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Yersinia pestis Lineages in Mongolia

Riehm, Julia M., Vergnaud, Gilles, Kiefer, Daniel, Damdindorj, Tserennorov, Dashdavaa, Otgonbaatar, Khurelsukh, Tungalag, Zöller, Lothar, Wölfel, Roman, Le Flèche, Philippe, Scholz, Holger C.·2012·PLoS ONE
DOI 10.1371/journal.pone.0030624PMC PMC3281858
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Figure 1 MLVA clustering and SNP branch assignment of 66 previously published Y. pestis microtus and pestis 0, 1 and 3 branches. Microtus and strains from the 0 and 1 branches so far investigated by MLVA25 and by SNP analysis are shown [5], [6]. Three Ulegeica, two Hissarica and nine Altaica strains not investigated by SNP analysis are also included. For completion, Table 1 gives further information about assignment of biovar, genotype, and origin. Colors reflect MLVA clustering as suggested by Li et al. [5]. The SNP branch assignment of each strain as defined by Morelli et al. is indicated (column Morelli2010) together with the strain ID and biovar designation [6]. The results of CRISPR analysis according to Cui et al. are shown in column group [18]. Bootstrap support values are indicated. The figure shows the satisfying terminal branches clustering achieved by MLVA but the sometimes incorrect and usually low bootstrap values of deep branching nodes illustrating the complementarity of the two methods.
Figure 1 MLVA clustering and SNP branch assignment of 66 previously published Y. pestis microtus and pestis 0, 1 and 3 branches. Microtus and strains from the 0 and 1 branches so far investigated by MLVA25 and by SNP analysis are shown [5], [6]. Three Ulegeica, two Hissarica and nine Altaica strains not investigated by SNP analysis are also included. For completion, Table 1 gives further information about assignment of biovar, genotype, and origin. Colors reflect MLVA clustering as suggested by Li et al. [5]. The SNP branch assignment of each strain as defined by Morelli et al. is indicated (column Morelli2010) together with the strain ID and biovar designation [6]. The results of CRISPR analysis according to Cui et al. are shown in column group [18]. Bootstrap support values are indicated. The figure shows the satisfying terminal branches clustering achieved by MLVA but the sometimes incorrect and usually low bootstrap values of deep branching nodes illustrating the complementarity of the two methods.CC BY · PubMed Central
Figure 2 MLVA clustering and SNP branch assignment of 68 previously published Y. pestis pestis branches 1 and 2. Sixty-eight strains from the 1 and 2 branches previously investigated by both MLVA25 and SNP analysis are displayed [5], [6]. For completion, Table 1 gives further information about assignment of biovar, genotype, and origin. Colors reflect MLVA clustering as suggested by Li et al. [5]. The SNP branch assignment of each strain as defined by Morelli et al. is indicated (column Morelli2010) together with the strain ID and biovar designation [6]. Bootstrap support values are indicated for each node. The results of CRISPR analysis according to Cui et al. are given in column group [18]. * This strain shows a Medievalis phenotype due to a different mutation in the napA gene compared to the mutation causing the Medievalis phenotype in the Medievalis biovar, as demonstrated by Pourcel et al. [13].
Figure 2 MLVA clustering and SNP branch assignment of 68 previously published Y. pestis pestis branches 1 and 2. Sixty-eight strains from the 1 and 2 branches previously investigated by both MLVA25 and SNP analysis are displayed [5], [6]. For completion, Table 1 gives further information about assignment of biovar, genotype, and origin. Colors reflect MLVA clustering as suggested by Li et al. [5]. The SNP branch assignment of each strain as defined by Morelli et al. is indicated (column Morelli2010) together with the strain ID and biovar designation [6]. Bootstrap support values are indicated for each node. The results of CRISPR analysis according to Cui et al. are given in column group [18]. * This strain shows a Medievalis phenotype due to a different mutation in the napA gene compared to the mutation causing the Medievalis phenotype in the Medievalis biovar, as demonstrated by Pourcel et al. [13].CC BY · PubMed Central
Figure 3 Minimal spanning tree of the strains as shown in Figures 1 and 2 using the same color code. The figure is based on the same data set as Fig. 1 and 2. Table 1 gives further information about assignment of biovar, genotype, and origin. Basic correlation and grouping of genotypes is similar compared to previously published Fig. 2 in Morelli et al. [6].
Figure 3 Minimal spanning tree of the strains as shown in Figures 1 and 2 using the same color code. The figure is based on the same data set as Fig. 1 and 2. Table 1 gives further information about assignment of biovar, genotype, and origin. Basic correlation and grouping of genotypes is similar compared to previously published Fig. 2 in Morelli et al. [6].CC BY · PubMed Central
