title: [A surveillance study on CRISPR/Cas molecular biomarker in Escherichia coli].
abstract: OBJECTIVE
  A 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.
  
  
  METHODS
  CRISPR/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.
  
  
  RESULTS
  With 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.
  
  
  CONCLUSIONS
  CRISPR/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.
authors.affiliation: 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.
authors.forename: W J
authors.initials: WJ
authors.lastname: Liang
authors.affiliation: Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou 450001, China.
authors.forename: R G
authors.initials: RG
authors.lastname: Zhang
authors.affiliation: 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.
authors.forename: G C
authors.initials: GC
authors.lastname: Duan
authors.affiliation: Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou 450001, China.
authors.forename: L J
authors.initials: LJ
authors.lastname: Hong
authors.affiliation: Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou 450001, China.
authors.forename: B
authors.initials: B
authors.lastname: Zhang
authors.affiliation: Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou 450001, China.
authors.forename: Y L
authors.initials: YL
authors.lastname: Xi
authors.affiliation: Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou 450001, China.
authors.forename: H Y
authors.initials: HY
authors.lastname: Yang
authors.affiliation: Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou 450001, China.
authors.forename: S Y
authors.initials: SY
authors.lastname: Chen
authors.affiliation: Laboratory Department, The First Affiliated Hospital of Xinxiang Medical University, Xinxiang 453100, China.
authors.forename: T Y
authors.initials: TY
authors.lastname: Lou
authors.affiliation: Laboratory Department, The Third Affiliated Hospital of Xinxiang Medical University, Xinxiang 453003, China.
authors.forename: Y X
authors.initials: YX
authors.lastname: Zhao
mesh_terms: D001483:Base Sequence; D015415:Biomarkers; D064112:Clustered Regularly Interspaced Short Palindromic Repeats; D004926:Escherichia coli / Q000235:genetics* / Q000302:isolation & purification; D005838:Genotype; D006801:Humans; D008969:Molecular Sequence Data; D010802:Phylogeny
chemical_list: D015415:Biomarkers