S. A. Portenko, E. V. Naidenova, D. A. Agafonov, D. A. Kuznetsova, A. V. Evteev, A. A. Tushinsky, L. N. Dmitrieva, A. D. Katyshev, V. E. Kuklev, N. Obissa, V. Mabiala, J. Loubano, M. Mpompolo, J.-C. Mobousse Misse, S. A. Shcherbakova, V. V. Kutyrev
{"title":"Organization of Joint Laboratory Studies during Sanitary and Epidemiological Interventions in the Republic of the Congo by Rospotrebnadzor Specialists","authors":"S. A. Portenko, E. V. Naidenova, D. A. Agafonov, D. A. Kuznetsova, A. V. Evteev, A. A. Tushinsky, L. N. Dmitrieva, A. D. Katyshev, V. E. Kuklev, N. Obissa, V. Mabiala, J. Loubano, M. Mpompolo, J.-C. Mobousse Misse, S. A. Shcherbakova, V. V. Kutyrev","doi":"10.21055/0370-1069-2024-2-167-177","DOIUrl":"https://doi.org/10.21055/0370-1069-2024-2-167-177","url":null,"abstract":"The study presents the data on organization of laboratory testing of clinical and environmental samples within the framework of establishing the etiology of the acute intestinal infections outbreak, performed by the specialists of the joint SAET of the Rospotrebnadzor in Dolisie (Republic of the Congo) in the period of 07–24 July, 2023.Materials and methods. In order to identify the causative agents of cholera and other acute intestinal infections of bacterial and viral nature, 177 clinical and environmental samples were tested, as well as cultures on solid nutrient media and bacterial suspensions. A total of 1023 tests were carried out by polymerase chain reaction (PCR) and 305 – using bacteriological method.Results and discussion. The causative agent of cholera has not been detected in any of the samples tested. Using the PCR method, markers of acute intestinal diseases agents (Salmonella spp., Shigella spp., Campylobacter spp., Rotavirus A) have been identified in 23 clinical samples and 1 sample of bacterial suspension. No DNA/RNA of pathogens has been detected in environmental samples. During culture studies, Salmonella enterica serovar Typhi have been isolated from 8 clinical samples, and their antibiotic sensitivity has been determined. Applying whole-genome nanopore sequencing, using the MinIon platform (Oxford Nanopore Technologies, UK), nucleotide sequences of 4 S. Typhi isolates have been investigated and deposited in the international database NCBI GenBank (No. CP141260, CP141193, CP141194, CP141195). Additionally, the analysis of initially sterile samples (blood, peritoneal fluid, intraoperational samples) from the patients of General and Reference hospitals of Dolisie has resulted in the identification of 5 cultures of non-fermenting bacteria, and their antibiotic sensitivity has been determined.","PeriodicalId":516710,"journal":{"name":"Problems of Particularly Dangerous Infections","volume":"10 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141681357","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
P. Mochalkin, V. Akimkin, S. Ugleva, E. S. Morozkin, E. A. Blinova, K. A. Sycheva, D. D. Skripnichenko, T. A. Bondarenko, Yu. O. Epik, M. Makenov, A. A. Kazak, A. K. Popova, M. A. Skotareva, O. V. Ivanova, B. R. Garifullin, N. V. Popov
{"title":"Combined Circulation of Puumala, Tula, Seewis Hantaviruses in the Territory of the Republic of Bashkortostan","authors":"P. Mochalkin, V. Akimkin, S. Ugleva, E. S. Morozkin, E. A. Blinova, K. A. Sycheva, D. D. Skripnichenko, T. A. Bondarenko, Yu. O. Epik, M. Makenov, A. A. Kazak, A. K. Popova, M. A. Skotareva, O. V. Ivanova, B. R. Garifullin, N. V. Popov","doi":"10.21055/0370-1069-2024-2-140-147","DOIUrl":"https://doi.org/10.21055/0370-1069-2024-2-140-147","url":null,"abstract":"The aim of the work was to study the species diversity of pathogenic and non-pathogenic hantaviruses circulating in populations of small mammals in the Republic of Bashkortostan using molecular-genetic methods.Materials and methods. Individual samples from small mammals were tested by the nested PCR using genus-specific primers that amplify the L segment of hantaviruses. The resulting PCR products were sequenced by the Sanger’s method from internal nested PCR primers. For samples containing Puumala virus, fragments of the S, M, and L segments of the viral genome were sequenced using Sanger’s method. The construction of phylogenetic trees was carried out using the MEGA X software.Results and discussion. Out of 300 examined samples of small mammals collected on the territory of the Republic of Bashkortostan in 2023, 14 samples have been found positive for