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Evolutionary causes and consequences of bacterial antibiotic persistence

Nature Reviews Microbiology volume 18, pages 479–490 (2020)Cite this article

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Abstract

Antibiotic treatment failure is of growing concern. Genetically encoded resistance is key in driving this process. However, there is increasing evidence that bacterial antibiotic persistence, a non-genetically encoded and reversible loss of antibiotic susceptibility, contributes to treatment failure and emergence of resistant strains as well. In this Review, we discuss the evolutionary forces that may drive the selection for antibiotic persistence. We review how some aspects of antibiotic persistence have been directly selected for whereas others result from indirect selection in disparate ecological contexts. We then discuss the consequences of antibiotic persistence on pathogen evolution. Persisters can facilitate the evolution of antibiotic resistance and virulence. Finally, we propose practical means to prevent persister formation and how this may help to slow down the evolution of virulence and resistance in pathogens.

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Fig. 1: Evolution of higher persistence.
Fig. 2: Selection for persistence.
Fig. 3: Evolutionary consequences of persistence.

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Acknowledgements

The authors would like to thank members of the Hardt laboratory for discussion. Work relevant to this review has been funded by grants from the Swiss National Science Foundation (SNF) (310030B-173338, 310030-192567 and the SNF NFP 72 407240-167121) and the Gebert Rüf Foundation to W.-D.H, a SNF professorship grant (PP00PP_176954) to M.D. and a Boehringer Ingelheim Fonds PhD Fellowship to E.B.

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  1. Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland

    Erik Bakkeren & Wolf-Dietrich Hardt

  2. Biozentrum, University of Basel, Basel, Switzerland

    Médéric Diard

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  1. Erik Bakkeren
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  2. Médéric Diard
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  3. Wolf-Dietrich Hardt
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The authors contributed equally to all aspects of the article.

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Correspondence to Médéric Diard or Wolf-Dietrich Hardt.

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Glossary

Antibiotic

An antimicrobial agent that either inhibits (bacteriostatic antibiotic) or kills (bactericidal antibiotic) bacteria.

Resistance

The genetically encoded ability of cells to grow in the presence of an antibiotic. Resistance increases the minimum inhibitory concentration of an antibiotic compared with susceptible cells. The offspring remains resistant, even if grown in the absence of antibiotics.

Persisters

Cells belonging to a subpopulation that is killed much slower than the rest of the population during exposure to bactericidal antibiotics. Typically, persisters halt growth during this survival. However, they can re-engage in fast growth when the antibiotic is removed.

Persistence

The phenomenon that for a population in which two or more distinct subpopulations exist (susceptible and tolerant), treatment with a bactericidal antibiotic will kill the susceptible subpopulation quickly, simultaneous with a much slower killing of the tolerant subpopulation. This leads to biphasic killing curves characteristic of persistence. Persistence is not heritable (clones isolated from the tolerant subpopulation will again give rise to a mix of susceptible and tolerant cells). Persistence can also be called heterotolerance.

Heteroresistance

The ability to grow a subpopulation of cells in the presence of an antibiotic. This subpopulation can be the result of rare resistant mutants that increase in frequency over time (polyclonal heteroresistance) or two distinct subpopulations (sensitive and resistant) that switch back and forth phenotypically even in the absence of antibiotics. In the latter case, the antibiotic exerts a selective pressure that can change the relative frequency of sensitive versus resistant cells (monoclonal heteroresistance). In standard minimum inhibitory concentration (MIC) assays, this increases the MIC of an antibiotic compared with a population of susceptible cells (when the inoculum is grown without antibiotics).

Tolerance

The ability of cells to survive in the presence of a bactericidal antibiotic to a higher extent than susceptible cells. This phenomenon pertains to all cells of the population and increases the minimum duration of killing in the presence of an antibiotic.

Horizontal gene transfer

(HGT). The transfer of genetic information from one organism to another. In bacteria, the main mechanisms are conjugation (mediated by plasmids), transduction (mediated by phages) or transformation (uptake of DNA from the environment).

Spontaneous persistence

Persistence observed without any stimulus; subpopulations of tolerant cells exist even during growth when environmental parameters are kept optimal.

Triggered persistence

Persistence that arises in response to a certain stimulus. This stimulus can result from stressful conditions in which it can be beneficial to maintain minimal metabolic activity in a subpopulation of cells.

Clinical persistence

The failure of either the immune system or antimicrobial therapy to eliminate the pathogen, resulting in the pathogen remaining in the host for long periods of time. That is, clinical persistence can be the result of either antibiotic persistence or persistent infection (for example, as a result of impaired immunity, immune subversion or evasion, biofilm formation or intracellular survival).

Persistent infection

The pathogen is not cleared from the host but remains in specific cells or compartments of the host for long periods of time, independently of antimicrobial treatment. Persistent infection can lead to clinical persistence.

Biofilms

A collection of microorganisms that adhere to each other and surfaces, embedded within an extracellular matrix. Exchange of nutrients, chemical messengers and genetic information is prominent, promoting a heterogeneous mixture of cells, including dormant cells. Biofilms are typically recalcitrant to antibiotic therapy (through poor antibiotic penetration, antibiotic persistence or both).

Stringent response

A stress response in bacteria as a result of nutrient limitation or other stress conditions that is mediated by accumulation of the alarmone (p)ppGpp. (p)ppGpp influences the transcriptional profile of the cell, for example to favour general metabolism maintenance rather than ribosome biosynthesis.

SOS response

A response to damage-inducing stresses detected by single-stranded breaks in DNA stalling the DNA polymerase. This induces LexA-repressed genes, which often include error-prone DNA repair and inhibitors of cell division.

Bet-hedging

An evolutionary strategy in which part of the population has decreased fitness in favourable conditions but is able to survive after a shift to more stressful environments. In bacteria, bet-hedging can occur when more than one phenotype is expressed at a population scale. One phenotype promotes optimal growth in the present environment, whereas others grow or survive suboptimally in this environment but would be more fit if the conditions changed. This mixture of phenotypes leads to an optimal fitness of the entire population over time under changing conditions.

Nutrient starvation

A cell is faced with no or insufficient nutrients to grow and must therefore use its own reserves, or rely on dormancy to survive.

Dormant

A state of reduced metabolic activity and halted growth that can protect bacterial cells against antibiotics that target aspects of cellular growth or metabolism. Dormancy is a mechanism by which cells are tolerant or persistent.

Responsive diversification

The generation of a range of different responses to a certain stimulus. In bacteria, for example, several subpopulations expressing different phenotypes can emerge in response to stressful conditions, favouring survival in changing environments.

Defectors

Mutants that do not pay a cost associated with production of a public good, as they do not produce it, but can still profit from the public good produced by others. This destabilizes cooperation in bacteria, as defectors are more fit (given the presence of the public good) and will therefore outcompete cooperators. Defectors can also be called ‘cheaters’.

Persistence as a social trait

An ecological explanation for persistence in which subpopulations of metabolically inactive, slow-growing and fast-growing cells exist so that nutrient competition is decreased among cells. This cooperative behaviour increases the growth efficiency at a population scale.

Persistence as stuff happens

An explanation for the existence of persistence in which persistence occurs owing to errors in cellular processes. Such errors occur in only a minor fraction of cells at a given time and could explain why metabolically inactive, survival-ready cells emerge in populations of otherwise susceptible growing cells.

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Bakkeren, E., Diard, M. & Hardt, WD. Evolutionary causes and consequences of bacterial antibiotic persistence. Nat Rev Microbiol 18, 479–490 (2020). https://doi.org/10.1038/s41579-020-0378-z

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