Potentiating antibiotic efficacy via perturbation of non-essential gene expression

Otoupal, Peter B.; Eller, Kristen A.; Erickson, Keesha E.; Campos, Jocelyn; Aunins, Thomas R.; Chatterjee, Anushree

doi:10.1038/s42003-021-02783-x

Potentiating antibiotic efficacy via perturbation of non-essential gene expression

Journal Article · Fri Nov 05 00:00:00 EDT 2021 · Communications Biology

DOI:https://doi.org/10.1038/s42003-021-02783-x· OSTI ID:2471775

Otoupal, Peter B. ^[1]; ^[2]; Erickson, Keesha E. ^[2]; Campos, Jocelyn ^[2]; Aunins, Thomas R. ^[2]; ^[3]

University of Colorado, Boulder, CO (United States); Joint Bioenergy Institute, Emeryville, CA (United States); Sandia National Laboratories (SNL-CA), Livermore, CA (United States)
University of Colorado, Boulder, CO (United States)
University of Colorado, Boulder, CO (United States); Antimicrobial Regeneration Consortium, Boulder, CO (United States)

Proliferation of multidrug-resistant (MDR) bacteria poses a threat to human health, requiring new strategies. Here we propose using fitness neutral gene expression perturbations to potentiate antibiotics. We systematically explored 270 gene knockout-antibiotic combinations in Escherichia coli, identifying 90 synergistic interactions. Identified gene targets were subsequently tested for antibiotic synergy on the transcriptomic level via multiplexed CRISPR-dCas9 and showed successful sensitization of E. coli without a separate fitness cost. These fitness neutral gene perturbations worked as co-therapies in reducing a Salmonella enterica intracellular infection in HeLa. Finally, these results informed the design of four antisense peptide nucleic acid (PNA) co-therapies, csgD, fnr, recA and acrA, against four MDR, clinically isolated bacteria. PNA combined with sub-minimal inhibitory concentrations of trimethoprim against two isolates of Klebsiella pneumoniae and E. coli showed three cases of re-sensitization with minimal fitness impacts. Our results highlight a promising approach for extending the utility of current antibiotics.

View Accepted Manuscript (DOE)

Research Organization:: Sandia National Laboratories (SNL-CA), Livermore, CA (United States)

Sponsoring Organization:: USDOE National Nuclear Security Administration (NNSA); National Science Foundation (NSF); National Science Foundation Graduate Research Fellowship; DARPA Young Faculty Award

Grant/Contract Number:: NA0003525

OSTI ID:: 2471775

Journal Information:: Communications Biology, Journal Name: Communications Biology Journal Issue: 1 Vol. 4; ISSN 2399-3642

Publisher:: Springer NatureCopyright Statement

Country of Publication:: United States

Language:: English

References (63)

