Historical and Modern Classifications of the Plague Agent

Abstract

The review presents the data on domestic and foreign phenotypic classifications of Yersinia pestis strains developed in the XX century; genetic classifications of the XXI century; as well as on the genealogy of ancient strains of the plague microbe, reconstructed using paleogenomic technologies. Since the discovery of the plague agent in 1894, many classifications were created that corresponded to the level of development of microbiology at that time. The intraspecific classification schemes of the XX century were based on three principles: phenotypic differences between strains, features of the species composition of carriers, and geographical affiliation. With the development of molecular microbiology early on in the XXI century, a genetic nomenclature of the branches of the pathogen evolution was developed and a number of classifications based on the analysis of the population structure of Y. pestis were created. Through the prism of the genetic diversity of Y. pestis strains from natural plague foci in Russia, near and far abroad countries, an improved classification with a division into seven subspecies has been developed: pestis, tibetica, caucasica, qinghaica, angolica, central asiatica, ulegeica, which allocates the subspecies according to the phylogenetic principle and epidemic significance. With the advancements in paleomicrobiology, prehistoric lineages of evolution have been included in the genealogy of Y. pestis, which expand the data on the intraspecific diversity of the plague microbe.

Molecular phylogenies of the plague microbe <i>Yersinia pestis</i>: an environmental assessment

“…The phylogenetics of the plague microbe is presently dominated by the MG approach. The most popular phylogenetic schemes are more often presented on dendrograms or cladograms [4] , [5] , [13] – [17] . The methodology most popular in recent years is based on the analysis of SNP traits, the theory of neutral evolution as the theoretical background of phylogenetic reconstructions of Y. pestis , and the use of such statistical methods as estimation of maximum likelihood and Bayesian Information Criterion.…”

“…The pika subspecies 0.PE5 ( Y. pestis ulegeica ) is believed to be the ‘youngest’ among the ‘vole’ subspecies. In MG phylogenies, it became the precursor of all highly virulent subspecies/genovariants [15] – [17] ( Figure 1 ). 0.PE5 circulates in populations of the Mongolian pika ( Ochotona pallasi pricei ) in the Mongolian and Gobi Altai.…”

“…A composite subspecies 0.PE4 ( Y. pestis central-asiatica ) [14] , [17] is comprised of genovariants circulating in populations of the Carruther's vole ( Microtus carruthersi ) on the Hisar Range, the Silver vole ( Alticola argentatus ) on the Talas Range, the Mongolian pika ( Ochotona pallasi pricei ) in the Altai Mountains and the Brandt's vole ( Lasiopodomys brandti ) in Northeast China. Integration of geographically separated populations of the plague microbe which circulate in foci with the major hosts belonging to different genera, families and even orders (Rodentia and Lagomorpha) of burrowing animals into a single subspecies solely on the basis of the nucleotide similarity of the selected molecular markers seems to be incorrect from the ecological point of view.…”

“…Therefore, the ‘archaeological’ taxa/subspecies Gok2, LNBA and the others are placed at the roots of phylogenetic trees of Y. pestis [15] , [16] ( Figure 1 ). No modern genotypes of the plague microbe with homologous ‘archaeological’ molecular markers have been found, and ‘archaeological’ taxa/subspecies are considered extinct [17] . However, environmental conditions in postglacial Europe are known to have been inappropriate for the persistence of natural plague foci.…”

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

“…комплексный анализ фенотипических и генетических свойств штаммов Yersinia pestis, выделенных в природных очагах кр в период 1928-1984 гг., показал, что они преимущественно относились к ветвям 0.ANT3 и 0.ANT5 античного биовара основного подвида, встречались также штаммы филогенетической ветви 2.MED1 средневекового биовара основного подвида [3]. в таласском высокогорном очаге установлена циркуляция штаммов филогенетической ветви 0.PE4t, которая в соответствии с усовершенствованной подвидовой классификацией относится к таласскому биовару центральноазиатского (неосновного) подвида [4]. в этом же очаге был изолирован штамм средневекового биовара основного подвида филогенетической ветви 2.MED1.…”