ISSN 0891-4168, Molecular Genetics, Microbiology and Virology, 2013, Vol. 28, No. 2, pp. 41–51. © Allerton Press, Inc., 2013. Original Russian Text © M.E. Platonov, V.V. Evseeva, S.V. Dentovskaya, A.P. Anisimov, 2013, published in Molekulyarnaya Genetika, Mikrobiologiya i Virusologiya, 2013, No. 2, pp. 3–12. 41 INTRODUCTION Plague is an extremely dangerous natural focal dis- ease transmitted through various pathways. The microbe causing plague, Yersinia pestis, was isolated and described for the first time by A. Yersin in 1894, at the beginning of the third plague pandemic, in Hong Kong [105]. That plague is transmitted through flea bites in rat populations was shown by Ogata in 1897 [82] and by Simond in 1898 [92]. Two other human pathogens of the genus Yersinia—Y. pseudotuberculo- sis and Y. enterocolitica—cause diseases of the alimen- tary tract accompanied by prolonged excretion of the pathogen with feces and subsequent alimentary infec- tion of new hosts [42, 44]. One of these pathogens— Y. pseudotuberculosis—is considered the ancestor of Y. pestis. These bacterial species diverged 15–20 thou- sand years ago [35, 36]. Emergence of a new species and subsequent intraspecies variability led to the for- mation of a wide range of intraspecies groups of Y. pes- tis (biovars, subspecies, ecotypes, proteinovars, plasmi- dovars, genotypes, etc.) differing in virulence and in the range of mammals sensitive to them [38, 47, 74, 109]. The plague microbe circulates in populations of more than 200 species of rodents and lagomorphs in natural plague foci and is transmitted by more than 120 spe- cies of fleas [38, 52, 84, 96]. The use of a wide range of hosts and vectors by the pathogen ensures the selection of genetic diversity in the genomes of Y. pestis strains circulating in ecosystems of geographically isolated natural plague foci. The highest intraspecies variety of the plague-causing pathogen was detected in the most ancient Eurasian natural foci of infection character- ized by a large diversity of rodent species that are the main (enzootic) hosts of Y. pestis [1, 2, 4, 27, 28, 33, 38, 47, 52, 80, 108–110]. The relative novelty of the plague-causing microbe, combined with the con- finedness of certain intraspecies populations to spe- cific natural foci, creates the necessary prerequisites for an assessment of the adequacy of molecular typing methods for the study of Y. pestis phylogenesis and epidemiological research. CURRENT STATE OF THE PROBLEM OF PLAGUE-CAUSING MICROBE TAXONOMY A. Yersin, who was the first to discover the plague- causing microbe [105], named it Bacterium pestis. Var- ious synonyms—“Bacterium pestis” [73]; “Bacillus pestis” [73]; Migula, 1900, “Pasteurella pestis” [73]; Bergey et al., 1923, nom. cons., Pestisella pestis, Pas- teurella pestis, Bacterium pestis, Bacillus pestis, “Pes- tisella pestis” [73]; Dorofeev, 1947, Yersinia pseudotu- berculosis subsp. pestis, Yersinia pestis [73]; van Loghem, 1944 (Approved Lists 1980); and Yersinia pseudotuberculosis subsp. pestis [73] Bercovier et al. 1981 (http://mousecyc.jax.org/META/NEW-IMAGE? type=ORGANISM&object=TAX-623&detail-level =2)—were subsequently used for this microorganism. The taxonomic name Yersinia pestis [73] van Loghem 1944 is universally accepted today (http://zipcodezoo. com/Key/Bacteria/Yersinia_Genus.asp); the genus name Yersinia was suggested by van Loghem [103] to commemorate the name of the researcher who was first to discover the plague microbe [73, 93, 94, 103]. The genus Yersinia of the family Enterobacteriaceae currently includes 17 species [62, 81]. The typical spe- cies of the genus Yersinia is Y. pestis [5]. The typical strain of the genus is Y. pestis ATCC 19428 = CIP 80.26 = NCTC 5923 [65]. Devignat [49] and Tumanskii [32] divided Y. pestis into three intraspecies groups according to the ability of the bacteria to ferment glycerol, nitrify, and deni- trify. Devignat termed them antiqua, medievalis, and orientalis biovars, since they presumably caused “Jus- tinian plague,” “Black Death,” and the third plague pandemia, respectively. Tumanskii used an ecological approach instead of a historico-geographical one and named the same Y. pestis varieties marmot (var. mar- Molecular Typing of Yersinia pestis M. E. Platonov, V. V. Evseeva, S. V. Dentovskaya, and A. P. Anisimov State Research Center of Applied Microbiology and Biotechnology, Obolensk, Russia e-mail: anisimov@obolensk.org Abstract—The present review is focused on methods of Yersinia pestis genotyping that are reproducible in dif- ferent laboratories and allow for differentiation of individual bacterial isolates into intraspecies groups corre- sponding to subspecies, biovars, and natural foci. A variant of the intraspecies classification of Y. pestis com- pliant with the rules of the International Code of Nomenclature of Bacteria is presented. Keywords: molecular typing of Yersinia pestis DOI: 10.3103/S0891416813020067 REVIEW