Microbial epigenetics adds a piece to the puzzle of antibiotic resistance

Summary of Papaleo S, Alvaro A, Nodari R, Panelli S, Bitar I, Comandatore F. The red thread between methylation and mutation in bacterial antibiotic resistance: How third-generation sequencing can help to unravel this relationship. Front Microbiol. 2022 Sep 15;13:957901. doi: 10.3389/fmicb.2022.957901. PMID: 36188005; PMCID: PMC9520237.

The word “epigenetics” makes us always think about Eukaryotes, where this topic is extensively studied, but these DNA bases modifications concern also the microbial world, with important effects also on antibiotic resistance. Our poor knowledge of bacterial epigenetics is due mostly to its need for different methods of study compared to eukaryotic methylation, and because the suitable techniques are quite recent and very expensive. Anyway, when I joined the SkyNet group, we started to discuss the impact of bacterial epigenetics on many aspects of microbial physiology and, again, about its relation with antibiotic resistance.

All that went into this review article, where we analyzed how the most recent technique of sequencing, Single Molecule, Real-Time (SMRT) sequencing (Eid et al., 2009) and the Oxford Nanopore technology (ONT), can have an impact on the investigation of antibiotic resistance. Indeed, these sequencing technologies allow to simultaneously detect all the methylated bases along with the DNA sequencing, leading to a better understanding of bacterial epigenetics. 

Bacterial DNA methylation is mostly known for its role in the Restriction-Modification (R-M) system, a primitive, rudimental, bacterial immune system. In R-M systems a restriction endonuclease and a cognate methyltransferase cooperate to protect the bacterial cell from phage’s attack, limiting foreign DNA acquisition. But other aspects of bacterial physiology are controlled by bacterial DNA methylation: the maintenance of mobile genetic elements, the starting of DNA replication, the functioning of some DNA mismatch repair systems and the regulation of gene expression. DNA methylation patterns are maintained after the replication but they can change for various factors, including stress conditions such as the exposure to antibiotic drugs. These changes can result in reversible and fast-appearing Adaptive Antibiotic Resistance (AdR) phenotypes, such as strains overexpressing efflux pumps, that resist the antibiotic attack, throwing the antibiotic molecule off the cell, without having any resistance gene or mutations. As written above, DNA methylation is involved in DNA mismatch repair systems, therefore it can be related to the DNA mutational rate (also because there is evidence that methylated bases are well-known mutational hotspots). In this review we support the idea that the AdR process can be the first important step in the selection of antibiotic-resistant strains, allowing the survival of the bacterial population until more efficient resistant mutants emerge. In this scenario, this sequencing technology enables the study of epigenetic modifications in link with antibiotic resistance and will help to investigate the relationship between methylation and mutation in the development of stable mechanisms of resistance.