Strain typing using REP-PCR

Aiding to the need of our partners for root cause analysis or epidemiological purposes, we offer strain typing services. Strain typing provides additional information in regards to the underlying familiarity of strains.. For this BaseClear offers strain typing services using either our validated Multi-locus sequencing typing (MLST) for set of known bacteria and/or repetitive element palindromic PCR (rep-PCR).

This fine degree of resolution for strain typing applies to various microbial isolates, that are important to our partners. Quality control laboratories for instance pharmaceutical, biotechnological, food and health care industries use these techniques to track and trace possible microbial contaminations. Microbial isolates may be obtained from sources such as raw materials, in-process samples, the processing environment and final products.


Rep-PCR is a general method applicable for almost all microorganisms. This method generates a DNA fingerprint that is unique to the organism at the strain level. For this we use a combination of GTG5, ERIC1, ERIC2, BOX-A1-R and BOX-A2-R PCR protocols. With a comprehensive, dynamic picture of any microbial environment, technicians can track and manage data at the strain level, letting them pinpoint contamination with a high level of speed, ease and precision. In addtion, we offer GMP Microbial strain typing services through our GMP brand ProBase Pharma.

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Testimonial UMC Utrecht

For some bacteria we lack the biochemical tests that would allow us to detemine the partcular strain we are testing with the required degree of certainty. For this type of bacteria we have to rely on molecular identification, which is the part that BaseClear handles for us. BaseClear types (MLST), which allows us to establish to what extent within a given species the microorganisms are related. As such are for example, able to detemine whether different contaminations were caused by the same source.

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