Vol 31, No 2 (2016)

The population structure of Mycobacterium tuberculosis from Republic of Sakha (Yakutia) was studied using 24-loci MIRU-VNTR genotyping. Most of the studied 199 strains isolated from 199 pulmonary tuberculosis patients (34.2% or 68 of 199 strains) belonged to the Beijing genotype. Multiple drug resistant and extensively drug resistant (MDR/XDR) isolates were predominant (χ² = 15.5; p < 0.001) among representatives of the CC2/W148 subtype of the Beijing genotype (9.5% or 19 of 199 isolates). Strains of the genotype S (15.6% or 31 of 199 isolates) were the second most common genotype after Beijing. Most of the strains of S genotype had an identical profile, 233325153325141344222372. Among non-Beijing isolates, representatives of the S genotype included the most significant proportion of MDR or XDR ((χ² = 59.8; p < 0.001). Isolates of Ural genotype were the third most common (10% or 20 of 199 isolates). The strains belonging to LAM genotype (8.5% or 17 of 199) were genetically heterogeneous. Minor genotypes T and Haarlem were also highly heterogeneous. The epidemic spread of MBT isolates belonging to S genotype and CC2/W148 of the Beijing genotype in Yakutia was reconstructed based on a phylogenetic model. The probable time of origin was estimated using the scale proposed by M. Merker et al. (2015). It was shown that isolates of the CC2/W148 subtype divided into four phylogenetic sublineages and were introduced in the recent historical period (the 20th century). Phylogenetic relationships between 30 MIRU-VNTR profiles of S genotype representatives from Yakutia and 31 reference S-profiles profiles from Europe and Canada were studied. Profiles of the isolates of S-genotype from Yakutia formed compact phylogenetic group. It suggested that these strains have been evolving in Yakutia. It was revealed that the ancestral genotype S was imported onto the territory of Yakutia 300–600 years ago.

Assessment of genetic diversity of unisexual (parthenogenetic) species of vertebrates is among the major objectives of research in these species. Various nuclear or mitochondrial genome markers can be used for such an assessment. Microsatellite DNAs are among the most efficient genetic markers, since the mutation rate in these fragments is high. Identification and characterization of such markers are the basic stages of genetic research in parthenogenetic species. Allelic polymorphism of three microsatellite loci in populations of the parthenogenetic species Darevskia rostombekovi (n = 42) and bisexual parent species D. raddei (n = 6) and D. portschinskii (n = 6) has been assessed by locus-specific PCR for the first time. All representatives of the parthenogenetic species D. rostombekovi used in the present study turned out to be heterozygous. The number of alleles of the different loci ranged from two to five in the populations investigated. The nucleotide sequence of the allelic variants of the loci investigated has been determined. The differences between the alleles were apparently related to variation in the structure of microsatellite clusters and single-nucleotide substitutions in DNA fragments located in the vicinity of the clusters at fixed distances from the latter. Structural variants of the alleles formed allele-specific haplotype markers that were inherited from the bisexual parent species. The origin (inheritance from the maternal or paternal species) has been determined for each allele of the parthenogenetic species. The distribution, frequency of occurrence, and pattern of combination of the alleles of microsatellite loci in D. rostombekovi populations have been characterized; these features determined the identity of each population. The data obtained can be used for assessment of the clonal diversity of the parthenogenetic species D. rostombekovi and the identification of a possible scenario of the emergence of the diversity in the populations.

A real-time PCR (RT PCR) assay for Francisella tularensis DNA in ixodes ticks Ixodes trianguliceps (140 mature individuals and 211 nymph pools) found on small mammals from the Middle Ural forests (Chusovskoi district, Perm Region) has been performed for the first time. Francisella DNA was detected in 12 mature ticks and 4 nymph pools when the 16SrRNA gene (amplicon size 1165–1170 bp) was used as the target. Amplification of a shorter fragment of the same gene (221–222 bp) resulted in identification of additional positive samples among mature ticks (17 of 128) and nymph pools (16 of 89). All 49 RT-PCR positive samples were identified as F. tularensis DNA using primers and probes complementary to a fragment of the lpnA (tul4) gene and the ISFtu2 element. The data obtained are indicative of the possible involvement of I. trianguliceps ticks in tularemia pathogen circulation in natural foci of forest type.

The work presents the results of genetic identification of Crimean–Congo hemorrhagic fever (CCHF) virus isolates obtained in the Crimean federal district in the course of the 2015 epidemiological survey for a Crimean-Congo hemorrhagic fever case from Crimea. A PCR test for the presence of the CCHF virus RNA was performed for a single blood serum sample obtained from a patient and for 61 pools (506 individuals) of ixodic ticks collected during an epizootological study carried out in six administrative regions of the Crimean federal district. CCHF virus RNA was detected in the patient’s blood serum and in ten samples of ixodic ticks. Genetic identification of the CCHF virus isolates was performed by sequencing S, M, and L virus genome segments. The results of the molecular and genetic analysis showed that the RNAs of the CCHF viruses detected in the blood serum samples and three tick suspension samples are highly homologous to each other and belong to a new Crimea (Vd) genetic subgroup of the Europe 1 genotype. Whole genome sequences were obtained for two CCHF virus isolates from the Crimea subgroup (Vd). CCHF virus variants belonging to the Crimea subgroup (Vd) of the Europe 1 genotype have been described for the first time and are endemic for the Crimean peninsula.

In our S. aureus isolates methicillin resistance was 59%. The most frequent SCCmec type was SCCmecIII (77%). Our results demonstrated the spread of HA-MRSA isolates in the community and propagating CA-MRSA isolates in the studied hospitals.