Yersinia pestis Lineages in Mongolia

Abstract

BackgroundWhole 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 FindingsClustered 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/SignificanceWe 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.

Characterization and evolution of Salmonella CRISPR-Cas systems

“…By comparison, in an active CRISPR-Cas system such as that of Streptococcus thermophilus, 77 % of spacers have viral protospacer matches . Spacers of bacterial origin have been observed in other bacteria, for example in Yersinia pestis (Riehm et al, 2012). It is also interesting to note the imbalance of spacer maintenance where identical spacers are present in more than one serovar.…”

The Role of CRISPR-Cas Systems in Virulence of Pathogenic Bacteria

“…In Y. pestis, CRISPR typing was able to identify the origin of the ancestor strains that caused the black plague (36). Whereas it had been assumed that the black plague originated from Mongolia, CRISPR typing suggested that this region harbored a different, less virulent Yersinia species (Yersinia microtus clade) (37). A separate study had linked geographical sources to outbreaks of Y. pestis isolates based on sequence variation within the CRISPR array (38).…”

CRISPRs: Molecular Signatures Used for Pathogen Subtyping

“…Given the temporal organization of spacers, sequencing of CRISPR arrays has been a tremendously useful tool in investigating and constructing phylogenetic relationships between different bacterial lineages, specifically, in Yersinia species, Erwinia amylovora, E. coli, and Salmonella enterica and, most recently, in the periodontal pathogen Porphyromonas gingivalis (23,(31)(32)(33)(34)(35)(36)(37)(38). CRISPR analysis from metagenomic data can also be used to identify both the presence of and relationship between viruses and hosts within complex and diverse ecological niches (26,30,(39)(40)(41).…”