摘要
Objective:To investigate the epidemiology of Uropathogenic E.coli(UPEC) and other sources in China,using the combination method with PCR phylogrouping and mH SNP analysis.Materials & Methods:116 strains of E.coli strains including(3 references strains) were selected.Type B,A,and C samples were taken from Urine,sputum,and other sources of patients respectively.After the culture of samples,E.coli suspected colonies were separated and confirmed by biochemical tests.The bacteria Genomic DNA of the 113 E.coli strains collected 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.Result:For E.coli strains phylogroup,25%(28/113) were observed to belong to the group A,15%(17/113) were observed to belong to the group B1,14%(16/113) were observed to belong to the group B2,and 46%(52/113) were observed to belong to the group D.The comparison of type B strains and type C+A strains in different phylogroups show that group A is statistical significant than Bl in type A+C strains(P<0.05),group D is statistical significant than group A in type B strains(P<0.05).No significant found between other comparisons.75%(85/113) were fimH positive.fimH SNPs analysis for 50 isolated from clinical sample and 3 references with fimH positive found 60 SNPs at 57 polymorphic sites,the nucleotides sequencebased phylogenic tree found 24 terminal groups.12 terminal groups were distinct allelic variants.23 SNPs resulted to 22 amino-acid changes and 37 SNPs were silent substitution.The number of amino-acid variants and silent SNPs were observed more in type B strains than in type A and C.In additional the strains with the same amino-acids variants that were from the same source were belong to the same phylogroup.Conclusion:This combination method could serve as a rapid,relatively inexpensive,highly reproducible typing test for epidemiological studies of uropathogenic E.coli and other sources in the future.Large collection data of E.coli isolates could be compared with other clinical laboratories to more understand the epidemiology investigation of E.coli strains between different regions.
Objective:To investigate the epidemiology of Uropathogenic E.coli(UPEC) and other sources in China,using the combination method with PCR phylogrouping and mH SNP analysis.Materials & Methods:116 strains of E.coli strains including(3 references strains) were selected.Type B,A,and C samples were taken from Urine,sputum,and other sources of patients respectively.After the culture of samples,E.coli suspected colonies were separated and confirmed by biochemical tests.The bacteria Genomic DNA of the 113 E.coli strains collected 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.Result:For E.coli strains phylogroup,25%(28/113) were observed to belong to the group A,15%(17/113) were observed to belong to the group B1,14%(16/113) were observed to belong to the group B2,and 46%(52/113) were observed to belong to the group D.The comparison of type B strains and type C+A strains in different phylogroups show that group A is statistical significant than Bl in type A+C strains(P<0.05),group D is statistical significant than group A in type B strains(P<0.05).No significant found between other comparisons.75%(85/113) were fimH positive.fimH SNPs analysis for 50 isolated from clinical sample and 3 references with fimH positive found 60 SNPs at 57 polymorphic sites,the nucleotides sequencebased phylogenic tree found 24 terminal groups.12 terminal groups were distinct allelic variants.23 SNPs resulted to 22 amino-acid changes and 37 SNPs were silent substitution.The number of amino-acid variants and silent SNPs were observed more in type B strains than in type A and C.In additional the strains with the same amino-acids variants that were from the same source were belong to the same phylogroup.Conclusion:This combination method could serve as a rapid,relatively inexpensive,highly reproducible typing test for epidemiological studies of uropathogenic E.coli and other sources in the future.Large collection data of E.coli isolates could be compared with other clinical laboratories to more understand the epidemiology investigation of E.coli strains between different regions.
引文