A multiplexable assay for screening antibiotic lethality against drug-tolerant bacteria

Jonathan M Stokes; Arnaud Gutierrez; Allison J Lopatkin; Ian W Andrews; Shawn French; Ivan Matic; Eric D Brown; James J Collins

doi:10.1038/s41592-019-0333-y

A multiplexable assay for screening antibiotic lethality against drug-tolerant bacteria

Nat Methods. 2019 Apr;16(4):303-306. doi: 10.1038/s41592-019-0333-y. Epub 2019 Mar 11.

Authors

Jonathan M Stokes^{1

2}, Arnaud Gutierrez^{1

2

3}, Allison J Lopatkin^{1

2

4}, Ian W Andrews^{1

2

4}, Shawn French⁵, Ivan Matic^{3

6}, Eric D Brown⁵, James J Collins^{7

8

9

10}

Affiliations

¹ Institute for Medical Engineering & Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA.
² Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA, USA.
³ Inserm U1001, Faculté de Médecine Paris Descartes, Université Paris Descartes, Sorbonne Paris Cité, Paris, France.
⁴ Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.
⁵ Michael G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry & Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada.
⁶ Department of Life Sciences, Centre National de la Recherche Scientifique, Paris, France.
⁷ Institute for Medical Engineering & Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA. [email protected].
⁸ Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA, USA. [email protected].
⁹ Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA. [email protected].
¹⁰ Harvard-MIT Program in Health Sciences and Technology, Cambridge, MA, USA. [email protected].

PMID: 30858599
DOI: 10.1038/s41592-019-0333-y

Abstract

Antibiotic screens typically rely on growth inhibition to characterize compound bioactivity-an approach that cannot be used to assess the bactericidal activity of antibiotics against bacteria in drug-tolerant states. To address this limitation, we developed a multiplexed assay that uses metabolism-sensitive staining to report on the killing of antibiotic-tolerant bacteria. This method can be used with diverse bacterial species and applied to genome-scale investigations to identify therapeutic targets against tolerant pathogens.

Publication types

Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Anti-Bacterial Agents / pharmacology*
Bacteria / drug effects*
Ciprofloxacin / pharmacology
DNA Damage
Drug Resistance, Bacterial*
Escherichia coli / drug effects*
Escherichia coli / growth & development
Gene Deletion
In Situ Nick-End Labeling
Microbial Sensitivity Tests*
Microscopy, Fluorescence
Mutation
Phenotype
Species Specificity

Substances

Anti-Bacterial Agents
Ciprofloxacin