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Antibiotics
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Antibiotics and Antimicrobial Resistance in Aquaculture: Alternative and Complementary Treatment...
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Antibiotics and Antimicrobial Resistance in Aquaculture: Alternative and Complementary Treatment Methods

A special issue of Antibiotics (ISSN 2079-6382).

Deadline for manuscript submissions: closed (30 December 2025) | Viewed by 5622

Special Issue Editor

Dr. Jaime Romero

E-Mail Website
Guest Editor
Laboratorio de Biotecnología, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Macul, Santiago 7810000, Chile
Interests: diet-microbiota-host interaction; nutrition; aditives; probiotics; antibiotics; health; sustainable aquaculture
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue aims at addressing the pressing issue of antibiotic use and antimicrobial resistance (AMR) in aquaculture by exploring alternative and complementary treatment methods. The use of antibiotics in aquaculture has raised concerns about the development and spread of AMR, posing risks to both animal and human health. As editors with expertise in antibiotics and AMR in aquaculture, we recognize the importance of finding sustainable solutions to reduce antibiotic usage while maintaining effective disease management strategies.  

This Special Issue will provide a platform for researchers to share innovative approaches and methods aimed at mitigating the reliance on antibiotics in aquaculture. We welcome contributions that cover a wide range of topics, including but not limited to the following: 

  • Alternative antimicrobial agents (e.g., probiotics, prebiotics, phage therapy);
  • Immunostimulants and vaccination strategies;
  • Biosecurity measures and management practices to prevent disease outbreaks;
  • Nutritional interventions to enhance immune function and disease resistance;
  • Integrated multitrophic aquaculture systems;
  • The wide spread of AMR;
  • Regulatory frameworks and policy recommendations to promote responsible antibiotic use in aquaculture.

Dr. Jaime Romero
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 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. Antibiotics 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 2900 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

  • antibiotics
  • antimicrobial resistance
  • alternatives
  • aquaculture
  • probiotics
  • phage therapy

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Published Papers (4 papers)

