Identification and analysis of CRISPR/Cas systems structures in the genomes of antibiotic-resistant strains of <i>Klebsiella pneumoniae</i>

Abstract

Background. Klebsiella pneumoniae belongs to a group of opportunistic bacteria that can form multiple resistance to antibiotics and transmit it to various types of bacteria through horizontal gene transfer. These studies examine the structural and functional diversity of CRISPR/Cas systems that protect bacteria from foreign DNA. Their analysis using the example of antibiotic-resistant strains of Klebsiella pneumoniae will demonstrate their resistance to certain bacteriophages, which will make it possible to develop approaches to the treatment of complex infectious diseases caused by these microorganisms by creating targeted phage therapy.The aim. To perform a bioinformatics analysis of the identified structural components of CRISPR/Cas systems for screening bacteriophages through CRISPR cassette spacers using the example of antibiotic-resistant strains of Klebsiella pneumoniae.Materials and methods. The article analyzed 29 full-genome sequences of Klebsiella pneumoniae, in the genome of which the structures of CRISPR/Cas systems and  antibiotic resistance genes were determined (according to NCBI). To achieve this  goal, using software modeling methods, a search was made for Cas genes and CRISPR cassettes, and their structural and functional characteristics were given.Results. Using bioinformatic search algorithms in the genome of antibiotic-resistant strains, functionally active CRISPR/Cas systems with the presence of one or two CRISPR cassettes and belonging to Type  I Subtype  IE were identified. Groups of resistant strains with identical spacer composition of CRISPR cassettes have been identified. A phylogenetic analysis was carried out confirming their common origin. By analyzing the spacer sequences of CRISPR cassettes, the spectrum of diversity of phages of bacteria of the genus Klebsiella, Salmonella, belonging to the same family Enterobacteriaceae, was determined. Thus, information was obtained about the bacteriophages that are targeted by the action of CRISPR systems of Klebsiella pneumoniae strains that have antibiotic resistance.Conclusions. Analysis of the functional and structural features of the CRISPR/Cas systems of antibiotic resistant Klebsiella pneumoniae strains made it possible to obtain information about their evolutionary history and about the bacteriophages against which their action is directed, that is, about their phage resistance. The approach used in this study may further serve as the basis for the creation of personalized phage therapy