Identification and Characterization of the CRISPR/Cas System in Staphylococcus aureus Strains From Diverse Sources

Abstract

The CRISPR-Cas [clustered regularly interspaced short palindromic repeats and the CRISPR-associated genes (Cas)] system provides defense mechanisms in bacteria and archaea vs. mobile genetic elements (MGEs), such as plasmids and bacteriophages, which can either be harmful or add sequences that can provide virulence or antibiotic resistance. Staphylococcus aureus is a Gram-positive bacterium that could be the etiological agent of important soft tissue infections that can lead to bacteremia and sepsis. The role of the CRISPR-Cas system in S. aureus is not completely understood since there is a lack of knowledge about it. We analyzed 716 genomes and 1 genomic island from GENOMES-NCBI and ENA-EMBL searching for the CRISPR-Cas systems and their spacer sequences (SSs). Our bioinformatic analysis shows that only 0.83% (6/716) of the analyzed genomes harbored the CRISPR-Cas system, all of them were subtype III-A, which is characterized by the presence of the cas10/csm1 gene. Analysis of SSs showed that 91% (40/44) had no match to annotated MGEs and 9% of SSs corresponded to plasmids and bacteriophages, indicating that those phages had infected those S. aureus strains. Some of those phages have been proposed as an alternative therapy in biofilm-forming or infection with S. aureus strains, but these findings indicate that such antibiotic phage strategy would be ineffective. More research about the CRISPR/Cas system is necessary for a bigger number of S. aureus strains from different sources, so additional features can be studied.

Whole-Genome Analysis of Staphylococcus aureus Isolates from Ready-to-Eat Food in Russia

“…We would like to emphasize that the low number of CRISPR/Cas systems in S. aureus isolates of different geographic origins may indicate that the presence of such immune systems in this species is a spontaneous biological phenomenon, namely, that such systems could be acquired from some other bacterial species sharing the environment with S. aureus [ 53 ].…”

ATP-dependent restriction enzyme SauUSI fromStaphylococcus aureusis also abona fidesingle strand DNA endonuclease

“…Micrococcal Nuclease (MN), a secreted endonuclease encoded by nuc1, and the cell-wall bound nuclease encoded by nuc2 are involved in immune evasion thus increasing pathogenesis (49)(50)(51)(52). The diverse Cas nuclease repertoire of the CRISPR systems and the different types of R-M systems in S. aureus regulate the acquisition of foreign genetic material (2,18,(53)(54)(55)(56). The dsDNA cleavage activity of SauUSI has been identified as a potent barrier to the entry of methylated dsDNA either by transduction or transformation (2,(17)(18)(19).…”

Understanding the Mechanisms That Drive Phage Resistance in Staphylococci to Prevent Phage Therapy Failure

“…All research so far indicates that CRISPR-Cas systems are not very widespread in the genus Staphylococcus compared to other bacteria [ 27 ], even though several studies have searched for these systems in the genomes of staphylococci, especially S. aureus . For instance, a recent study that analyzed 716 whole genomes available in public databases found that only 0.83% carried CRISPR-Cas systems, all of which belonged to subtype IIIA [ 28 ]. A similar percentage had already been observed by Cao et al [ 29 ] after probing the genomes of 616 clinical isolates.…”

“…On the other hand, identification of potential spacer sequences (SSc) in the genome of a target strain would help predict which phages are the most adequate for treatment. For instance, a recent study found spacer sequences (SSc) in the genome of S. aureus strains from various sources that matched sequences corresponding to phages that had previously been considered as a treatment against this pathogen [ 28 ].…”