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Research

21 pages, 7924 KB  
Article
Genomic and GWAS-Based Insights into Antimicrobial Resistance in Shewanella algae Isolated from Penaeus monodon
by Ponsit Sathapondecha, Wichai Pornthanakasem, Timpika Thepsuwan, Pacharaporn Angthong, Wiyada Chumpol, Kamonwan Lunha, Suganya Yongkiettrakul and Wanilada Rungrassamee
Antibiotics 2026, 15(4), 405; https://doi.org/10.3390/antibiotics15040405 - 16 Apr 2026
Viewed by 715
Abstract
Background/Objectives: The emergence of antimicrobial-resistant (AMR) pathogens in aquaculture ecosystems poses a significant risk to both food security and human health. Shewanella species are recognized as significant AMR reservoirs, yet their prevalence and resistance mechanisms within a shrimp-related ecosystem remain poorly characterized. This [...] Read more.
Background/Objectives: The emergence of antimicrobial-resistant (AMR) pathogens in aquaculture ecosystems poses a significant risk to both food security and human health. Shewanella species are recognized as significant AMR reservoirs, yet their prevalence and resistance mechanisms within a shrimp-related ecosystem remain poorly characterized. This study aimed to perform a genotypic and phenotypic characterization of S. algae VK101, isolated from wild-caught black tiger shrimp (Penaeus monodon) broodstock. Methods: A complete 5.21 Mb genome was generated using a hybrid Illumina and Oxford Nanopore sequencing approach. Antimicrobial susceptibility was evaluated for 21 antibiotics via Minimum Inhibitory Concentration (MIC) testing. Comparative pangenomics and genome-wide association studies (GWAS) across 125 S. algae genomes were conducted to identify novel resistance determinants. Results: MIC analysis revealed that VK101 was resistant to ampicillin (>16 µg/mL) and colistin (8 µg/mL), while showing intermediate susceptibility to imipenem and ciprofloxacin. In silico analysis identified 205 antimicrobial resistance genes (ARGs), including a perfect hit for the fluoroquinolone resistance gene qnrA3. Notably, no mcr genes were detected. Although VK101 exhibited moderate resistance (8 µg/mL), GWAS across the broader S. algae population linked a specific lptA mutation (K140N) to high-level resistance (64 µg/mL). Other GWAS-identified genes (e.g., czcA, ampC, and oprM) likely represent indirect associations driven by genetic linkage or clade-specific markers rather than direct causal factors. Conclusions: These findings highlighted the presence of multidrug-resistant S. algae in wild-caught P. monodon broodstock, reflecting the occurrence of antimicrobial resistance in aquatic environments. Colistin resistance in these isolates was primarily mediated by chromosomal variants rather than mobile mcr elements, indicating the need for integrated genomic surveillance within the aquaculture value chain. Full article
(This article belongs to the Special Issue Antibiotics and Antimicrobial Resistance in Aquaculture: Alternative and Complementary Treatment Methods)
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20 pages, 4280 KB  
Article
Silybin Interferes with the Intracellular Replication of Piscirickettsia salmonis in SHK-1 Cells and Confers Protection in Salmo salar
by Mick Parra, Meraiot Rubio, Katherin Izquierdo, Valentina Barsotti, Ana María Sandino and Brenda Modak
Antibiotics 2026, 15(2), 219; https://doi.org/10.3390/antibiotics15020219 - 17 Feb 2026
Viewed by 646
Abstract
Background/Objectives: The salmon industry plays an important role in the Chilean economy, positioning the country as the second-largest producer of salmonids worldwide after Norway. However, this rapid growth has led to an increase in outbreaks of infectious diseases, which cause significant economic [...] Read more.
Background/Objectives: The salmon industry plays an important role in the Chilean economy, positioning the country as the second-largest producer of salmonids worldwide after Norway. However, this rapid growth has led to an increase in outbreaks of infectious diseases, which cause significant economic losses to the industry. The pathogen that most affects the salmon industry is the bacterium Piscirickettsia salmonis, accounting for 43.1% of infection-related deaths. In the search for new treatment alternatives against P. salmonis, we have previously reported that the effect of co-incubating silybin at sub-IC50 concentrations decreases the intracellular presence of P. salmonis in SHK-1 cells. Methods: This article evaluates the effect of silybin on the immune response and oxidative stress of SHK-1 cells infected with P. salmonis, as well as the reduction in intracellular bacterial replication during the first 72 h of infection. Furthermore, we assess the ability of silybin administration to modulate the immune response in S. salar and protect against P. salmonis infection. Results: The results show that co-incubation of silybin during infection in SHK-1 cells modulates the expression levels of the genes gsh-px, cat, tnf-α, and il-1β and also decreases the levels of intracellular ROS generated by the infection. Furthermore, the mechanism of action of silybin in SHK-1 cells is related to interference with the intracellular replication of P. salmonis after 72 h of infection and not to adherence or internalization of the bacteria. Finally, silybin is able to generate protection in S. salar infected with P. salmonis independently of stimulation of the immune response. Conclusions: In conclusion, silybin administration may be an effective treatment against P. salmonis in salmonids; however, further studies are needed to clarify the mechanism of action. Full article
