Vol 99, No 4 (2022)

Introduction. Since the registration of the first cases of COVID-19 in the PRC, due to the high migration activity of the population, the new coronavirus infection has spread throughout the world, including the Russian Federation.

Aim. To establish the features of the spread of a new coronavirus infection in the Rostov Region. Materials and methods.The analysis of 81 cases of the importation of a new coronavirus infection by persons who arrived in the Rostov Region from abroad or other regions of the Russian Federation was carried out based on the data of the Rostov Region office of the Federal Service for Supervision of Consumer Protection and Human Welfare. The dynamics of the spread of COVID-19 in the administrative territories of the Rostov Region has been analyzed. The data of viral genome-wide sequencing (n = 155) carried out in the Rostov-on-Don Research Anti-Plague Institute were used in this study.

Results. In the period from 03/21/2020 to 03/28/2020, cases imported both from abroad and from other regions of the Russian Federation were registered in the Rostov Region, , mainly on the territory of the Rostov urban agglomeration. The vector of the spread of the disease was directed from the administrative center of the region to the periphery. The emergence of a new genetic line B.617.2 (Delta) probably led to a significant increase in the incidence in the Rostov Region.

Conclusions. The spread of a new coronavirus infection in the Rostov Region was facilitated by the one of the main social factors of epidemiological risk, the population migration, which led to the importation of the infection to the administrative center of the subject, Rostov-on-Don city. Taking into account peculiarities of the Rostov region, the largest proportion of COVID-19 cases was recorded in the Rostov urban agglomeration. Against the background of the dominance of the “Delta” variant of the virus on the territory of the Rostov region, there was a tendency towards an increase in the number of cases.

The aim: In vitro identification of targets for antagonism factors in klebsiellas and enterococci for Candida albicans isolated from the intestinal microbiome of HIV infected patients.

Materials and methods. The tests were performed using 38 Candida albicans strains, 28 Klebsiella pneumoniae strains, and 30 Enterococcus faecalis strains isolated from the intestinal microbiome of 89 HIV infected children. The mean age of the patients was 24 ± 2 months; the group consisted of 49 (55%) boys and 40 (45%) girls. Microorganisms were isolated from the intestinal biotope using such selective media as HiChrome Candida Agar, HiChrome Klebsiella Selective Agar Base, and Enterococcus Agar; the study included identification of species. Model experiments were performed to study anti-catalase activity of E. faecalis exometabolites and the impact of K. pneumoniae on morphological transformation of C. albicans fungi.

Results. Klebsiellas decrease the intensity of germ tube formation in C. albicans by 58.7% (p < 0.01). When cocultured, 12.3% of the yeast cells produce germ tubes, while 29.8% of transformed cells was detected in the fungal monoculture. It has been found that exometabolites of 65.7% of E. faecalis strains decrease production of catalase in C. albicans. The initial catalase level in untreated cultures of C. albicans averages 1.02 µmol/min of optical density; after they are treated with E. faecalis exometabolites, the level decreases to 0.55 µmol/min, i.e. by 46.1% (p < 0.05).

Conclusions. K. pneumoniae and E. faecalis demonstrate antagonism of different intensity toward C. albicans. Morphological transformation and catalase production are targets for antagonism factors of facultative microbiota in C. albicans.

Introduction. Klebsiella pneumoniae in human microbiota may appear as a part of commensal microbiota, and as hypervirulent pathogen, for example, hypermucoid pathotype. This pathotype is characterized by certain genetic determinants, leading to the possibility of detecting the pathogenic potential of isolates by PCR.

 Aim of the study: to evaluate and compare pathogenic potential of K. pneumoniae isolates from practically healthy people, patients with inflammatory bowel disease (IBD) and extraintestinal infections (ExII).

Materials and methods. Testing was performed with the set of nucleotides for multiplex PCR analysis targeting eight potentially virulent genes with the following functions: ferrum uptake (ybsT, kfu, iutA), adhesion and invasion (mrkD), hypermucoid phenotype and virulent serotypes (mrkD, magA, rmpA, k2) and metabolism of allantoin (allS). PCR assay was used to screen Klebsiella pneumoniae isolates from feces of patients with IBD (69 isolates) and of practically healthy people (68 isolates), and multiresistant isolates from biological material (blood, urine, surgical wounds, bronchoalveolar lavage) of patients with extraintestinal infections (mrExII, 25 isolates).

