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...
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| creator | Qin, Jingliang Shi, Liyuan Wu, Yarong Kong, Jinjiao Qian, Xiuwei Zhang, Xianglilan Zuo, Xiujuan Fan, Hang Guo, Yan Cui, Mengnan Dong, Shanshan Tan, Hongli Zhong, Youhong Song, Yajun Yang, Ruifu Wang, Peng Cui, Yujun |
| description | 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. |
| doi_str_mv | 10.1371/journal.pntd.0011527 |
| format | Article |
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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.</description><identifier>ISSN: 1935-2735</identifier><identifier>ISSN: 1935-2727</identifier><identifier>EISSN: 1935-2735</identifier><identifier>DOI: 10.1371/journal.pntd.0011527</identifier><identifier>PMID: 37549110</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Analysis ; Biological diversity ; Biology and Life Sciences ; Casualties ; Causes of ; China ; China - epidemiology ; Cladistics ; Computer and Information Sciences ; Disease control ; Disease prevention ; Epidemics ; Epidemiology ; Fatalities ; Genetic aspects ; Genetic diversity ; Genetic variation ; Genomes ; Genomic analysis ; Genomics ; Humans ; Identification and classification ; Infectious diseases ; Medicine and Health Sciences ; Microbiological research ; Patient outcomes ; Phylogenetics ; Phylogeny ; Plague ; Plague - epidemiology ; Plague - microbiology ; Rodents ; Software ; Statistics ; Strains ; Transmission ; Tropical diseases ; Yersinia infections ; Yersinia pestis</subject><ispartof>PLoS neglected tropical diseases, 2023-08, Vol.17 (8), p.e0011527-e0011527</ispartof><rights>Copyright: © 2023 Qin et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.</rights><rights>COPYRIGHT 2023 Public Library of Science</rights><rights>2023 Qin et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2023 Qin et al 2023 Qin et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c508t-5b64508901db2d1f755c19d88ca5e1ecadec6104107ecbb1feefe7b0a046dc9a3</cites><orcidid>0000-0002-3350-1835 ; 0000-0001-7236-2412</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC10406180/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC10406180/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,2915,23845,27901,27902,53766,53768,79342,79343</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/37549110$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Qin, Jingliang</creatorcontrib><creatorcontrib>Shi, Liyuan</creatorcontrib><creatorcontrib>Wu, Yarong</creatorcontrib><creatorcontrib>Kong, Jinjiao</creatorcontrib><creatorcontrib>Qian, Xiuwei</creatorcontrib><creatorcontrib>Zhang, Xianglilan</creatorcontrib><creatorcontrib>Zuo, Xiujuan</creatorcontrib><creatorcontrib>Fan, Hang</creatorcontrib><creatorcontrib>Guo, Yan</creatorcontrib><creatorcontrib>Cui, Mengnan</creatorcontrib><creatorcontrib>Dong, Shanshan</creatorcontrib><creatorcontrib>Tan, Hongli</creatorcontrib><creatorcontrib>Zhong, Youhong</creatorcontrib><creatorcontrib>Song, Yajun</creatorcontrib><creatorcontrib>Yang, Ruifu</creatorcontrib><creatorcontrib>Wang, Peng</creatorcontrib><creatorcontrib>Cui, Yujun</creatorcontrib><title>Genomic epidemiological analysis of county-scale Yersinia pestis spread pattern over 50 years in a Southwest Chinese prefecture</title><title>PLoS neglected tropical diseases</title><addtitle>PLoS Negl Trop Dis</addtitle><description>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.</description><subject>Analysis</subject><subject>Biological diversity</subject><subject>Biology and Life Sciences</subject><subject>Casualties</subject><subject>Causes of</subject><subject>China</subject><subject>China - epidemiology</subject><subject>Cladistics</subject><subject>Computer and Information Sciences</subject><subject>Disease control</subject><subject>Disease prevention</subject><subject>Epidemics</subject><subject>Epidemiology</subject><subject>Fatalities</subject><subject>Genetic aspects</subject><subject>Genetic diversity</subject><subject>Genetic variation</subject><subject>Genomes</subject><subject>Genomic analysis</subject><subject>Genomics</subject><subject>Humans</subject><subject>Identification and classification</subject><subject>Infectious diseases</subject><subject>Medicine and Health Sciences</subject><subject>Microbiological research</subject><subject>Patient outcomes</subject><subject>Phylogenetics</subject><subject>Phylogeny</subject><subject>Plague</subject><subject>Plague - 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>PLoS neglected tropical diseases</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Qin, Jingliang</au><au>Shi, Liyuan</au><au>Wu, Yarong</au><au>Kong, Jinjiao</au><au>Qian, Xiuwei</au><au>Zhang, Xianglilan</au><au>Zuo, Xiujuan</au><au>Fan, Hang</au><au>Guo, Yan</au><au>Cui, Mengnan</au><au>Dong, Shanshan</au><au>Tan, Hongli</au><au>Zhong, Youhong</au><au>Song, Yajun</au><au>Yang, Ruifu</au><au>Wang, Peng</au><au>Cui, Yujun</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Genomic epidemiological analysis of county-scale Yersinia pestis spread pattern over 50 years in a Southwest Chinese prefecture</atitle><jtitle>PLoS neglected tropical diseases</jtitle><addtitle>PLoS Negl Trop Dis</addtitle><date>2023-08-01</date><risdate>2023</risdate><volume>17</volume><issue>8</issue><spage>e0011527</spage><epage>e0011527</epage><pages>e0011527-e0011527</pages><issn>1935-2735</issn><issn>1935-2727</issn><eissn>1935-2735</eissn><abstract>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.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>37549110</pmid><doi>10.1371/journal.pntd.0011527</doi><orcidid>https://orcid.org/0000-0002-3350-1835</orcidid><orcidid>https://orcid.org/0000-0001-7236-2412</orcidid><oa>free_for_read</oa></addata></record> |
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| identifier | ISSN: 1935-2735 |
| ispartof | PLoS neglected tropical diseases, 2023-08, Vol.17 (8), p.e0011527-e0011527 |
| issn | 1935-2735 1935-2727 1935-2735 |
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| source | MEDLINE; DOAJ Directory of Open Access Journals; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; PubMed Central; PubMed Central Open Access; Public Library of Science (PLoS) |
| subjects | Analysis Biological diversity Biology and Life Sciences Casualties Causes of China China - epidemiology Cladistics Computer and Information Sciences Disease control Disease prevention Epidemics Epidemiology Fatalities Genetic aspects Genetic diversity Genetic variation Genomes Genomic analysis Genomics Humans Identification and classification Infectious diseases Medicine and Health Sciences Microbiological research Patient outcomes Phylogenetics Phylogeny Plague Plague - epidemiology Plague - microbiology Rodents Software Statistics Strains Transmission Tropical diseases Yersinia infections Yersinia pestis |
| title | Genomic epidemiological analysis of county-scale Yersinia pestis spread pattern over 50 years in a Southwest Chinese prefecture |
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