Uncovering Endolysins against Methicillin-Resistant Staphylococcus aureus Using a Microbial Single-Cell Genome Database

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 these endolysins is vital. We propose here 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 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.