Environmental, mechanistic and evolutionary landscape of antibiotic persistence

Abstract

Recalcitrant infections pose a serious challenge by prolonging antibiotic therapies and contributing to the spread of antibiotic resistance, thereby threatening the successful treatment of bacterial infections. One potential contributing factor in persistent infections is antibiotic persistence, which involves the survival of transiently tolerant subpopulations of bacteria. This review summarizes the current understanding of antibiotic persistence, including its clinical significance and the environmental and evolutionary factors at play. Additionally, we discuss the emerging concept of persister regrowth and potential strategies to combat persister cells. Recent advances highlight the multifaceted nature of persistence, which is controlled by deterministic and stochastic elements and shaped by genetic and environmental factors. To translate in vitro findings to in vivo settings, it is crucial to include the heterogeneity and complexity of bacterial populations in natural environments. As researchers continue to gain a more holistic understanding of this phenomenon and develop effective treatments for persistent bacterial infections, the study of antibiotic persistence is likely to become increasingly complex.

Keywords: antibiotic persistence; evolution; persistent infections; persister recovery; tolerance.

Figure 1. Distinguishing between resistance, tolerance, and persistence and the possible clinical implication of persistence

(A) Antibiotic‐resistant cells are characterized by their ability to grow during antibiotic treatment (blue). This is in contrast to antibiotic tolerance (pink) and persistence (green). In case of antibiotic tolerance, the decreased population‐wide sensitivity results in slower killing, which implies that prolonged antibiotic treatment is required to eradicate the population (pink). Antibiotic persistence is a survival strategy where only a small subpopulation is highly tolerant to the antibiotic. This results in characteristic biphasic killing, where the majority of sensitive cells are rapidly killed and the subpopulation of persister cells survives. However, note that killing of persister cells can still happen at a slow rate (green). (B) A patient suffering from, for example, a urinary tract infection receives antibiotic treatment. The pathogen load in the urinary tract rapidly decreases, resulting in a seemingly successful treatment. However, once the antibiotic treatment is ceased, surviving persister cells can again increase the pathogen load, resulting in a chronic infection.

Figure 2. Formation and heterogeneity of antibiotic persisters

(A) Two categories of persister cells are depicted: spontaneous and triggered persistence. Spontaneous persisters arise stochastically due to cellular noise, whereas triggered persisters form in response to environmental stressors, such as abiotic stress, macrophage‐ or biofilm‐associated stresses. Abbreviations: ROS, reactive oxygen species; QS, Quorum sensing molecules. (B) and (C) present the models that explain how both types of persisters arise heterogeneously in a population. (B) Spontaneous persisters arise from random variation in persister protein expression, coupled with feedback loops, resulting in bistable phenotypic differentiation. (C) Triggered persisters, on the contrary, represent a subset of cells with the highest level of antibiotic tolerance within a population with varying levels of susceptibility arising from developmental noise in various tolerance mechanisms. The proportion of persisters depends on both the (1) mean (μ) and (2) variance (σ) of this distribution as well as the (3) specific antibiotic conditions and duration. Perturbing the mean, such as through environmental triggers or genetic mutations, can increase the fraction of cells surviving antibiotic exposure. Increasing the variance of this distribution, through environmental heterogeneity or genetic changes in buffering or potentiating genes, can also increase the fraction of survivors.

Figure 3. Mechanisms of persistence defense, recovery, and regrowth

(A) During the course of antibiotic treatment, persister cells utilize various defense mechanisms to survive the effects of antibiotics. Once the treatment ceases, persister cells first recover from the inflicted damage before regrowing and forming a new population, where other cells can switch to the persister state. This recovery period involves repairing DNA damage and resuming critical cellular processes, such as DNA replication, transcription, and translation. (B) Persister cells can defend themselves from antibiotic damage by lowering their metabolism through inhibition of DNA replication, transcription, and translation. These pathways can be inhibited by expressing pathway‐specific toxins, by sequestering essential proteins of these pathways in aggregates or by depleting the ATP needed for their functioning. Additionally, persister cells might protect themselves from more antibiotic‐induced damage by increasing antibiotic efflux. For their recovery, persister cells need to repair the inflicted DNA damage. Moreover, they need to increase their metabolism to be able to regrow by restarting DNA replication, transcription and translation. To reactivate these processes, persister cells need to replete their ATP levels and remove the aggregates present in the cell.

Figure 4. Strategies to combat persistence

(1) Direct targeting of persister cells using single‐drug therapy with novel antibiotics or combinatorial therapy with existing antibiotics. (2) Combining existing antibiotics with a potentiating compound to enhance the efficacy of the antibiotic against the whole population, including both persister and nonpersister cells. Potentiating compounds can inhibit persister formation, trigger persister recovery and regrowth, and increase antibiotic uptake or decrease antibiotic efflux. (3) Preventing evolution of increased levels of persisters, which may also limit the evolution and spread of resistance via persistence.