the presence of hantavirus RNA: Seewis (8), Tula (3), Puumala (3). The circulation of the non-pathogenic hantavirus Seewis and the opportunistic hantavirus Tula has been established for the first time in the Republic of Bashkortostan. The circulation of the Seewis hantavirus has been confirmed in populations of the common shrew (Sorex araneus) and the pygmy shrew (S. minutus); the Tula hantavirus – in populations of the common vole (Microtus arvalis). Results of phylogenetic analysis substantiate the reassortment origin of one of the genetic variants of the Puumala hantavirus on the territory of the Republic of Bashkortostan. The prerequisites for the formation of combined natural foci of hantaviruses Puumala, Seewis, and Tula on the territory of the Republic of Bashkortostan are discussed.","PeriodicalId":516710,"journal":{"name":"Problems of Particularly Dangerous Infections","volume":"13 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141683430","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
A. Tyurina, N. E. Gaevskaya, I. A. Ivanova, A. Filippenko, N. D. Omel’chenko, A. Trufanova, M. Pogozhova, A. O. Anoprienko, Yu. V. Sizova, N. Pasyukova
{"title":"Assessment of the Effectiveness of Cholera Bacteriophages for Prevention of Experimental Cholera","authors":"A. Tyurina, N. E. Gaevskaya, I. A. Ivanova, A. Filippenko, N. D. Omel’chenko, A. Trufanova, M. Pogozhova, A. O. Anoprienko, Yu. V. Sizova, N. Pasyukova","doi":"10.21055/0370-1069-2024-2-193-195","DOIUrl":"https://doi.org/10.21055/0370-1069-2024-2-193-195","url":null,"abstract":"The possibility of cholera importation into our country and the increase in the number of Vibrio cholerae strains that are resistant to antibacterial agents necessitate the development of alternative therapeutic and prophylactic biological products based on bacteriophages.The aim of the work was to study the effectiveness of application of cholera bacteriophages for the prevention of experimental cholera.Materials and methods. The work involved cholera bacteriophages Rostov-M3, Rostov-13, active against cholera vibrios of the O1 serogroup; and FB1, which has lytic activity against the O139 serogroup. The effectiveness of cholera prevention was assessed using a model of an isolated loop of the small intestine in an adult rabbit.Results and discussion. The use of Rostov-M3 and Rostov-13 for five and especially seven days before infection with virulent strains of V. cholerae O1 serogroup prevents the development of infection in the small intestine of experimental animals. Bacteriophage FB1 did not have that ability against V. cholerae O139. These studies indicate the effectiveness of using phages Rostov-M3 and Rostov-13 for the prevention of experimental cholera caused by V. cholerae O1 serogroup.","PeriodicalId":516710,"journal":{"name":"Problems of Particularly Dangerous Infections","volume":"20 S36","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141683768","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
M. Patyashina, E. P. Sizova, L. Avdonina, G. G. Badamshina, L. V. Stavropolskaya, A. G. Aleshina, I. A. Karpova, A. V. Goncharova, A. R. Nurtdinova, A. Antonov
{"title":"Epidemiological Aspects of the Incidence of West Nile Fever in the Republic of Tatarstan in 2023","authors":"M. Patyashina, E. P. Sizova, L. Avdonina, G. G. Badamshina, L. V. Stavropolskaya, A. G. Aleshina, I. A. Karpova, A. V. Goncharova, A. R. Nurtdinova, A. Antonov","doi":"10.21055/0370-1069-2024-2-157-166","DOIUrl":"https://doi.org/10.21055/0370-1069-2024-2-157-166","url":null,"abstract":"The aim of the work was to study the epidemiological situation on West Nile fever (WNF) in the Republic of Tatarstan in 2023.Materials and methods. An operational epidemiological analysis of WNF cases registered in the Republic of Tatarstan in 2023 was performed. In order to establish sources and risk factors for infection of the population, 987 samples of zoo-entomological material were examined for the presence of West Nile virus (WNV) markers. A set of laboratory diagnostic methods was used: ELISA, RT-PCR, sequencing.Results and discussion. It has been established that all cases of WNF were registered in the region in the summer-autumn period of 2023, mainly in August, among residents of the city of Kazan who had not traveled outside the Russian Federation and the Republic of Tatarstan over the past six months. The incidence rate of WNF in the Republic of