Trypanosoma cruzi persisters that survive benznidazole treatment in vitro and in vivo are in a transient non-replicative state

Benznidazole is the front-line drug used to treat infections with Trypanosoma cruzi, the causative agent of Chagas disease. However, for reasons that are unknown, treatment failures are common. To assess the nature of parasites that persist after treatment, we first exposed infected mammalian cell monolayers to a benznidazole regimen that reduces the intracellular amastigote population to <1% of the pre-treatment level. Of host cells that remained infected, the vast majority contained only one or two surviving intracellular amastigotes. Analysis, using incorporation of the thymidine analogue EdU, revealed these surviving parasites to be in a transient non-replicative state. Furthermore, treatment with benznidazole led to widespread damage to parasite DNA. When parasites that survived treatment in mice were examined using in vivo and ex vivo bioluminescence imaging, we found that recrudescence is not due to persistence of parasites in a specific organ or tissue that preferentially protects them from drug activity. Surviving parasites were widely distributed and located in host cells where the vast majority contained only one or two amastigotes. Therefore, infection relapse does not arise from a small number of intact large nests. Rather, persisters are either survivors of intracellular populations where co-located parasites have been killed, or amastigotes in single/low-level infected cells exist in a state where they are less susceptible to benznidazole. Assessment by EdU incorporation revealed that the small number of parasites which persist in mice after treatment are initially non-replicative. A possible explanation could be that triggering of the T. cruzi DNA damage response pathway by the activity of benznidazole metabolites results in exit from the cell cycle as parasites attempt DNA repair, and that metabolic changes associated with non-proliferation act to reduce drug susceptibility. Alternatively, a small percentage of the parasite population may pre-exist in this non-replicative state prior to treatment. Author Summary Trypanosoma cruzi is the causative agent of Chagas disease, the most important parasitic infection in Latin America. For reasons that are not established, the front-line drug benznidazole often fails to achieve sterile cure. Here, we used highly sensitive imaging technology to investigate the impact of benznidazole on T. cruzi infected mice. Following non-curative treatment, we found that persistence is not restricted to a specific organ or tissue that preferentially protects the parasite from drug activity. Rather, surviving parasites are widely distributed, although overall tissue levels are extremely low. These persisters are located in host cells that typically contain only one or two non-replicating intracellular amastigotes. However, these parasites re-initiate DNA replication within several days of treatment cessation and begin to proliferate. Therefore, being in a non-replicative state seems to confer protection against drug-mediated trypanocidal activity. Benznidazole treatment results in widespread damage to parasite DNA. One possibility therefore, is that this triggers the T. cruzi DNA damage response pathway, resulting in exit from the cell cycle as parasites attempt DNA repair. Alternatively, persisters may be derived from a small parasite sub-population that pre-exists in a non-replicative state prior to treatment.