A Minimal Packaging Signal Enables Production of High-Purity Phage-Like Particles for CRISPR-Cas Antimicrobials in Staphylococcus aureus

Abstract

Precision phage therapeutics provide a promising strategy to combat multidrug-resistant pathogens, including Staphylococcus aureus. Efficient, specific packaging of genetic cargoes remains challenging. Using modular design principles, we report a minimal phagemid packaging signal consisting of the phage terminase small subunit under its native promoter that significantly outperforms conventional packaging signals. The utility of this synthetic terS operon was demonstrated through production of highly concentrated and genetically pure CRISPR-Cas antimicrobials. To circumvent CRISPR-mediated self-targeting during antimicrobial generation, a terS-deficient strain was engineered to express the anti-CRISPR protein AcrIIA4, enabling titers above 1010 transducing units per milliliter (TRU/mL) with over 94% purity. With a high-copy origin of replication module, CRISPR-Cas phage-like particle titers could approach 1012 TRU/mL. We discovered that pure CRISPR-Cas antimicrobials are potent and can be amplified in hosts possessing prophages. Taken altogether, this study defines the minimal and optimal genetic requirements for efficient, specific creation of phage-based technologies. Technological ReadinessThe described system for engineering phage-like particles has reached a technological readiness level (TRL) of 4-5 based on the provided laboratory validation and strong literature support from other engineered phage therapies applied to in vivo models. Previous systems have demonstrated high-purity phage-like particle preparation, but always at the cost of severely reduced productivity. Therefore, our demarcation of a specific, efficient, and minimal system for packaging nucleic acid cargoes into phage vectors is a critical step toward real-world use. Despite this, low levels of contaminating host/phage DNA remain a key barrier to phage-based therapies. Protein and strain engineering efforts can help mitigate terminase nonspecificity, but care must be taken to not compromise productivity. More generally, widespread adoption will require deeper understanding of host-pathogen-phage interactions, development of scalable GMP manufacturing processes, and harmonized regulatory guidance that recognizes the dynamic nature of phage-derived technologies.