Tatarstan was 0.20 per 100 thousand population, the mortality rate reached 12.5 %. Signs of damage to the central nervous system were present in 6 out of 8 (75 %) patients. The majority of people with severe clinical symptoms belonged to older age groups and had concomitant diseases. Cases of the infection were reported in all age groups, with the exception of children and adolescents. The spatial characteristics of morbidity have been investigated, indicating the diffuse nature of the distribution of cases. The integrated use of methods, consisting in the concurrent use of polymerase chain reaction and enzyme-linked immunosorbent assay, made it possible to laboratory confirm cases of WNF in patients at different stages of the disease. The circulation of a subvariant of the WNV of the second genotype in the Republic of Tatarstan, currently dominant in the southern and central regions of Russia, has been established. A set of measures has been proposed to optimize epidemiological surveillance and control of WNF in the Republic of Tatarstan.","PeriodicalId":516710,"journal":{"name":"Problems of Particularly Dangerous Infections","volume":"13 S17","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141683429","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
N. A. Osina, D. A. Sitmbetov, O. A. Morozov, E. G. Bulgakova, A. V. Osin, S. S. Chekmareva, E. V. Sazanova, A. M. Senichkina, O. Lyashova, T. Polunina, Yaroslav M. Krasnov, Z. Devdariani, S. A. Shcherbakova
{"title":"Intraspecific Differentiation of Francisella tularensis Strains Using Molecular-Genetic Methods. Complex Approach","authors":"N. A. Osina, D. A. Sitmbetov, O. A. Morozov, E. G. Bulgakova, A. V. Osin, S. S. Chekmareva, E. V. Sazanova, A. M. Senichkina, O. Lyashova, T. Polunina, Yaroslav M. Krasnov, Z. Devdariani, S. A. Shcherbakova","doi":"10.21055/0370-1069-2024-2-148-156","DOIUrl":"https://doi.org/10.21055/0370-1069-2024-2-148-156","url":null,"abstract":"The aim of the study was to develop an algorithm for intraspecific differentiation of tularemia agent strains using a set of approaches based on amplification and sequencing technologies.Materials and methods. 97 strains of Francisella tularensis of various subspecies, biovars and subpopulations from the State Collection of Pathogenic Bacteria of the Russian Research Anti-Plague Institute “Microbe” were used in the work. The intraspecific identification of tularemia agent strains was carried out using the “F. tularensis-4c” system; analysis of the variability of the RD1 differentiation region, the sdhA gene, by applying the disk diffusion method using disks with erythromycin. Fragment Sanger sequencing was performed on a 3500 XL genetic analyzer (Applied Biosystems, USA) taking into account the manufacturer’s recommendations. Sequence homology assessment was conducted using the BLAST algorithm, the GenBank NCBI database, MEGA11 v11.0.13 and Unipro UGENE v50.0 software.Results and discussion. Subspecies- and biovarspecific mutations have been detected in the 23S rRNA gene. Promising regions of this gene for further investigation have been identified using fragment sequencing. A comprehensive scheme for intraspecific differentiation of tularemia microbe strains has been put forward, where at the first stage the subspecies and biovar japonica are determined, and at the second stage, the results are verified based on the determination of mutations in the 23S rRNA gene. The effectiveness of the proposed integrated approach has been confirmed in a study of 97 collection strains of tularemia agent. The conducted research allows for rapid identification of tularemia agent strains of different subspecies and verification of their taxonomic appurtenance using molecular-genetic methods, expanding data on the circulation of various subspecies, biovars and subpopulations of the pathogen in Europe, Asia and other regions of the world.","PeriodicalId":516710,"journal":{"name":"Problems of Particularly Dangerous Infections","volume":" 61","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141680490","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
A. Shipovalov, G. Kudrov, E. Ivleva, V. V. Omigov, O. V. Pyankov, O. Taranov
