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Phylogenetic analysis using insertion sequence fingerprinting in Escherichia coli.

J G Lawrence1, D E Dykhuizen, R F DuBose

  • 1Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110.

Molecular Biology and Evolution
|January 1, 1989
PubMed
Summary

Phylogenetic analysis of insertion sequences (IS) in pathogenic Escherichia coli strains revealed a stable genomic distribution pattern. This IS element analysis aids in distinguishing bacterial strains and supports their use in epidemiological studies.

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Area of Science:

  • Microbiology
  • Genetics
  • Bioinformatics

Background:

  • Pathogenic Escherichia coli strains present challenges in differentiation using traditional biochemical and electrophoretic methods.
  • Insertion sequences (IS) are mobile genetic elements with potential for genomic analysis.

Purpose of the Study:

  • To develop a robust method for distinguishing closely related pathogenic Escherichia coli strains.
  • To investigate the phylogenetic utility of insertion sequence distribution in bacterial genomes.
  • To explore the dynamics of IS element evolution, including insertion, deletion, and recombination.

Main Methods:

  • Digestion and probing of chromosomal DNA from 23 pathogenic Escherichia coli strains for five specific insertion sequences (IS1, IS2, IS4, IS5, IS30).
  • Parsimony analysis of IS element distribution to construct a phylogenetic tree.

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  • Reexamination of IS element distribution in the context of inferred phylogenetic relationships.

    • Main Results:

    • A unique phylogenetic tree was generated, successfully differentiating strains with identical biochemical and electrophoretic profiles.
    • Consistent phylogenetic signals were observed across multiple, unrelated insertion elements.
    • The distribution pattern of IS elements was found to be stable enough for epidemiological applications.
    • Evidence suggesting at least two recombinational events, potentially via conjugation, was identified.

    Conclusions:

    • Insertion sequence profiling provides a powerful tool for bacterial strain differentiation and epidemiological tracking.
    • The genomic distribution of IS elements is a stable marker, offering insights into bacterial evolution and population dynamics.
    • IS element analysis can reveal complex genetic events such as recombination, even in strains with seemingly low recombination rates.