Simultaneous detection and differentiation of Escherichia coli populations from environmental freshwaters by means of sequence variations in a fragment of the β-D-glucuronidase gene

Andreas H. Farnleitner, Norbert Kreuzinger, Gerhard G. Kavka, Sonja Grillenberger, Johannes Rath, Robert L. Mach

Research output: Journal article (peer-reviewed)Journal article

66 Citations (Scopus)

Abstract

A PCR-based denaturing-gradient gel electrophoresis (DGGE) approach was applied to a partial sequence of the β-D-glucuronidase gene (uidA) for specific detection and differentiation of Escherichia coli populations according to their uidA sequence variations. Detection of sequence variations by PCRoDGGE and by PCR with direct sequencing correlated perfectly. Screening of 50 E. coli freshwater isolates and reference strains revealed 11 sequence types, showing nine polymorphic sites and an average number of pairwise differences between alleles of the uidA gene fragments (screened fragment length, 126 bp) of 2.3%. Among the analyzed strains a range of dominating to more rarely and/or uniquely observed E. coli sequence types was revealed. PCR-DGGE applied to fecally polluted river water samples simultaneously detected E. coli and generated a fingerprint of the mixed populations by separating the polymorphic uidA amplicons. No significant differences between non-cultivation-based and cultivation-based profiles were observed, suggesting that at least some members of all occurring sequence types could be cultivated. As E. coli is frequently used as a fecal indicator, this work is considered an important step towards a new, practical tool for the differentiation and tracing of fecal pollution in all kinds of waters.

Original languageEnglish
Pages (from-to)1340-1346
Number of pages7
JournalApplied and Environmental Microbiology
Volume66
Issue number4
DOIs
Publication statusPublished - Apr 2000
Externally publishedYes

Keywords

  • Electrophoresis, Polyacrylamide Gel/methods
  • Escherichia coli/classification
  • Fresh Water/microbiology
  • Genetic Variation
  • Glucuronidase/genetics
  • Polymerase Chain Reaction/methods
  • Sequence Analysis, DNA
  • Water Microbiology

ASJC Scopus subject areas

  • Applied Microbiology and Biotechnology
  • Food Science
  • Biotechnology
  • Ecology

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