Comparison of five rep-PCR genomic fingerprinting methods for differentiation of  fecalEscherichia colifrom humans, poultry and wild birds

Abstract

The development of a methodology to identify the origin of fecal pollution is important both for assessing the degree of risk posed to public health and for developing strategies to mitigate the environmental loading of pathogens associated with waterborne disease transmission. Five rep-PCR genomic fingerprinting methods, such as rep-PCR, enterobacterial repetitive intergenic consensus (ERIC)-PCR, ERIC2-PCR, BOX-PCR and (GTG)(5)-PCR, were assessed for their potential in differentiation of 232 fecal Escherichia coli isolates obtained from humans, poultry (chicken, duck and turkey) and wild birds (Canada goose and gull). Based on the results of cluster analysis and discriminant function analysis, (GTG)(5)-PCR was found to be the most suitable method for molecular typing of fecal E. coli, followed by BOX-PCR, REP-PCR, ERIC-PCR and ERIC2-PCR. A discriminant function analysis of (GTG)(5)-PCR fingerprints showed that 94.1%, 79.8%, 80.5%, 74.4%, 86.7% and 88.6% of turkey, chicken, duck, Canada goose, gull and human E. coli isolates were classified into the correct host group, respectively. Subsequently, (GTG)(5)-PCR was tested for its ability to track the origin of 113 environmental E. coli isolated from natural pond water. In conclusion, the (GTG)(5)-PCR genomic fingerprinting method can be considered as a promising genotypic tool for epidemiological surveillance of fecal pollution in aquatic environments.

Genetic heterogeneity of Escherichia coli isolated from pasteurized milk in State of Paraná, Brazil

“…ERIC-PCR is effective in typing E. coli isolates from animals (Mohapatra, Broersma, Mazumder, 2007;Prabu et al, 2010;Wan et al, 2011;De la Fé Rodriguez et al, 2012) and water (Casarez, Pillai, Di Giovanni, 2007). However, some reports indicated that ERIC-PCR is not effective in typing E. coli isolated from humans, animals, and food (Giammanco et al, 2002;Leung et al, 2004;Costa et al, 2006).…”

(CGG) 4 -Based PCR as a Novel Tool for Discrimination of Uropathogenic Escherichia coli Strains: Comparison with Enterobacterial Repetitive Intergenic Consensus-PCR

“…Also, (GTG) 5 -PCR was tested for its ability to track the origins of E. coli, Lactobacillus spp., and Enterococcus spp. isolated from various sources (12,24,25,39). We propose an improved PCR methodology that employs an N 6 (CGG) 4 primer with a high annealing temperature.…”

Seroprevalence and molecular epidemiology of EAST1 gene-carrying Escherichia coli from diarrheal patients and raw meats

“…DNA fingerprinting of EAST1-EC serotype O15 was performed using enterobacterial repetitive intergenic consensus (ERIC) 2-PCR and BOX-PCR using ERIC2 and BOX-A1R primers, respectively [21]. PCR was performed in a 25-μL reaction mixture containing 0.2 μM of each primer, 0.2 mM dNTPs, 1× GoTaq DNA polymerase buffer, 3.0 mM MgCl 2 , 1.25 U GoTaq DNA polymerase, and 50 ng of DNA template (prepared using glass fiber matrix spin column; Geneaid, Taiwan).…”