The role of DNA damage repair in Salmonella persister survival and relapse during infection

Abstract

The rise of antibiotic treatment failure represents a serious global health problem. Along with antibiotic resistance, antibiotic tolerance and persistence make up the three phenomena underlying the ability of bacteria to survive treatment with bactericidal antibiotics. Primarily distinguished by their penetrance within a bacterial population, antibiotic tolerance and persistence are superficially similar phenomena, with both relying on low antibiotic uptake or target activity due to slow or arrested bacterial growth. As such, it is widely assumed that similar mechanisms underpin the ability of persistent and tolerant bacteria to survive antibiotic exposure. However, to date, little evidence directly supports mechanistic equivalence between these two forms of antibiotic recalcitrance. In this thesis, I compare the molecular mechanisms enabling the survival of antibiotic tolerant and persistent Salmonella Typhimurium during macrophage infection. First, I identify purA as a multidrug antibiotic tolerant Salmonella mutant. Using this mutant, I then directly compare the physiological states adopted by antibiotic tolerant Salmonella and wild type persisters during macrophage infection. Specifically, I show that tolerant Salmonella adopt a near-dormant state, undergoing minimal DNA damage during macrophage infection. In contrast, persisters retain an active but vulnerable physiological state that is prone to the accumulation of double-stranded DNA (dsDNA) breaks during macrophage infection. In view of these initial observations, I next explore the dependence of Salmonella persisters on various DNA repair pathways for survival during macrophage infection, uncovering that these bacteria rely extensively on RecA-mediated DNA repair to overcome their inherent vulnerability to the intramacrophage environment. Finally, I compare the relative ability of tolerant and persistent bacteria to initiate infection relapse after cessation of antibiotic treatment. This revealed that, despite their vulnerability, persisters retain the ability to initiate infection relapse as long as they are protected by RecA-mediated DNA repair. Overall, this work highlights the importance of RecA-mediated DNA repair for wild type Salmonella persisters to survive within the host during antibiotic treatment and to initiate infection relapse following drug withdrawal.