Modification detection in Enterococcus faecalis OG1RF. Enterococcus faecalis OG1RF

Enterococcus faecalis is a Gram-positive bacterium that natively colonizes the human gastrointestinal tract and opportunistically causes life-threatening infections in compromised hosts. Multidrug-resistant (MDR) E. faecalis strains have emerged, reducing treatment options for these infections. MDR E. faecalis have large genomes containing abundant mobile genetic elements (MGEs) encoding antibiotic resistance and virulence determinants. Bacteria commonly possess genome defense mechanisms to block MGE acquisition, and we hypothesize that genome defense mechanisms have been compromised in MDR E. faecalis. In restriction-modification (R-M) defense, the bacterial genome is methylated at cytosine (C) or adenine (A) residues by a methyltransferase (MTase) such that non-self DNA can be distinguished from self DNA. A cognate restriction endonuclease digests improperly modified non-self DNA. Little is known about R-M in E. faecalis. Here, we use genome resequencing to identify genome modifications occurring in the oral isolate OG1RF. OG1RF has one of the smallest E. faecalis genomes sequenced to date, and possesses few MGEs. Single Molecule Real Time (SMRT) sequencing was used to identify modified bases in the OG1RF genome, and bisulfite sequencing was used to specifically interrogate N4-methylcytosine (m4C) and 5-methylcytosine (m5C) occurrence. SMRT and bisulfite sequencing revealed that OG1RF has global m5C methylation at 5’-GCWGC-3’ motifs. A Type II R-M system was found to be responsible for the global m5C modification, and disruption of this system impacts transfer of the pheromone-responsive plasmid pCF10. Based on these results, we conclude that R-M is a barrier to MGE acquisition and limits antibiotic resistance gene dissemination in the faecalis species.