Harnessing Broad-Specificity Phage Recombinases for Universal Bacterial Editing platforms

PROJECT SUMMARY The vast array of genetic elements within a bacterial genome dictates its potential to cause disease. These elements influence virulence, antibiotic susceptibility, and the ability to evade the immune response. Understanding and manipulating these genetic components are crucial for identifying the drivers of bacterial pathogenicity. However, a significant challenge arises because efficient genetic systems are typically limited to laboratory-adapted strains. This limitation leaves many virulent clinical pathogens genetically intractable. To address this challenge, we developed a genome editing platform on phage recombinase that works across a broad range of species. Editing bacteria with phage recombinases, a process termed recombineering, has been transformative in E coli. However, its reliance on host factors causes species-specificity that has limited its broader impact. We discovered a phage protein that is conserved across bacterial phyla that can used to identify broadly functioning phage recombinase systems. Leveraging this protein, we developed a recombineering system that operates in both Gram-positive and Gram-negative bacteria. To further explore the potential of phage-based genetic engineering, we have established a high-throughput selection to identify phage recombinases from genomic material without relying on homology to existing recombinases. Coupling the ubiquity of recombination modules in dsDNA phages with the vast diversity of genetic information encoded by phage, we anticipate identifying numerous new phage-based recombination systems. Initial results have demonstrated levels of genetic editing in the important human pathogen Staphylococcus aureus comparable to recombineering in E coli. This work will transform the way we genetically manipulate bacteria, enabling us to directly probe the genetic elements driving pathogenicity in clinically relevant strains.