Progresses of ancient plague pandemics investigations with paleomicrobiological insights
SONG Kai1, QI Zhi-zhen2,3, YANG Rui-fu1,3, SONG Ya-jun1,3
1.State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China; 2.Qinghai Institute for Endemic Disease Prevention and Control, Xining 811062, China; 3.Key Laboratory for Plague Prevention and Control of Qinghai Province, Xining 811062, China
Abstract：Plague is a notorious infectious disease caused by Yersinia pestis that has caused three devastating pandemics in the human history. In recent years, the development of paleomicrobiology has allowed researchers to explore the historical plague pandemics in further details, providing a much deeper understanding of certain controversial issues, such as the origin and dissemination of plague, and the molecular evolution of Y. pestis. This paper briefly reviews the progresses in ancient plague pandemics investigations with the help of paleomicrobiological techniques: PCR, proteomic and genomic analysis on the ruins of victims confirmed that Y. pestis was indeed the causative agent of historic plague pandemics, including the Justinian Plague and the Black Death; human plague cases occurred no later than Late Neolithic to the Bronze Age; and the speciation time of Y. pestis was pin-pointed to 5, 000 to 7, 500 years ago. Paleomicrobiological methods will not only speed researches on specific topics of plague and Y. pestis, but also shed light on the studies of other historical infectious disease pandemics.
宋凯, 祁芝珍, 杨瑞馥, 宋亚军. 鼠疫历史疫情的考古微生物学研究进展[J]. 中国人兽共患病学报, 2018, 34(12): 1142-1146.
SONG Kai, QI Zhi-zhen, YANG Rui-fu, SONG Ya-jun. Progresses of ancient plague pandemics investigations with paleomicrobiological insights. Chinese Journal of Zoonoses, 2018, 34(12): 1142-1146.
[1] Morelli G, Song Y, Mazzoni C J, et al. Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity[J]. Nat Genet, 2010, 42(12): 1140-1143. DOI:10.1038/ng.705 [2] Wagner D M, Klunk J, Harbeck M, et al. Yersinia pestis and the plague of Justinian 541-543 AD: a genomic analysis[J]. Lancet Infect Dis, 2014, 14(4): 319-326. DOI:10.1016/S1473-3099(13)70323-2 [3] Drancourt M, Raoult D. Molecular history of plague[J]. Clin Microbiol Infect, 2016, 22(11): 911-915. DOI:10.1016/j.cmi.2016.08.031 [4] 伍连德. 鼠疫概论[M]. 上海: 卫生署海港检疫处, 1937:20-38. [5] Pollitzer R. Plague, Geneva[M]. World Health Organization: Monograph Series, 1954: 22. [6] Cui Y, Yu C, Yan Y, et al. Historical variations in mutation rate in an epidemic pathogen, Yersinia pestis[J]. Proc Natl Acad Sci U S A, 2013, 110(2): 577-582. DOI:10.1073/pnas.1205750110 [7] Spyrou M A, Tukhbatova R I, Feldman M, et al. Historical Y. pestis genomes reveal the european black death as the source of ancient and modern plague pandemics[J]. Cell Host Microbe, 2016, 19(6): 874-881. DOI:10.1016/j.chom.2016.05.012 [8] Aboudharam G. Sources of Materials for Paleomicrobiology[J]. Microbiol Spectr, 2016, 4(4). DOI:10.1128/microbiolspec.PoH-0016-2015 [9] Seth-Smith H. Beyond the palaeomicrobiology[J]. Nat Rev Microbiol, 2012, 10(4): 240. DOI:10.1038/nrmicro2768 [10] Drancourt M, Aboudharam G, Signoli M, et al. Detection of 400-year-old Yersinia pestis DNA in human dental pulp: an approach to the diagnosis of ancient septicemia[J]. Proc Natl Acad Sci U S A, 1998, 95(21): 12637-12640. DOI:10.1073/pnas.95.21.12637 [11] Raoult D, Aboudharam G, Crubezy E, et al. Molecular identification by "suicide PCR" of Yersinia pestis as the agent of medieval black death[J]. Proc Natl Acad Sci U S A, 2000, 97(23): 12800-12803. DOI:10.1073/pnas.220225197 [12] Wiechmann I, Grupe G. Detection of Yersinia pestis DNA in two early medieval skeletal finds from Aschheim (Upper Bavaria, 6th century A.D.)