In Silico Analysis of the Structural Diversity of CRISPR-Cas Systems in Genomes of Salmonella enterica and Phage Species Detected by Them
Authors:   Irkutsk State University, Borisenko A. Yu. , Arefieva N. A. ,   Scientific Сentre for Family Health and Human Reproduction Problems,   Irkutsk Anti-Plague Research Institute of Siberia and Far East of Rospotrebnadzor,   Irkutsk State Medical University,   Irkutsk State University, Dzhioev Yu. P. ,   Irkutsk State Medical University, Erdyneev S. V. ,   Irkutsk State Medical University,   Irkutsk Anti-Plague Research Institute of Siberia and Far East of Rospotrebnadzor, Bukin Yu. S. ,   Limnological Institute SB RAS,   Irkutsk State University, Teterina G. A. ,   Irkutsk State University, Pristavka A. A. ,   Irkutsk State University, Yurinova G. V. ,   Irkutsk State University, Antipin D. A. ,   Irkutsk State Medical University, Kahiani K. B. ,   Irkutsk State Medical University, Makarova A. E. ,   Irkutsk State Medical University, Salovarova V. P. ,   Irkutsk State University, Zlobin V. I. ,   Irkutsk State Medical University,   Gamaleya National Research Center for Epidemiology and Microbiology
Published: March 2024

The problem of resistance of pathogenic bacteria to antibiotics has become global and, therefore, there is renewed interest in the use of bacteriophages. However, bacteria also have phage defense structures, the CRISPR/Cas system. Therefore, the analysis of the structural diversity of CRISPR-Cas systems in the genomes of pathogenic bacteria and phages is an important fundamental and applied direction. The aim. Investigation of the diversity of structures of CRISPR/Cas systems in the genomes of S. enterica strains from the NCBI database using bioinformatics programs and assessment of the possibilities to identify phage protection of strains through spacers in CRISPR cassettes. The studies were carried out with the genomes of 449 S. enterica strains from the NCBI database. A number of bioinformation software methods were used: 1) MacSyFinder, 2) CRISPR Interactive database, 3) CRISPR R Tool, 4) CRISPI: a CRISPR Interactive database, 5) CRISPRFinder. Screening of phages through spacers CRISPR cassettes was used: 1) CRISPRTarget, 2) Mycobacteriophage Database, 3) Phages database. In the genomes of the studied strains of S. enterica, one type of CRISPR/Cas system, I-E, was identified. Protein genes were present in each locus of the CRISPR/Cas systems: Cas1_0_I-E_7, Cas2_0_I-E_8, Cas3_0_I_1, Cas5_0_I-E_5, Cas6_0_I-E_6, Cas7_0_I-E_4, Cse1_0_I-E_2, Cse2_0_I-E_3. The number of cassettes was from 1 to 3, and the spacers in them varied from 8 to 30. Repeats in CRISPR cassettes varied from 27 to 29 base pairs. The identified phages belonged to bacteria of the genera: Salmonella – 60%, Escherichia – 18%, Enterobacter – 9%, Salmonella – 8%, and Staphylococcus and Enterococcus were up to 5%. The obtained data on the diversity of CRISPR/Cas systems in the genomes of the studied S. enterica strains demonstrate their unique structures. The homogeneity of CRISPR/Cas systems and the rooting of CAS types I-E in genomes can be explained by their participation in the interspecific transmission of these CRISPR systems.