Uncovering novel endolysins against methicillin-resistant Staphylococcus aureus using microbial single-cell genome sequencing

Endolysins, peptidoglycan hydrolases derived from bacteriophages (phages), are being developed as a promising alternative to conventional antibiotics. To obtain highly active endolysins, a diverse library of endolysins is vital. We here propose microbial single-cell genome sequencing as an efficient tool to discover dozens of previously unknown endolysins, owing to its culture-independent sequencing method. As a proof-of-concept, we analyzed and recovered endolysin genes within prophage regions of Staphylococcus single-amplified genomes (SAGs) in human skin microbiome samples. We constructed a library of chimeric endolysins by shuffling domains of the natural endolysins and performed high-throughput screening against Staphylococcus aureus . One of the lead endolysins, bbst1027, exhibited desirable antimicrobial properties such as rapid bactericidal activity, no detectable resistance development, and in vivo efficacy. We foresee that this endolysin discovery pipeline is in principle applicable to any bacterial target, and boost the development of novel antimicrobial agents.