Figure 4 Sampling sites in Mongolia and observed genotypes. The map of Mongolia shows the sampling sites 1 to 35 and associated clusters (in color). Sizes of circles correlate to the number of collected strains. The exact geographic position of plague foci, and further background data of strains is listed in Table S1. Genotypes are explained in Table 1. Some previously published natural plague foci are shown in ovals. Colors match the corresponding lineage found in Mongolia: Mountain-Altai, Russia (#36), a reservoir for 0.PE1/Altaica strains. Tuva (Mongun-Taigin), Russia (#37), populated with 3.ANT genotype strains. Khentii province (KP), Mongolia [4], associated with the 2.ANT3 lineage. Bayanölgie province (BP), Mongolia [18] associated with the Ulegeica biovar. Chinese natural plague foci are present in Ningxia, Hebei, Shanxi, and Inner Mongolia, (I), Inner Mongolia, Jilin, Heilongjiang (H), and Inner Mongolia (L). Different lineages have been isolated here as shown by Li et al. [5].
Figure 4 Sampling sites in Mongolia and observed genotypes. The map of Mongolia shows the sampling sites 1 to 35 and associated clusters (in color). Sizes of circles correlate to the number of collected strains. The exact geographic position of plague foci, and further background data of strains is listed in Table S1. Genotypes are explained in Table 1. Some previously published natural plague foci are shown in ovals. Colors match the corresponding lineage found in Mongolia: Mountain-Altai, Russia (#36), a reservoir for 0.PE1/Altaica strains. Tuva (Mongun-Taigin), Russia (#37), populated with 3.ANT genotype strains. Khentii province (KP), Mongolia [4], associated with the 2.ANT3 lineage. Bayanölgie province (BP), Mongolia [18] associated with the Ulegeica biovar. Chinese natural plague foci are present in Ningxia, Hebei, Shanxi, and Inner Mongolia, (I), Inner Mongolia, Jilin, Heilongjiang (H), and Inner Mongolia (L). Different lineages have been isolated here as shown by Li et al. [5].CC BY · PubMed Central
Figure 5 MLVA25 assignment of four clusters of the investigated Mongolian Y. pestis strains. MLVA25 tree of 16 investigated Mongolian Y. pestis strains (marked with color and boxes) representing four of the 6 clusters, and various Y. pestis strains originating from microtus and pestis biovars. For each strain, the tentative SNP branch or node according to Morelli et al. [6] as deduced by the presence of a linking strain in the same MLVA cluster is indicated by a question mark. Strain name, CRISPR profile as investigated in this study, and the sampling site (Focus) are listed.
Figure 5 MLVA25 assignment of four clusters of the investigated Mongolian Y. pestis strains. MLVA25 tree of 16 investigated Mongolian Y. pestis strains (marked with color and boxes) representing four of the 6 clusters, and various Y. pestis strains originating from microtus and pestis biovars. For each strain, the tentative SNP branch or node according to Morelli et al. [6] as deduced by the presence of a linking strain in the same MLVA cluster is indicated by a question mark. Strain name, CRISPR profile as investigated in this study, and the sampling site (Focus) are listed.CC BY · PubMed Central
Figure 6 MLVA25 assignment of two clusters of the Mongolian Y. pestis strains. MLVA25 tree of two clusters comprising 84 investigated Mongolian Y. pestis strains (marked with color and boxes) compared to various previously typed Y. pestis strains. For each strain, the tentative SNP branch or node according to Morelli et al. [6] as deduced by the presence of a linking strain in the same MLVA cluster is indicated by a question mark. Strain name, CRISPR profile as investigated in this study, and the sampling site (Focus) are listed.
Figure 6 MLVA25 assignment of two clusters of the Mongolian Y. pestis strains. MLVA25 tree of two clusters comprising 84 investigated Mongolian Y. pestis strains (marked with color and boxes) compared to various previously typed Y. pestis strains. For each strain, the tentative SNP branch or node according to Morelli et al. [6] as deduced by the presence of a linking strain in the same MLVA cluster is indicated by a question mark. Strain name, CRISPR profile as investigated in this study, and the sampling site (Focus) are listed.CC BY · PubMed Central
Figure 7 MST tree of the main Mongolian clade. MST tree of the 78 Mongolian Y. pestis strains, determined as 3.ANT genotype and showing CRISPR spacer b48 (blue). The seven strains previously described by Li et al. and associated to the Mongolian cluster were included (yellow) [5], suggesting distinct clustering. Numbers refer to the sampling sites given in Fig. 4.
Figure 7 MST tree of the main Mongolian clade. MST tree of the 78 Mongolian Y. pestis strains, determined as 3.ANT genotype and showing CRISPR spacer b48 (blue). The seven strains previously described by Li et al. and associated to the Mongolian cluster were included (yellow) [5], suggesting distinct clustering. Numbers refer to the sampling sites given in Fig. 4.CC BY · PubMed Central

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Cited by

Metadata

Authors
Riehm, J. M., Vergnaud, G., Kiefer, D., Damdindorj, T., Dashdavaa, O., Khurelsukh, T., Zöller, L., Wölfel, R., Le Flèche, P., & Scholz, H. C.
Venue
PLoS ONE
Publisher
Public Library of Science (PLoS)
Published
2012-02-17
Volume
7
Issue
2
Pages
e30624
ISSN
1932-6203
DOI
10.1371/journal.pone.0030624
PMC
PMC3281858
Cited by
65
References
0
Language
en
Licence
creativecommons.org/licenses/by/4.0/ (unspecified)

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