Analysis of the gene structure of antiphage systems of non-toxigenic strains of <i>Vibrio cholerae</i> O1 biovar El Tor

Introduction. The presence and structure of antiphage systems that contribute to the resistance of cholera vibrios to lytic phages in non-toxigenic strains of Vibrio cholerae O1 biovar El Tor isolated in the Russian Federation and neighboring countries has not been studied. The aim of the study is the detection and analysis of antiphage systems of non-toxigenic strains of V. cholerae O1 biovar El Tor. Materials and methods. The study involved 126 non-toxigenic (ctxAB–tcpA+ and ctxAB–tcpA–) strains of V. cholerae O1 El Tor isolated from 1972 to 2018. DNA sequencing was performed on the MGI DNBSEQ-G50 platform. For bioinformatics analysis, the following programs were used: fastp v. 0.23, unicycler v. 0.4.7, Blast 2.16.0, MEGA X, CRISPRCasty-per and CRISPRCasFinder. Results. Phage-inducible islands of the PLE, BREX and DISARM systems were not detected in the genome of the studied strains. It was found that 80% of ctxAB–tcpA+ strains contain the type I restriction-modification system, while this system was not detected in ctxAB–tcpA– isolates. The genes of the CBASS system were detected in single strains of both groups. In the genome of 35 (32%) studied ctxAB–tcpA– strains isolated in different regions of the Russian Federation and neighboring countries, the presence of the CRISPR–Cas system of class 1 types I (subtypes I-E, I-F, I-C) and III (subtype III-B) was established. The number of spacers in this system varied from 0 to 80 and their sequence was homologous to the protospacer regions of DNA of lytic and temperate phages, transposons, plasmids of V. cholerae, representatives of the genus Vibrio and unrelated bacteria. The presence in a number of strains of spacers homologous to the genetic material of the phage circulating in endemic territories may indicate the imported nature of these strains. Conclusion. The heterogeneity of the studied non-toxigenic strains of V. cholerae O1 El Tor in the presence of antiphage systems was revealed, which expands the information on their genetic organization. In their genome, restriction-modification systems of type I (ctxAB–tcpA+), CBASS (ctxAB–tcpA+ and ctxAB–tcpA–) and CRISPR–Cas class 1 types I (subtypes I-E, I-F, I-C) and III (ctxAB–tcpA–) were identified. The detection of several types and subtypes of the CRISPR–Cas system in the genome of a number of ctxAB–tcpA strains may indicate its repeated acquisition through horizontal transfer.