Heterogeneous bacterial persisters and engineering approaches to eliminate them
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.
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