Annual Report of the Chief Medical Officer: infection and the rise of antimicrobial resistance Davies, Sally C.; Fowler, Tom; Watson, John The Lancet, Vol. 381, Issue 9878 https://doi.org/10.1016/S0140-6736(13)60604-2	journal	May 2013
The mar regulon: multiple resistance to antibiotics and other toxic chemicals Alekshun, Michael N.; Levy, Stuart B. Trends in Microbiology, Vol. 7, Issue 10 https://doi.org/10.1016/S0966-842X(99)01589-9	journal	October 1999
The dinB Gene Encodes a Novel E. coli DNA Polymerase, DNA Pol IV, Involved in Mutagenesis Wagner, Jérôme; Gruz, Petr; Kim, Su-Ryang Molecular Cell, Vol. 4, Issue 2 https://doi.org/10.1016/S1097-2765(00)80376-7	journal	August 1999
Phenotypic Landscape of a Bacterial Cell Nichols, Robert J.; Sen, Saunak; Choo, Yoe Jin Cell, Vol. 144, Issue 1 https://doi.org/10.1016/j.cell.2010.11.052	journal	January 2011
Creeping baselines and adaptive resistance to antibiotics Fernández, Lucía; Breidenstein, Elena B. M.; Hancock, Robert E. W. Drug Resistance Updates, Vol. 14, Issue 1 https://doi.org/10.1016/j.drup.2011.01.001	journal	February 2011
Combination drugs, an emerging option for antibacterial therapy Cottarel, Guillaume; Wierzbowski, Jamey Trends in Biotechnology, Vol. 25, Issue 12 https://doi.org/10.1016/j.tibtech.2007.09.004	journal	December 2007
Sequence-Specific Peptide Nucleic Acid-Based Antisense Inhibitors of TEM-1 β-Lactamase and Mechanism of Adaptive Resistance Courtney, Colleen M.; Chatterjee, Anushree ACS Infectious Diseases, Vol. 1, Issue 6 https://doi.org/10.1021/acsinfecdis.5b00042	journal	May 2015
Gene Expression Variability Underlies Adaptive Resistance in Phenotypically Heterogeneous Bacterial Populations Erickson, Keesha E.; Otoupal, Peter B.; Chatterjee, Anushree ACS Infectious Diseases, Vol. 1, Issue 11 https://doi.org/10.1021/acsinfecdis.5b00095	journal	September 2015
AcrAB–TolC Inhibition by Peptide-Conjugated Phosphorodiamidate Morpholino Oligomers Restores Antibiotic Activity in Vitro and in Vivo Sturge, Carolyn R.; Felder-Scott, Christina F.; Pifer, Reed ACS Infectious Diseases, Vol. 5, Issue 8 https://doi.org/10.1021/acsinfecdis.9b00123	journal	May 2019
CRISPR Perturbation of Gene Expression Alters Bacterial Fitness under Stress and Reveals Underlying Epistatic Constraints Otoupal, Peter B.; Erickson, Keesha E.; Escalas-Bordoy, Antoni ACS Synthetic Biology, Vol. 6, Issue 1 https://doi.org/10.1021/acssynbio.6b00050	journal	September 2016
Peptide Nucleic Acid. A Molecule with Two Identities Nielsen, Peter E. Accounts of Chemical Research, Vol. 32, Issue 7 https://doi.org/10.1021/ar980010t	journal	July 1999
Bactericidal antisense effects of peptide–PNA conjugates Good, Liam; Awasthi, Satish Kumar; Dryselius, Rikard Nature Biotechnology, Vol. 19, Issue 4 https://doi.org/10.1038/86753	journal	April 2001
Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants the Keio collection Baba, Tomoya; Ara, Takeshi; Hasegawa, Miki Molecular Systems Biology, Vol. 2, Article No. 2006.0008 https://doi.org/10.1038/msb4100050	journal	February 2006
Structure of the AcrAB–TolC multidrug efflux pump Du, Dijun; Wang, Zhao; James, Nathan R. Nature, Vol. 509, Issue 7501 https://doi.org/10.1038/nature13205	journal	April 2014
Exploiting CRISPR-Cas nucleases to produce sequence-specific antimicrobials Bikard, David; Euler, Chad W.; Jiang, Wenyan Nature Biotechnology, Vol. 32, Issue 11 https://doi.org/10.1038/nbt.3043	journal	October 2014
Combating bacteria and drug resistance by inhibiting mechanisms of persistence and adaptation Smith, Peter A.; Romesberg, Floyd E. Nature Chemical Biology, Vol. 3, Issue 9 https://doi.org/10.1038/nchembio.2007.27	journal	August 2007
