Correlation between type IIIA CRISPR-Cas system and SCCmec in Staphylococcus epidermidis

Area of Science:

• Microbiology
• Genomics
• Bacterial Genetics

Background:

• A subculture of Staphylococcus epidermidis (S. epidermidis) strain ATCC35984, amenable to genetic manipulation, was identified.
• This mutant strain displayed methicillin susceptibility, unlike its resistant parent strain.

Purpose of the Study:

• To elucidate the genetic mechanism behind the methicillin susceptibility in the S. epidermidis mutant.
• To investigate the role of CRISPR-Cas systems in bacterial genome remodeling and mobile genetic element dynamics.

Main Methods:

• Whole-genome sequencing of the S. epidermidis mutant and its parent strain.
• Comparative genomic analysis to identify genetic differences.
• Bioinformatics analysis, including MLST typing and phylogenetic analysis.
• Investigation of CRISPR-Cas system location and flanking regions in staphylococci.

Main Results:

• A large DNA fragment, including the CRISPR-Cas system, type I restriction-modification system, and SCCmec element, was deleted in the mutant.
• Similar large deletions associated with CRISPR-Cas systems were observed spontaneously and induced in other bacterial species.
• S. epidermidis strains harboring CRISPR-Cas systems showed a higher prevalence of the SCCmec element, originating from multiple events.
• CRISPR-Cas systems are consistently located near the orfX gene, with conserved flanking loci acting as recombination hotspots.

Conclusions:

• CRISPR-Cas systems can drive bacterial genome remodeling by facilitating the deletion of integrated mobile genetic elements (MGEs).
• The proximity of CRISPR-Cas systems to the orfX gene and conserved flanking regions may promote the dissemination of neighboring MGEs like SCCmec.
• Incomplete immune protection by CRISPR-Cas systems can contribute to the spread of mobile genetic elements within bacterial populations.