(This article belongs to the Special Issue Antibiotics and Antimicrobial Resistance in Aquaculture: Alternative and Complementary Treatment Methods)
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13 pages, 405 KB  
Article
Functional Potential of Red Dragon Fruit (Hylocereus polyrhizus) Juice By-Products as a Natural Feed Additive for Juvenile Red Seabream (Pagrus major): Implications for Antibiotic-Free Aquaculture
by Hwa Yong Oh, Ki-Tae Kim, Tae Hoon Lee, Da Ye Kang, Do-Hyun Kwon, Young Wook Kim and Hee Sung Kim
Antibiotics 2025, 14(11), 1096; https://doi.org/10.3390/antibiotics14111096 - 1 Nov 2025
Viewed by 1246
Abstract
Background: The extensive use of antibiotics in aquaculture has raised serious concerns, emphasizing the need for sustainable and natural alternatives. This study evaluated the potential of red dragon fruit (Hylocereus polyrhizus) juice by-products (RJB) as a functional feed additive for juvenile [...] Read more.
Background: The extensive use of antibiotics in aquaculture has raised serious concerns, emphasizing the need for sustainable and natural alternatives. This study evaluated the potential of red dragon fruit (Hylocereus polyrhizus) juice by-products (RJB) as a functional feed additive for juvenile red seabream (Pagrus major). Materials and Methods: The bioactive composition and antioxidant capacity of RJB were analyzed, and five experimental diets containing 0, 0.2, 0.4, 0.8, and 1% RJB were fed to fish for 56 days. Results: Growth performance, feed utilization, body composition, antioxidant enzyme activities, and lysozyme activity were evaluated. RJB contained substantial levels of phenolic and flavonoid compounds and exhibited strong radical-scavenging activity. Dietary inclusion of up to 1% RJB did not significantly affect growth, feed efficiency, or plasma biochemistry. However, fish fed the 1% RJB diet showed increased catalase and glutathione levels, significantly enhanced lysozyme activity, and improved survival following Edwardsiella tarda infection. Conclusion: These results demonstrate that RJB can be safely incorporated into marine fish diets to enhance antioxidant capacity and innate immune defense. The valorization of fruit-processing by-products such as RJB offers a promising strategy for developing antibiotic-free and sustainable aquaculture practices. Full article
(This article belongs to the Special Issue Antibiotics and Antimicrobial Resistance in Aquaculture: Alternative and Complementary Treatment Methods)
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12 pages, 1705 KB  
Communication
Unveiling Hidden Allies: In Silico Discovery of Prophages in Tenacibaculum Species
by Carolina Ramírez and Jaime Romero
Antibiotics 2024, 13(12), 1184; https://doi.org/10.3390/antibiotics13121184 - 5 Dec 2024
Cited by 3 | Viewed by 2053
Abstract
Tenacibaculosis, caused by Tenacibaculum species, is a significant disease in aquaculture, leading to high mortality and economic losses. Antibiotic treatment raises concerns about resistance, making phage therapy an interesting alternative. Analyzing phage traces in Tenacibaculum genomes is crucial for developing these bacteriophage-based strategies. [...] Read more.
Tenacibaculosis, caused by Tenacibaculum species, is a significant disease in aquaculture, leading to high mortality and economic losses. Antibiotic treatment raises concerns about resistance, making phage therapy an interesting alternative. Analyzing phage traces in Tenacibaculum genomes is crucial for developing these bacteriophage-based strategies. Methods: We assessed the presence of prophages in 212 Tenacibaculum genomes/assemblies available in the NCBI repository, comprising several species and global locations, using the PHASTEST program. Then, we focused on those regions classified as intact, evaluating the most common phages found using VICTOR. The protein of interest discovered in the prophages was evaluated using the ProtParam, DeepTMHMM, InterPro, and Phyre2 tools. In addition, we evaluated the presence of antiphage defense systems in those genomes with intact prophages using the DefenseFinder tool. Results: We identified 25 phage elements in 24 out of the 212 Tenacibaculum genomes/assemblies analyzed, with 11% of the assemblies containing phage elements. These were concentrated in T. maritimum and T. mesophilum, which harbored 10 and 7 prophage regions, respectively. Of the identified elements, six were classified as intact, including four in T. maritimum, with the most common phages belonging to the Pippivirus and Siphoviridae families. Bioinformatic analysis showed that the putative endolysin is a stable protein of 432 amino acids and 49.8 kDa, with three transmembrane helices and a CHAP domain, structurally similar to the CHAP lytic domain of S. aureus bacteriophage K. Conclusions: Key prophage elements in Tenacibaculum, especially in T. maritimum, show promise for phage therapy against tenacibaculosis, supporting sustainable, antibiotic-free treatments in aquaculture. Full article
(This article belongs to the Special Issue Antibiotics and Antimicrobial Resistance in Aquaculture: Alternative and Complementary Treatment Methods)
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