β-lactam antibiotics promote bacterial mutagenesis via an RpoS-mediated reduction in replication fidelity Gutierrez, A.; Laureti, L.; Crussard, S. Nature Communications, Vol. 4, Issue 1 https://doi.org/10.1038/ncomms2607	journal	March 2013
Functional classification of drugs by properties of their pairwise interactions Yeh, Pamela; Tschumi, Ariane I.; Kishony, Roy Nature Genetics, Vol. 38, Issue 4 https://doi.org/10.1038/ng1755	journal	March 2006
Photoexcited quantum dots for killing multidrug-resistant bacteria Courtney, Colleen M.; Goodman, Samuel M.; McDaniel, Jessica A. Nature Materials, Vol. 15, Issue 5 https://doi.org/10.1038/nmat4542	journal	January 2016
Fast gapped-read alignment with Bowtie 2 Langmead, Ben; Salzberg, Steven L. Nature Methods, Vol. 9, Issue 4 https://doi.org/10.1038/nmeth.1923	journal	March 2012
CRISPR interference (CRISPRi) for sequence-specific control of gene expression Larson, Matthew H.; Gilbert, Luke A.; Wang, Xiaowo Nature Protocols, Vol. 8, Issue 11 https://doi.org/10.1038/nprot.2013.132	journal	October 2013
Exploring protein fitness landscapes by directed evolution Romero, Philip A.; Arnold, Frances H. Nature Reviews Molecular Cell Biology, Vol. 10, Issue 12 https://doi.org/10.1038/nrm2805	journal	December 2009
A CRISPRi screen in E. coli reveals sequence-specific toxicity of dCas9 Cui, Lun; Vigouroux, Antoine; Rousset, François Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-04209-5	journal	May 2018
Multiplexed deactivated CRISPR-Cas9 gene expression perturbations deter bacterial adaptation by inducing negative epistasis Otoupal, Peter B.; Cordell, William T.; Bachu, Vismaya Communications Biology, Vol. 1, Issue 1 https://doi.org/10.1038/s42003-018-0135-2	journal	September 2018
Facile accelerated specific therapeutic (FAST) platform develops antisense therapies to counter multidrug-resistant bacteria Eller, Kristen A.; Aunins, Thomas R.; Courtney, Colleen M. Communications Biology, Vol. 4, Issue 1 https://doi.org/10.1038/s42003-021-01856-1	journal	March 2021
Antisense PNA Accumulates in Escherichia coli and Mediates a Long Post-antibiotic Effect Nikravesh, Abbas; Dryselius, Rikard; Faridani, Omid R. Molecular Therapy, Vol. 15, Issue 8 https://doi.org/10.1038/sj.mt.6300209	journal	August 2007
Accelerated evolution of resistance in multidrug environments Hegreness, M.; Shoresh, N.; Damian, D. Proceedings of the National Academy of Sciences, Vol. 105, Issue 37 https://doi.org/10.1073/pnas.0805965105	journal	September 2008
Targeting a bacterial stress response to enhance antibiotic action Lee, S.; Hinz, A.; Bauerle, E. Proceedings of the National Academy of Sciences, Vol. 106, Issue 34 https://doi.org/10.1073/pnas.0903619106	journal	August 2009
Antibiotics induce redox-related physiological alterations as part of their lethality Dwyer, D. J.; Belenky, P. A.; Yang, J. H. Proceedings of the National Academy of Sciences, Vol. 111, Issue 20 https://doi.org/10.1073/pnas.1401876111	journal	May 2014
Transcriptome-based design of antisense inhibitors potentiates carbapenem efficacy in CRE Escherichia coli Aunins, Thomas R.; Erickson, Keesha E.; Chatterjee, Anushree Proceedings of the National Academy of Sciences, Vol. 117, Issue 48 https://doi.org/10.1073/pnas.1922187117	journal	November 2020
Long-Term Experimental Evolution in Escherichia coli. I. Adaptation and Divergence During 2,000 Generations Lenski, Richard E.; Rose, Michael R.; Simpson, Suzanne C. The American Naturalist, Vol. 138, Issue 6 https://doi.org/10.1086/285289	journal	December 1991
The Sequence Alignment/Map format and SAMtools Li, H.; Handsaker, B.; Wysoker, A. Bioinformatics, Vol. 25, Issue 16 https://doi.org/10.1093/bioinformatics/btp352	journal	June 2009
BEDTools: a flexible suite of utilities for comparing genomic features Quinlan, Aaron R.; Hall, Ira M. Bioinformatics, Vol. 26, Issue 6 https://doi.org/10.1093/bioinformatics/btq033	journal	January 2010
