Antibiotics that target multiple cellular functions are anticipated to be less prone
to bacterial resistance. Here we hypothesize that while dual targeting is crucial,
it is not sufficient in preventing resistance. Only those antibiotics that simultaneously
target membrane integrity and block another cellular pathway display reduced resistance
development. To test the hypothesis, we focus on three antibiotic candidates, POL7306,
Tridecaptin M152-P3 and SCH79797, all of which fulfill the above criteria. Here we
show that resistance evolution against these antibiotics is limited in ESKAPE pathogens,
including Escherichia coli , Klebsiella pneumoniae , Acinetobacter baumannii and Pseudomonas
aeruginosa , while dual-target topoisomerase antibiotics are prone to resistance.
We discover several mechanisms restricting resistance. First, de novo mutations result
in only a limited elevation in resistance, including those affecting the molecular
targets and efflux pumps. Second, resistance is inaccessible through gene amplification.
Third, functional metagenomics reveal that mobile resistance genes are rare in human
gut, soil and clinical microbiomes. Finally, we detect rapid eradication of bacterial
populations upon toxic exposure to membrane targeting antibiotics. We conclude that
resistance mechanisms commonly found in natural bacterial pathogens provide only limited
protection to these antibiotics. Our work provides guidelines for the future development
of antibiotics.
