Heterogeneous bacterial persisters and engineering approaches to eliminate them

https://doi.org/10.1016/j.mib.2011.09.002Get rights and content

Bacterial persistence is a state in which a subpopulation of cells (persisters) survives antibiotic treatment, and has been implicated in the tolerance of clinical infections and the recalcitrance of biofilms. There has been a renewed interest in the role of bacterial persisters in treatment failure in light of a wealth of recent findings. Here we review recent laboratory studies of bacterial persistence. Further, we pose the hypothesis that each bacterial population may contain a diverse collection of persisters and discuss engineering strategies for persister eradication.

Highlights

► Review of current laboratory research on persisters, including the roles of growth heterogeneity, stationary phase, and the SOS-response. ► History and phenotypes associated with hipA. ► Hypothesis that each bacterial population contains many different persisters with different tolerance mechanisms. ► Engineering strategies for eradicating bacterial persisters.

Introduction

Bacterial persistence is a phenomenon in which a subpopulation of cells survives antibiotic treatment [1•, 2•, 3, 4, 5, 6, 7]. In contrast to resistant bacteria, persisters do not grow in the presence of antibiotics and their tolerance arises from physiological processes rather than genetic mutations in a subpopulation of bacteria. Persistence was first described by Joseph Bigger in 1944 [8] while attempting to sterilize cultures of pathogenic Staphylococcus aureus with penicillin. He found that a small number of cells ‘persisted’ and could later form colonies even after treatment with high antibiotic concentrations.

The possible clinical implications of persisters were apparent: antibiotics might not sterilize infections and remaining bacteria could later cause recurrence once treatment ended [9••]. Early clinical studies of in vivo persistence in S. aureus, S. pneumoniae, and M. tuberculosis demonstrated that the phenotype was indeed an important and distinct problem in the treatment of infections [9••, 10••]. Driven by an abundance of recent laboratory findings [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24], there is renewed interest in clinical persistence [25, 26••], which has led to the demonstration that high-persistent mutants can arise during treatment of chronic infections [26••]. Here, we review some of the recent laboratory studies of bacterial persistence in E. coli [1•, 2•, 3] and propose that persistence might be explained by variance in the many processes governing stress responses and antibiotic lethality, suggesting that a single population of bacteria contains a collection of distinct persisters.

Section snippets

hipA and the dawn of persister genetics

The first paper in persister genetics was published in 1983 by Moyed and Bertrand, who presented the results of a mutagenesis-and-selection scheme designed to create mutants with high persistence to penicillin [27]. After 24 independent attempts, they created four high-persistence strains, two of which were found to have mutations in the same gene, named hipA (for ‘high persistence’). 1% of the hipA mutant cells persisted treatment with multiple antibiotics targeting peptidoglycan synthesis [28

More than one way to make a persister

There have been many laboratory studies on persistence in the past decade, many of which have uncovered previously unrecognized conditions and processes contributing to the phenotype. Here, we focus on three of these: heterogeneous growth, nutrient limitation, and the SOS response.

Persisters and physiological heterogeneity

The diversity of the pathways implicated in bacterial persistence suggests that, in addition to there being more than one way to make a persister, there may be different types of persisters. This raises the possibility that each persister has its own specific tolerances to antibiotics.

Total dormancy of a subpopulation is an attractive model for persistence as it simplifies the phenotype and suggests a possible unified theory of persistence. However, this model does not fit the growing body of

Engineering treatments for persisters

The clinical importance of developing anti-persister strategies is self-evident, though there have been few attempts to target the elimination of persisters. It has been suggested that drugs and methods could be developed to target the genetic determinants leading to persister formation so as to prevent or reverse persistence [2]. Given the number of genes involved in persistence, such an approach may prove difficult. Toward development of treatments for a diversity of persisters, it may be

Conclusion

Studies over the past decade have implicated a multiplicity of processes contributing to bacterial persistence. Given the physiological complexity of each bacterial cell, it seems plausible that persistence may be the result of fluctuations and variance in different tolerance-associated processes. This suggests, that in a single bacterial population, there may be many different types of persisters, each with distinct mechanisms for evading the lethal effects of bactericidal antibiotics.

