Two-Step Source Tracing Strategy of Yersinia pestis and Its Historical Epidemiology in a Specific Region
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{"title"=>"Two-step source tracing strategy of yersinia pestis and its historical epidemiology in a specific region", "type"=>"journal", "authors"=>[{"first_name"=>"Yanfeng", "last_name"=>"Yan", "scopus_author_id"=>"24729717900"}, {"first_name"=>"Hu", "last_name"=>"Wang", "scopus_author_id"=>"56094903200"}, {"first_name"=>"Dongfang", "last_name"=>"Li", "scopus_author_id"=>"50361509100"}, {"first_name"=>"Xianwei", "last_name"=>"Yang", "scopus_author_id"=>"55278100500"}, {"first_name"=>"Zuyun", "last_name"=>"Wang", "scopus_author_id"=>"8542368500"}, {"first_name"=>"Zhizhen", "last_name"=>"Qi", "scopus_author_id"=>"9278826700"}, {"first_name"=>"Qingwen", "last_name"=>"Zhang", "scopus_author_id"=>"55699330600"}, {"first_name"=>"Baizhong", "last_name"=>"Cui", "scopus_author_id"=>"9278773100"}, {"first_name"=>"Zhaobiao", "last_name"=>"Guo", "scopus_author_id"=>"7404657441"}, {"first_name"=>"Chang", "last_name"=>"Yu", "scopus_author_id"=>"55265116200"}, {"first_name"=>"Jun", "last_name"=>"Wang", "scopus_author_id"=>"56034096100"}, {"first_name"=>"Jian", "last_name"=>"Wang", "scopus_author_id"=>"56048867500"}, {"first_name"=>"Guangming", "last_name"=>"Liu", "scopus_author_id"=>"55706577200"}, {"first_name"=>"Yajun", "last_name"=>"Song", "scopus_author_id"=>"8542368300"}, {"first_name"=>"Yingrui", "last_name"=>"Li", "scopus_author_id"=>"23766780600"}, {"first_name"=>"Yujun", "last_name"=>"Cui", "scopus_author_id"=>"24480809600"}, {"first_name"=>"Ruifu", "last_name"=>"Yang", "scopus_author_id"=>"55547041600"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "pui"=>"372730879", "doi"=>"10.1371/journal.pone.0085374", "sgr"=>"84897411734", "scopus"=>"2-s2.0-84897411734", "isbn"=>"1000422100", "pmid"=>"24416399"}, "id"=>"5a1796b7-fdc5-3ef3-ad81-4e7eff3c324d", "abstract"=>"Source tracing of pathogens is critical for the control and prevention of infectious diseases. Genome sequencing by high throughput technologies is currently feasible and popular, leading to the burst of deciphered bacterial genome sequences. Utilizing the flooding genomic data for source tracing of pathogens in outbreaks is promising, and challenging as well. Here, we employed Yersinia pestis genomes from a plague outbreak at Xinghai county of China in 2009 as an example, to develop a simple two-step strategy for rapid source tracing of the outbreak. The first step was to define the phylogenetic position of the outbreak strains in a whole species tree, and the next step was to provide a detailed relationship across the outbreak strains and their suspected relatives. Through this strategy, we observed that the Xinghai plague outbreak was caused by Y. pestis that circulated in the local plague focus, where the majority of historical plague epidemics in the Qinghai-Tibet Plateau may originate from. The analytical strategy developed here will be of great help in fighting against the outbreaks of emerging infectious diseases, by pinpointing the source of pathogens rapidly with genomic epidemiological data and microbial forensics information.", "link"=>"http://www.mendeley.com/research/twostep-source-tracing-strategy-yersinia-pestis-historical-epidemiology-specific-region", "reader_count"=>25, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>2, "Researcher"=>6, "Student > Ph. D. Student"=>6, "Student > Postgraduate"=>1, "Student > Master"=>2, "Other"=>2, "Student > Bachelor"=>3, "Lecturer"=>2, "Professor"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>2, "Researcher"=>6, "Student > Ph. D. Student"=>6, "Student > Postgraduate"=>1, "Student > Master"=>2, "Other"=>2, "Student > Bachelor"=>3, "Lecturer"=>2, "Professor"=>1}, "reader_count_by_subject_area"=>{"Biochemistry, Genetics and Molecular Biology"=>3, "Agricultural and Biological Sciences"=>17, "Medicine and Dentistry"=>2, "Design"=>1, "Pharmacology, Toxicology and Pharmaceutical Science"=>1, "Computer Science"=>1}, "reader_count_by_subdiscipline"=>{"Design"=>{"Design"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>17}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>3}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>1}}, "reader_count_by_country"=>{"Sweden"=>1, "United States"=>1}, "group_count"=>1}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1344644"], "description"=>"<p>(A) MSTree of strains in the phylogroup 1.IN2 (a to q), 2009 outbreak strains (r), and historical strains in Xinghai County (s, t, u, and 0.PE7b). The circle size represents the number of strains it contains. The designation of hypothetical nodes was obtained from previous research <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0085374#pone.0085374-Cui2\" target=\"_blank\">[32]</a>, and the SNP numbers (>2) between the nodes are labeled in gray on each branch. Strains that were close to the MRCA of phylogroup 1.IN2 (node N12) are marked in blue, strains isolated from Xinghai are in green, and the other strains are in yellow. (B) Geographic distribution of strains used in MSTree.