{"title":"Comparative Study of Pathomorphological Changes in Animal Lung Tissue when Modeling Infection Caused by the SARS-CoV-2 Virus","authors":"A. Shipovalov, G. Kudrov, E. Ivleva, V. V. Omigov, O. V. Pyankov, O. Taranov","doi":"10.21055/0370-1069-2024-2-178-187","DOIUrl":"https://doi.org/10.21055/0370-1069-2024-2-178-187","url":null,"abstract":"The aim of the work was to study the features of the infectious process in the lungs of animals used as models for assessing SARS-CoV-2 pathogenicity.Materials and methods. The strain of SARS-CoV-2 alpha variant virus was used in the work. The experiments were carried out on linear and transgenic mice, Syrian hamsters, guinea pigs, ferrets and two types of primates: rhesus macaques and green monkey. The pathomorphological examination was performed by optical microscopy of histological lung preparations using a computerized microscope with digital microphotography.Results and discussion. A comparative histological analysis of the lungs in six different types of laboratory animals was carried out when modeling a new coronavirus infection; similar morphometric signs of the severity of the disease caused by the SARS-CoV-2 virus in sensitive animals were determined, and a dose-dependent correlation of pathological changes in lung tissues with intranasal administration of various infectious doses was revealed. The features of pathomorphological changes in six different animal species in the simulation of a new coronavirus infection have been characterized, and their dose-dependent nature determined. The presented research results can be used to select a model animal for the purpose of in-depth study of the pathogenesis of COVID-19 caused by newly isolated coronavirus variants, the dynamics of immune reactions of the body during the development of the disease, as well as in vivo studies of the protective effect of promising therapeutic drugs and vaccines.","PeriodicalId":516710,"journal":{"name":"Problems of Particularly Dangerous Infections","volume":"62 1‐2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141682493","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
E. Monakhova, V. D. Kruglikov, A. S. Vodopyanov, Yaroslav M. Krasnov, S. D. Katyshev, N. A. Sharapova, L. Alekseeva, E. A. Men’shikova, V. V. Evdokimova, M. I. Ezhova, A. Noskov
{"title":"Characteristics of Vibrio cholerae O1 CTX+ Strain Isolated from the Temernik River in Rostov-on-Don in 2023","authors":"E. Monakhova, V. D. Kruglikov, A. S. Vodopyanov, Yaroslav M. Krasnov, S. D. Katyshev, N. A. Sharapova, L. Alekseeva, E. A. Men’shikova, V. V. Evdokimova, M. I. Ezhova, A. Noskov","doi":"10.21055/0370-1069-2024-2-132-139","DOIUrl":"https://doi.org/10.21055/0370-1069-2024-2-132-139","url":null,"abstract":"The aim of the work was to determine the pheno- and genotypic features of the aquatic CTX+ strain of Vibrio cholerae isolated in 2023 and a comparative bioinformatic analysis of whole-genome sequencing data.Materials and methods. Whole-genome sequencing was performed on MiSeq (Illumina) and MinIon Oxford Nanopore Technologies (ONT) platforms; hybrid assembly of the whole genome was carried out using the Trycycler algorithm; assembly errors were eliminated by means of the Medaka algorithm and the Pilon program. Dendrogram construction and bioinformatics analysis were carried out with the help of the scipy and Graphviz packages, BioEdit, BLASTN, BLASTP, CARD, ICE Genotyper, and Vector NTI programs. The ability to produce cholera toxin was tested using the GM1ELISA.Results and discussion. The isolated strain was identified as V. cholerae O1 Ogawa, sensitive to most antibiotics. Based on the totality of genetic properties, it was classified as the first genovariant, distinct from the typical El Tor strains only by the presence of ctxB1 gene of classical type instead of ctxB3 of the El Tor type. It has been established that it contains a tandemly duplicated CTX prophage on the small chromosome and a tandem of two copies of RS1 prophage on the large chromosome. Thereat, the rstR gene of the CTX prophage belonged to the classical type, and the RS1 prophage – to the El Tor type. The remaining criteria of epidemic hazard – tcpAelt, rtxA1 and intact VSP-II did not differ from the prototypes. The genome of the strain carries the ICE element VchBan11, which contains the trimethoprim resistance gene dfrA1, and phenotypically the strain is resistant to this antibiotic. Under in vitro conditions, the strain did not produce cholera toxin, as shown by ELISA results. This may be due to the presence of a deletion within the toxR regulatory gene. Strains similar to the 2023 isolate are mainly attributed to the second wave of the seventh pandemic. Currently, they are almost replaced by new genovariants, but occasionally can emerge and even cause diseases. Therefore, their importation into Russian territory potentially pose a threat to public health.","PeriodicalId":516710,"journal":{"name":"Problems of Particularly Dangerous Infections","volume":"22 1‐2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141683742","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