References and recommended reading

Papers of particular interest, published within the period of review, have been highlighted as:

  • • of special interest

  • •• of outstanding interest

Acknowledgements

We thank Daniel J. Dwyer and D. Ewen Cameron for helpful suggestions on the manuscript. This work was supported by the NIH Director's Pioneer Award Program and the Howard Hughes Medical Institute.

References (69)

  • N. Dhar et al.

    Microbial phenotypic heterogeneity and antibiotic tolerance

    Curr Opin Microbiol

    (2007)
  • W. McDermott

    Microbial persistence

    Yale J Biol Med

    (1958)
  • W. McDermott

    Inapparent infection: relation of latent and dormant infections to microbial persistence

    Public Health Rep

    (1959)
  • N.Q. Balaban et al.

    Bacterial persistence as a phenotypic switch

    Science

    (2004)
  • O. Gefen et al.

    Single-cell protein induction dynamics reveals a period of vulnerability to antibiotics in persister bacteria

    Proc Natl Acad Sci USA

    (2008)
  • E. Rotem et al.

    Regulation of phenotypic variability by a threshold-based mechanism underlies bacterial persistence

    Proc Natl Acad Sci USA

    (2010)
  • X. Wang et al.

    Toxin-antitoxin systems influence biofilm and persister cell formation and the general stress response

    Appl Environ Microbiol

    (2011)
  • B.L. Brown et al.

    Structure of the Escherichia coli antitoxin mqsA (ygiT/b3021) bound to its gene promoter reveals extensive domain rearrangements and the specificity of transcriptional regulation

    J Biol Chem

    (2011)
  • Y. Kim et al.

    Escherichia coli toxin/antitoxin pair mqsR/mqsA regulate toxin cspD

    Environ Microbiol

    (2010)
  • A.L. Spoering et al.

    Biofilms and planktonic cells of Pseudomonas aeruginosa have similar resistance to killing by antimicrobials

    J Bacteriol

    (2001)
  • A.L. Spoering et al.

    GlpD and plsB participate in persister cell formation in Escherichia coli

    J Bacteriol

    (2006)
  • D. Shah et al.

    Persisters: a distinct physiological state of E. coli

    BMC Microbiol

    (2006)
  • I. Keren et al.

    Persister cells and tolerance to antimicrobials

    FEMS Microbiol Lett

    (2004)
  • I. Keren et al.

    Specialized persister cells and the mechanism of multidrug tolerance in Escherichia coli

    J Bacteriol

    (2004)
  • T. Dorr et al.

    Ciprofloxacin causes persister formation by inducing the tisB toxin in Escherichia coli

    PLoS Biol

    (2010)
  • M.D. Lafleur et al.

    Patients with long-term oral carriage harbor high-persister mutants of Candida albicans

    Antimicrob Agents Chemother

    (2010)
  • L.R. Mulcahy et al.

    Emergence of Pseudomonas aeruginosa strains producing high levels of persister cells in patients with cystic fibrosis

    J Bacteriol

    (2010)
  • H.S. Moyed et al.

    HipA, a newly recognized gene of Escherichia coli K-12 that affects frequency of persistence after inhibition of murein synthesis

    J Bacteriol

    (1983)
  • J.V. Holtje

    Growth of the stress-bearing and shape-maintaining murein sacculus of Escherichia coli

    Microbiol Mol Biol Rev

    (1998)
  • S.B. Korch et al.

    Characterization of the hipA7 allele of Escherichia coli and evidence that high persistence is governed by (p)ppGpp synthesis

    Mol Microbiol

    (2003)
  • R. Scherrer et al.

    Conditional impairment of cell division and altered lethality in hipA mutants of Escherichia coli K-12

    J Bacteriol

    (1988)
  • S.B. Korch et al.

    Ectopic overexpression of wild-type and mutant hipA genes in Escherichia coli: effects on macromolecular synthesis and persister formation

    J Bacteriol

    (2006)
  • A. Tomasz et al.

    Multiple antibiotic resistance in a bacterium with suppressed autolytic system

    Nature

    (1970)
  • E.W. Goodell et al.

    Suppression of lytic effect of beta lactams on Escherichia coli and other bacteria

    Proc Natl Acad Sci USA

    (1976)
  • Cited by (0)

    View full text