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The origin of Yersinia pestis and the early stages of its evolution are fundamental subjects of investigation given its high virulence and mortality that resulted from past pandemics. Although the earliest evidence of Y. pestis infections in humans has been identified in Late Neolithic/Bronze Age Eurasia (LNBA 5000-3500y BP), these strains lack key genetic components required for flea adaptation, thus making their mode of transmission and disease presentation in humans unclear. Here, we reconstruct ancient Y. pestis genomes from individuals associated with the Late Bronze Age period (~3800 BP) in the Samara region of modern-day Russia. We show clear distinctions between our new strains and the LNBA lineage, and suggest that the full ability for flea-mediated transmission causing bubonic plague evolved more than 1000 years earlier than previously suggested. Finally, we propose that several Y. pestis lineages were established during the Bronze Age, some of which persist to the present day.

The communication substantiates the opinion that the theory of natural nidality of plague; which is based on the fundamental recognition that fleas play a leading role in the transmission and accumulation of the plague pathogen, cannot be disproved or substantially changed on the alternative weakly reasoned assumptions and hypotheses. All its "bottlenecks" are quite understandable when considering the long-term volumetric materials that have been gathered directly in nature and generalized in multiple publications. Plague is an obligate transmissive infection; its, agent is a highly specialized parasite that is completely associated in its vital activity with the only group of the blood-sucking insects--fleas and that is transmitted through periodic colonization of warm-blooded animals for a short time. All other types of plague microbe persistence in nature are either occasional or minor and do not play any significant role in pathogen persistence in the natural foci of this disease. There are no strong grounds for seriously considering the attempts to revise the main points of the theory of natural nidality of plague, which are widely held in current academic publications.

There is evidence that in 1923-2014 the sharp aggravations of the epizootic situation of plague in the area of its Caspian sandy natural focus after long interepizootic periods are in time with the ups of the Caspian Sea in the extrema of 11-year solar cycles. There were cases of multiple manifestations of plague in the same areas in the epizootic cycles of 1946-1954, 1979-1996, 2001, and 2013-2014. The paper considers the possible role of amebae of the genus Acanthamoeba and nematodes, the representatives of the orders Rhabditida and Tylenchida in the microfocal pattern of plague manifestations.

The relative number of plague pathogen strains isolated from some flea species in different Gorno-Altai natural plague foci substantially varies; this indicator also varies with time. These patterns are due to the difference in the structure of multispecies communities of ectoparasites in these areas and their long-term transformation. As of now, the three species Paradoxopsyllus scorodumovi, Ctenophyllus hirticrus, and Amphalius runatus are widely involved in pathogen transmission in all three foci. These ectoparasites should be referred to as main plague vectors. In each focus, they are joined by other flea species, such as Rhadinopsylla dahurica and Amphipsylla primaris in the Ulandryk focus, Frontopsylla hetera, R. dahurica, Paradoxopsyllus kalabukhovi, and Paramonopsyllus scalodae in the Tarkhatin focus, and P. scalonae and P. kalabukhovi in the Kurai focus, which should be classified as an additional vector.

The paper characterizes the seasonal phenomena of the life cycle of fleas in relation to the intensity of epizootias in the natural foci of plague in the Caucasus. A situation determined by the vital activity of several species of fleas, the parasites of a major vehicle, is, in terms of pathogen transmission, established in each of 9 natural plague foci. They are combined by the nesting-borrow type of parasitism, which provides the wide distribution of plague pathogen among rodents. In each focus, there are the most intensive epizootias in the period of high feeding and reproductive activity of transmitters.