Multiplexed deactivated CRISPR-Cas9 gene expression perturbations deter bacterial adaptation by inducing negative epistasis

Peter B Otoupal; William T Cordell; Vismaya Bachu; Madeleine J Sitton; Anushree Chatterjee

doi:10.1038/s42003-018-0135-2

Multiplexed deactivated CRISPR-Cas9 gene expression perturbations deter bacterial adaptation by inducing negative epistasis

Commun Biol. 2018 Sep 3:1:129. doi: 10.1038/s42003-018-0135-2. eCollection 2018.

Authors

Peter B Otoupal¹, William T Cordell¹, Vismaya Bachu¹, Madeleine J Sitton¹, Anushree Chatterjee^{2

3}

Affiliations

¹ Department of Chemical and Biological Engineering, University of Colorado at Boulder, Boulder, CO, 80303, USA.
² Department of Chemical and Biological Engineering, University of Colorado at Boulder, Boulder, CO, 80303, USA. chatterjee@colorado.edu.
³ BioFrontiers Institute, University of Colorado at Boulder, Boulder, CO, 80303, USA. chatterjee@colorado.edu.

Abstract

The ever-increasing threat of multi-drug resistant bacteria, a shrinking antibiotic pipeline, and the innate ability of microorganisms to adapt necessitates long-term strategies to slow the evolution of antibiotic resistance. Here we develop an approach, dubbed Controlled Hindrance of Adaptation of OrganismS or CHAOS, involving induction of epistasis between gene perturbations to deter adaption. We construct a combinatorial library of multiplexed, deactivated CRISPR-Cas9 devices to systematically perturb gene expression in Escherichia coli. While individual perturbations improved fitness during antibiotic exposure, multiplexed perturbations caused large fitness loss in a significant epistatic fashion. Strains exhibiting epistasis adapted significantly more slowly over three to fourteen days, and loss in adaptive potential was shown to be sustainable. Finally, we show that multiplexed peptide nucleic acids increase the antibiotic susceptibility of clinically isolated Carbapenem-resistant E. coli in an epistatic fashion. Together, these results suggest a new therapeutic strategy for restricting the evolution of antibiotic resistance.