Strain-typing of Isolates

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Strain typing of isolates allows to compare and differentiate strains of the same species. For this purpose we use specific PCR techniques.

Typical applications for strain typing are:

  • confirming the identity of production strains
  • confirming the identity of reference strains
  • identifying the source(s) of contaminating microorganisms
  • grouping of isolates / phylogenetic analysis

Depending on the microorganism different methods are used for strain typing:

  • for bacteria: DAF-PCR or ERIC-PCR
  • for eucaryotes: microsatellite PCR


In addition to the isolate to test a defined reference isolate is required. The PCR products are separated on acrylamid gels (v. fig.). The band pattern is analysed with a specific program for densitometric analyses. This generates a phylogenetic tree to display the genetic similarities (v. fig)