Natural Plague Foci Research Articles

Historical Assessment and Mapping of Human Plague, Kazakhstan, 1926-2003.

Understanding Kazakhstan's plague history is crucial for early warning and effective health disaster management. We used descriptive-analytical methods to analyze spatial data for human cases in natural plague foci in Kazakhstan during 1926-2003. The findings revealed 565 human cases across 82 outbreaks in Almaty (32.22%), Aktobe (1.59%), Atyrau (4.42%), Mangystau (21.24%), and Kyzylorda (40.53%) oblasts. Before antibiotic drugs were introduced in 1947-1948, major plague outbreaks occurred in 1926, 1929, 1945, 1947, and 1948, constituting 80.7% of human transmission. Plague spread through flea bites, camel handling, wild animal contact, aerosol transmissions, and rodent bites. Patients were up to 86 years of age; 49.9% were male and 50.1% female. Pulmonary cases were reported most frequently (72.4%), and person-to-person infection occurred at an incidence rate of 0.29 cases/10,000 population. Risk increased with human expansion into natural plague foci areas. Swift diagnosis and treatment are essential for curbing plague outbreaks in Kazakhstan.

The principle of ecological and molecular consensus in reconstructed plague microbe <i>Yersinia pestis</i> phylogeny

In the second half of the 20th century, through the efforts of scientists from many countries, a coherent theory of natural plague foci (sylvatic plague) was formulated, attempted to describe the history of the origin and evolution of the causative agent of plague infection, the microbeYersinia pestis. But the accumulated knowledge in this regard remained extremely limited. Envisioned by the modern phylogenetics, the methods of phylogenetic constructions in the pregenomic time were rather primitive, “manual”, characteristic of early empirico-intuitive Haeckel phylogenetics. Since the beginning of the 21st century, the introduction of genomic methodologies in the study of the plague pathogen allowed to detail the intraspecific diversity (subspecies, genovariants) of this particularly dangerous pathogen at the level of geographical and local populations (individual natural foci) around the world and to bring the diagnostics and description of intraspecific diversity to a high degree of perfection. Two important discoveries were made. First, the direct ancestor of the plague microbe was reliably established, it turned out to be the causative agent of intestinal infection — Far Eastern scarlet-like fever (Y. pseudotuberculosis0:1b). Secondly, the evolutionary youth of the plague pathogen was shown, the “molecular clock” showed the time of its divergence from the ancestral population no earlier than 30 thousand years ago. Thus, the root of the phylogenetic tree ofY. pestiswas fully characterized. Nevertheless, molecular genetic (MG) achievements do not yet allow to reveal the secrets of its phylogeny, i.e. the origin and sequence of world expansion. The most important reason is the high dependence of the MG of phylogeny reconstructions on the choice of evolutionary model for the analyzed characters: the model of neutral evolution is traditionally accepted, but its adequacy in relation toY. pestisphylogeny is questioned by many well-known ecological (in the broad sense) facts. At the same time, MG achievements contributed to the creation of an ecological (ECO) approach based on the provisions of the theory of natural plague foci in an updated version, according to which the plague pathogen is an evolutionarily young pathogen descended from a psychrophilic pseudotuberculous ancestor. The presumptive ECO scenario has no obvious natural-scientific and historical contradictions and can serve as a null hypothesis for improving the MG methodology of phylogenetic constructions for plague and other similar microbes. It is suggested that the creation of a real phylogeny of the plague microbe is possible only based on integration of MG and ECO approaches.

Performance Capabilities of a Mobile Laboratory for Supporting Immunological Monitoring in Natural Plague Foci

Performance Capabilities of a Mobile Laboratory for Supporting Immunological Monitoring in Natural Plague Foci

Ecological and faunistic features of fleas in the Transcaucasian mounthill natural plague foci in Azerbaijan

