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.
References (69)
The bactericidal action of penicillin on Staphylococcus pyogenes
Ir J Med Sci
(1944)- et al.
Three dimensional structure of the mqsR:mqsA complex: a novel TA pair comprised of a toxin homologous to rele and an antitoxin with unique properties
PLoS Pathog
(2009) - et al.
SOS response induces persistence to fluoroquinolones in Escherichia coli
PLoS Genet
(2009) - et al.
Microfluidic devices for measuring gene network dynamics in single cells
Nat Rev Genet
(2009) - et al.
The importance of being persistent: heterogeneity of bacterial populations under antibiotic stress
FEMS Microbiol Rev
(2009) Persister cells
Annu Rev Microbiol
(2010)Persister cells, dormancy and infectious disease
Nat Rev Microbiol
(2007)- et al.
Non-inherited antibiotic resistance
Nat Rev Microbiol
(2006) - et al.
Combating bacteria and drug resistance by inhibiting mechanisms of persistence and adaptation
Nat Chem Biol
(2007) Bacterial persistence: some new insights into an old phenomenon
J Biosci
(2008)
Microbial phenotypic heterogeneity and antibiotic tolerance
Curr Opin Microbiol
Microbial persistence
Yale J Biol Med
Inapparent infection: relation of latent and dormant infections to microbial persistence
Public Health Rep
Bacterial persistence as a phenotypic switch
Science
Single-cell protein induction dynamics reveals a period of vulnerability to antibiotics in persister bacteria
Proc Natl Acad Sci USA
Regulation of phenotypic variability by a threshold-based mechanism underlies bacterial persistence
Proc Natl Acad Sci USA
Toxin-antitoxin systems influence biofilm and persister cell formation and the general stress response
Appl Environ Microbiol
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
Escherichia coli toxin/antitoxin pair mqsR/mqsA regulate toxin cspD
Environ Microbiol
Biofilms and planktonic cells of Pseudomonas aeruginosa have similar resistance to killing by antimicrobials
J Bacteriol
GlpD and plsB participate in persister cell formation in Escherichia coli
J Bacteriol
Persisters: a distinct physiological state of E. coli
BMC Microbiol
Persister cells and tolerance to antimicrobials
FEMS Microbiol Lett
Specialized persister cells and the mechanism of multidrug tolerance in Escherichia coli
J Bacteriol
Ciprofloxacin causes persister formation by inducing the tisB toxin in Escherichia coli
PLoS Biol
Patients with long-term oral carriage harbor high-persister mutants of Candida albicans
Antimicrob Agents Chemother
Emergence of Pseudomonas aeruginosa strains producing high levels of persister cells in patients with cystic fibrosis
J Bacteriol
HipA, a newly recognized gene of Escherichia coli K-12 that affects frequency of persistence after inhibition of murein synthesis
J Bacteriol
Growth of the stress-bearing and shape-maintaining murein sacculus of Escherichia coli
Microbiol Mol Biol Rev
Characterization of the hipA7 allele of Escherichia coli and evidence that high persistence is governed by (p)ppGpp synthesis
Mol Microbiol
Conditional impairment of cell division and altered lethality in hipA mutants of Escherichia coli K-12
J Bacteriol
Ectopic overexpression of wild-type and mutant hipA genes in Escherichia coli: effects on macromolecular synthesis and persister formation
J Bacteriol
Multiple antibiotic resistance in a bacterium with suppressed autolytic system
Nature
Suppression of lytic effect of beta lactams on Escherichia coli and other bacteria
Proc Natl Acad Sci USA
Cited by (155)
The classification of bacterial survival strategies in the presence of antimicrobials
2021, Microbial PathogenesisCitation Excerpt :There are several classification approaches concerning the mechanisms of BRHM subpopulation genesis. The theory of bacterial stress response to negative changes in the extracellular environment is considered the most popular theory [31]. These negative changes include starvation, osmotic stress, acid shock, cold or heat shock, oxidative DNA damage, antibiotic stress, etc.
Delayed host mortality and immune response upon infection with P. aeruginosa persister cells
2023, Infection and ImmunityResuscitation dynamics reveal persister partitioning after antibiotic treatment
2023, Molecular Systems BiologyLocal Regulator AcrR Regulates Persister Formation by Repression of AcrAB Efflux Pump during Exponential Growth in Aeromonas veronii
2023, Antimicrobial Agents and Chemotherapy