title: [Genotyping by CRISPR and regional distribution ofYersinia pestisin Qinghai-plateau from 1954 to 2011].
abstract: Objective:To investigate the CRISPR genotypes (clusters) and regional distribution ofYersinia pestisin Qinghai-plateau.Methods:One hundred and two isolates ofY. pestisisolated from human plague patients, host animal and insect vectors from Qinghai-plateau were selected. The DNAs were extracted using the traditional sodium dodecyl sulfate decomposition and phenol-chloroform method. Three CRISPR loci YPa, YPb and YPc of 102 isolates ofY. pesitswere amplified and sequenced, and then the CRISPR sequence analysis was carried out by comparing the latest published CRISPR spacer dictionary and the NCBI database to identify the spacer and spacer array. CRISPR genotyping of isolates ofY. pesitswere finally conducted according to the polymorphism of the spacer arrays and the regional distribution pattern of isolates ofY. pesitsin Qinghai-plateau was described.Results:Forty spacers including 22 of YPa, 13 of YPb and 5 of YPc were observed among 102 isolates ofY. pestisin Qinghai-plateau, of which 5 spacers (a1', a103, a104, b4'' and b4''') were firstly identified. Meanwhile, 16, 10, and 5 different spacer arrays were obtained in YPa, YPb and YPc respectively, including 11 new spacer arrays detected in this study. One hundred and two isolates were divided into 24 CRISPR genotypes and classified into 9 CRISPR clusters (Cb4, Cb4', Cb2, Ca37, Ca7, Ca7', CaΔ5', Ca35' and Cc3'). Each dominant cluster presented significant aggregation geographically: Ca7 were found in Yushu, Nangqian, Chenduo, Zaduo, Zhiduo and Qumalai countries. Ca7' were found in Xunhua, Tongren, Zeku, Tongde, Maqin and Guinan countries. CaΔ5' were restricted to Qilian, Gangcha, Menyuan and Datong countries. CaΔ35' were found in Huangyuan, Haiyan, Gangcha, Tianjun, Delingha, Wulan, Doulan, Gonghe, Xinghai, Guide and Tongde countries.Conclusion:CRISPR-based genotyping analyses showed complicated population ofY. pestisin Qinghai-plateau. Four clusters, Ca7, Ca7', CaΔ5' and Ca35' were the most epidemic dominant four clusters and presented obvious regional distribution patterns, which instructed us to strengthen the surveillance and prevention and control by CRISPR-genotyping technique.
authors.affiliation: Qinghai Institute for Endemic Diseases Prevention and Control, Key Laboratory for Plague Prevention and Control of Qinghai Province, Xining 811602, China.
authors.forename: X Q
authors.initials: XQ
authors.lastname: Xu
authors.forename: Y Q
authors.initials: YQ
authors.lastname: Xin
authors.forename: X
authors.initials: X
authors.lastname: Li
authors.forename: Q W
authors.initials: QW
authors.lastname: Zhang
authors.forename: X Y
authors.initials: XY
authors.lastname: Yang
authors.forename: Y
authors.initials: Y
authors.lastname: Jin
authors.forename: H H
authors.initials: HH
authors.lastname: Zhao
authors.forename: X
authors.initials: X
authors.lastname: Jin
authors.forename: Z Z
authors.initials: ZZ
authors.lastname: Qi
mesh_terms: D000818:Animals; D001483:Base Sequence; D064112:Clustered Regularly Interspaced Short Palindromic Repeats / Q000235:genetics*; D005838:Genotype; D006801:Humans; D010930:Plague / Q000235:genetics*; D011110:Polymorphism, Genetic; D015010:Yersinia pestis / Q000235:genetics* / Q000302:isolation & purification
keywords: Genotype; Qinghai-plateau; Yersinia pestis