Among all vectors of natural focal infections, fleas are the most active. In this respect, entomological and epizootological monitoring has always been of great importance. This article, based on the material collected from the Transcaucasian foothill natural plague focus, presents the results of a study of flea species diversity, the landscape and geographical area of their distribution. The goal of this work was to determine the diversity of flea species, their distribution and abundance based on the results of epizootological studies conducted in areas with different landscapes in the Transcaucasian foothill natural plague focus of Azerbaijan. The material for the study was obtained during epizootological studies and observations conducted in the spring and autumn seasons of 2020–2023. in the Transcaucasian foothill natural plague focus of Azerbaijan (Bozchol, Mil-Mugan, Eastern and Western Jeyranchel, Gobustan, Absheron, semi-deserts of Kilazi, Sitalchay). Collection, packaging, transportation, and marketing of the material were carried out on the basis of relevant biosafety rules and delivered for further study to the Special Dangerous İnfections Control Center. In total, 61,087 nest tracks were examined, and 7,939 fleas were collected and delivered. The material was processed and identified in the laboratory in accordance with the current regulatory and methodological document on the safety of working with pathogenic biological agents (PBA) of pathogenicity groups I–IV. As a result of sample identification, the species composition of fleas was determined and grouped by geographical areas and landscapes. Research was also carried out (using the PCR method) for the presence of the plague causative agent - Yersinia pestis. According to the results of the study, it was found that, regardless of the biocenotic and climatic characteristics of individual sectors of the Transcaucasian foothill natural plague focus of Azerbaijan, there may be enough carriers of infectious diseases and their growth increases over the years. The frequency of occurrence of the prevailing genera of fleas - Xenopsylla and Nosopsyllus- depends on the natural and climatic conditions of the focus being studied. The analysis for the presence of the plague causative agent among all fleas caught and studied did not give positive results. For the timely detection of epizootics among wild rodents and bloodsuckers, it is important to conduct regular epizootic surveys in enzootic areas for plague.

Fleas (Siphonaptera) of Gerbils in the Caucasus

Representatives of the gerbil subfamily (Gerbillinae) are the main components of biocenoses in deserts and semi-deserts. They are the hosts of many flea species and the main vectors of the causative plague agent in a number of natural plague foci. The taxonomic diversity, distribution pattern and host-parasite relationships of flea species noted as parasites of gerbils in the Caucasus are analyzed. Gerbils and their fleas entered the Caucasus from southwest Asia in the Pliocene in parallel to the migration of floral psammophilic complexes. In the Holocene, semi-desert and desert Turanian plants were introduced from the northeast to the Pre-Caucasus, and the fauna of gerbils and their fleas was replenished with several species and subspecies. In accordance with the settlement of carriers and vectors, sandy natural plague foci in Transcaucasia could have existed already in the Pliocene, and in the Pre-Caucasus they were formed no earlier than the Holocene.

Hybrid Assembly of Complete Genomes of <I>Yersinia pestis</I> Strains

The aim of the study was to assemble full-length nucleotide sequences of the chromosome and plasmids for 13 Yersinia pestis strains from 11 natural plague foci located in the Russian Federation, using data from two sequencing technologies.Materials and methods. Y. pestis strains were grown on Hottinger’s agar (pH 7.2) at 37 °C. DNA was isolated using phenol-chloroform extraction. For the MinIon genetic analyzer (Oxford Nanopore), DNA fragments were prepared by ligation according to a modified protocol. For the Ion S5 genetic analyzer (IonTorrent), sample preparation was carried out according to the standard protocol for obtaining a library with a DNA fragment size of 400 nucleotide pairs (bp). The resulting single reads were filtered by average quality Q30 for IonTorrent and Q7 for Oxford Nanopore.Results and discussion. DNA fragments containing 50 000 or more nucleotide pairs were prepared for subsequent sequencing using nanopore sequencing technology (Oxford Nanopore). The Trycycler algorithm was applied for hybrid assembly of the genome of Y. pestis strains and correction of errors arising during this process, allowing the obtainment of full-length nucleotide sequences of the chromosome and plasmids for each genome of the strain. The nucleotide sequences of the chromosomes of 13 Y. pestis strains from 11 natural foci of plague located in the Russian Federation have been deposited in the international genetic database NCBI GenBank. It has been established that to assemble full-length genomes of Y. pestis strains, a significant number of reads with a size of 50 000 bp or more is required, and the use of the Trycycler algorithm allows one to generate a more accurate assembly of complete bacterial genomes.

