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Int J Mol Epidemiol Genet 2011;2(4):339-353

Original Article
Epidemiologic investigation of extra-intestinal pathogenic E. coli (ExPEC)
based on PCR phylogenetic group and fimH single nucleotide polymorphisms
(SNPs) in China

Kamal Said Abdallah, Yang Cao, Dian-Jun Wei

Department of Clinical Laboratory, Second Hospital of Tianjin Medical University, 300211 Tianjin; Tianjin Institute of Infection
Diseases, Second Hospital of Tianjin Medical University, Tianjin, China.

Received August 23, 2011; accepted November 6, 2011; Epub November 15, 2011; published December 15, 2011

Abstract: Using the combination method with PCR phylogrouping and fimH SNPs analysis, this study investigates the
epidemiology of Extra-intestinal pathogenic E. coli in China. 116 E. coli strains including (74 from Urine, 39 from other extra-
intestinal sources and 3 references strains) were collected. The bacteria Genomic DNA were extracted; phylogroup and the
fimH gene amplifications were determined by two-step triplex PCR-based phylogrouping and simple PCR amplification assay
respectively. Finally the fimH SNPs analysis and phylogenetic analysis and construction of tree were carried out using DNAMAN
Version and MEGA4, ClustalW and CLC Bio software respectively for 50 E. coli strains isolated from clinical sample
and 3 references ; K-12 E. coli strain was used as reference comparison. For E. coli strains phylogroup, 25% (28/113) were
observed to belong to the group A, 15% (17/113) to the group B1, 14% (16/113) to the group B2, and 46% (52/113) to the group
D. 75% (85/113) were fimH positive. fimH SNPs analysis for 50 isolated from clinical sample and 3 references found 60 SNPs
at 57 polymorphic sites. The number of amino-acid variants and silent SNPs were observed more in UPEC strains than in
other extra-intestinal E. coli strains. Most of the UPEC strains with the same amino-acid variants were belong to the same
phylogroup. This combination method could serve as a rapid, highly reproducible typing test for epidemiological studies of
ExPEC. Large collection data could be compared with other clinical laboratories that the sequence data are accessible.  

Key words: Polymerase chain reaction (PCR), single nucleotide polymorphisms (SNPs), extra-intestinal E.coli (ExPEC),

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Address all correspondence to:
Dr. Dian-Jun Wei
Department of Clinical Laboratory
Second Hospital of Tianjin Medical University
Tianjin 300211, China
E-mail: weidianjun@gmail.com