Understanding the genetic; evolutionary; and ecological interactions between drug resistance and phage resistance

Project Summary/AbstractBacterial pathogens are increasingly evolving drug resistance under natural selection from antibiotics inmedicine, agriculture, and nature. Meanwhile, bacteria ubiquitously encounter bacteriophages and rapidlyevolve phage resistance. However, the role of phages in driving drug resistance and sensitivity remains unclear.Phage selection can specifically interact with antibiotic selection in complex ways. For instance, the evolution ofbacterial resistance to some phages increases resistance to antibiotics. On the other hand, some phages forcebacteria into evolutionary tradeoffs between phage and antibiotic resistance. We have previously shown thatphage which force such tradeoffs can drive the evolution of restored drug sensitivity in bacteria through thealteration of phage-targeted antibiotic efflux pumps. However, there are many non-efflux pump genes associatedwith drug resistance. For instance, Escherichia coli has 283 genes associated with drug resistance, only three ofwhich are characterized efflux-related genes. It is unknown how phages interact with uncharacterized crypticdrug resistance-associated genes and the conditions where selection by phages that use drug-associated genesmay restore drug sensitivity. To better understand the interactions of phage and antibiotic resistance, we willidentify phages that use cryptic drug resistance genes and, importantly, we will identify conditions in whichphage selection drives the evolution of increased drug sensitivity. Extending our previous work into a studysystem with excellent genetic tools, we will use microbiological, evolutionary, and molecular approaches tocharacterize interactions between our collection of phages and drug resistance associated genes in E. coli. Thiswork focuses on the ecological and evolutionary mechanisms not addressed in previous studies. We will screenour E. coli phage collection (33 phages) against a collection of 283 E. coli gene knockouts to identify phages thatspecifically rely on drug-resistance-associated alleles. We will then test how microbial community dynamics areinfluenced by phages and in turn alter the evolution of antibiotic resistance, characterizing general and drug-related evolutionary tradeoffs in communities of increasing complexity. Finally, we will analyze drug-resistance-targeting phage through life cycle characterization and whole genome sequencing and annotation, generatingwell-characterized phages for future study. This proposal leverages existing molecular biology knowledge of E.coli to survey every gene associated with drug resistance and determine whether phages interact with those genesand how phage selection alters the evolution of drug sensitivity. Within microbial evolutionary biology, thisproject will reveal how microbial communities mediate and alter evolutionary tradeoffs. More broadly formedical microbiology, this work will uncover relationships between drug resistance and phage resistance,increasing our understanding of the mechanisms by which drug resistance ? and sensitivity ? can evolve atclinical timescales. Should lytic phage be broadly applied in medicine, our project fills fundamental knowledgegaps required for their effectiveness and sustainability.