The Experience in Using the MaxEnt Model to Rank the Territory of the Caspian Sandy Natural Plague Focus (43) according to the Risk of Epizooty Registration

The aim of this work was to rank the territory of the Caspian sandy natural plague focus (43) by the risk of epizooty emergence using the MaxEnt model.Materials and methods. The archival data on epizootic manifestations of plague over the past 35 years, aggregated by the Stavropol Anti-Plague Institute of the Rospotrebnadzor, the Dagestan, Elista, Astrakhan PCSs of the Rospotrebnadzor, were used for model design. 615 archive plague detection points were converted into the coordinate system (1980–2015). 87 publicly available bioclimatic variables BioClim were deployed to construct the MaxEnt model. Applied weather and climatic factors of the BioClim database are averaged over a multiyear period.Results and discussion. The MaxEnt model has a very high degree of reliability (AUC=0.975), with a sufficiently high predictive ability (AUC=0.973). According to the generated model, the Caspian sandy natural plague focus has a heterogeneous structure in terms of the probability of epizooty registration and can be divided into five zones. The most significant factors for the model are the following indicators: the average temperature of the wettest quarter, solar radiation in November, the average temperature of the driest quarter, the amount of precipitation in the coldest quarter, wind speed in May, the amount of precipitation in the wettest quarter, and the average air temperature in September. The data obtained allow for targeted search for plague epizootics and can be used to adjust boundaries of a surveyed natural focus in the future.

Epidemiological Situation on Plague around the World. Forecast of Epizootic Activity of Natural Plague Foci in the Russian Federation for 2024

The aim of the review was to assess the epidemiological situation in natural plague foci in the Russian Federation, near and far abroad countries in 2023 and to forecast their epizootic activity for 2024. In 2023, cases of plague were registered in five countries worldwide: the Democratic Republic of the Congo (60 cases), the Republic of Madagascar (14), the United States of America (2), the People’s Republic of China (3), and Mongolia (5). A total of 84 cases of plague were recorded, of which 22 (26.2 %) were fatal. In the Russian Federation, in 2023, epidemic risks in epizootically active natural foci were significantly reduced due to the implementation of a set of preventive measures carried out by Rospotrebnadzor institutions, which was the guarantor of ensuring epidemiological well-being as regards plague. Plague epizootics were detected on the territory of two (Gorno-Altai high-mountain and Tuva mountain) out of 11 natural plague foci in the Russian Federation in 2023. Epizootics were reported on the territory of the Kosh-Agach district of the Altai Republic and the Mongun-Taiginsky kozhuun of the Tuva Republic. The total area of epizootics was 731.2 km2 (in 2022 – 248.3 km2). In total, 55 cultures of the antique biovar of the main subspecies Yersinia pestis pestis were isolated in 2023 (19 in 2022). The forecast for continuation of the tense epidemiological situation in the territory of the Altai and Tuva Republics in 2024 is substantiated. The trend of sustained growth in the epizootic potential of the East Caucasus high-mountain and Dagestan plain-piedmont plague foci is outlined. The prospects for introducing an automated electronic system for assessing the epidemic potential of natural plague foci into practice are explained.

Assessment of the Current State of the Hissar High-Mountain Natural Plague Focus in the Republic of Tajikistan

The review is devoted to discussing the results of survey in the Hissar high-mountain natural plague focus on the territory of the Republic of Tajikistan in 2015–2023. Regular examination of the focus was carried out in 1970–1991. According to its results, the main carrier of the plague pathogen was the juniper vole, in the population of which a strain of the non-main subspecies central asiatica (0.PE4) of Hissar biovar (0.PE4h) was steadily circulating, the strain considered avirulent for humans. During that period, 853 strains were isolated in the focus, of which 799 (93.7%) were from the juniper vole and its fleas. Secondary carriers – the silver vole, the pygmy wood mouse, and the gray hamster – were rarely involved in epizootics. The red marmot, which has epidemiological significance due to its hunting by the local population, occupies a special position in the focus. Socio-political phenomena at the end of the 20th – early 21st century caused a long break in the work of the Tajik Plague Control Station. In 2008, the Station was transformed into the Republican Center for Combating Quarantine Diseases under the Ministry of Health and Social Protection of the Population of the Republic of Tajikistan. In 2015, studies were resumed, but carried out on a small scale. In 2021–2023, epizootiological monitoring in the Hissar focus was performed jointly with Russian specialists with the testing of field material samples for plague and other natural-focal infections. Currently, against the background of low numbers and population density of small mammals and their blood-sucking ectoparasites – potential carriers and vectors of zoonoses – the circulation of agents of plague, tularemia, pseudotuberculosis, tick-borne viral encephalitis, Ixodidae tick-borne borreliosis, human granulocytic anaplasmosis, human monocytic ehrlichiosis has not been registered. Markers (DNA) of causative agents of leptospirosis and intestinal yersiniosis have been identified. Joint Tajik-Russian cooperation on issues of ensuring the epidemiological well-being of the population of the Republic of Tajikistan must be continued.

