A novel DNA microarray design for accurate and straightforward identification of Escherichia coli safety and laboratory strains

Andreas Peter Bauer, Wolfgang Ludwig, Karl Heinz Schleifer

Research output: Contribution to journalArticlepeer-review

11 Scopus citations

Abstract

Escherichia coli K-12, B, C and W strains and their derivates are declared in biological safety guidelines as risk group 1 organisms as they are unable to colonise the human gut. Differentiation and identification of these safety strains is mainly based on pulsed-field gel electrophoresis (PFGE), phage sensitivity tests or PCR-based methods. However, these methods are either tedious and time consuming (phage sensitivity, PFGE) or based on single specific fragments (PCR) or patterns (PFGE) lacking additional information for further differentiation of the strains. In the current study, subtractive hybridisation techniques were applied to detect specific DNA fragments which were used to design a microarray (chip) for accurate and simple identification of these organisms, and to differentiate them from other E. coli strains. The chip can be used to identify E. coli safety strains and monitor them during ongoing experiments for changes in their genome and culture purity. The hybridisation layout of the microarray was arranged in such a way that the respective lineages of safety strains could be easily identified as distinct letters (K, B, C or W). Differentiation of single strains or subtyping was possible with further probes. In addition, a set of probes targeting genes coding for common virulence factors has been included, both to differentiate safety strains from pathogenic variants and to make sure that no transfer of these genes happens during handling or storage. The reliability of the approach has been tested on a comprehensive selection of E. coli laboratory strains and pathogenic representatives.

Original languageEnglish
Pages (from-to)50-61
Number of pages12
JournalSystematic and Applied Microbiology
Volume31
Issue number1
DOIs
StatePublished - 19 Mar 2008
Externally publishedYes

Keywords

  • Escherichia coli safety strains
  • Identification
  • Laboratory strains
  • Microarray

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