RESUMO
Objective To analyze the effect of the identification and evaluation of Escherichia (E.) coli and Shigella,based on the upstream flanking sequences of CRISPR1.Methods Both CRISPR and cas sequences were obtained through the BLAST with repeating sequences against the publicly complete genome in GenBank that related to E.coli and Shigella.Clustal X was used to perform multi-sequences alignment of the flanking sequences.PCR method was used to amplify the upstream flanking sequences of CRISPR1 in order to appraise the effect of identification and evaluation of upstream flanking sequences on E.coli and Shigella,which were based on the upstream flanking sequences of CRISPR1.Results The results showed that 73.4％ of the strains containing the I-E CRISPR/Cas that belonged to the phylogroups A,B1,D while 8.4％ strains carried the I-F CRISPR/Cas.Another 17.2％ of the strains owned CRISPR3-4 (non-CRISPR/Cas) only belonged to the phylogroups B2.All the Shigella strains carried I-E CRISPR/Cas.More than 99％ of similarity the CRISPR1 upstream-flanking sequences was seen in E.coli (except B2) and Shigella and E.coli (B2).Both sensitivity and specificity were greater than 91％ after PCR amplification in the region to identify the E.coli and Shigella.Conclusion The upstream of CRISPR1 could achieve a preliminary identification effect on E.coli and Shigella.
RESUMO
Objective To analyze the effect of the identification and evaluation of Escherichia (E.) coli and Shigella,based on the upstream flanking sequences of CRISPR1.Methods Both CRISPR and cas sequences were obtained through the BLAST with repeating sequences against the publicly complete genome in GenBank that related to E.coli and Shigella.Clustal X was used to perform multi-sequences alignment of the flanking sequences.PCR method was used to amplify the upstream flanking sequences of CRISPR1 in order to appraise the effect of identification and evaluation of upstream flanking sequences on E.coli and Shigella,which were based on the upstream flanking sequences of CRISPR1.Results The results showed that 73.4％ of the strains containing the I-E CRISPR/Cas that belonged to the phylogroups A,B1,D while 8.4％ strains carried the I-F CRISPR/Cas.Another 17.2％ of the strains owned CRISPR3-4 (non-CRISPR/Cas) only belonged to the phylogroups B2.All the Shigella strains carried I-E CRISPR/Cas.More than 99％ of similarity the CRISPR1 upstream-flanking sequences was seen in E.coli (except B2) and Shigella and E.coli (B2).Both sensitivity and specificity were greater than 91％ after PCR amplification in the region to identify the E.coli and Shigella.Conclusion The upstream of CRISPR1 could achieve a preliminary identification effect on E.coli and Shigella.
RESUMO
Objective To investigate the association between phage-mediated shiga toxin and molecular distribution of CRISPR in Escherichia (E.) coli O26:H11 or NM.Methods A total of 135 E.coli O26:H11 or NM strains were collected from NCBI database.Software CRT and CRISPR Finder were used to extract CRISPR and Excel was used to assign the spacer of unique number and type CRISPR.And the relationship between CRISPR and stx phage was analyzed.Results All the 135 E.coli O26:H11 or NM strains had the CRISPR.For CRISPRI,CRISPR2.1,CRISPR2.2 and CRISPR3-4,19,22,1 and 1 subtypes were found,respectively.According to the four CRISPR sites,the strains could be divided into 40 subtypes.Stx-phage was only observed in the group C of CRISPR.Compared with E.coli of stx-phage negative,E.coli with stx-phage harbored more spacers.Conclusions CRISPR loci was extensively existed in E.coli O26:H11 or NM,and many subtypes were found in these strains.The presence of stx-phage was related to the molecular distribution of CRISPR in E.coli O26:H11 or NM.CRISPR might be a valuable biomarker to identify strains with high virulent potential.
RESUMO
Objective To investigate the association between phage-mediated shiga toxin and molecular distribution of CRISPR in Escherichia (E.) coli O26:H11 or NM.Methods A total of 135 E.coli O26:H11 or NM strains were collected from NCBI database.Software CRT and CRISPR Finder were used to extract CRISPR and Excel was used to assign the spacer of unique number and type CRISPR.And the relationship between CRISPR and stx phage was analyzed.Results All the 135 E.coli O26:H11 or NM strains had the CRISPR.For CRISPRI,CRISPR2.1,CRISPR2.2 and CRISPR3-4,19,22,1 and 1 subtypes were found,respectively.According to the four CRISPR sites,the strains could be divided into 40 subtypes.Stx-phage was only observed in the group C of CRISPR.Compared with E.coli of stx-phage negative,E.coli with stx-phage harbored more spacers.Conclusions CRISPR loci was extensively existed in E.coli O26:H11 or NM,and many subtypes were found in these strains.The presence of stx-phage was related to the molecular distribution of CRISPR in E.coli O26:H11 or NM.CRISPR might be a valuable biomarker to identify strains with high virulent potential.
