Yersinia pestis Lineages in Mongolia

BACKGROUND: Whole genome sequencing allowed the development of a number of high resolution sequence based typing tools for Yersinia (Y.) pestis. The application of these methods on isolates from most known foci worldwide and in particular from China and the Former Soviet Union has dramatically improved our understanding of the population structure of this species. In the current view, Y. pestis including the non or moderate human pathogen Y. pestis subspecies microtus emerged from Yersinia pseudotuberculosis about 2,600 to 28,600 years ago in central Asia. The majority of central Asia natural foci have been investigated. However these investigations included only few strains from Mongolia. METHODOLOGY/PRINCIPAL FINDINGS: Clustered Regularly Interspaced Short Prokaryotic Repeats (CRISPR) analysis and Multiple-locus variable number of tandem repeats (VNTR) analysis (MLVA) with 25 loci was performed on 100 Y. pestis strains, isolated from 37 sampling areas in Mongolia. The resulting data were compared with previously published data from more than 500 plague strains, 130 of which had also been previously genotyped by single nucleotide polymorphism (SNP) analysis. The comparison revealed six main clusters including the three microtus biovars Ulegeica, Altaica, and Xilingolensis. The largest cluster comprises 78 isolates, with unique and new genotypes seen so far in Mongolia only. Typing of selected isolates by key SNPs was used to robustly assign the corresponding clusters to previously defined SNP branches. CONCLUSIONS/SIGNIFICANCE: We show that Mongolia hosts the most recent microtus clade (Ulegeica). Interestingly no representatives of the ancestral Y. pestis subspecies pestis nodes previously identified in North-western China were identified in this study. This observation suggests that the subsequent evolution steps within Y. pestis pestis did not occur in Mongolia. Rather, Mongolia was most likely re-colonized by more recent clades coming back from China contemporary of the black death pandemic, or more recently in the past 600 years

Molecular Epidemiological Study of Bacillus anthracis Isolated in Mongolia by Multiple-Locus Variable-Number Tandem-Repeat Analysis for 8 Loci (MLVA-8)

SUMMARY: The incidence of anthrax, which is caused by Bacillus anthracis, in the human and animal population of Mongolia has increased recently, and control of this infection is a nationwide concern. In this study, 29 isolates obtained from animals and various regions in Mongolia from 2001 to 2007 were analyzed by performing multiple-locus variable-number tandem-repeat analysis for 8 loci (MLVA-8) to understand the genetic relationship between the Mongolian B. anthracis isolates. We found that all the Mongolian isolates can be classified into A3 cluster along with the Japanese and the Chinese B. anthracis isolates. Our data revealed that MLVA-8 is useful for studying the molecular epidemiology of the Mongolian B. anthracis isolates and would help characterize B. anthracis infections in Mongolia

Protospacers for newly identified spacers a6′, a85–88, and b48–49.

<p>Protospacers for newly identified spacers a6′, a85–88, and b48–49.</p

CRISPR genotypes.

<p>CRISPR genotypes.</p

MLVA25 assignment of four clusters of the investigated Mongolian <i>Y. pestis</i> strains.

<p>MLVA25 tree of 16 investigated Mongolian <i>Y. pestis</i> strains (marked with color and boxes) representing four of the 6 clusters, and various <i>Y. pestis</i> strains originating from <i>microtus</i> and <i>pestis</i> biovars. For each strain, the tentative SNP branch or node according to Morelli et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030624#pone.0030624-Morelli1" target="_blank">[6]</a> 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.</p

Minimal spanning tree of the strains as shown in <b>Figures 1</b> and <b>2</b> using the same color code.

<p>The figure is based on the same data set as <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030624#pone-0030624-g001" target="_blank">Fig. 1</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030624#pone-0030624-g002" target="_blank">2</a>. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030624#pone-0030624-t001" target="_blank">Table 1</a> gives further information about assignment of biovar, genotype, and origin. Basic correlation and grouping of genotypes is similar compared to previously published <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030624#pone-0030624-g002" target="_blank">Fig. 2</a> in Morelli et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030624#pone.0030624-Morelli1" target="_blank">[6]</a>.</p

MLVA clustering and SNP branch assignment of 68 previously published <i>Y. pestis pestis</i> branches 1 and 2.

<p>Sixty-eight strains from the 1 and 2 branches previously investigated by both MLVA25 and SNP analysis are displayed <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030624#pone.0030624-Li1" target="_blank">[5]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030624#pone.0030624-Morelli1" target="_blank">[6]</a>. For completion, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030624#pone-0030624-t001" target="_blank">Table 1</a> gives further information about assignment of biovar, genotype, and origin. Colors reflect MLVA clustering as suggested by Li et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030624#pone.0030624-Li1" target="_blank">[5]</a>. The SNP branch assignment of each strain as defined by Morelli et al. is indicated (column <i>Morelli2010</i>) together with the strain ID and biovar designation <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030624#pone.0030624-Morelli1" target="_blank">[6]</a>. Bootstrap support values are indicated for each node. The results of CRISPR analysis according to Cui et al. are given in column <i>group </i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030624#pone.0030624-Cui1" target="_blank">[18]</a>. * 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. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030624#pone.0030624-Pourcel1" target="_blank">[13]</a>.</p

Overview of <i>Y. pestis</i> subspecies, biovar, genotype, and natural foci as suggested by different authors [4], [5], [6], [7], [18], and as deduced in this study.

<p>*abbreviations as defined by Achtman et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030624#pone.0030624-Achtman1" target="_blank">[7]</a> and Morelli et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030624#pone.0030624-Morelli1" target="_blank">[6]</a>: PE – pestoides (<i>microtus</i>), ANT – Antiqua, IN – Intermedium, ORI – Orientalis, and MED – Medievalis; Intermedium in Morelli et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030624#pone.0030624-Morelli1" target="_blank">[6]</a> has not the same meaning as intermedium defined by Li et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030624#pone.0030624-Li1" target="_blank">[5]</a> which refers to Rhamnose positive <i>Y. pestis pestis</i> isolates.</p><p># prefix refers to foci as described by Anisimov et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030624#pone.0030624-Anisimov1" target="_blank">[4]</a>. Numbers without # refer to Mongolian foci as shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030624#pone-0030624-g004" target="_blank">Figure 4</a>.</p

CRISPR spacer signatures.

<p>*<b>bold print:</b> first described in this study.</p