Evolution of <I>Yersinia pestis</I> as the Causative Agent of a Vector-Borne Disease Transmitted by Arthropods

The review summarizes the data of modern domestic and foreign studies on the mechanisms of evolutionary adaptation of the plague pathogen to transmissive spread by arthropods. The data on the molecular basis of the rapid formation of a highly pathogenic bacterium due to the acquisition of new genetic information; structural and functional changes in the genome, causing the disruption of functionality of some genes that prevent survival in the vector are presented. The stage of the complex life cycle of the pathogen associated with the peculiarities of its stay in the vector’s organism and its tactics of evasion from the action of antibacterial substances formed by the flea is considered. The importance of biofilm formation for effective transmission of the pathogen is discussed. A complex cascade of transcriptional regulators of biofilm in Yersinia pestis is considered, which includes activators and repressors of biofilm formation, as well as regulators of synthesis or modification/transport of exopolysaccharide. The hms-dependent mechanism of biofilm formation in Y. pestis is described in detail, as well as the impact on biofilm formation through the regulation of LPS-related genes and its role in the modification and transport of biofilm exopolysaccharide. The data from our own studies on the variability of genes involved in biofilm formation in the main subspecies of the plague pathogen in comparison with non-main subspecies of the plague pathogen, as well as on the ability of strains of different subspecies to form biofilm not only in the proventriculus of the flea, but also on the cuticle of soil nematodes of the Tylenchida and Rhabditida orders and the genus Panagrolaimus are presented. The latter allows us to assume the possible participation of soil and entomoparasitic nematodes in the removal of Y. pestis biofilms from the soil to the above-ground biocoenosis of the natural plague focus.

High genetic diversity of the himalayan marmot relative to plague outbreaks in the Qinghai-Tibet Plateau, China

Plague, as an ancient zoonotic disease caused by Yersinia pestis, has brought great disasters. The natural plague focus of Marmota himalayana in the Qinghai-Tibet Plateau is the largest, which has been constantly active and the leading source of human plague in China for decades. Understanding the population genetics of M. himalayana and relating that information to the biogeographic distribution of Yersinia pestis and plague outbreaks are greatly beneficial for the knowledge of plague spillover and arecrucial for pandemic prevention. In the present research, we assessed the population genetics of M. himalayana. We carried out a comparative study of plague outbreaks and the population genetics of M. himalayana on the Qinghai-Tibet Plateau. We found that M. himalayana populations are divided into two main clusters located in the south and north of the Qinghai-Tibet Plateau. Fourteen DFR genomovars of Y. pestis were found and exhibited a significant region-specific distribution. Additionally, the increased genetic diversity of plague hosts is positively associated with human plague outbreaks. This insight gained can improve our understanding of biodiversity for pathogen spillover and provide municipally directed targets for One Health surveillance development, which will be an informative next step toward increased monitoring of M. himalayana dynamics.

Modern Diagnostic Technologies in the Study of the Field Material Collected from the Natural Plague Foci of the Kyrgyz Republic in 2023

