Use of repetitive DNA sequences and the PCR to differentiate Escherichia coli isolates from human and animal sources

The rep-PCR DNA fingerprint technique, which uses repetitive intergenic DNA sequences, was investigated as a way to differentiate between human and animal sources of fecal pollution. BOX and REP primers were used to generate DNA fingerprints from Escherichia coli strains isolated from human and anim...

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Bibliographic Details
Published in:Applied and environmental microbiology 2000-06, Vol.66 (6), p.2572-2577
Main Authors: DOMBEK, P. E, JOHNSON, L. K, ZIMMERLEY, S. T, SADOWSKY, M. J
Format: Article
Language:English
Subjects:
Animals
Bacteria
Bacteriological methods and techniques used in bacteriology
Bacteriology
Biological and medical sciences
BOX 1R primer
BOX A1R primer
Cattle
Cluster Analysis
Contamination
Deoxyribonucleic acid
DNA
DNA Fingerprinting
DNA Primers
Escherichia coli
Escherichia coli - classification
Escherichia coli - genetics
Escherichia coli - isolation & purification
Escherichia coli Infections - microbiology
Feces - microbiology
Fundamental and applied biological sciences. Psychology
Humans
Microbiology
Multivariate Analysis
Pollution
Polymerase Chain Reaction - methods
Public Health Microbiology
Repetitive Sequences, Nucleic Acid
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Summary:The rep-PCR DNA fingerprint technique, which uses repetitive intergenic DNA sequences, was investigated as a way to differentiate between human and animal sources of fecal pollution. BOX and REP primers were used to generate DNA fingerprints from Escherichia coli strains isolated from human and animal sources (geese, ducks, cows, pigs, chickens, and sheep). Our initial studies revealed that the DNA fingerprints obtained with the BOX primer were more effective for grouping E. coli strains than the DNA fingerprints obtained with REP primers. The BOX primer DNA fingerprints of 154 E. coli isolates were analyzed by using the Jaccard band-matching algorithm. Jackknife analysis of the resulting similarity coefficients revealed that 100% of the chicken and cow isolates and between 78 and 90% of the human, goose, duck, pig, and sheep isolates were assigned to the correct source groups. A dendrogram constructed by using Jaccard similarity coefficients almost completely separated the human isolates from the nonhuman isolates. Multivariate analysis of variance, a form of discriminant analysis, successfully differentiated the isolates and placed them in the appropriate source groups. Taken together, our results indicate that rep-PCR performed with the BOX A1R primer may be a useful and effective tool for rapidly determining sources of fecal pollution.
ISSN:0099-2240
1098-5336
DOI:10.1128/AEM.66.6.2572-2577.2000