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Two-Step Source Tracing Strategy of Yersinia pestis and Its Historical Epidemiology in a Specific Region

Yan, Yanfeng, Wang, Hu, Li, Dongfang, Yang, Xianwei, Wang, Zuyun, Qi, Zhizhen, Zhang, Qingwen, Cui, Baizhong, Guo, Zhaobiao, Yu, Chang, Wang, Jun, Wang, Jian, Liu, Guangming, Song, Yajun, Li, Yingrui, Cui, Yujun, Yang, Ruifu·2014·PLoS ONE
DOI 10.1371/journal.pone.0085374PMC PMC3887043
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Figure 1 CPU running time and RAM consumption of phylogenetic reconstruction based on simulated mega dataset. 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.
Figure 1 CPU running time and RAM consumption of phylogenetic reconstruction based on simulated mega dataset. 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.CC BY · PubMed Central
Figure 2 First step of source tracing: defining the phylogenetic position of outbreak strains. (A) MLTree of 2009 outbreak strains and 24 representative Y. pestis 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 Y. pseudotuberculosis, 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.
Figure 2 First step of source tracing: defining the phylogenetic position of outbreak strains. (A) MLTree of 2009 outbreak strains and 24 representative Y. pestis 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 Y. pseudotuberculosis, 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.CC BY · PubMed Central
Figure 3 Second step of source tracing: Investigating the phylogenetic relationship within the particular phylogroup and historical isolates in the outbreak region. (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 [32], 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.
Figure 3 Second step of source tracing: Investigating the phylogenetic relationship within the particular phylogroup and historical isolates in the outbreak region. (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 [32], 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.CC BY · PubMed Central

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Cited by

Metadata

Authors
Yan, Y., Wang, H., Li, D., Yang, X., Wang, Z., Qi, Z., Zhang, Q., Cui, B., Guo, Z., Yu, C., Wang, J., Wang, J., Liu, G., Song, Y., Li, Y., Cui, Y., & Yang, R.
Venue
PLoS ONE
Publisher
Public Library of Science (PLoS)
Published
2014-01-09
Volume
9
Issue
1
Pages
e85374
ISSN
1932-6203
DOI
10.1371/journal.pone.0085374
PMC
PMC3887043
Cited by
9
References
2
Language
en
Licence
creativecommons.org/licenses/by/4.0/ (vor)

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