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The CRISPR/Cas system as an antimicrobial resistance strategy in aquatic ecosystems

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With the growing population, demand for food has dramatically increased, and fisheries, including aquaculture, are expected to play an essential role in sustaining demand with adequate quantities of protein and essential vitamin supplements, employment generation, and GDP growth. Unfortunately, the incidence of emerging/re-emerging AMR pathogens annually occurs because of anthropogenic activities and the frequent use of antibiotics in aquaculture. These AMR pathogens include the WHO's top 6 prioritized ESKAPE pathogens (nosocomial pathogens: Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.), extended-spectrum beta lactases (ESBLs) and carbapenemase-producing E. coli, which pose major challenges to the biomagnification of both nonnative and native antibiotic-resistant bacteria in capture and cultured fishes. Although implementing the rational use of antibiotics represents a promising mitigation measure, this approach is practically impossible due to the lack of awareness among farmers about the interplay between antimicrobial use and the emergence of antimicrobial resistance (AMR). Nevertheless, to eradicate these ‘superbugs,’ CRISPR/Cas (clustered regularly interspersed short palindromic repeats/CRISPR associate protein) has turned out to be a novel approach owing to its ability to perform precise site-directed targeting/knockdown/reversal of specific antimicrobial resistance genes in vitro and to distinguish AMR-resistant bacteria from a plethora of commensal aquatic bacteria. Along with highlighting the importance of virulent multidrug resistance genes in bacteria, this article aims to provide a holistic picture of CRISPR/Cas9-mediated genome editing for combating antimicrobial-resistant bacteria isolated from various aquaculture and marine systems, as well as insights into different types of CRISPR/Cas systems, delivery methods, and challenges associated with developing CRISPR/Cas9 antimicrobial agents.

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The authors would like to express their acknowledgment to the Indian Council of Medical Research- Department of Health Research (ICMR-DHR), New Delhi, ICAR-DARE, New Delhi and Director, ICAR-CIFT, Cochin, Kerala, India and the University of Southampton, UK.


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Authors and Affiliations



Sobin Sonu Gupta: Draft manuscript preparation, Visualization.

Muneeb Hamza: Assisted in drawing the figures and editing.

Collin Sones: Conceptualization, supervision.

Xunli Zhang: Conceptualization, supervision, manuscript review and editing.

Gopalan Krishnan Sivaraman: Conceptualization, Design, supervision, Review & Editing.

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Correspondence to Gopalan Krishnan Sivaraman.

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Gupta, S.S., Hamza KH, M., Sones, C.L. et al. The CRISPR/Cas system as an antimicrobial resistance strategy in aquatic ecosystems. Funct Integr Genomics 24, 110 (2024).

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