P. Loti, S. S. Nyirenda, F. K. Chisulo, A. Chama, M. Singogo, D. B. Chileshe, J. L. Mwansa
{"title":"Investigation of Malaria Parasitemia among Asymptomatic Individuals in Designated Districts of Central and Muchinga Provinces of Zambia – A Cross Sectional Study","authors":"P. Loti, S. S. Nyirenda, F. K. Chisulo, A. Chama, M. Singogo, D. B. Chileshe, J. L. Mwansa","doi":"10.21055/0370-1069-2024-2-188-192","DOIUrl":"https://doi.org/10.21055/0370-1069-2024-2-188-192","url":null,"abstract":"The aim of the study was to investigate asymptomatic malaria in health-conscious population across four selected districts. Malaria is a life-threatening disease caused by Plasmodium spp. transmitted through bites of infected female Anopheles mosquitoes. Asymptomatic malaria refers to the presence of malaria parasites in vivo without symptoms, which usually provides a reservoir for the disease transmission.Materials and methods. Blood collected in EDTA underwent testing through RDT (SD Bioline one-step malaria antigen P.f. (HRP-II) rapid test kits), while thin and thick blood smears Giemsa stained were microscopically examined.Results and discussion. Out of 385 individuals examined, 84 people (21.8 %) tested positive for malaria using RDT and 101/385 (26.2 %) – through microscopy. Microscopic examination further identified 27 individuals (7.0 %) with gametocytes and 74 (19.2 %) – with trophozoites. Intriguingly, 17 (4.4 %) samples showed negative results in RDT but exhibited trophozoites and gametocytes upon smear examination. District-wise analysis demonstrated the highest malaria positivity rate in Kanchibiya district, with 32 cases (8.3 %) detected by RDT and 35 (8.5 %) – through microscopy. Chitambo district followed closely: with RDT and microscopy values of 25 (6.5 %) and 33 (8.4 %), respectively; while Mpika and Serenje districts had 13 (3.4 %) and 14 (3.6 %) prevalence, respectively, with RDT and microscopy at 12 (3.1 %) in both districts [x2 =16.3, p-value=0.0118]. The study also revealed that 365/385 (95 %) of the participants demonstrated knowledge and positive attitudes toward malaria. Our findings accentuate the presence of asymptomatic malaria, encompassing trophozoites and gametocytes, among seemingly healthy individuals which poses a health risk to the community. Therefore, it is imperative to implement preventive chemotherapy and strengthen vector control efforts against malaria in order to reduce the infection rate.","PeriodicalId":516710,"journal":{"name":"Problems of Particularly Dangerous Infections","volume":"81 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141681982","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
L. V. Mironova, I. S. Fedotova, Yu. P. Galach’yants, A. S. Ponomareva, S. V. Erdyneev, Zh. Yu. Khunkheeva, E. A. Basov, A. V. Fortunatova, S. V. Balakhonov
{"title":"Genomic Analysis of Vibrio cholerae Strains Isolated in Siberia and the Far East during the Seventh Cholera Pandemic: Determining the Appurtenance to Global Phylogenetic Lines","authors":"L. V. Mironova, I. S. Fedotova, Yu. P. Galach’yants, A. S. Ponomareva, S. V. Erdyneev, Zh. Yu. Khunkheeva, E. A. Basov, A. V. Fortunatova, S. V. Balakhonov","doi":"10.21055/0370-1069-2024-2-122-131","DOIUrl":"https://doi.org/10.21055/0370-1069-2024-2-122-131","url":null,"abstract":"The aim was to determine the phylogenetic position and features of the genome organization of individual groups of Vibrio cholerae strains isolated in Siberia and the Far East under different epidemiological situations during the seventh cholera pandemic.Materials and methods. We examined 275 V. cholerae strains, isolated during epidemic complications and during the cholera-free period in Siberia and the Far East, with different profiles of the main genomic loci of pathogenicity. The genomes of 969 V. cholerae strains from GenBank were used for phylogenetic analysis. The phylogeny reconstruction was carried out through calculating the distances between strains based on the