A Robust Method for Generating, Quantifying, and Testing Large Numbers of Escherichia coli Persisters

Silke R Vedelaar, Jakub L Radzikowski, Matthias Heinemann*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

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Bacteria can exhibit phenotypes that render them tolerant against antibiotics. However, often only a few cells of a bacterial population show the so-called persister phenotype, which makes it difficult to study this health-threatening phenotype. We recently found that certain abrupt nutrient shifts generate Escherichia coli populations that consist almost entirely of antibiotic-tolerant cells. These nearly homogeneous persister cell populations enable assessment with population-averaging experimental methods, such as high-throughput methods. In this chapter, we provide a detailed protocol for generating a large fraction of tolerant cells using the nutrient-switch approach. Furthermore, we describe how to determine the fraction of cells that enter the tolerant state upon a sudden nutrient shift and we provide a new way to assess antibiotic tolerance using flow cytometry. We envision that these methods will facilitate research into the important and exciting phenotype of bacterial persister cells.

Original languageEnglish
Pages (from-to)41-62
Number of pages22
JournalMethods in molecular biology (Clifton, N.J.)
Publication statusPublished - 30-Sep-2021


  • Antibiotic tolerance
  • Flow cytometry
  • Nutrient shift
  • Tolerant cells
  • Persister cells
  • Escherichia coli

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