title: Computational prediction and experimental validation of novel markers for detection of STEC O157:H7.
abstract: OBJECTIVE
  To identify and assess the novel makers for detection of Shiga toxin producing Escherichia coli (STEC) O157:H7 with an integrated computational and experimental approach.
  
  
  METHODS
  High-throughput NCBI blast (E-value cutoff e-5) was used to search homologous genes among all sequenced prokaryotic genomes of each gene encoded in each of the three strains of STEC O157:H7 with complete genomes, aiming to find unique genes in O157:H7 as its potential markers. To ensure that the identified markers from the three strains of STEC O157:H7 can serve as general markers for all the STEC O157:H7 strains, a genomic barcode approach was used to select the markers to minimize the possibility of choosing a marker gene as part of a transposable element. Effectiveness of the markers predicted was then validated by running polymerase chain reaction (PCR) on 18 strains of O157:H7 with 5 additional genomes used as negative controls.
  
  
  RESULTS
  The blast search identified 20, 16 and 20 genes, respectively, in the three sequenced strains of STEC O157:H7, which had no homologs in any of the other prokaryotic genomes. Three genes, wzy, Z0372 and Z0344, common to the three gene lists, were selected based on the genomic barcode approach. PCR showed an identification accuracy of 100% on the 18 tested strains and the 5 controls.
  
  
  CONCLUSIONS
  The three identified novel markers, wzy, Z0372 and Z0344, are highly promising for the detection of STEC O157:H7, in complementary to the known markers.
authors.affiliation: Department of Pathogenobiology, Norman Bethune Medical College of Jilin University, Changchun 130000, Jilin Province, China.
authors.forename: Guo-Qing
authors.initials: GQ
authors.lastname: Wang
authors.forename: Feng-Feng
authors.initials: FF
authors.lastname: Zhou
authors.forename: Victor
authors.initials: V
authors.lastname: Olman
authors.forename: Ying-Ying
authors.initials: YY
authors.lastname: Su
authors.forename: Ying
authors.initials: Y
authors.lastname: Xu
authors.forename: Fan
authors.initials: F
authors.lastname: Li
mesh_terms: D000818:Animals; D004927:Escherichia coli Infections / Q000175:diagnosis*; D019453:Escherichia coli O157 / Q000235:genetics*; D005819:Genetic Markers; D016680:Genome, Bacterial; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction; D015203:Reproducibility of Results; D022603:Shiga Toxins
chemical_list: D005819:Genetic Markers; D022603:Shiga Toxins