</p>", "links"=>[], "tags"=>["genomics", "Comparative genomics", "Genome evolution", "Genome sequencing", "microbiology", "Emerging infectious diseases", "Medical microbiology", "Microbial evolution", "Population biology", "population genetics", "Genetic polymorphism", "epidemiology", "Molecular epidemiology", "Infectious diseases", "Bacterial diseases", "Plagues", "Yersinia pestis", "Infectious disease control", "investigating", "phylogenetic", "phylogroup", "isolates", "outbreak"], "article_id"=>898973, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Yanfeng Yan", "Hu Wang", "Dongfang Li", "Xianwei Yang", "Zuyun Wang", "Zhizhen Qi", "Qingwen Zhang", "Baizhong Cui", "Zhaobiao Guo", "Chang Yu", "Jun Wang", "Jian Wang", "Guangming Liu", "Yajun Song", "Yingrui Li", "Yujun Cui", "Ruifu Yang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0085374.g003", "stats"=>{"downloads"=>1, "page_views"=>17, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Second_step_of_source_tracing_Investigating_the_phylogenetic_relationship_within_the_particular_phylogroup_and_historical_isolates_in_the_outbreak_region_/898973", "title"=>"Second step of source tracing: Investigating the phylogenetic relationship within the particular phylogroup and historical isolates in the outbreak region.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-09 03:58:05"}
  • {"files"=>["https://ndownloader.figshare.com/files/1344645"], "description"=>"<p>: MSTree ID refers to the strain ID in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0085374#pone-0085374-g003\" target=\"_blank\">Figure 3A</a>.</p><p>#: AT stands for antibiotic treatment.</p><p>: The two dogs that died in the outbreak were buried on July 22 and 23, 2009, respectively <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0085374#pone.0085374-Wang1\" target=\"_blank\">[31]</a>. For the epidemic investigation, the bodies were exhumed, and strains 090958 and 090959 were successfully isolated from the necropsy samples on August 5, 2009.</p>", "links"=>[], "tags"=>["genomics", "Comparative genomics", "Genome evolution", "Genome sequencing", "microbiology", "Emerging infectious diseases", "Medical microbiology", "Microbial evolution", "Population biology", "population genetics", "Genetic polymorphism", "epidemiology", "Molecular epidemiology", "Infectious diseases", "Bacterial diseases", "Plagues", "Yersinia pestis", "Infectious disease control", "strains", "sequenced"], "article_id"=>898974, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Yanfeng Yan", "Hu Wang", "Dongfang Li", "Xianwei Yang", "Zuyun Wang", "Zhizhen Qi", "Qingwen Zhang", "Baizhong Cui", "Zhaobiao Guo", "Chang Yu", "Jun Wang", "Jian Wang", "Guangming Liu", "Yajun Song", "Yingrui Li", "Yujun Cui", "Ruifu Yang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0085374.t001", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Bacterial_strains_sequenced_in_this_study_/898974", "title"=>"Bacterial strains sequenced in this study.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-01-09 03:58:05"}
  • {"files"=>["https://ndownloader.figshare.com/files/1344642"], "description"=>"<p>The points represent the CPU running time (panel A) and RAM consumption (panel B) for reconstructing the MLTree based on different numbers of genomes and variations. The red curves represent the changes of both running time and RAM consumption, which follow the power function according to the formulas in the figure.</p>", "links"=>[], "tags"=>["genomics", "Comparative genomics", "Genome evolution", "Genome sequencing", "microbiology", "Emerging infectious diseases", "Medical microbiology", "Microbial evolution", "Population biology", "population genetics", "Genetic polymorphism", "epidemiology", "Molecular epidemiology", "Infectious diseases", "Bacterial diseases", "Plagues", "Yersinia pestis", "Infectious disease control", "ram", "phylogenetic", "reconstruction", "simulated", "mega"], "article_id"=>898971, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Yanfeng Yan", "Hu Wang", "Dongfang Li", "Xianwei Yang", "Zuyun Wang", "Zhizhen Qi", "Qingwen Zhang", "Baizhong Cui", "Zhaobiao Guo", "Chang Yu", "Jun Wang", "Jian Wang", "Guangming Liu", "Yajun Song", "Yingrui Li", "Yujun Cui", "Ruifu Yang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0085374.g001", "stats"=>{"downloads"=>1, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_CPU_running_time_and_RAM_consumption_of_phylogenetic_reconstruction_based_on_simulated_mega_dataset_/898971", "title"=>"CPU running time and RAM consumption of phylogenetic reconstruction based on simulated mega dataset.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-09 03:58:05"}