occurrence of k-mers. The search, analysis and visualization of the loci structure in mobile genetic elements in V. cholerae genomes were performed using the blastn and Prokka programs and the author’s R and Python scripts.Results and discussion. Strains of V. cholerae isolated in Siberia and the Far East have been included in three global phylogenetic lines – L2, L3, L4. The distribution of strains from Siberia and the Far East along phylogenetic lines corresponds to the epidemiological situation in which they were isolated. We have identified the differentiation of strains by groups consistent with the global waves of spread of the etiological agent of the seventh cholera pandemic. We also traced potential paths for the import of the cholera pathogen into the territory of the Russian Federation. It has been revealed that spontaneous mutants that lost cholera toxin genes during storage and cultivation on nutrient media belong to the L2 phylogenetic lineage as well as toxigenic El Tor vibrios. The structural analysis confirms the differences in their genome organization and strains that do not have a CTX prophage during primary PCR screening. We recommend a two-stage algorithm of phylogenetic analysis within the framework of genomic monitoring of cholera agent: the first stage is a simplified assessment based on the occurrence of k-mers for express epidemiological analysis; the second stage is an in-depth analysis of genomes using a complex of phylogenetic methods for the reconstruction of links in individual epidemic complications, to establish patterns of origin and time of divergence of the pathogen clones.","PeriodicalId":516710,"journal":{"name":"Problems of Particularly Dangerous Infections","volume":"330 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141686538","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
V. V. Kutyrev, S. A. Shcherbakova, A. V. Ivanova, V. E. Kuklev, Zh. A. Kas’yan, I. G. Karnaukhov
{"title":"Russia and Venezuela: New Strategic Partnership in the Field of Response to Biological Threats and Prospects for Cooperation","authors":"V. V. Kutyrev, S. A. Shcherbakova, A. V. Ivanova, V. E. Kuklev, Zh. A. Kas’yan, I. G. Karnaukhov","doi":"10.21055/0370-1069-2024-2-115-121","DOIUrl":"https://doi.org/10.21055/0370-1069-2024-2-115-121","url":null,"abstract":"The paper considers the key areas of international activities of the Federal Service for Surveillance on Consumers’ Rights Protection and Human Well-being in strengthening cooperation with specialized agencies of foreign countries in the global provision of sanitary-epidemiological welfare of the population at the current stage. Consistent work to strengthen the international network to counter emergency situations of a sanitary and epidemiological nature through effective interaction in the field of rapid response with partner countries in the near and far abroad, including through the organization of joint scientific and practical centers for the study and prevention of infectious diseases is presented. It is shown that the programs being implemented are aimed at strengthening the national healthcare structures of partner countries to achieve independence in the implementation of monitoring and anti-epidemic measures and building a single epidemiological space, independent of the influence of global and regional geopolitical fluctuations. The relevance of increasing interstate cooperation in the field of analysis and control of biological threats, primarily infectious diseases with the potential for emergencies of a sanitary and epidemiological nature of international concern, in the South American region is considered. The currently expanding strategic biosecurity collaboration with the Bolivarian Republic of Venezuela through the establishment of the first joint research center in the South American region is described. The first results of the joint work of Russian and Venezuelan specialists are presented, confirming the successful integration of Russian experience in monitoring and preventing biological threats into the system of ensuring the sanitary and epidemiological well-being of the Venezuelan population. Promising areas for further joint research are discussed.","PeriodicalId":516710,"journal":{"name":"Problems of Particularly Dangerous Infections","volume":"22 8","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141685647","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}