Research Article | Volume: 7, Issue: 11, November, 2017

In silico Pulsed Field Gel Electrophoresis and Molecular characterization of Escherichia coli

Nusrat Nahar Samia Naz Sharmeen Asad Md. Shariful Islam D. A. Anwar Al Aman Nurul Islam Setu Tufael Ahmed Md. Kamrul Islam Muhammed Mahfuzur Rahman Md. Abdul Bari Ridwan Bin Rashid   

Open Access   

Published:  Nov 30, 2017

DOI: 10.7324/JAPS.2017.71124

Sixty-five isolates were analyzed for virulence, antibiotic resistance and adherence genes by in silico tools. Thirteen virulence genes were selected to classify Escherichia coli isolates. The most prevalent virulence gene was shiga toxin, stx2 (13.85%). Out of the 65 isolates, 3 isolates were harbouring heat labile enterotoxin (LT1) and isolate NC_017633 Escherichia coli ETEC H10407 and NC_017641 Escherichia coli UMNK 88 harboured STI and STII genes, respectively, both of which were representative of ETEC. Six isolates were positive for vt1; and none of the isolates had the vt2 gene. The intimin gene, eaeA was detected in seven isolates (10.77%). The presence of Escherichia coli O157 was confirmed by rfbE genes that were present in five isolates (7.69%). Among the 8 hlyA positive isolates, 5 were positive for both hlyA and eaeA genes that classified the isolates into typical EHEC. Two isolates (NC_013941 Escherichia coli O55:H7 str. CB9615 and NC_017656 Escherichia coli O55:H7 str. RM12579) were classified as atypical EPEC as contained only eaeA gene and no bfpA gene. Five isolates (7.69%) were positive for astA gene and four isolates (6.15%) had the aggR gene. So most prevalent verotype was EHEC (11 isolates), followed by ETEC. No Enteroinvasive E. coli (EIEC) was found. Eleven isolates (16.92%) had the sulfonamide resistance gene, sul2. The curli genes, csgA and crl were seen in 31 (47.69%) and 40 isolates (61.54%), respectively. Eleven isolates (16.92%) had the type 1 fimbriae and these isolates were likely to form biofilm on abiotic surfaces. The sfa gene was detected in 5 isolates and hence these isolates might be able to bind to receptors containing sialic acid residues. None of the isolates had the genes papC which are required for colonization on uroepithelial cells. In silico pulsed-field gel electrophoresis (PFGE) was able to group isolates into 25 genotypes. Genotype 8 was more virulent and contained only EHEC isolates. Genotype 17 contained all antibiotic resistance genes except tetC, sul3 and catA1 genes. Genotype 17 also contained three adhesive genes. Virulence profile analyzed in this study helps to compare the genes with previously published human pathogenic strains and verify possible genetic similarities and assess the distribution of these genes based on genotypes. This study helps to select antibiotic for treatment and improve the outcomes with severe bacterial infections based on genotyping.

Keyword:     Adhesin genes Antibiotic resistance genes Escherichia coliGenotyping PCR PFGE Virulence genes.


Nahar N, Naz S, Asad S, Islam MS, Al Aman DA, Setu NI, Ahmed T, Islam MK, Rahman MM, Bari MA, Rashid RB. In silico Pulsed Field Gel Electrophoresis and Molecular characterization of Escherichia coli. J App Pharm Sci, 2017; 7 (11): 159-167.

Copyright: © The Author(s). This is an open-access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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