Antimicrobial resistance (AMR) and persistence are associated with an elevated risk of treatment failure and relapsing infections. They are thus important drivers of increased morbidity and mortality rates resulting in growing healthcare costs. Antibiotic resistance is readily identifiable with standard microbiological assays, and the threat imposed by antibiotic resistance has been well recognized. Measures aiming to reduce resistance development and spreading of resistant bacteria are being enforced. However, the phenomenon of bacteria surviving antibiotic exposure despite being fully susceptible, so-called antibiotic persistence, is still largely underestimated. In contrast to antibiotic resistance, antibiotic persistence is difficult to measure and therefore often missed, potentially leading to treatment failures. In this review, we focus on bacterial mechanisms allowing evasion of antibiotic killing and discuss their implications on human health. We describe the relationship between antibiotic persistence and bacterial heterogeneity and discuss recent studies that link bacterial persistence and tolerance with the evolution of antibiotic resistance. Finally, we review persister detection methods, novel strategies aiming at eradicating bacterial persisters and the latest advances in the development of new antibiotics.

Antibiotic resistance and persistence-Implications for human health and treatment perspectives.

Bacterial Heterogeneity and Antibiotic Survival: Understanding and Combatting Persistence and Heteroresistance.

Insufficient development of new antibiotics and the rising resistance of bacteria to those that we have are putting the world at risk of losing the most widely curative class of medicines currently available Preventing deaths from antimicrobial resistance (AMR) will require exploiting emerging knowledge not only about genetic AMR conferred by horizontal gene transfer or de novo mutations but also about phenotypic AMR, which lacks a stably heritable basis This Review summarizes recent advances and continuing limitations in our understanding of AMR and suggests approaches for combating its clinical consequences, including identification of previously unexploited bacterial targets, new antimicrobial compounds, and improved combination drug regimens

Biology of antimicrobial resistance and approaches to combat it

Stress Can Induce Transcription of Toxin-Antitoxin Systems without Activating Toxin

Persisters represent a small subpopulation of non- or slow-growing bacterial cells that are tolerant to killing by antibiotics. Despite their prominent role in the recalcitrance of chronic infections to antibiotic therapy, the mechanism of their formation has remained elusive. We show that sorted cells of Escherichia coli with low levels of energy-generating enzymes are better able to survive antibiotic killing. Using microfluidics time-lapse microscopy and a fluorescent reporter for in vivo ATP measurements, we find that a subpopulation of cells with a low level of ATP survives killing by ampicillin. We propose that these low ATP cells are formed stochastically as a result of fluctuations in the abundance of energy-generating components. These findings point to a general "low energy" mechanism of persister formation.

Bacterial persisters are a stochastically formed subpopulation of low-energy cells.

Clarifying the Link between Toxin-Antitoxin Modules and Bacterial Persistence.

The vulnerable versatility of Salmonella antibiotic persisters during infection.

Antibiotic persistence and tolerance: not just one and the same.

This chapter contains the latest version of essential protocols established to study Salmonella persisters during macrophage infection . These methods, which can be applied to other pathogens, allow researchers to quantify, visualize, and characterize bacterial persisters within a population and within immune cells consistent with the recent consensus statement published by the research community working on antibiotic persistence (Balaban et al, Nat Rev Microbiol 17:441-448, 2019). These protocols notably allow the discrimination between tolerance and persistence during infection , which is essential to clarify which phenomenon is actually reported. Methods described in this chapter may contribute to the determination of key bacterial and host genes that contribute to antibiotic persistence.

Séverin Ronneau

Papers

Clarifying the Link between Toxin-Antitoxin Modules and Bacterial Persistence.

The vulnerable versatility of Salmonella antibiotic persisters during infection.

Antibiotic persistence and tolerance: not just one and the same.

Studying Antibiotic Persistence During Infection.