The aim of the work was to analyze the results of investigating the field material obtained from natural plague foci of the Kyrgyz Republic (KR) in 2023, using modern diagnostic technologies.Materials and methods. 1435 biological samples from the Tien Shan, Alai and Talas high-mountain foci of the Kyrgyz Republic were studied using conventional methods of laboratory diagnosis of plague: microbiological, immunological, biological; as well as modern molecular-genetic methods. Testing of the obtained samples for the presence of plague pathogen DNA was carried out using RT-PCR; and the presence of antibodies to the plague microbe was detected by enzyme-linked immunosorbent assay (ELISA). Molecular identification of Yersinia pestis strains according to their appurtenance to subspecies, biovars, and phylogenetic lineages was performed by RT-PCR using the method of identifying single-nucleotide substitutions based on the analysis of melting curves of products.Results and discussion. An approach to the molecular identification of Y. pestis strains from plague foci of the KR has been developed and validated through identifying singlenucleotide substitutions using the analysis of product melting curves (HMR-analysis) with a set of designed primers. It has been established that Y. pestis strains isolated in the Sarydzhaz autonomous focus of the Tien Shan high-mountain focus belong to the biovar antiqua of the main subspecies, phylogenetic branch 0.ANT5. The phylogenetic relation of Y. pestis strains isolated in 2023 was studied based on genome-wide SNP analysis. Areas of epizootic activity in Eastern Alai have been identified. The data obtained indicate the sustained activation of plague foci in the KR. Areas of the territory of the KR that are promising for paleogenomic research are also discussed.

Анализ биотопической приуроченности мышевидных грызунов на территориях природных очагов чумы и туляремии Республики Дагестан

Mouse-like rodents in natural plague foci occupy an important place as potential reservoirs of the causative agent of this dangerous disease, acting in some cases as the main or secondary carriers of the pathogen. On the territory of the Republic of Dagestan, characterized by a variety of natural conditions – from flat dry deserts to foothills and highlands, with an abundance of anthropogenic biotopes, this group of small mammals is quite widely represented in terms of species diversity. This work is based on the analysis of the results of long-term epizootological monitoring over the period 2010–2021 carried out in three natural foci of plague: Dagestan plain-foothill, Caspian sandy and East Caucasian high-mountain and tularemia (Plain-foothill steppe, Terek-Kuma floodplain-marsh and Highmountain foothill-mountain-stream). To assess the selectivity of a species in choosing a biotope, the authors used the degree of biotopic confinement Fij (Y.A. Pesenko, 1982). All calculations were carried in Microsoft Office Excel. In these calculations, eurytopic species dominated, which can participate in the epizootic process during periods of activation of foci, contributing to the spread of infectious agents. It was revealed that most species are confined to moist biotopes of river banks and canals, which can be habitats for small mammals during periods of population depression. In this biotope, it is necessary to conduct a more thorough epizootological examination for tularemia and other particularly dangerous infections. The proposed method will make it possible to streamline the control of mouse-like rodents and optimize the work of epizootological examination on the territory of the Republic of Dagestan.

ГАМАЗОВЫЕ КЛЕЩИ (GAMASINA) ГНЕЗД ОБЫКНОВЕННОЙ ПОЛЕВКИ ПРИСЕВАНСКОГО МЕЗООЧАГА ЗАКАВКАЗСКОГО ВЫСОКОГОРНОГО ПРИРОДНОГО ОЧАГА ЧУМЫ

The paper highlights new data on the species composition of gamasid ticks living in the nests of the common vole of the Prisevan meso-foci of the Transcaucasian high-mountain natural plague foci of the Republic of Armenia. As a result of the research conducted in the studied territory, the fauna of gamasid ticks is represented by nine species, including two species that were not previously found in the nests of the common vole. Key words: gamasid ticks, common vole, parasitic arthropods, Prisevan meso-foci, Transcaucasian high-mountain natural plague foci.

Молекулярно-генетический анализ штаммов Yersinia pestis, выделенных в различные эпизоотические периоды на территории Урало-Эмбенского пустынного природного очага чумы в ХХ веке

