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Open Access Highly Accessed Open Badges Research article

Persisters: a distinct physiological state of E. coli

Devang Shah1, Zhigang Zhang23, Arkady B Khodursky34, Niilo Kaldalu5, Kristi Kurg5 and Kim Lewis1*

Author Affiliations

1 Department of Biology, Northeastern University, 134 Mugar Hall, 360 Huntington Ave, Boston, MA 02115, USA

2 Department of Chemical Engineering and Materials Science, University of Minnesota, St Paul, MN 55108, USA

3 BioTechnology Institute, University of Minnesota, St Paul, MN 55108, USA

4 Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St Paul, MN 55108, USA

5 Institute of Technology, Tartu University, Tartu 50411, Estonia

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BMC Microbiology 2006, 6:53  doi:10.1186/1471-2180-6-53

Published: 12 June 2006



Bacterial populations contain persisters, phenotypic variants that constitute approximately 1% of cells in stationary phase and biofilm cultures. Multidrug tolerance of persisters is largely responsible for the inability of antibiotics to completely eradicate infections. Recent progress in understanding persisters is encouraging, but the main obstacle in understanding their nature was our inability to isolate these elusive cells from a wild-type population since their discovery in 1944.


We hypothesized that persisters are dormant cells with a low level of translation, and used this to physically sort dim E. coli cells which do not contain sufficient amounts of unstable GFP expressed from a promoter whose activity depends on the growth rate. The dim cells were tolerant to antibiotics and exhibited a gene expression profile distinctly different from those observed for cells in exponential or stationary phases. Genes coding for toxin-antitoxin module proteins were expressed in persisters and are likely contributors to this condition.


We report a method for persister isolation and conclude that these cells represent a distinct state of bacterial physiology.