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

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 6.0.3.93 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.