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”.

Borisenko Andrei Yurievich, Assistant, Irkutsk State Medical University, 1, Krasnogo Vosstania st., Irkutsk, 664003, Russian Federation, e-mail: 89500720225@mail.ru 

Dzhioev Yuri Pavlovich, Candidate of Sciences (Biology), Senior Research Scientist, Head of Laboratory, Irkutsk State Medical University, 1, Krasnogo Vosstania st., Irkutsk, 664003, Russian Federation, e-mail: alanir07@mail.ru 

Stepanenko Lilia Alexandrovna, Candidate of Sciences (Medicine), Senior Research Scientist, Irkutsk State Medical University, 1, Krasnogo Vosstania st., Irkutsk, 664003, Russian Federation, e-mail: steplia@mail.ru 

Zemlyanskaya Julia Mikhailovna, Senior Lecturer, Irkutsk State Medical University, 1, Krasnogo Vosstania st., Irkutsk, 664003, Russian Federation, e-mail: yuliyazemlya84@mail.ru 

Peretolchina Nadezhda Pavlovna, Junior Research Scientist, Irkutsk State Medical University, 1, Krasnogo Vosstania st., Irkutsk, 664003, Russian Federation, e-mail: nadine1lenz@gmail.com 

Arefieva Nadezhda Aleksandrovna, Student, Irkutsk State University, 1, Karl Marx st., Irkutsk, 664003, Russian Federation, e-mail: arefieva.n4@gmail.com 

Bukin Yuri Sergeevich, Candidate of Sciences (Biology), Senior Research Scientist, Limnological Institute SB RAS, 3, Ulan-Batorskaya st., Irkutsk, 664033, Russian Federation, e-mail: bukinys@lin.irk.ru 

Rakova Elena Borisovna, Candidate of Sciences (Biology), Associate Professor, Irkutsk State Medical University, 1, Krasnogo Vosstania st., Irkutsk, 664003, Russian Federation, e-mail: lenova_@mail.ru 

Kokorina Lyubov Aleksandrovna, Assistant, Irkutsk State Medical University, 1, Krasnogo Vosstania st., Irkutsk, 664003, Russian Federation, e-mail: lubovkokorina1990@yandex.ru

Portnaya Yana Alekseevna, Student, Irkutsk State Medical University, 1, Krasnogo Vosstania st., Irkutsk, 664003, Russian Federation, e-mail: portnaya.yana.1997@yandex.ru 

Vyatchina Olga Fedorovna, Candidate of Sciences (Biology), Associate Professor, Irkutsk State University, Russian Federation, 664003, Irkutsk, st. Karl Marx, 1, e-mail: olgairk3@rambler.ru 

Martynova Alena Sergeevna, Undergraduate, Irkutsk State University, 1, Karl Marx st., Irkutsk, 664003, Russian Federation, e-mail: martynovalen@mail.ru 

Frantseva Lada Andreevna, Student, Irkutsk State University, 1, Karl Marx st., Irkutsk, 664003, Russian Federation, e-mail: ladafrantseva@yandex.ru 

Vasiliev Valery Vladimirovich, Research Scientist, Irkutsk Anti-plague Research Institute of Siberia and Far East of Rospotrebnadzor, 78, Trilisser st., Irkutsk, 664047, Russian Federation, e-mail: marmakeda_007@mail.ru 

Teterina Galina Aleksandrovna, Graduate Student, Irkutsk State University, 1, Karl Marx st., Irkutsk, 664003, Russian Federation, e-mail: galina.teterina.91@mail.ru 

Salovarova Valentina Petrovna, Doctor of Sciences (Biology), Professor, Head of Department, Irkutsk State University, 1, Karl Marx st., Irkutsk, 664003, Russian Federation, e-mail: vsalovarova@rambler.ru 

Simonova Elena Vasilievna, Doctor of Sciences (Biology), Professor, Irkutsk State Medical University, 1, Krasnogo Vosstania st., Irkutsk, 664003, Russian Federation, e-mail: ev.simonova@yandex.ru 

Zlobin Vladimir Igorevich, Doctor of Sciences (Medicine), Professor, Academician of RAS, Head of Department, Director of the Research Institute of Biomedical Technologies, Irkutsk State Medical University, 1, Krasnogo Vosstania st., Irkutsk, 664003, Russian Federation, e-mail: vizlobin@mail.ru

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genome of strain of Staphylococcus aureus ST228, program methods of bioinformatics, CRISPR/Cas-system, spacers, repeats, protospisers, bacteriophages

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