CRISPR-Cas–Mediated Precision Antimicrobial Strategies for Targeting Multidrug-Resistant Bacteria: Mechanisms, Delivery Systems, and Clinical Potential

Abstract

The escalating crisis of antimicrobial resistance (AMR) has outpaced conventional antibiotic discovery, necessitating innovative, sequence-specific therapeutic modalities. This review critically evaluates CRISPR-Cas–mediated antimicrobial strategies as a programmable alternative for eradicating multidrug-resistant (MDR) bacterial pathogens. We synthesize current evidence on mechanistic platforms, including DNA/RNA-targeting nucleases (Cas9, Cas12a, Cas13) and transcriptional modulators (CRISPRi/a), highlighting their capacity for precise pathogen elimination, resistance plasmid curing, and antibiotic resensitization. Furthermore, we assess emerging delivery architectures, engineered bacteriophages, lipid nanoparticles, and conjugative plasmids, detailing their tropism specificity, payload stability, and in vivo pharmacokinetic profiles. Despite robust preclinical efficacy and microbiome-sparing advantages, clinical translation remains constrained by delivery inefficiencies in complex host environments, bacterial counter-adaptations (e.g., anti-CRISPR proteins, PAM mutations), and the absence of standardized regulatory and pharmacological frameworks. We propose actionable recommendations for effector multiplexing, adaptive clinical trial design, GMP-scale manufacturing, and One Health–aligned ecological stewardship. CRISPR-Cas antimicrobials represent a transformative frontier in infectious disease therapeutics; realizing their clinical potential demands interdisciplinary convergence, regulatory modernization, and rigorous translational validation to safeguard global health in the post-antibiotic era.