Mining the Methylome Reveals Extensive Diversity in Staphylococcus epidermidis Restriction Modification

Area of Science:

• Microbiology and Molecular Biology
• Genomics and Bioinformatics

Background:

• Staphylococcus epidermidis is a major cause of hospital-acquired infections, particularly with medical devices.
• Genetic manipulation of S. epidermidis has been difficult due to restriction-modification (RM) systems limiting foreign DNA entry.
• Existing knowledge on RM systems in Staphylococcus aureus does not fully apply to S. epidermidis.

Purpose of the Study:

• To perform systematic genomic and methylomic analyses of type I RM systems in S. epidermidis and S. aureus.
• To understand the diversity and characteristics of RM systems in S. epidermidis.
• To develop an efficient method for genetically manipulating diverse and previously intractable S. epidermidis clinical isolates.

Main Methods:

• Whole-genome sequencing and methylome analysis of seven diverse S. epidermidis isolates.
• Comparative genomic analysis of type I RM systems in S. epidermidis and S. aureus.
• Functional experiments using Escherichia coli plasmid artificial modification (PAM) to express S. epidermidis hsdMS genes.
• Electroporation efficiency assays to assess DNA uptake.

Main Results:

• Significant differences in type I RM system gene arrangement, location, and mobility were found between S. epidermidis and S. aureus.
• S. epidermidis type I RM systems exhibit extensive diversity, even within single genetic lineages, contrary to prior assumptions.
• Expression of S. epidermidis hsdMS via PAM successfully overcame restriction barriers, achieving high electroporation efficiencies.
• Genomic data can predict RM system functionality and strain electroporation proficiency.
• A restriction-defective, multidrug-resistant S. epidermidis isolate (BPH0736) was identified as ideal for molecular studies.

Conclusions:

• The study provides the first comprehensive analysis of barriers to foreign DNA uptake in S. epidermidis, distinct from S. aureus.
• An efficient strategy for genetic manipulation of diverse S. epidermidis strains, including previously intractable ones, has been established.
• These findings will facilitate molecular studies of S. epidermidis, aiding research into hospital-acquired infections and device-related complications.