ISSN Print 2500–1094
ISSN Online 2542–1204
BIOMEDICAL JOURNAL OF PIROGOV UNIVERSITY (MOSCOW, RUSSIA)
ORIGINAL RESEARCH
The search and analysis of a CRISPR-Cas system in Escherichia coli HS with subsequent scanning for the corresponding phage races based on the spacers of the detected CRIPSR array using bioinformatic methods
About authors
1 Scientific Center for Family Health and Human Reproduction Problems, Irkutsk
2 Research Institute for Biomedical Technologies of Irkutsk State Medical University, Irkutsk
Correspondence should be addressed: Elena Ivanova
Timiryazeva 16, Irkutsk, 66400; moc.liamg@mei.avonavi
Received: 2018-03-15
Accepted: 2018-03-24
Published online: 2018-06-27
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CRISPR-Cas is an immune system of prokaryotes that protects them against alien replicons, mainly viruses and plasmids. Short sequences (spacers) complementary to the regions of a viral or plasmid genome are inserted into a CRISPR array conferring resistance to reinfection. Infections caused by Escherichia coli still present a serious challenge for clinical medicine. The aim of this study was to scan the genome of Escherichia coli HS for CRISPR-Cas components. The search was conducted using MacSyFinder (Macromolecular System Finder, ver. 1.0.2.), a program for bioinformatic modelling. Sequence homology searches were done using makeblastdb (ver. 2.2.28) and HMMER (ver. 3.0) tools. Bioinformatics-based methods allowed us to detect one CRISPR-Cas system in the studied genome of Escherichia coli HS and read the spacer sequences of its CRIPSR array. The protospacer regions complementary to the spacer sequences of the detected CRISPR array are typical for a few types of phages. Based on these findings, one can assess the degree of bacterial resistance to alien genetic elements.
Keywords: bioinformatics, CRISPR-Cas system, Escherichia coli HS, bacteriophage