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. 2007 May 9:157–171. doi: 10.1016/B978-012088483-4/50011-1

TABLE 8.8.

Examples of genotypic methods used in epidemiologic investigations

Restriction endonuclease-based methods
  • A.
    Restriction fragment length polymorphism (RFLP) without hybridization
    • —Frequent cutter (4–6bp recognition site) coupled with conventional electrophoresis to separate restriction fragments
    • —Infrequent cutter (generally 6–8 bp recognition site) coupled with pulsed-field gel electrophoresis (PFGE) to separate restriction fragments
  • B.
    RFLP with hybridization
    • —Frequent cutter (4–6bp recognition site) coupled with conventional electrophoresis to separate restriction fragments followed by Southern transfer to nylon membrane. The power and efficacy of typing method depends on the probe.
    • —16S and 23S rRNA (ribotyping)
    • —Insertion sequences (e.g., IS6110 of Mycobacterium tuberculosis)
Amplification-based methods
  • A.

    Random amplification of polymorphic DNA (RAPD) analysis; arbitrarily primed PCR (APPCR)

  • B.

    Amplified fragment length polymorphism (AFLP) method

  • C.

    Repetitive element PCR (REP-PCR) method; variable number tandem repeat (VNTR) fingerprinting

Sequence-based methods
  • A.

    Multilocus sequence typing (MLST)

  • B.

    Electrophoretic karyotyping