RT Journal Article
SR Electronic
T1 Potentiating antibiotic treatment using fitness-neutral gene expression perturbations
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 736058
DO 10.1101/736058
A1 Peter B. Otoupal
A1 Keesha E. Erickson
A1 Kristen A. Eller
A1 Jocelyn Campos
A1 Thomas R. Aunins
A1 Anushree Chatterjee
YR 2019
UL http://biorxiv.org/content/early/2019/08/15/736058.abstract
AB The rapid proliferation of multidrug-resistant (MDR) bacteria poses a critical threat to human health, for which new antimicrobial strategies are desperately needed. Here we outline a strategy for combating bacterial infections by administering fitness neutral gene expression perturbations as co-therapies to potentiate antibiotic lethality. We systematically explored the fitness of 270 gene knockout-drug combinations in Escherichia coli, identifying 114 synergistic interactions. Genes revealed in this screen were subsequently perturbed at the transcriptome level via multiplexed CRISPR-dCas9 interference to induce antibiotic synergy. These perturbations successfully sensitized E. coli to antibiotic treatment without imposing a separate fitness cost. We next administered these fitness neutral gene perturbations as co-therapies to potentiate antibiotic killing of Salmonella enterica in intracellular infections of HeLa epithelial cells, demonstrating therapeutic applicability. Finally, we utilized these results to design peptide nucleic acid (PNA) co-therapies for targeted gene expression reduction in four MDR, clinically isolated bacteria. Two isolates of Klebsiella pneumoniae and E. coli were each exposed to PNAs targeting homologs of the genes csgD, fnr, recA and acrA in the presence of sub-minimal inhibitory concentrations of trimethoprim. We successfully increased each strain’s susceptibility to trimethoprim treatment and identified eight cases in which re-sensitization occurred without a direct fitness impact of the PNA on MDR strains. Our results highlight a promising approach for combating MDR bacteria which could extend the utility of our current antibiotic arsenal.CRISPRclustered regularly interspaced short palindromic repeats.Cas9CRISPR-associated protein 9.dCas9catalytically deactivated-Cas9.sgRNAsingle-guide RNA.PAMprotospacer adjacent motif.CFUcolony forming unit.Ntnucleotide.aTcanhydrous tetracycline.AMPampicillin.TETtetracycline.ERYerythromycin.PUROpuromycin.CIPciprofloxacin.CROceftriaxone.CMchloramphenicol.TMPtrimethoprim.SDIsulfadimidine.GENgentamicin.KANkanamycin.