Abstract
Staphylococcus aureus (S. aureus), which is one of the most important species of Staphylococci, poses a great threat to public health. Clustered regularly interspaced short palindromic repeats (CRISPR) and their CRISPR-associated proteins (Cas) are an adaptive immune platform to combat foreign mobile genetic elements (MGEs) such as plasmids and phages. The aim of this study is to describe the distribution and structure of CRISPR-Cas system in S. aureus, and to explore the relationship between CRISPR and horizontal gene transfer (HGT). Here, we analyzed 67 confirmed CRISPR loci and 15 companion Cas proteins in 52 strains of Staphylococci with bioinformatics methods. Comparing with the orphan CRISPR loci in Staphylococci, the strains harboring complete CRISPR-Cas systems contained multiple CRISPR loci, direct repeat sequences (DR) forming stable RNA secondary structures with lower minimum free energy (MFE), and variable spacers with detectable protospacers. In S. aureus, unlike the orphan CRISPRs away from Staphylococcal cassette chromosome mec (SCCmec), the complete CRISPR-Cas systems were in J1 region of SCCmec. In addition, we found a conserved motif 5′-TTCTCGT-3′ that may protect their downstream sequences from DNA interference. In general, orphan CRISPR locus in S. aureus differed greatly from the structural characteristics of the CRISPR-Cas system. Collectively, our results provided new insight into the diversity and characterization of the CRISPR-Cas system in S. aureus.
Highlights
Staphylococcus is a genus of Gram-positive bacteria that can be found in the air, water, dust, and the skin and mucous membranes of humans and other organisms
The confirmed CRIPSR loci were found in 42 strains of S. aureus and the complete Clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated proteins (Cas) system was identified in 15 strains of Staphylococci by the CRISPR Finder
19 ST, 20 spa types, and 8 Staphylococcal cassette chromosome mec (SCCmec) types were found among the 42 strains of S. aureus, of which the most representative was ST398-t034-Vc
Summary
Staphylococcus is a genus of Gram-positive bacteria that can be found in the air, water, dust, and the skin and mucous membranes of humans and other organisms. In recent years, numerous studies have reported the detection of MRSA or multidrug-resistant S. aureus (MDRSA) in retail food worldwide (de Lencastre et al, 2017; Ge et al, 2017; Tang et al, 2017; Wang et al, 2017), indicating a shift to non-special locations. This is directly related to the popularization of antibiotics and the frequent horizontal transfer of mobile genetic elements (MGEs), such as phages, plasmids, transposons, and Staphylococcal cassette chromosomes (SCC) (Holden et al, 2013; Lindsay, 2014; Strommenger et al, 2014). It is obvious that these exogenous genes provide additional advantages for the survival of bacteria, but they cause unavoidable problems, such as bacterial lysis caused by bacteriophage infection
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