Engineering Next-Generation Bacteriophage and CRISPR-Based Strategies for Precision Control of Antimicrobial-Resistant Pathogens

Abstract

Antimicrobial resistance (AMR) represents a major global public health challenge, necessitating innovative therapeutic strategies against multidrug-resistant (MDR) bacterial pathogens. This study framework evaluated the potential of engineered bacteriophages and CRISPR–Cas systems, individually and in combination, for precision antimicrobial targeting. An illustrative dataset comprising 150 bacterial isolates representing five clinically important species was used to compare antimicrobial resistance profiles, bacteriophage host-range coverage, antibacterial efficacy, biofilm inhibition, and treatment-associated resistance. Multidrug resistance was identified in 74.7% of isolates, with the highest prevalence observed in Acinetobacter baumannii (86.7%). Engineered bacteriophages increased host-range coverage from 69.3% to 85.3% and achieved a bacterial reduction of 3.64 ± 0.35 log₁₀ CFU/mL. CRISPR–Cas treatment demonstrated a reduction of 3.18 ± 0.32 log₁₀ CFU/mL. Notably, the integrated bacteriophage–CRISPR platform exhibited the greatest antibacterial activity (5.21 ± 0.41 log₁₀ CFU/mL), substantial biofilm inhibition (82.4 ± 4.3%), and the lowest frequency of reduced treatment susceptibility (7.0%). Additionally, meropenem susceptibility improved, with a fourfold reduction in minimum inhibitory concentration against Klebsiella pneumoniae. Collectively, these illustrative findings suggest that integrated bacteriophage–CRISPR strategies warrant further investigation as targeted antimicrobial approaches. Experimental validation and comprehensive biosafety assessments remain essential before clinical translation.

Keywords: Antimicrobial resistance, Engineered bacteriophages, CRISPR–Cas systems, Multidrug-resistant pathogens and Precision antimicrobial therapy.