We performed a molecular genetic analysis of Yersinia pestis strains isolated in the Ural-Embensky desert natural plague focus area in the twentieth century. We studied 24 strains of Y. pestis isolated on this territory since 1945 to1991, as well as 21 strains of Y. pestis from adjacent territories. All of the strains studied from the Ural-Embensky natural focus of plague belonged to the highly virulent and epidemically significant medieval biovar of the main subspecies Y. pestis. According to the results of the WG-SNP analysis and subsequent phylogenetic reconstruction based on 1353 SNPs, the maximum likelihood method (Maximum Likelihood, GTR model) revealed 6 key phylopopulations, which included strains isolated during different periods of epidemic and epizootic activity in the study area. It has been established that there were three waves of spread of the 2.MED1 branch of the medieval biovar to the territory of Ural-Embensky desert natural plague focus. Strains isolated before 1945 belong to the first wave of spread of the 2.MED1 branch to the territory of the Northern Caspian Region. The second wave is considered to be the 1968–1974 strains. They have close genetic similarities with strains from the Mangyshlak (1978) and Ustyurt desert plague foci (1962 and 1975). The third wave includes strains isolated after 1966. They are genetically close to the strains from the North Aral foci (1945). The data obtained will be used for molecular-genetic detailing of the certification of foci in which this highly virulent medieval Y. pestis biovar circulates. They are important for determining the patterns of spatiotemporal distribution of highly virulent strains of the 2.MED1 branch of the medieval biovar in the 20th century and for long-term forecasting of the epizootic activity of plague foci in the North-Eastern Caspian region in the current 21st century.

Mapping Plague Risk Using Super Species Distribution Models and Forecasts for Rodents in the Zhambyl Region, Kazakhstan.

One of the most extensive natural plague centers, or foci, is located in Central Asia, in particular, the Zhambyl region in Southern Kazakhstan. Here, we conducted plague surveillance from 2000 to 2020 in the Zhambyl region in Kazakhstan and confirmed 3,072 cases of infected wild animals. We used Species Distribution Modeling by employing MaxEnt, and identified that the natural plague foci are primarily located in the Moiynqum, Betpaqdala, and Tauqum Deserts. The Zhambyl region's central part, including the Moiynqum and Sarysu districts, has a high potential risk of plague outbreak for the rural towns and villages. Since the phenomenon of climate change has been identified as a determinant that affects the rodent populations, thereby elevating the likelihood of an outbreak of plague, we investigated the potential dissemination routes of the disease under the changing climate conditions, thus creating Species Distribution Forecasts for the rodent species in southern part of Kazakhstan for the year 2100. By 2100, in case of increasing temperatures, the range of host species is likely to expand, leading to a higher risk of plague outbreaks. The highest risk of disease transmission can be expected at the outer limits of the modeled total distribution range, where infection rates are high, but antibody presence is low, making many species susceptible to the pathogen. To mitigate the risk of a potential plague outbreak, it is necessary to implement appropriate sanitary-epidemiological measures and climate mitigation policies.

Genomic diversity of Yersinia pestis from Yunnan Province, China, implies a potential common ancestor as the source of two plague epidemics

Plague, caused by Yersinia pestis, is a zoonotic disease that can reemerge and cause outbreaks following decades of latency in natural plague foci. However, the genetic diversity and spread pattern of Y. pestis during these epidemic-silent cycles remain unclear. In this study, we analyze 356 Y. pestis genomes isolated between 1952 and 2016 in the Yunnan Rattus tanezumi plague focus, China, covering two epidemic-silent cycles. Through high-resolution genomic epidemiological analysis, we find that 96% of Y. pestis genomes belong to phylogroup 1.ORI2 and are subdivided into two sister clades (Sublineage1 and Sublineage2) characterized by different temporal-spatial distributions and genetic diversity. Most of the Sublineage1 strains are isolated from the first epidemic-silent cycle, while Sublineage2 strains are predominantly from the second cycle and revealing a west to east spread. The two sister clades evolved in parallel from a common ancestor and independently lead to two separate epidemics, confirming that the pathogen responsible for the second epidemic following the silent interval is not a descendant of the causative strain of the first epidemic. Our results provide a mechanism for defining epidemic-silent cycles in natural plague foci, which is valuable in the prevention and control of future plague outbreaks.

The complex genomic diversity of Yersinia pestis on the long-term plague foci in Qinghai-Tibet plateau.

