Data mining reveals the diversity of prophage endolysins targeting pathogenic enterococci

Antimicrobial resistance poses a critical global health threat, with enterococci among the leading contributors due to their intrinsic and acquired resistance to antibiotics. Clinically relevant species, including Enterococcus faecalis and Enterococcus faecium as well as the emerging poultry pathogen Enterococcus cecorum, highlight the need for alternative therapeutics across human and agricultural settings. Bacteriophages and their derived enzymes, particularly endolysins, offer promising antibacterial strategies but challenges such as phage resistance and limited lysin diversity hinder their application. In this study, we performed a large-scale analysis of prophage-encoded endolysins across these three enterococcal opportunistic pathogens, characterizing over 48,000 sequences. We identified 33 distinct domain architectures combining diverse catalytic and cell wall-binding domains (CBDs) including novel putative CBDs. These findings expand the known diversity of enterococcal lysins and provide a comprehensive resource for the rational design of stable, recombinant ‘enzybiotics’ to combat multidrug-resistant enterococcal infections.