CRISPR is revolutionizing disease diagnosis in aquaculture species

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By Milthon Lujan

Working mechanism of various CRISPR-Cas systems used for disease diagnostics. Source: Bohara et al., (2024); SSRN.
Working mechanism of various CRISPR-Cas systems used for disease diagnostics. Source: Bohara et al., (2024); SSRN.

Traditional diagnostic methods in aquaculture, although effective, can be time-consuming and expensive. Fortunately, a revolutionary technology called CRISPR is emerging as a game changer in disease detection in aquaculture.

A team of scientists from the University of Arkansas at Pine Bluff (USA) and Delaware State University (USA) consolidated and summarized the characteristics, applicability, and limitations of various CRISPR-based diagnostic methods developed specifically for aquaculture.

The Challenge: Diagnosing Diseases in Aquaculture

The delicate balance between farmed fish, pathogens, and the environment is easily disrupted by factors such as climate change and high-density aquaculture practices. This disruption leads to disease outbreaks, affecting both fish health and farm profitability. Moreover, many diseases lack effective treatments or vaccines, highlighting the importance of early and accurate diagnosis.

Traditional Methods: Effective but Limited

Currently, methods such as polymerase chain reaction (PCR) and cell culture are the standard for diagnosing aquatic diseases. Environmental DNA/RNA testing is also promising, but detecting degraded nucleic acids in water is challenging.

While these methods offer high sensitivity and specificity, they often require significant time and specialized equipment, limiting their accessibility for on-site testing.

The Promise of CRISPR Diagnostics

CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) is a revolutionary gene-editing tool that scientists have used to develop disease-resistant fish and improve the breeding and production of aquaculture species. However, it also has intriguing applications in disease diagnostics.

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Researchers are now leveraging CRISPR’s potential to develop rapid, sensitive, and cost-effective diagnostic assays for aquaculture.

How CRISPR Diagnostics Work

CRISPR diagnostics utilize CRISPR-associated enzymes (Cas), such as Cas9, Cas12, or Cas13. These enzymes target specific sequences in the pathogen’s genetic material. Upon successful detection, a reporter signal is activated, indicating the presence of the disease. Pre-amplification techniques can further enhance sensitivity by increasing the detectable amount of pathogen DNA or RNA.

Revolutionizing Disease Detection in Aquaculture

CRISPR-based diagnostics have immense potential to transform disease detection and monitoring in aquaculture. Here are some key areas of impact:

1. Rapid and Specific Pathogen Detection: CRISPR diagnostics can quickly identify pathogens with high accuracy, enabling early intervention and disease control. Advantages include:

    • Speed: Faster turnaround times compared to traditional methods.
    • Sensitivity: Highly sensitive, allowing early pathogen detection.
    • Portability: Portable systems could enable on-site testing at fish farms.
    • Cost-Effectiveness: Potential for affordable testing, benefiting small-scale farmers.

    2. Point-of-Care Testing: Unlike traditional methods that require laboratory facilities, CRISPR-based assays can potentially be designed for on-site testing, providing farmers with real-time disease information.

    3. High-Throughput Screening: These diagnostics could potentially be used for large-scale screening of fish populations, enabling proactive disease management.

    4. Antimicrobial Resistance Detection: CRISPR can identify antibiotic-resistant pathogens, facilitating appropriate treatment strategies.

    5. Customizable Detection Platforms: The technology can be tailored to detect various pathogens, creating a versatile diagnostic tool.

      A Diverse Toolkit: Cas Systems for Different Needs

      Researchers are exploring various CRISPR-Cas systems, each with its own advantages, to develop assays for diagnosing aquatic diseases. This review delves into these systems, exploring:

      • Characteristics: Key features and functionalities of different Cas systems.
      • Applicability: How each system can be used to diagnose specific diseases in aquaculture.
      • Limitations: Potential challenges associated with each system.
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      While CRISPR diagnostics offer a bright future for aquaculture, further research is needed to fully unlock their potential. A comprehensive understanding of different Cas systems and their suitability for various pathogens is crucial. Additionally, optimizing assay design and developing user-friendly platforms for on-site testing are important areas of focus.


      By understanding the strengths and limitations of various CRISPR-based diagnostic methods, researchers and fish farmers can choose the most suitable tool for specific disease detection needs.

      CRISPR diagnostics are poised to revolutionize disease detection in aquaculture. By enabling rapid, sensitive, and cost-effective diagnostics, this technology can empower aquaculturists to safeguard their fish populations and ensure a healthy, sustainable food source for the future.

      Reference (open access)
      Bohara, Kailash and Parsaeimehr, Ali and Bhattarai, Sujan, CRISPR-based diagnostic in aquaculture: Application, Potential/Opportunities, and Limitations (May 2, 2024). Available at SSRN: https://ssrn.com/abstract=4815342 or http://dx.doi.org/10.2139/ssrn.4815342