title: Insight into microevolution of Yersinia pestis by clustered regularly interspaced short palindromic repeats.
abstract: BACKGROUND
  Yersinia pestis, the pathogen of plague, has greatly influenced human history on a global scale. Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR), an element participating in immunity against phages' invasion, is composed of short repeated sequences separated by unique spacers and provides the basis of the spoligotyping technology. In the present research, three CRISPR loci were analyzed in 125 strains of Y. pestis from 26 natural plague foci of China, the former Soviet Union and Mongolia were analyzed, for validating CRISPR-based genotyping method and better understanding adaptive microevolution of Y. pestis.
  
  
  RESULTS
  Using PCR amplification, sequencing and online data processing, a high degree of genetic diversity was revealed in all three CRISPR elements. The distribution of spacers and their arrays in Y. pestis strains is strongly region and focus-specific, allowing the construction of a hypothetic evolutionary model of Y. pestis. This model suggests transmission route of microtus strains that encircled Takla Makan Desert and ZhunGer Basin. Starting from Tadjikistan, one branch passed through the Kunlun Mountains, and moved to the Qinghai-Tibet Plateau. Another branch went north via the Pamirs Plateau, the Tianshan Mountains, the Altai Mountains and the Inner Mongolian Plateau. Other Y. pestis lineages might be originated from certain areas along those routes.
  
  
  CONCLUSIONS
  CRISPR can provide important information for genotyping and evolutionary research of bacteria, which will help to trace the source of outbreaks. The resulting data will make possible the development of very low cost and high-resolution assays for the systematic typing of any new isolate.
authors.affiliation: State Key laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Beijing, China.
authors.forename: Yujun
authors.initials: Y
authors.lastname: Cui
authors.forename: Yanjun
authors.initials: Y
authors.lastname: Li
authors.forename: Olivier
authors.initials: O
authors.lastname: Gorgé
authors.forename: Mikhail E
authors.initials: ME
authors.lastname: Platonov
authors.forename: Yanfeng
authors.initials: Y
authors.lastname: Yan
authors.forename: Zhaobiao
authors.initials: Z
authors.lastname: Guo
authors.forename: Christine
authors.initials: C
authors.lastname: Pourcel
authors.forename: Svetlana V
authors.initials: SV
authors.lastname: Dentovskaya
authors.forename: Sergey V
authors.initials: SV
authors.lastname: Balakhonov
authors.forename: Xiaoyi
authors.initials: X
authors.lastname: Wang
authors.forename: Yajun
authors.initials: Y
authors.lastname: Song
authors.forename: Andrey P
authors.initials: AP
authors.lastname: Anisimov
authors.forename: Gilles
authors.initials: G
authors.lastname: Vergnaud
authors.forename: Ruifu
authors.initials: R
authors.lastname: Yang
mesh_terms: D019143:Evolution, Molecular; D014644:Genetic Variation; D016680:Genome, Bacterial; D005838:Genotype; D006801:Humans; D020071:Interspersed Repetitive Sequences; D011110:Polymorphism, Genetic; D015010:Yersinia pestis / Q000145:classification / Q000235:genetics*