STRING v10: protein–protein interaction networks, integrated over the tree of life Szklarczyk, Damian; Franceschini, Andrea; Wyder, Stefan Nucleic Acids Research, Vol. 43, Issue D1 https://doi.org/10.1093/nar/gku1003	journal	October 2014
The EcoCyc database: reflecting new knowledge about Escherichia coli K-12 Keseler, Ingrid M.; Mackie, Amanda; Santos-Zavaleta, Alberto Nucleic Acids Research, Vol. 45, Issue D1 https://doi.org/10.1093/nar/gkw1003	journal	November 2016
Overexpression of marA, soxS , or acrAB produces resistance to triclosan in laboratory and clinical strains of Escherichia coli Mcmurry, Laura M.; Oethinger, Margret; Levy, Stuart B. FEMS Microbiology Letters, Vol. 166, Issue 2 https://doi.org/10.1111/j.1574-6968.1998.tb13905.x	journal	September 1998
Potentiating antibiotics in drug-resistant clinical isolates via stimuli-activated superoxide generation Courtney, Colleen M.; Goodman, Samuel M.; Nagy, Toni A. Science Advances, Vol. 3, Issue 10 https://doi.org/10.1126/sciadv.1701776	journal	October 2017
SOS Response Induction by ß-Lactams and Bacterial Defense Against Antibiotic Lethality Miller, Christine; Thomsen, Line Elnif; Gaggero, Carina Science, Vol. 305, Issue 5690 https://doi.org/10.1126/science.1101630	journal	September 2004
Multidrug evolutionary strategies to reverse antibiotic resistance Baym, M.; Stone, L. K.; Kishony, R. Science, Vol. 351, Issue 6268 https://doi.org/10.1126/science.aad3292	journal	December 2015
Cloning, Nucleotide Sequencing, and Analysis of the AcrAB-TolC Efflux Pump of Enterobacter cloacae and Determination of Its Involvement in Antibiotic Resistance in a Clinical Isolate Pérez, Astrid; Canle, Delia; Latasa, Cristina Antimicrobial Agents and Chemotherapy, Vol. 51, Issue 9 https://doi.org/10.1128/AAC.00072-07	journal	September 2007
Antibiotic Sensitivity Profiles Determined with an Escherichia coli Gene Knockout Collection: Generating an Antibiotic Bar Code Liu, A.; Tran, L.; Becket, E. Antimicrobial Agents and Chemotherapy, Vol. 54, Issue 4 https://doi.org/10.1128/AAC.00906-09	journal	January 2010
Involvement of the AcrAB-TolC Efflux Pump in the Resistance, Fitness, and Virulence of Enterobacter cloacae Pérez, Astrid; Poza, Margarita; Fernández, Ana Antimicrobial Agents and Chemotherapy, Vol. 56, Issue 4 https://doi.org/10.1128/AAC.05509-11	journal	January 2012
Killing by Ampicillin and Ofloxacin Induces Overlapping Changes in Escherichia coli Transcription Profile Kaldalu, Niilo; Mei, Rui; Lewis, Kim Antimicrobial Agents and Chemotherapy, Vol. 48, Issue 3 https://doi.org/10.1128/AAC.48.3.890-896.2004	journal	March 2004
Functional Genomic Study of Exogenous n-Butanol Stress in Escherichia coli Rutherford, B. J.; Dahl, R. H.; Price, R. E. Applied and Environmental Microbiology, Vol. 76, Issue 6 https://doi.org/10.1128/AEM.02323-09	journal	January 2010
Role of DNA Polymerase IV in Escherichia coli SOS Mutator Activity Kuban, Wojciech; Banach-Orlowska, Magdalena; Schaaper, Roel M. Journal of Bacteriology, Vol. 188, Issue 22 https://doi.org/10.1128/JB.01088-06	journal	November 2006
Complete and SOS-Mediated Response of Staphylococcus aureus to the Antibiotic Ciprofloxacin Cirz, Ryan T.; Jones, Marcus B.; Gingles, Neill A. Journal of Bacteriology, Vol. 189, Issue 2 https://doi.org/10.1128/JB.01464-06	journal	November 2006
Determination of Antibiotic Hypersensitivity among 4,000 Single-Gene-Knockout Mutants of Escherichia coli Tamae, C.; Liu, A.; Kim, K. Journal of Bacteriology, Vol. 190, Issue 17 https://doi.org/10.1128/JB.01982-07	journal	July 2008
Functional Genomics: Expression Analysis ofEscherichia coli Growing on Minimal and Rich Media Tao, Han; Bausch, Christoph; Richmond, Craig Journal of Bacteriology, Vol. 181, Issue 20 https://doi.org/10.1128/JB.181.20.6425-6440.1999	journal	October 1999