[J]. Am J Phys Anthropol, 2005, 126(1): 48-55. DOI:10.1002/ajpa.10276 [13] Vergnaud G. Yersinia pestis genotyping[J]. Emerg Infect Dis, 2005, 11(8): 1317-1318. DOI:10.3201/eid1108.040942 [14] Drancourt M, Roux V, Dang LV, et al. Genotyping, Orientalis-like Yersinia pestis, and plague pandemics[J]. Emerg Infect Dis, 2004, 10(9): 1585-1592. DOI:10.3201/eid1009.030933 [15] Harbeck M, Seifert L, Hansch S, et al. Yersinia pestis DNA from skeletal remains from the 6(th) century AD reveals insights into Justinianic Plague[J]. PLoS Pathog, 2013, 9(5): e1003349. DOI:10.1371/journal.ppat.1003349 [16] Haensch S, Bianucci R, Signoli M, et al. Distinct clones of Yersinia pestis caused the black death[J]. PLoS Pathog, 2010, 6(10): e1001134. DOI:10.1371/journal.ppat.1001134 [17] Tran-Hung L, Tran-Thi N, Aboudharam G, et al. A new method to extract dental pulp DNA: application to universal detection of bacteria[J]. PLoS One, 2007, 2(10): e1062. DOI:10.1371/journal.pone.0001062 [18] Wadsworth C, Buckley M. Proteome degradation in fossils: investigating the longevity of protein survival in ancient bone[J]. Rapid Commun Mass Spectrom, 2014, 28(6): 605-615. DOI:10.1002/rcm.6821 [19] Zavialov AV, Berglund J, Pudney AF, et al. Structure and biogenesis of the capsular F1 antigen from Yersinia pestis: preserved folding energy drives fiber formation[J]. Cell, 2003, 113(5): 587-596. DOI:10.1016/s0092-8674(03)00351-9 [20] Pusch C M, Rahalison L, Blin N, et al. Yersinial F1 antigen and the cause of Black Death[J]. Lancet Infect Dis, 2004, 4(8): 484-5. DOI:10.1016/S1473-3099(04)01099-0 [21] Bianucci R, Rahalison L, Ferroglio E, et al. A rapid diagnostic test for plague detects Yersinia pestis F1 antigen in ancient human remains[J]. C R Biol, 2007, 330(10): 747-754. DOI:10.1016/j.crvi.2007.07.007 [22] Malou N, Tran TN, Nappez C, et al. Immuno-PCR--a new tool for paleomicrobiology: the plague paradigm[J]. PLoS One, 2012, 7(2): e31744. DOI:10.1371/journal.pone.0031744 [23] Barbieri R, Mekni R, Levasseur A, et al. Paleoproteomics of the Dental Pulp: The plague paradigm[J]. PLoS One, 2017, 12(7): e0180552. DOI:10.1371/journal.pone.0180552 [24] D'Amato A, Zilberstein G, Zilberstein S, et al. Of mice and men: Traces of life in the death registries of the 1630 plague in Milano[J]. J Proteomics, 2018, 180: 128-37. DOI:10.1016/j.jprot.2017.11.028 [25] McNally A, Thomson NR, Reuter S, et al. 'Add, stir and reduce': Yersinia spp. as model bacteria for pathogen evolution[J]. Nat Rev Microbiol, 2016, 14(3): 177-190. DOI:10.1038/nrmicro.2015.29 [26] Bos KI, Schuenemann VJ, Golding GB, et al. A draft genome of Yersinia pestis from victims of the Black Death[J]. Nature, 2011, 478(7370): 506-510. DOI:10.1038/nature10549 [27] Bos K I, Herbig A, Sahl J, et al. Eighteenth century Yersinia pestis genomes reveal the long-term persistence of an historical plague focus[J]. Elife, 2016, 5: e12994. DOI:10.7554/eLife.12994 [28] Schmid B V, Buntgen U, Easterday W R, et al. Climate-driven introduction of the Black Death and successive plague reintroductions into Europe[J]. Proc Natl Acad Sci U S A, 2015, 112(10): 3020-3025. DOI:10.1073/pnas.1412887112 [29] Rasmussen S, Allentoft M E, Nielsen K, et al. Early divergent strains of Yersinia pestis in Eurasia 5,000 years ago[J]. Cell, 2015, 163(3): 571-582. DOI:10.1016/j.cell.2015.10.009 [30] Andrades Valtuena A, Mittnik A, Key F M, et al. The Stone Age Plague and Its Persistence in Eurasia[J]. Curr Biol, 2017, 27(23): 3683-3691 e8. DOI:10.1016/j.cub.2017.10.025 [31] Spyrou M A, Tukhbatova R I, Wang C C, et al. Analysis of 3800-year-old Yersinia pestis genomes suggests Bronze Age origin for bubonic plague[J]. Nat Commun, 2018, 9(1): 2234. DOI:10.1038/s41467-018-04550-9 [32] Burki T. Plague in Madagascar[J]. Lancet Infect Dis, 2017, 17(12): 1241. DOI:10.1016/S1473-3099(17)30647-3 [33] Tran T N, Raoult D, Drancourt M. Yersinia pestis DNA sequences in late medieval skeletal finds, Bavaria[J]. Emerg Infect Dis, 2011, 17(5): 955-957; author reply 7. DOI:10.3201/eid1705.101777 [34] Tran T N, Forestier C L, Drancourt M, et al. Brief communication: co-detection of Bartonella quintana and Yersinia pestis in an 11th-15th burial site in Bondy, France[J]. Am J Phys Anthropol, 2011, 145(3): 489-494. DOI:10.1002/ajpa.21510
2018, Vol. 34 