Results. Results of the testing demonstrated association of four of targeted determinants with the patients diagnoses. YbtS gene was significantly more often found in isolates from IBD (р = 0.024) and mrExII (p < 0.001) groups. RmpA gene was significantly more often detected in IBD group (р = 0.038). Extraintestinal infectious isolates were significantly (р ≤ 0.001) enriched with mrkD and allS genes (р = 0.032).

Conclusion. The most potentially virulent group was isolated from patients with extraintestinal infections, the least virulent — isolates from feces of practically healthy people. The most frequently detected virulence genes were involved in adhesion and hypermucoid phenotype formation.

Introduction. The published and our own data show that CTAG and, to a lesser extent, TCGA tetra-nucleotides have significantly lower concentrations in frequency profiles (FPs) of herpesvirus DNAs compared to other complete, bilaterally symmetrical tetra-nucleotides.

The aim of the study is to present a comparative analysis of CTAG and TCGA tetra-nucleotide FPs in viral DNAs.

Materials and methods. We have analyzed FPs and other characteristics of the two above tetramers in DNAs of at least one species of viruses of each genus (or each subfamily, if the classification into genera was not available), complying with the size limit requirements (minimum 100,000 base pairs) — a total of more than 200 species of viruses. The analysis was performed using the GenBank database.

Results. Two groups of characteristics of TCGA and CTAG tetramers have been described. One of them covers the results of the FP analysis for these tetranucleotides in viral DNAs and shows that DNAs with GC:AT > 2 are characterized by nCGn FP symmetries while these symmetries are frequently distorted in nTAn FP due to CTAG underrepresentation. The other group of tetramer characteristics demonstrates differences in their FPs in complete viral DNAs and in their genomes (a coding part, which can reach 80% in some studied viruses, thus making the analysis of their DNAs more significant than the analysis of DNAs of cellular live forms) and suggests that these tetramers may have participated in the origin of the universal genetic code.

Discussion. Assumedly, the genetic code started evolving amid C+G prevailing in "pre-code" DNA polymers; then the initial code forms evolved further to their final structure where TCGA and CTAG tetramers hold a central position, encapsulating the previous stages of this evolution. The nCGn FP symmetries typical of the "complete" DNA of Herpes simplex viruses disappear in the sequence of the second codon letters of the genome of these viruses, implying that their functions differ from functions of other letters and emphasizing the reasonableness of presenting the genetic code as a calligram where the second line is not symmetrical.

Introduction. In 2017–2020 for the first time in many years strains of Vibrio cholerae nonO1/nonO139 (NAGs) were isolated in Russia from patients with otitis.

Aim — bioinformatic analysis of whole genome sequences (WGSs) and sequences of individual genes of NAG strains - causative agents of otitis isolated in Russia.

Materials and methods. Analysis of WGSs of eight NAG clinical isolates obtained on the MiSeq Illumina platform was carried out using BioEdit, BLASTN, BLASTP, Vector NTI programs; antibiotic resistance was determined according to MUK 4.2.2495-09.

Results. The strains differed in SNP content, sets of determinants of pathogenicity/persistence factors and their alleles. All lacked CTX, preCTX, RS1 prophages, VPI pathogenicity island, thermostable toxin gene, mobile elements associated with antibiotic resistance, pandemicity island VSP-I; two strains contained VSP-II island. Genes of a number of proteases, cholix toxin, type 3 secretion system (T3SS) cluster and additional T6SS clusters formed different combinations. Products of the altered genes retained or lost their characteristic active domains. In the cytotoxin MARTX of 6 strains, the key ACD domain was absent; in 4 strains a new rtxA-like domain was revealed. Biofilm gene clusters varied in their structure. The presence of genes for antibiotic resistance did not always correlate with antibioticograms. All strains were susceptible to most antibiotics, but some showed resistance to 1–4 drugs.

Conclusion. All the studied strains — causative agents of otitis, in spite of revealed differences, have sufficient sets of determinants responsible for realization of pathogenic and persistent potential. Due to discrepancy between the genotypic and phenotypic characteristics of antibiotic resistance, one should rely mainly on the phenotype when choosing drugs for the etiotropic therapy of NAG infections. Emergence of patients with otitis caused by NAG-vibrios in Russia indicates the advisability of the inclusion of tests for their identification in the scheme of bacteriological analysis for extraintestinal infections and, in cases of their isolation, for prompt determination of sensitivity to antibiotics.