Identification and evaluation on methods with upstream flank sequences of CRISPR1, regarding Escherichia coli and Shigella.
10.3760/cma.j.issn.0254-6450.2018.12.013
- VernacularTitle:CRISPR1上游侧翼序列用于大肠埃希菌和志贺菌鉴定的效果评价
- Author:
W J LIANG
1
,
2
;
C C CUI
1
,
2
;
G C DUAN
2
,
3
;
H Y LIU
4
;
Y K XU
4
;
Y L XI
4
;
H Y YANG
4
;
S Y CHEN
4
Author Information
1. Department of Epidemiology and Statistics, School of Public Health, Xinxiang Medical University, Xinxiang 453003, China
2. Henan Innovation Center of Molecular Diagnosis and Laboratory Medicine, Xinxiang Medical University, Xinxiang 453003, China.
3. Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou 450001, China
4. Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou 450001, China.
- Publication Type:Journal Article
- Keywords:
Clustered regularly interspaced short palindromic repeats;
Escherichia coli;
Flanking sequence;
Identification;
Shigella
- MeSH:
Clustered Regularly Interspaced Short Palindromic Repeats/genetics*;
DNA, Bacterial/genetics*;
Escherichia coli/isolation & purification*;
Genotype;
Humans;
Molecular Sequence Data;
Sequence Analysis, DNA;
Shigella/isolation & purification*
- From:
Chinese Journal of Epidemiology
2018;39(12):1607-1610
- CountryChina
- Language:Chinese
-
Abstract:
Objective: To analyze the effect of the identification and evaluation of Escherichia (E.) coli and Shigella, based on the upstream flanking sequences of CRISPR1. Methods: Both CRISPR and cas sequences were obtained through the BLAST with repeating sequences against the publicly complete genome in GenBank that related to E. coli and Shigella. Clustal X was used to perform multi-sequences alignment of the flanking sequences. PCR method was used to amplify the upstream flanking sequences of CRISPR1 in order to appraise the effect of identification and evaluation of upstream flanking sequences on E. coli and Shigella, which were based on the upstream flanking sequences of CRISPR1. Results: The results showed that 73.4% of the strains containing the I-E CRISPR/Cas that belonged to the phylogroups A, B1, D while 8.4% strains carried the I-F CRISPR/Cas. Another 17.2% of the strains owned CRISPR3-4 (non-CRISPR/Cas) only belonged to the phylogroups B2. All the Shigella strains carried I-E CRISPR/Cas. More than 99% of similarity the CRISPR1 upstream-flanking sequences was seen in E. coli (except B2) and Shigella and E. coli (B2). Both sensitivity and specificity were greater than 91% after PCR amplification in the region to identify the E.coli and Shigella. Conclusion: The upstream of CRISPR1 could achieve a preliminary identification effect on E.coli and Shigella.
