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

• Published in: Applied and environmental microbiology Vol. 66; no. 6; pp. 2572 - 2577
• Main Authors: DOMBEK, P. E, JOHNSON, L. K, ZIMMERLEY, S. T, SADOWSKY, M. J
• Format: Journal Article
• Language: English
• Published: Washington, DC American Society for Microbiology 01-06-2000
• 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; Human; Polymerase chain reaction; Repeated sequence; Animal; Escherichia coli; Fingerprint method; Bacteria; Isolate; Spacer DNA; Water pollution; Feces; Enterobacteriaceae
• DOI: 10.1128/AEM.66.6.2572-2577.2000
• EISSN: 1098-5336
• ISSN: 0099-2240

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.