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

Distinguished by their penetrance within a population, antibiotic tolerance and persistence are superficially similar phenomena by which growth-restricted bacteria survive treatment with bactericidal antibiotics. Owing to their apparent similarity, it is often assumed that the same physiological states and molecular mechanisms underlie the ability of individual antibiotic tolerant and persistent bacteria to survive treatment. Experimentally, antibiotic persistence is an extremely challenging phenomenon to study due to both its transience and the co-existence of persisters with non-persisters in the population of interest. In contrast, antibiotic tolerance operates at the whole population level as a result of bacteria acquiring genetic mutations or encountering environmental conditions that result in growth restriction. Therefore, studying antibiotic tolerance is often used as a convenient way to understand the molecular mechanisms governing antibiotic persistence. In this opinion, we discuss our current understanding of these two phenomena, outlining how tolerance and persistence can be distinguished experimentally. We argue that this approach will help avoid controversies in the field, especially in instances where the two phenomena co-exist. Finally, we evaluate the clinical evidence implicating tolerance and persistence in recalcitrance and relapse of bacterial infections.

De novo DNA methylation drives 5hmC accumulation in mouse zygotes.

Zygotic epigenetic reprogramming entails genome-wide DNA demethylation that is accompanied by Tet methylcytosine dioxygenase 3 (Tet3)-driven oxidation of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC; refs 1-4). Here we demonstrate using detailed immunofluorescence analysis and ultrasensitive LC-MS-based quantitative measurements that the initial loss of paternal 5mC does not require 5hmC formation. Small-molecule inhibition of Tet3 activity, as well as genetic ablation, impedes 5hmC accumulation in zygotes without affecting the early loss of paternal 5mC. Instead, 5hmC accumulation is dependent on the activity of zygotic Dnmt3a and Dnmt1, documenting a role for Tet3-driven hydroxylation in targeting de novo methylation activities present in the early embryo. Our data thus provide further insights into the dynamics of zygotic reprogramming, revealing an intricate interplay between DNA demethylation, de novo methylation and Tet3-driven hydroxylation.