Molecular Epidemiology
A surveillance study on CRISPR/Cas molecular biomarker in Escherichia coli
Wenjuan Liang, Rongguang Zhang, Guangcai Duan, Lijuan Hong, Bing Zhang, Yuanlin Xi, Haiyan Yang, Shuaiyin Chen, Tingye Lou, Yongxin Zhao
Published 2016-08-10
Cite as Chin J Epidemiol, 2016, 37(8): 1080-1086. DOI: 10.3760/cma.j.issn.0254-6450.2016.08.005
Abstract
ObjectiveA new method related to molecular biomarker with CRISPR/Cas (clustered regularly interspaced short palindromic repeats-cas) in Escherichia (E.) coli was developed and used for surveillance programs.
MethodsCRISPR/Cas sequence that containing 135 strains with complete sequence and 203 strains with whole genome shotgun sequence of E. coli in GenBank by BLAST and 361 strains of E. coli (including 38 strains of E. coli O157∶H7) in laboratory were identified by PCR and analyzed with the CRISPR Finder. Spacers were compared with DANMAN and the phylogenetic trees of cas gene were constructed under Clustal Ⅹ and Mega 5.1.
ResultsWith new perspective, a descriptive method was developed targeting on the position of CRISPR/cas in E. coli. The CRISPR1 was detected in 77.04%, 100.00% and 75.62% and the CRISPR2 was detected in 74.81%, 100.00% and 92.24% and the CRISPR3 and CRISPR4 were detected in 11.85%, 0 and 1.39% for 135 strains with complete sequence, 203 strains with whole genome shotgun sequence and 361 strains in the laboratory, respectively. One strain downloaded in GenBank with whole genome sequencing and 2 strains in the our laboratory were identified that containing four CRISPR locus. The other E. coli strain was with insertion sequence in downstream of the non-cas CRISPR1. The unique CRISPR was found in 8 strains of O55∶H7, in 180 strains of O157∶H7, in 8 strains of O157∶HNM, in 40 strains of O104∶H4, in 4 strains of O145∶H28, in all the 699 E. coli strains. The phylogenetic tree could be divided into two groups-cas with type I-E or type I-F.
ConclusionsCRISPR/Cas might be used as a valuable molecular biomarker in epidemiological surveillance studies to identify the high virulent strains or new strains of E. coli. Phage night be related to the missing or obtaining of spacers.
Key words:
Escherichia coli; Clustered regularly interspaced short palindromic repeats/cas; Molecular biomarker
Contributor Information
Wenjuan Liang
Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou 450001, China
Henan Innovation Center of Molecular Diagnosis and Laboratory Medicine, Xinxiang Medical University, Xinxiang 453003
Rongguang Zhang
Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou 450001, China
Guangcai Duan
Henan Innovation Center of Molecular Diagnosis and Laboratory Medicine, Xinxiang Medical University, Xinxiang 453003
Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou 450001, China
Lijuan Hong
Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou 450001, China
Bing Zhang
Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou 450001, China
Yuanlin Xi
Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou 450001, China
Haiyan Yang
Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou 450001, China
Shuaiyin Chen
Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou 450001, China
Tingye Lou
Laboratory Department, The First Affiliated Hospital of Xinxiang Medical University, Xinxiang 453100, China
Yongxin Zhao
Laboratory Department, The Third Affiliated Hospital of Xinxiang Medical University, Xinxiang 453003, China
