Structures of the CRISPR/Cas System in the Genome of the Staphylococcus aureus ST228 Strain and Phage Races Detected by Bioinformatics

Abstract

In the modern world, infections caused by multidrug-resistant (MDR) bacteria have become carriers of global threats to human health. Today these pathogenic bacteria have come to be referred to as "superbugs" and their number and aggressiveness is growing. This group of "superbugs" also includes Staphylococcus aureus. It is capable of infecting almost any tissue in the human body. Therefore, it became necessary to find alternative antibiotic methods of treating bacterial infections. The use of bacteriophages is again among them. We propose a new approach in the search for strain-specific (target) phages through the structures of the CRISPR/Cas-systems of bacteria. As is known, CRISPR/Cas systems are the most ancient system of "adaptive immunity" in bacteria. This system makes bacteria resistant to phages and plasmids. This approach is based on the use of methods of structural genomics and software bioinformatics modeling. Using them, an algorithm was developed to search for the structures of CRISPR/Cas systems in bacterial genomes presented in the NCBI databases and screening through their CRISPR cassettes of phages with which a particular strain could meet. The design of the developed algorithm was tested on the genome of methicillin-resistant S. aureus strain (ST228-MRSA-I) from the GenBank database. The results of the search for loci and structures of the CRISPR/Cas system in the genome of this strain showed that the identified system belongs to type III-A. It was found that the cas genes and the CRISPR cassette are located at a distance from each other and between them are located several genes that perform other functions in the genome of the S. aureus strain. It was shown that the structures of spacers in the detected CRISPR cassette are identical to protospacers of phages, the hosts of which are bacteria of the following genera – Staphylococcus, Mycobacterium, Streptococcus, Bacillus, Gordonia, Arthrobacter, Streptomyces. Thus, it can be stated that the developed algorithm of software methods for searching for loci of CRISPR/Cas systems and screening for phages makes it possible to type both the system itself and through its spacers to detect and identify phage races with which a particular bacterial strain could meet. The degree of resistance of a particular bacterial strain to specific phages is also determined, which in the long term should ensure the effectiveness of targeted phage therapy for infections caused by pathogenic bacteria, including "superbugs".