through a hemolysis test and bacterial challenge experiments. Morphological characterization, 16S rRNA gene sequence-based molecular identification and biochemical tests showed that strain H27 belonged to the genus of Pseudoalteromonas, a dominant genus in the diseased tissue of C. gigas revealed by bacterial community structure analysis. The clinical signs originally observed in naturally diseased C. gigas were reproduced in strain H27-challenged adults, both with the red mantle and adductor. Histopathological analysis was further performed on the diseased tissues of the latter, which showed a significantly increased accumulation of pigment granules in the cytoplasm of the diseased mantle as well as enlarged muscle fiber distances in the diseased adductor. In addition, strain H27 was re-isolated from tissues of the moribund C. gigas after bacterial challenge, indicating the fulfillment of Koch’s postulate. Our results help to enrich the knowledge of C. gigas diseases, possibly contributing to disease prevention and control. Full article
(This article belongs to the Special Issue Infectious Diseases in Aquaculture)
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16 pages, 8810 KiB  
Article
Streptococcus agalactiae Infection in Wild Trahira (Hoplias malabaricus) and Farmed Arapaima (Arapaima gigas) in Brazil: An Interspecies Transmission in Aquatic Environments Shared with Nile Tilapia (Oreochromis niloticus)
by Carlos Augusto Gomes Leal, Rafael Gariglio Clark Xavier, Guilherme Alves de Queiroz, Tarcísio Martins França Silva, Júnia Pacheco Teixeira, Flávia Figueira Aburjaile and Guilherme Campos Tavares
Microorganisms 2024, 12(12), 2393; https://doi.org/10.3390/microorganisms12122393 - 22 Nov 2024
Viewed by 948
Abstract
Streptococcus agalactiae is an important pathogen responsible for cases of high mortality in farmed and wild fish worldwide. In Brazil, this bacterium has been commonly associated with outbreaks in Nile tilapia farms, but other native fish species are also susceptible. Since floating cages [...] Read more.
Streptococcus agalactiae is an important pathogen responsible for cases of high mortality in farmed and wild fish worldwide. In Brazil, this bacterium has been commonly associated with outbreaks in Nile tilapia farms, but other native fish species are also susceptible. Since floating cages are one of the most common culture systems used in the country, the close contact between farmed tilapia and native fish species presents a risk concerning the transmission of this pathogen. In this study, we characterized a mortality outbreak in free-living trahira and in farmed arapaima, as well as the genetic and antimicrobial susceptibility patterns of the isolates obtained. During the outbreaks, moribund fish were sampled and subjected to bacterial examination, after which the isolates were identified via MALDI-ToF analysis. Genotyping was evaluated using repetitive sequence-based PCR (REP-PCR) and multilocus sequence typing (MLST). Antimicrobial susceptibility was evaluated using disc diffusion assays. In addition, whole-genome analysis also was performed. S. agalactiae was identified in all diseased fish, all of which belonged to serotype Ib; however, trahira strains were classified as non-typeable lineages in the MLST assay, while arapaima strains were classified as ST260. These isolates were shown to be similar to the main genotype found in Nile tilapia in Brazil, using REP-PCR, MLST and phylogenomic analysis. The pathogenicity of the bacterium was confirmed by Koch’s postulates for both fish species. The antimicrobial susceptibility assay showed variable results to the same antibiotics among the isolates, prompting four of the isolates to be classified as multidrug-resistant. This study represents the first report of a natural outbreak of Streptococcus agalactiae infection in wild trahira and farmed arapaima inhabiting the same aquatic environment as Nile tilapia. Full article
(This article belongs to the Special Issue Infectious Diseases in Aquaculture)
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