The evolution of antimicrobial peptide resistance in Pseudomonas aeruginosa is shaped by strong epistatic interactions.

Nicholas Jochumsen,Rune Lyngklip Jensen,Rasmus L Marvig,Lars Jelsbak,Søren Molin,Anders Folkesson,Søren Damkiær,Wilhelm Paulander

doi:10.1038/ncomms13002

Nicholas Jochumsen, Rune Lyngklip Jensen + Show 6 more

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https://doi.org/10.1038/ncomms13002

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Abstract

Colistin is an antimicrobial peptide that has become the only remaining alternative for the treatment of multidrug-resistant Gram-negative bacterial infections, but little is known of how clinical levels of colistin resistance evolve. We use in vitro experimental evolution and whole-genome sequencing of colistin-resistant Pseudomonas aeruginosa isolates from cystic fibrosis patients to reconstruct the molecular evolutionary pathways open for high-level colistin resistance. We show that the evolution of resistance is a complex, multistep process that requires mutation in at least five independent loci that synergistically create the phenotype. Strong intergenic epistasis limits the number of possible evolutionary pathways to resistance. Mutations in transcriptional regulators are essential for resistance evolution and function as nodes that potentiate further evolution towards higher resistance by functionalizing and increasing the effect of the other mutations. These results add to our understanding of clinical antimicrobial peptide resistance and the prediction of resistance evolution.

Highlights

Colistin is an antimicrobial peptide that has become the only remaining alternative for the treatment of multidrug-resistant Gram-negative bacterial infections, but little is known of how clinical levels of colistin resistance evolve
We show that the evolution of high-level colistin resistance is a complex, multistep process requiring mutations in at least five independent loci that act synergistically to create the phenotype and demonstrating that complex resistance mechanisms can readily evolve de novo under the right conditions such as drug gradients or stepwise selection
We sequenced the genomes of B3-1811, B3-208, B3-20M and B3-CFI, which are four P. aeruginosa isolates isolated from consecutive sputum samples from a cystic fibrosis patient with a long-term chronic P. aeruginosa lung infection[31]

Summary

Introduction

Colistin is an antimicrobial peptide that has become the only remaining alternative for the treatment of multidrug-resistant Gram-negative bacterial infections, but little is known of how clinical levels of colistin resistance evolve. We use in vitro experimental evolution and whole-genome sequencing of colistin-resistant Pseudomonas aeruginosa isolates from cystic fibrosis patients to reconstruct the molecular evolutionary pathways open for high-level colistin resistance. Mutations in transcriptional regulators are essential for resistance evolution and function as nodes that potentiate further evolution towards higher resistance by functionalizing and increasing the effect of the other mutations These results add to our understanding of clinical antimicrobial peptide resistance and the prediction of resistance evolution. We show that the evolution of high-level colistin resistance is a complex, multistep process requiring mutations in at least five independent loci that act synergistically to create the phenotype and demonstrating that complex resistance mechanisms can readily evolve de novo under the right conditions such as drug gradients or stepwise selection. The identification and understanding of the genetic basis of colistin resistance and the evolutionary process driving resistance evolution may facilitate the development of tools to predict and manage resistance

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