Epigenetic regulation and antimicrobial resistance: functional roles of DNA methylation

The global rise of antimicrobial resistance (AMR) demands urgent attention. While genetic drivers are well studied, epigenetic mechanisms, particularly DNA methylation, are emerging as key contributors to bacterial adaptation under antibiotic pressure. This review examines the roles of N6-methyladenine (m6A), N4-methylcytosine (m4C), and 5-methylcytosine (m5C), each catalysed by distinct DNA methyltransferases (MTases), in regulating resistance-related processes, such as efflux pump expression, β-lactamase activity, and stress responses. Advances in long-read sequencing technologies, including SMRT and ONT, now enable single-base resolution detection of methylation and support strain-specific methylome mapping. These efforts reveal methylation patterns that are dynamic, strain-dependent, and environmentally responsive, complicating resistance profiling. Emerging applications for tackling methylation-linked AMR include methylation-aware diagnostics and CRISPR-based epigenetic editing. Tools like CRISPR-dCas9 fused to DNA methyltransferases enable targeted, reversible suppression of resistance genes regulated by methylation. Current findings position DNA methylation as both a regulator of AMR and a promising target for next-generation diagnostics and therapeutics. However, challenges remain, including the lack of validated biomarkers, inconsistent protocols, and difficulty interpreting mixed-species data. Integrating methylation profiles with transcriptomic and phenotypic data will be essential to fully understand and target resistance mechanisms.