Plague is a typical natural focus disease that circulates in different ecology of vectors and reservoir hosts. We conducted genomic population and phylogenetic analyses of the Yersinia pestis collected from the 12 natural plague foci in China with more than 20 kinds of hosts and vectors. Different ecological landscapes with specific hosts, vectors, and habitat which shape various niches for Y. pestis. The phylogeographic diversity of Y. pestis in different kinds plague foci in China showed host niches adaptation. Most natural plague foci strains are region-and focus-specific, with one predominant subpopulation; but the isolates from the Qinghai-Tibet plateau harbor a higher genetic diversity than other foci. The Y. pestis from Marmota himalayana plague foci are defined as the ancestors of different populations at the root of the evolutionary tree, suggesting several different evolutionary paths to other foci. It has the largest pan-genome and widest SNP distances with most accessory genes enriched in mobilome functions (prophages, transposons). Geological barriers play an important role in the maintenance of local Y. pestis species and block the introduction of non-native strains. This study provides new insights into the control of plague outbreaks and epidemics, deepened the understanding of the evolutionary history of MHPF (M. himalayana plague focus) in China. The population structure and identify clades among different natural foci of China renewed the space cognition of the plague.

Natural foci of plague in Kazakhstan in the space-time continuum

The relevance of the problem of the stated topic lies in the fact that the causative agent of the plague infection demonstrates high survival while maintaining high virulence in the territories, which are enzootic in terms of the plague. The study aimed to investigate the geographic distribution and genetic diversity of the plague pathogen in endemic regions through molecular genetic research. The work included the results of laboratory studies of 3058 samples, including soil – 1154, burrow substrates – 549, the contents of the feeding chamber – 349, bone remains – 18, biological objects – 988 samples of sera and suspensions from carriers and vectors of plague infection collected from 14 autonomous plague foci of Kazakhstan for the period 2021–2022. The leading method in the study was a laboratory experiment, thanks to which, using a new advanced technology on a microbiological analyser VITEK 2 COMPACT 30, it was possible to study pathogenic and non-pathogenic strains of the genus Yersinia isolated during field experiment. As a result of experimental work, it was shown that during a long inter-epizootic period, the plague pathogen can persist in the soil in symbiosis with soil microorganisms, and in this area, it chooses soil with a low-quality index of 10 points, where soils with a low total microbial number and species landscape prevail.

Species-level microbiota of ticks and fleas from Marmota himalayana in the Qinghai-Tibet Plateau.

Ticks and fleas, as blood-sucking arthropods, carry and transmit various zoonotic diseases. In the natural plague foci of China, monitoring of Yersinia pestis has been continuously conducted in Marmota himalayana and other host animals, whereas other pathogens carried by vectors are rarely concerned in the Qinghai-Tibet Plateau. In this study, we investigated the microbiota of ticks and fleas sampling from M. himalayana in the Qinghai-Tibet Plateau, China by metataxonomics combined with metagenomic methods. By metataxonomic approach based on full-length 16S rDNA amplicon sequencing and operational phylogenetic unit (OPU) analyses, we described the microbiota community of ticks and fleas at the species level, annotated 1,250 OPUs in ticks, including 556 known species and 492 potentially new species, accounting for 48.50% and 41.71% of the total reads in ticks, respectively. A total of 689 OPUs were detected in fleas, consisting of 277 known species (40.62% of the total reads in fleas) and 294 potentially new species (56.88%). At the dominant species categories, we detected the Anaplasma phagocytophilum (OPU 421) and potentially pathogenic new species of Wolbachia, Ehrlichia, Rickettsia, and Bartonella. Using shotgun sequencing, we obtained 10 metagenomic assembled genomes (MAGs) from vector samples, including a known species (Providencia heimbachae DFT2), and six new species affliated to four known genera, i.e., Wolbachia, Mumia, Bartonella, and Anaplasma. By the phylogenetic analyses based on full-length 16S rRNA genes and core genes, we identified that ticks harbored pathogenic A. phagocytophilum. Moreover, these potentially pathogenic novel species were more closely related to Ehrlichia muris, Ehrlichia muris subsp. eauclairensis, Bartonella rochalimae, and Rickettsia limoniae, respectively. The OPU 422 Ehrlichia sp1 was most related to Ehrlichia muris and Ehrlichia muris subsp. eauclairensis. The OPU 230 Bartonella sp1 and Bartonella spp. (DTF8 and DTF9) was clustered with Bartonella rochalimae. The OPU 427 Rickettsia sp1 was clustered with Rickettsia limoniae. The findings of the study have advanced our understanding of the potential pathogen groups of vectors in marmot (Marmota himalayana) in the Qinghai-Tibet Plateau.