Draft Genome Sequence for a Clinical Isolate of Vancomycin-Resistant Enterococcus faecalis Erickson, Keesha E.; Madinger, Nancy E.; Chatterjee, Anushree Genome Announcements, Vol. 4, Issue 3 https://doi.org/10.1128/genomeA.00584-16	journal	June 2016
Draft Genome Sequences of Clinical Isolates of Multidrug-Resistant Acinetobacter baumannii Erickson, Keesha E.; Madinger, Nancy E.; Chatterjee, Anushree Genome Announcements, Vol. 5, Issue 5 https://doi.org/10.1128/genomeA.01547-16	journal	February 2017
Programmable Removal of Bacterial Strains by Use of Genome-Targeting CRISPR-Cas Systems Gomaa, Ahmed A.; Klumpe, Heidi E.; Luo, Michelle L. mBio, Vol. 5, Issue 1 https://doi.org/10.1128/mBio.00928-13	journal	January 2014
Quinolone Resistance Reversion by Targeting the SOS Response Recacha, E.; Machuca, J.; Díaz de Alba, P. mBio, Vol. 8, Issue 5 https://doi.org/10.1128/mBio.00971-17	journal	November 2017
Transcriptome-Level Signatures in Gene Expression and Gene Expression Variability during Bacterial Adaptive Evolution Erickson, Keesha E.; Otoupal, Peter B.; Chatterjee, Anushree mSphere, Vol. 2, Issue 1 https://doi.org/10.1128/mSphere.00009-17	journal	February 2017
Mechanisms of Solvent Tolerance in Gram-Negative Bacteria Ramos, Juan L.; Duque, Estrella; Gallegos, María-Trinidad Annual Review of Microbiology, Vol. 56, Issue 1 https://doi.org/10.1146/annurev.micro.56.012302.161038	journal	October 2002
Inhibition of Mutation and Combating the Evolution of Antibiotic Resistance Cirz, Ryan T.; Chin, Jodie K.; Andes, David R. PLoS Biology, Vol. 3, Issue 6 https://doi.org/10.1371/journal.pbio.0030176	journal	May 2005
Quantifying the Determinants of Evolutionary Dynamics Leading to Drug Resistance Chevereau, Guillaume; Dravecká, Marta; Batur, Tugce PLOS Biology, Vol. 13, Issue 11 https://doi.org/10.1371/journal.pbio.1002299	journal	November 2015
Sequence-Specific Targeting of Bacterial Resistance Genes Increases Antibiotic Efficacy Ayhan, Dilay Hazal; Tamer, Yusuf Talha; Akbar, Mohammed PLOS Biology, Vol. 14, Issue 9 https://doi.org/10.1371/journal.pbio.1002552	journal	September 2016
Mapping the Environmental Fitness Landscape of a Synthetic Gene Circuit Nevozhay, Dmitry; Adams, Rhys M.; Van Itallie, Elizabeth PLoS Computational Biology, Vol. 8, Issue 4 https://doi.org/10.1371/journal.pcbi.1002480	journal	April 2012
Positive Epistasis Drives the Acquisition of Multidrug Resistance Trindade, Sandra; Sousa, Ana; Xavier, Karina Bivar PLoS Genetics, Vol. 5, Issue 7 https://doi.org/10.1371/journal.pgen.1000578	journal	July 2009
Genomic Library Screens for Genes Involved in n-Butanol Tolerance in Escherichia coli Reyes, Luis H.; Almario, Maria P.; Kao, Katy C. PLoS ONE, Vol. 6, Issue 3 https://doi.org/10.1371/journal.pone.0017678	journal	March 2011
Parallel Mapping of Antibiotic Resistance Alleles in Escherichia coli Weiss, Sophie J.; Mansell, Thomas J.; Mortazavi, Pooneh PLOS ONE, Vol. 11, Issue 1 https://doi.org/10.1371/journal.pone.0146916	journal	January 2016
Statistical determination of synergy based on Bliss definition of drugs independence Demidenko, Eugene; Miller, Todd W. PLOS ONE, Vol. 14, Issue 11 https://doi.org/10.1371/journal.pone.0224137	journal	November 2019
DinB Upregulation Is the Sole Role of the SOS Response in Stress-Induced Mutagenesis in Escherichia coli Galhardo, Rodrigo S.; Do, Robert; Yamada, Masami Genetics, Vol. 182, Issue 1 https://doi.org/10.1534/genetics.109.100735	journal	March 2009

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Potentiating antibiotic efficacy via perturbation of non-essential gene expression

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