New Genotype of Yersinia pestis Found in Live Rodents in Yunnan Province, China

Hotspots of genetic change in Yersinia pestis

The relative contributions of mutation rate variation, selection, and recombination in shaping genomic variation in bacterial populations remain poorly understood. Here we analyze 3318 Yersinia pestis genomes, spanning nearly a century and including 2336 newly sequenced strains, to shed light on the patterns of genetic diversity and variation distribution at the population level. We identify 45 genomic regions ("hot regions", HRs) that, although comprising a minor fraction of the genome, are hotbeds of genetic variation. These HRs are distributed non-randomly across Y. pestis phylogenetic lineages and are primarily linked to regulatory genes, underscoring their potential functional significance. We explore various factors contributing to the shaping and maintenance of HRs, including genomic context, homologous recombination, mutation rate variation and natural selection. Our findings suggest that positive selection is likely the primary driver behind the emergence of HRs, but not the sole force, as evidenced by the pronounced trend of variation purging within these regions.

Prevalence and genetic diversity of Anaplasma phagocytophilum in wild small mammals from western Yunnan province, China

Anaplasma phagocytophilum (A. phagocytophilum) is an emerging zoonotic pathogen causing human granulocytic anaplasmosis, linked to small mammal reservoirs that harbor various zoonotic pathogens, underscoring their importance in public health and ecology. This study seeks to determine the prevalence of A. phagocytophilum in small mammals using PCR, then sequence and genotype positive samples, and assess infection risk factors. Small mammals were seasonally captured and a nested polymerase chain reaction (nested-PCR) was conducted targeting the 16S rRNA gene on spleen samples to detect A. phagocytophilum infection from three counties in western Yunnan province, China. Positive samples were sequenced and genotyped, revealing genetic diversity and regional clustering of the pathogen. A total of 1,605 small mammals belonging to 30 species, 18 genera, 6 families, 3 orders were captured seasonally and screened in this region, yielding a 0.93% infection rate with A. phagocytophilum (15/1605). Significant variations in infection rates were observed across different species, counties, and habitats. The 16Sr RNA genes of A. phagocytophilum were categorized into two distinct clades, indicating notable genetic diversity. The identification of genetic variants in spleen samples underscores the potential public health risk and the critical importance of the One Health approach in disease surveillance. Our findings emphasize the necessity for continuous monitoring and highlight the value of nested-PCR testing on spleen samples for accurate prevalence assessment.

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.

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.

Genomic epidemiological analysis of county-scale Yersinia pestis spread pattern over 50 years in a Southwest Chinese prefecture

Plague, one of the most devastating infectious diseases in human history, is caused by the bacterium Yersinia pestis. Since the 1950s, the Dehong Dai-Jingpo Autonomous Prefecture (DH) in Yunnan Province, China, has recorded plague outbreaks that have resulted in 1,153 human cases and 379 deaths. The genetic diversity and transmission characteristics of Y. pestis strains in this region remain unknown. Here, we performed high-resolution genomic epidemiological analysis of 175 Y. pestis strains isolated from five counties and 19 towns in DH between 1953 and 2007. Phylogenetic analysis revealed that most DH strains were located in lineage 1.ORI2, which could be further subdivided into seven sub-phylogroups (SPG1-SPG7). The dominant sub-phylogroups of Y. pestis in DH varied during different periods and presented a population shift. Genomic evidence showed that plague might have emerged from the southwest of DH (e.g., Longchuan or Ruili counties) or its bordering countries, and subsequently spread to the northeast in multiple waves between 1982 and 2007. Our study infers a fine-scale phylogeny and spread pattern of the DH Y. pestis population, which extends our knowledge regarding its genetic diversity and provides clues for the future prevention and control of plague in this region.