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

A subculture of S.epidermidis strain ATCC35984 that is amenable to genetically manipulate was occasionally found in our laboratory. This mutant exhibited susceptibility to methicillin in contrast to its parent strain. To unveil the underlying mechanism, whole-genome sequencing of the mutant was performed. A comparative analysis revealed that a large DNA fragment encompassing the CRISPR-Cas system, type I R-M system and the SCCmec element was deleted from the mutant. The large chromosomal deletion associated with CRISPR-Cas system was also observed to occur spontaneously in S. epidermidis in another independent laboratory, or artificially induced by introducing engineering crRNAs in other bacterial species. These findings imply the CRISPR-Cas systems can affect bacterial genome remodeling through deletion of the integrated MGEs (mobile genetic elements). Further bioinformatics analysis identified a higher carriage rate of SCCmec element in the S. epidermidis strains harboring the CRISPR-Cas system. MLST typing and phylogenetic analysis of those CRIPSR-Cas-positive S. epidermidis strains revealed multiple origins. In addition, distinct types of SCCmec carried in those strains suggested that acquisition of this MGE originated from multiple independent recombination events. Intriguingly, CRISPR-Cas systems are found to be always located in the vicinity of orfX gene among staphylococci. Allelic analysis of CRISPR loci flanking cas genes disclosed that the loci distal to the orfX gene are considerably stable and conserved, which probably serve as recombination hotspot between CRISPR-Cas system and phage or plasmid. Therefore, the findings generally support the notion that incomplete immune protection of CRISPR-Cas system can promote dissemination of its neighboring SCCmec element.

Automated summary

A genetically manipulable subculture of S.epidermidis strain ATCC35984 was found in the laboratory, showing susceptibility to methicillin due to a large chromosomal deletion encompassing the CRISPR-Cas system. This study suggests that the incomplete immune protection of the CRISPR-Cas system can promote the dissemination of the adjacent SCCmec element, leading to genetic remodeling in bacterial genomes. The findings also indicate the presence of multiple origins and recombination events in the acquisition of the SCCmec element among the CRISPR-Cas-positive S.epidermidis strains.