title: Yersinia pestis lineages in Mongolia.
abstract: 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.
  
  
  RESULTS
  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
  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.
authors.affiliation: Bundeswehr Institute of Microbiology, Munich, Germany. juliariehm@bundeswehr.org
authors.forename: Julia M
authors.initials: JM
authors.lastname: Riehm
authors.forename: Gilles
authors.initials: G
authors.lastname: Vergnaud
authors.forename: Daniel
authors.initials: D
authors.lastname: Kiefer
authors.forename: Tserennorov
authors.initials: T
authors.lastname: Damdindorj
authors.forename: Otgonbaatar
authors.initials: O
authors.lastname: Dashdavaa
authors.forename: Tungalag
authors.initials: T
authors.lastname: Khurelsukh
authors.forename: Lothar
authors.initials: L
authors.lastname: Zöller
authors.forename: Roman
authors.initials: R
authors.lastname: Wölfel
authors.forename: Philippe
authors.initials: P
authors.lastname: Le Flèche
authors.forename: Holger C
authors.initials: HC
authors.lastname: Scholz
mesh_terms: D001483:Base Sequence; D016000:Cluster Analysis; D005838:Genotype; D060005:Genotyping Techniques; D005843:Geography; D006801:Humans; D018598:Minisatellite Repeats / Q000235:genetics; D008969:Molecular Sequence Data; D008986:Mongolia; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D013045:Species Specificity; D015010:Yersinia pestis / Q000235:genetics* / Q000302:isolation & purification