Combined analysis of genome-wide DNA methylome and transcriptome reveals the first epigenetic-based antibiotic-resistance mechanism in Acinetobacter baumannii

Abstract

The World Health Organization (WHO) has defined carbapenem-resistant Acinetobacter baumannii (A. baumannii) as a critical species for which new therapeutic strategies are needed. In this tragic context, the discovery of new antibiotics with innovative pharmacological targets is essential. Currently, limited information is available on the relationship between epigenetic changes of m5C/m6A DNA and drug resistance in A. baumannii. In this study, we used Oxford Nanopore sequencing to analyze m5C/m6A epigenetic marks and Illumina RNA-Seq to evaluate the transcriptome of 5 A. baumanni isolates with different resistance profiles. The data clearly demonstrated that the m5C pattern of resistant strains globally differs from the multi susceptible strain, with more than 600 hypo- and hypermethylated sites for each resistant strain. For m6A, less severe changes occurred, however, more than 40 hyper- and hypomethylated sites were still found between each resistant and susceptible strain. Combined whole-genome DNA methylome and transcriptome analysis revealed a greater involvement of m5C modification in drug resistance processes. This study provides a new understanding of the epigenetic regulation of antibiotic resistance in A. baumannii and has potential implications for future antibiotic resistance research.