Utilizing CRISPR-Cas Systems to Combat Antibacterial Resistance

The escalating crisis of antimicrobial resistance (AMR) represents an existential threat to global health. The emergence and rapid global dissemination of "superbugs" capable of evading multiple antibiotics severely undermine our ability to treat common infections, threatening to revert modern medicine to a pre-antibiotic era where routine medical procedures become unacceptably risky. This challenge is multifaceted, driven by antibiotic misuse, inadequate infection control, and a critical shortfall in the development of genuinely novel antimicrobial agents. With millions of deaths directly attributable to resistant infections each year, the urgent need for innovative, precise, and multi-pronged strategies is paramount.

In this critical context, CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeats-CRISPR-associated proteins) systems have emerged as a groundbreaking and remarkably versatile paradigm for combating bacterial threats. Originally discovered as bacterial adaptive immune systems, CRISPR-Cas technologies have been ingeniously repurposed into highly precise and programmable genetic tools. Their unparalleled ability to specifically target and manipulate DNA or RNA sequences offers unprecedented avenues not only to directly disarm resistant bacteria but also to develop entirely new antibacterial modalities and enhance host defenses.

Beyond the direct degradation of antibiotic resistance genes (ARGs) on mobile genetic elements or bacterial chromosomes, CRISPR-Cas systems provide powerful means to disrupt essential bacterial genes for direct killing, interfere with bacterial communication and virulence, and even modulate host immune responses to improve infection clearance. Their programmable nature allows for the rational design of highly specific therapeutics. Furthermore, CRISPR's inherent connection to bacteriophages opens unique avenues for targeted delivery and synergistic therapies, while its precision makes it invaluable for rapid diagnostics and surveillance of resistant pathogens.

While the therapeutic and diagnostic promise of CRISPR-Cas is immense, practical challenges persist, including efficient and specific delivery into target cells, ensuring system stability in vivo, and mitigating potential off-target effects. Understanding and overcoming these hurdles, along with anticipating bacterial resistance mechanisms to CRISPR-based interventions, are crucial for successful clinical translation. This special issue aims to provide a comprehensive collection of cutting-edge research and insightful reviews that explore the full spectrum of CRISPR-Cas applications, from foundational mechanisms and computational design to innovative delivery, advanced diagnostics, and critical clinical considerations, in the global imperative to combat antibacterial resistance.

Suggested sub-topics:

1. Mechanisms of CRISPR-Cas Action against Antibiotic Resistance Genes (ARGs): Deep dives into how different CRISPR-Cas types (e.g., Type I, II, V, VI) are engineered for precise targeting and degradation of plasmid-borne or chromosomal ARGs, including CRISPR-mediated gene deletion and repression (CRISPRi).

2. CRISPR-Cas as a Direct Antibacterial Agent: Targeting Essential Bacterial Genes and Metabolic Pathways: Research on utilizing CRISPR-Cas to disrupt fundamental bacterial processes, leading to cell death or growth inhibition, thereby providing novel drug-independent antibacterial strategies.

3. Modulating Bacterial Virulence Factors, Biofilms, and Communication Systems: Studies on CRISPR-Cas applications to interfere with bacterial pathogenicity, including the suppression of virulence gene expression, inhibition of biofilm formation, interference with quorum sensing mechanisms, and targeting of drug efflux pumps.

4. Targeting Host Factors Modulating Bacterial Survival, Growth, and Immune Evasion: Investigations into using CRISPR-Cas or CRISPR-based screens to identify and modulate host genes or pathways that facilitate bacterial persistence (e.g., intracellular survival), promote immune evasion, or otherwise contribute to infection pathogenesis.

5. Enhancing Host Immune Responses for Bacterial Clearance via CRISPR-Cas: Studies on CRISPR-mediated modulation of host immune cells (e.g., macrophages, neutrophils) or specific immune pathways to bolster intrinsic anti-bacterial defenses, mitigate hyperinflammation, and improve overall host resilience against resistant infections.

6. CRISPR-Cas for Antibiotic Repurposing and Sensitization: Explorations into strategies where CRISPR-Cas systems are employed to restore the susceptibility of resistant bacterial strains to conventional antibiotics, thus revitalizing the efficacy of currently ineffective drugs.

7. Advanced Delivery Strategies for CRISPR-Cas Antimicrobials: Innovations in designing and optimizing delivery platforms for CRISPR-Cas components (e.g., engineered phages, nanoparticles, bacterial outer membrane vesicles, liposomes) to achieve targeted delivery, stability, and efficacy in vivo.

8. CRISPR-Phage Synergies and Engineering for Antimicrobial Applications: Research on the combined use of CRISPR-Cas with bacteriophages, including phage-mediated delivery of CRISPR components and the engineering of phages with enhanced lytic capabilities or broadened host ranges using CRISPR tools.

9. CRISPR-Based Diagnostics and Surveillance for AMR: Applications of CRISPR-Cas systems in developing rapid, sensitive, and specific diagnostics for identifying resistant bacterial strains, detecting ARGs in clinical samples, and facilitating surveillance of AMR dissemination.

10. Computational Design, Optimization, and In Silico Analysis of CRISPR Systems: Methodological advancements in bioinformatics and computational approaches for designing optimal guide RNAs, predicting off-target effects, analyzing bacterial resistance mechanisms to CRISPR, and simulating CRISPR-Cas therapeutic outcomes.

11. Challenges, Bacterial Resistance Mechanisms to CRISPR-Cas, and Counter-Strategies: Studies investigating potential bacterial countermeasures against CRISPR-Cas therapies (e.g., anti-CRISPR proteins, PAM mutations, target gene mutations) and the development of strategies to overcome these emerging resistances.

12. Clinical Translation, Safety, and Regulatory Considerations: Comprehensive reviews and original research on the current status of CRISPR-Cas-based antibacterial therapies from bench to bedside, detailed safety assessments, ethical implications, and the regulatory pathways for their eventual clinical adoption.

In this Research Topic we welcome the following article types: Original Research, Review, Mini Review, Perspective and Methods.

Article types and fees

This Research Topic accepts the following article types, unless otherwise specified in the Research Topic description:

• Brief Research Report
• Case Report
• Classification
• Clinical Trial
• Editorial
• FAIR² Data
• FAIR² DATA Direct Submission
• General Commentary
• Hypothesis and Theory
• ... View all formats

Articles that are accepted for publication by our external editors following rigorous peer review incur a publishing fee charged to Authors, institutions, or funders.

Article types

This Research Topic accepts the following article types, unless otherwise specified in the Research Topic description:

• Brief Research Report
• Case Report
• Classification
• Clinical Trial
• Editorial
• FAIR² Data
• FAIR² DATA Direct Submission
• General Commentary
• Hypothesis and Theory
• Methods
• Mini Review
• Opinion
• Original Research
• Perspective
• Review
• Systematic Review
• Technology and Code

Keywords: CRISPR-Cas, Antimicrobial Resistance (AMR), Bacterial Pathogens, Gene Editing, Host-Directed Therapies, Bacteriophages

Important note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.