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Background  IncA/C plasmids play important roles in the development and dissemination of multidrug resistance in bacteria. These plasmids carry three methylase genes, two of which show cytosine specificity. The effects of such a plasmid on the host methylome were observed by single-molecule, real-time (SMRT) and bisulfite sequencing in this work.    Results  The results showed that the numbers of methylation sites on the host chromosomes were changed, as were the sequences recognized by MTase. The host chromosomes were completely remodified by the plasmid with a methylation pattern different from that of the host itself. When the three  dcm  genes were deleted, the transferability of the plasmid into other  Vibrio cholerae  and  Escherichia coli  strains was lost. During deletion of the  dcm  genes, except for the wild-type strains and the targeted deletion strains, 18.7%~ 38.5% of the clones lost the IncA/C plasmid and changed from erythromycin-, azithromycin- and tetracycline-resistant strains to strains that were sensitive to these antibiotics.    Conclusions  Methylation of the IncA/C plasmid was a new mobile restriction modification (RM) barrier against foreign DNA. By actively changing the host’s methylation pattern, the plasmid crossed the barrier of the host’s RM system, and this might be the simplest and most universal method by which plasmids acquire a broad host range. Elimination of plasmids by destruction of plasmid stability could be a new effective strategy to address bacterial multidrug resistance.    Electronic supplementary material  The online version of this article (10.1186/s13100-019-0168-1) contains supplementary material, which is available to authorized users.

A mobile restriction modification system consisting of methylases on the IncA/C plasmid