Three novel strains of Gram-stain-negative, obligately anaerobic, spore-forming straight or slightly curved rods with pointed ends occurring singly or in pairs were isolated from the faeces of healthy human children. The strains were characterized by mesophilic fermentative metabolism and production of acetate, ethanol and H₂ as the end metabolic products. Strains ASD3451 and ASD5720^T were motile, fermented lactose and raffinose, and weakly fermented maltose. Strain ASD4241^T was non-motile and did not ferment the carbohydrates listed above but fermented starch. Strains ASD3451 and ASD5720^T shared average nucleotide identity higher than 98.5 % with each other, while ASD4241^T had only 88.5-89 % identity to them. Based on phylogenetic and chemotaxonomic analyses, we propose Diplocloster agilis gen. nov., sp. nov. (ASD5720^T=JCM 34353^T=VKM B-3497^T) and Diplocloster modestus sp. nov. (ASD4241^T=JCM 34351^T=VKM B-3498^T) within the family Lachnospiraceae .

Human seasonal coronaviruses (hCoVs) are a group of viruses that affect the upper respiratory tract. While seasonal patterns and the annual variability of predominant hCoV species are well-documented, their genetic and species diversity in St. Petersburg and across Russia remains largely unexplored. In this study, we developed a two-pool, long-amplicon (900–1100 bp) PCR primer panel for the whole-genome sequencing of four seasonal hCoV species. The panel was validated using nasopharyngeal swab samples collected within the Global Influenza Hospital Surveillance Network (GIHSN) project. Over a period of six epidemiological seasons from 2017 to 2023, we retrospectively analyzed 14,704 nasopharyngeal swabs collected from patients hospitalized in St. Petersburg clinics. Of these samples, 5010 (34.07%) tested positive for respiratory viruses, with 424 (2.88% of all samples) identified as seasonal human coronaviruses. The assessment of species diversity showed that predominant hCoV species alternate between seasons. Whole-genome sequences for 85 seasonal human coronaviruses (hCoVs) with >70% genome coverage were obtained, including 23 hCoV-OC43, 6 hCoV-HKU1, 39 hCoV-229E, and 17 hCoV-NL63. These represent the first near-complete genomes of seasonal hCoVs from the Russian Federation, addressing a significant gap in the genomic epidemiology of these viruses. A detailed phylogenetic analysis of the sequenced genomes was conducted, highlighting the emergence of hCoV-229E subclades 7b.1 and 7b.2, which carry numerous substitutions in the Spike protein. Additionally, we sequenced a historical hCoV-229E isolate collected in the USSR in 1979, the oldest sequenced 229E virus from Eurasia, and demonstrated that it belongs to Genotype 2. The newly developed PCR-based sequencing protocol for seasonal hCoVs is straightforward and well-suited for genomic surveillance, providing a valuable tool to enhance our understanding of the genetic diversity of human seasonal coronaviruses.

The spread of antibiotic-resistant human bacterial pathogens is a serious threat to modern medicine. Antibiotic susceptibility testing is essential for treatment regimens optimization and preventing dissemination of antibiotic resistance. Therefore, development of antibiotic susceptibility testing methods is a priority challenge of laboratory medicine. The aim of this review is to analyze the capabilities of the bioinformatics tools for bacterial whole genome sequence data processing. The PubMed database, Russian scientific electronic library eLIBRARY, information networks of World health organization and European Society of Clinical Microbiology and Infectious Diseases (ESCMID) were used during the analysis. In this review, the platforms for whole genome sequencing, which are suitable for detection of bacterial genetic resistance determinants, are described. The classic step of genetic resistance determinants searching is an alignment between the query nucleotide/protein sequence and the subject (database) nucleotide/protein sequence, which is performed using the nucleotide and protein sequence databases. The most commonly used databases are Resfinder, CARD, Bacterial Antimicrobial Resistance Reference Gene Database. The results of the resistance determinants searching in genome assemblies is more correct in comparison to results of the searching in contigs. The new resistance genes searching bioinformatics tools, such as neural networks and machine learning, are discussed in the review. After critical appraisal of the current antibiotic resistance databases we designed a protocol for predicting antibiotic resistance using whole genome sequence data. The designed protocol can be used as a basis of the algorithm for qualitative and quantitative antimicrobial susceptibility testing based on whole genome sequence data.

INTRODUCTION. Spontaneous mutations often arise and accumulate in the genome of RNA-containing viruses, for example measles, rubella and mumps. Modern requirements for the production of vaccine products containing live vaccine viruses suggest control of the genetic stability of production strains. The method of high throughput sequencing allows to determine all mutations arisen in viral population, and to assess genetic stability of production strains. AIM. Analysis of nucleotide sequence of the genomes of seed and production strains of measles (Leningrad-16), rubella (RA27/3) and mumps (Leningrad-3) viruses, in comparison with the reference nucleotide sequences of vaccine strains genomes (submitted in the Gen-Bank database). MATERIALS AND METHODS. Production strains of vaccines (measles culture live, rubella culture live and mumps culture live) were used in this study. Whole genome sequencing was performed using the MGI DNBSEQ G-400 and Illumina NextSeq2000 genetic analyzers. When processing and analyzing the sequencing data, the following programs and tools were used: FastQC v.0.12.1, FastP v.0.23.4, BWA-MEM2 v.2.2.1, VizCoV tool. RESULTS. Analysis of single nucleotide polymorphisms (SNPs) within the viral population in the studied samples revealed a number of minor variants that, and after further accumulation, may lead to changes in the consensus sequences of the vaccine strains proteins. For the studied measles virus samples, no SNPs were found in the main measles virus antigen H protein, however, a nonsynonymous polymorphism was detected in the F protein, occurring in 30.0–40.9% of the viral genomes. SNPs were found in the capsid protein C and in the surface glycoprotein E2 rubella virus, occurring in the viral population with a frequency of up to 30%. SNPs were found in surface antigens hemagglutinin neuraminidase HN and fusion protein F of mumps virus, occurring in the genomes of less than 20% of viral population. Mutations in the genomes of production strains that could affect the immunogenicity of measles, rubella, and mumps vaccines were not detected. CONCLUSIONS. The identified set of minor variants with a frequency of occurrence in viral population of more than 10%, which, with further accumulation, can lead to changes in the consensus sequences of vaccine strains, makes the monitoring of vaccine strains stability using high-throughput sequencing relevant.

The aim of this controlled study was to identify polymorphisms in the genome of COVID­19 patients associated with the frequency of hospitalization.Materials and methods: Two groups of patients were formed: the main group – 56 patients with COVID­19, hospitalized at least twice during the study period, and the control group – 107 patients for whom only one hospitalization with COVID­19 was confirmed during the study period. Wholeexome sequencing of residual nasopharyngeal swabs from patients hospitalized with COVID­19 was performed on the MGI platform, followed by bioinformatics analysis and gene enrichment analysis.Result: For the first time, exome sequencing was performed from oropharyngeal swabs from 163 patients hospitalized with COVID­19 using the MGI platform. In the main group, unique variants of genetic polymorphisms were identified, including six previously undescribed ones.Conclusion: No genetic variants were statistically significantly associated with single or multiple hospitalizations of COVID­19 patients in the study. Nasopharyngeal swabs can be used for whole exome sequencing. Further studies are needed to identify unique genetic variants responsible for susceptibility to infectious diseases. Nasopharyngeal swabs can be used for whole­exome sequencing. Further studies are needed to identify unique genetic variants responsible for susceptibility to infectious diseases.

In the traditional myxomycete classification, the order Liceales was defined by the absence of a capillitium and columella, along with bright-colored spores. Historically, the composition of this o...