Wang GQ, Zhou FF, Olman V, Su YY, Xu Y, Li F. Computational prediction and experimental validation of novel markers for detection of STEC O157:H7. World J Gastroenterol 2011; 17(14): 1910-1914 [PMID: 21528067 DOI: 10.3748/wjg.v17.i14.1910]
Corresponding Author of This Article
Fan Li, Professor, Norman Bethune Medical College of Jilin University, Changchun 130021, Jilin Province, China. lifan@jlu.edu.cn
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Wang GQ, Zhou FF, Olman V, Su YY, Xu Y, Li F. Computational prediction and experimental validation of novel markers for detection of STEC O157:H7. World J Gastroenterol 2011; 17(14): 1910-1914 [PMID: 21528067 DOI: 10.3748/wjg.v17.i14.1910]
World J Gastroenterol. Apr 14, 2011; 17(14): 1910-1914 Published online Apr 14, 2011. doi: 10.3748/wjg.v17.i14.1910
Computational prediction and experimental validation of novel markers for detection of STEC O157:H7
Guo-Qing Wang, Feng-Feng Zhou, Victor Olman, Ying-Ying Su, Ying Xu, Fan Li
Guo-Qing Wang, Ying-Ying Su, Fan Li, Department of Pathogenobiology, Norman Bethune Medical College of Jilin University, Changchun 130000, Jilin Province, China
Guo-Qing Wang, Feng-Feng Zhou, Victor Olman, Ying Xu, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, United States
Ying Xu, Department of Bioinformatics, College of Computer Science and Technology, Jilin University, Changchun 130000, Jilin Province, China
Author contributions: Wang GQ designed and performed the research; Zhou FF and Olman V analyzed the data and generated the genomic barcode tool; Su YY performed the experiments; Li F and Xu Y designed the study and provided the financial support for this work; Wang GQ wrote the manuscript.
Supported by National Natural Science Foundation of China, No. 30872415, in part by National Science Foundation, No. DBI-0354771, ITR-IIS-0407204, DBI-0542119, CCF0621700, National Institutes of Health, No. 1R01GM075331 and 1R01GM081682, and grant from BioEnergy Science Center, US Department of Energy BioEnergy Research Center supported by the Office of Biological and Environmental Research in DOE Office of Science
Correspondence to: Fan Li, Professor, Norman Bethune Medical College of Jilin University, Changchun 130021, Jilin Province, China. lifan@jlu.edu.cn
Telephone: +86-431-85619574 Fax: +86-431-85619574
Received: October 15, 2010 Revised: February 12, 2011 Accepted: February 19, 2011 Published online: April 14, 2011
Abstract
AIM: 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.
CONCLUSION: 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.
