Comparative efficacy of five different rep-PCR methods to discriminate Escherichia coli populations in aquatic environments

Water Science and Technology : a Journal of the International Association on Water Pollution Research
Bidyut R Mohapatra, Asit Mazumder

Abstract

Development of efficient techniques to discriminate the sources of E. coli in aquatic environments is essential to improve the surveillance of fecal pollution indicators, to develop strategies to identify the sources of fecal contamination, and to implement appropriate management practices to minimize gastrointestinal disease transmission. In this study the robustness of five different rep-PCR methods, such as REP-PCR, ERIC-PCR, ERIC2-PCR, BOX-PCR and (GTG)(5)-PCR were evaluated to discriminate 271 E. coli strains isolated from two watersheds (Lakelse Lake and Okanagan Lake) located in British Columbia, Canada. Cluster analysis of (GTG)(5)-PCR, BOX-PCR, REP-PCR, ERIC-PCR and ERIC2-PCR profiles of 271 E. coli revealed 43 clusters, 35 clusters, 28 clusters, 23 clusters and 14 clusters, respectively. The discriminant analysis of rep-PCR genomic fingerprints of 271 E. coli isolates yielded an average rate of correct classification (watershed-specific) of 86.8%, 82.3%, 78.4%, 72.6% and 55.8% for (GTG)(5)-PCR, BOX-PCR, REP-PCR, ERIC-PCR and ERIC2-PCR, respectively. Based on the results of cluster analysis and discriminant function analysis, (GTG)(5)-PCR was found to be the most robust molecular tool for differentiation of E. coli pop...Continue Reading

Citations

Oct 22, 2011·Environmental Monitoring and Assessment·Kasi MuruganKuppusamy Sekar
Jan 20, 2016·Infection Control and Hospital Epidemiology : the Official Journal of the Society of Hospital Epidemiologists of America·Miriam D IsmailBetsy Foxman
Sep 9, 2009·Journal of Applied Microbiology·M A JohnstonL F Webster
Oct 15, 2013·The Journal of Animal Ecology·Kimberly L VanderwaalBrenda McCowan
Nov 22, 2014·Microbiology·Monalessa F PereiraDenise Ms Bazzolli
Apr 30, 2015·Environmental Science and Pollution Research International·Song LiZengmin Miao
Apr 18, 2015·Frontiers in Cellular and Infection Microbiology·Pallavi SinghShannon D Manning
Dec 3, 2014·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Debasish KarRaj Kumar Singh
Jul 13, 2019·The Journal of Animal Ecology·Tatiana ProbosteJennifer M Seddon
Feb 27, 2015·Journal of Water and Health·Matthew AijukaElna M Buys
Sep 12, 2018·BMC Research Notes·Novi PuspariniEva Nikastri
May 16, 2019·The ISME Journal·Jonathan N V MartinsonSeth T Walk
Mar 5, 2020·Journal of Water and Health·Kevin L LabradorWindell L Rivera
Nov 17, 2016·Frontiers in Microbiology·Xiao LiangPhilip M Dixon
Sep 27, 2020·EcoSal Plus·Jonathan N V Martinson, Seth T Walk

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