Harnessing antibiotic metabolic dependence to design therapies for tolerance and persistence with improved efficacy and safety

Abstract

Chronic and recurrent bacterial infections are a cause of debilitating disease that can progress for years and are a burden on healthcare systems. Infection relapse is thought to be due to incomplete clearance of the infection during treatment and has been linked to antibiotic tolerance and persistence, where metabolically repressed bacteria survive antibiotic lethality. As most antibiotics are ineffective in low metabolic contexts, tolerant and persister cells are protected from antibiotic killing, allowing for re-establishment of the infection once treatment has ceased. However, recent discoveries of anti-tolerant and anti-persister compounds have shown that there may be antibiotics with varying metabolic dependencies that remain effective even against these dormant cells, though many of these compounds are associated with patient toxicity and thus may not be suitable for clinical use. This research aims to characterize differences in metabolic dependence between these emerging compounds and conventional antibiotics, and to design combination strategies that eradicate and prevent establishment of persister and tolerant cells, while minimizing dosage of toxic drugs. Chapter 2 describes the development of a new metric to determine antibiotic metabolic dependence. We demonstrate that conventional antibiotics are strongly dependent on metabolism (SDM), while in contrast, anti-persister compounds are weakly dependent on metabolism (WDM). In the following two chapters we provide examples of how this classification of SDM versus WDM can be harnessed to design treatments that are effective in metabolically repressed contexts and that minimize use of toxic antibiotics. We design a combination treatment where antibiotics are specifically used to target either metabolically active or dormant bacteria, a strategy which allows reduction of the WDM antibiotic concentration (Chapter 3). Chapter 4 investigates the effect of antibiotic metabolism-dependence on evolutionary trajectories and details a method to delay the evolution of tolerance by cycling SDM and WDM antibiotics. Finally, in Chapter 5, we report a novel mechanism of SDM antibiotic tolerance through loss of the sodium/proton antiporter nhaA, causing downregulation of metabolic processes. Together, these findings demonstrate the importance of taking bacterial metabolism into account when designing antibiotic therapies and provides strategies for the prevention and treatment of antibiotic tolerance and persistence.