  • {"files"=>["https://ndownloader.figshare.com/files/1344643"], "description"=>"<p>(A) MLTree of 2009 outbreak strains and 24 representative <i>Y. pestis</i> strains with global diversity. The branch length reveals genetic distance between isolates, except for the branch of 0.PE3, which was truncated for visual effect. The root was defined by the ancestor <i>Y. pseudotuberculosis</i>, IP32953. Each strain is labeled with different symbols and colors that correspond to its geographical distribution on the map in panel B. Strains that are not mapped in panel B are labeled with an asterisk. As no variations exist across outbreak strains, the corresponding branches were collapsed in the tree. All nodes have a bootstrap support of more than 90%. (B) Geographic information of the strains in the MLTree.</p>", "links"=>[], "tags"=>["genomics", "Comparative genomics", "Genome evolution", "Genome sequencing", "microbiology", "Emerging infectious diseases", "Medical microbiology", "Microbial evolution", "Population biology", "population genetics", "Genetic polymorphism", "epidemiology", "Molecular epidemiology", "Infectious diseases", "Bacterial diseases", "Plagues", "Yersinia pestis", "Infectious disease control", "phylogenetic", "outbreak"], "article_id"=>898972, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Yanfeng Yan", "Hu Wang", "Dongfang Li", "Xianwei Yang", "Zuyun Wang", "Zhizhen Qi", "Qingwen Zhang", "Baizhong Cui", "Zhaobiao Guo", "Chang Yu", "Jun Wang", "Jian Wang", "Guangming Liu", "Yajun Song", "Yingrui Li", "Yujun Cui", "Ruifu Yang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0085374.g002", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_First_step_of_source_tracing_defining_the_phylogenetic_position_of_outbreak_strains_/898972", "title"=>"First step of source tracing: defining the phylogenetic position of outbreak strains.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-09 03:58:05"}
  • {"files"=>["https://ndownloader.figshare.com/files/1344646", "https://ndownloader.figshare.com/files/1344647", "https://ndownloader.figshare.com/files/1344648", "https://ndownloader.figshare.com/files/1344649", "https://ndownloader.figshare.com/files/1344650"], "description"=>"<div><p>Source tracing of pathogens is critical for the control and prevention of infectious diseases. Genome sequencing by high throughput technologies is currently feasible and popular, leading to the burst of deciphered bacterial genome sequences. Utilizing the flooding genomic data for source tracing of pathogens in outbreaks is promising, and challenging as well. Here, we employed <i>Yersinia pestis</i> genomes from a plague outbreak at Xinghai county of China in 2009 as an example, to develop a simple two-step strategy for rapid source tracing of the outbreak. The first step was to define the phylogenetic position of the outbreak strains in a whole species tree, and the next step was to provide a detailed relationship across the outbreak strains and their suspected relatives. Through this strategy, we observed that the Xinghai plague outbreak was caused by <i>Y. pestis</i> that circulated in the local plague focus, where the majority of historical plague epidemics in the Qinghai-Tibet Plateau may originate from. The analytical strategy developed here will be of great help in fighting against the outbreaks of emerging infectious diseases, by pinpointing the source of pathogens rapidly with genomic epidemiological data and microbial forensics information.</p></div>", "links"=>[], "tags"=>["genomics", "Comparative genomics", "Genome evolution", "Genome sequencing", "microbiology", "Emerging infectious diseases", "Medical microbiology", "Microbial evolution", "Population biology", "population genetics", "Genetic polymorphism", "epidemiology", "Molecular epidemiology", "Infectious diseases", "Bacterial diseases", "Plagues", "Yersinia pestis", "Infectious disease control", "two-step", "tracing"], "article_id"=>898975, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Yanfeng Yan", "Hu Wang", "Dongfang Li", "Xianwei Yang", "Zuyun Wang", "Zhizhen Qi", "Qingwen Zhang", "Baizhong Cui", "Zhaobiao Guo", "Chang Yu", "Jun Wang", "Jian Wang", "Guangming Liu", "Yajun Song", "Yingrui Li", "Yujun Cui", "Ruifu Yang"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0085374.s001", "https://dx.doi.org/10.1371/journal.pone.0085374.s002", "https://dx.doi.org/10.1371/journal.pone.0085374.s003", "https://dx.doi.org/10.1371/journal.pone.0085374.s004", "https://dx.doi.org/10.1371/journal.pone.0085374.s005"], "stats"=>{"downloads"=>1, "page_views"=>20, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Two_Step_Source_Tracing_Strategy_of_Yersinia_pestis_and_Its_Historical_Epidemiology_in_a_Specific_Region/898975", "title"=>"Two-Step Source Tracing Strategy of <i>Yersinia pestis</i> and Its Historical Epidemiology in a Specific Region", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-01-09 03:58:05"}

PMC Usage Stats | Further Information

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Relative Metric

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