Root cause analysis

In case of a microbial contamination it is necessary to determine the root cause of the contamination problem. BaseClear offers all-inclusive microbial typing services for microbial root cause analysis (RCA). Different microorganisms occupy a diverse range of habitats. The only way to determine the origin of a contaminating microorganism is to characterize it as a specific strain and match this with control strains, or other strain present somewhere else in the environment.

Strain typing services

Strain typing provides in-depth information in regards to the underlying familiarity of strains. Quality control laboratories for instance pharmaceutical, biotechnological, food and health care industries use these techniques for root cause analysis of microbial contaminations. Microbial isolates may be obtained from sources such as raw materials, in-process samples, the processing environment and final products.


We offer GMP Microbial strain typing services through our daughter company ProBase Pharma. ProBase Pharma uses the power of DNA to not only identify the genus/species of contaminants, but also provide deeper, strain-level typing at the same time. This fine degree of resolution applies to environmental isolates, pathogens, spoilage organisms, control strains, beneficial organisms or any other bacteria that are important to the industry.

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Strain typing services BaseClear

Root cause analysis methods

For root cause investigation BaseClear Quality Solutions offers microbial typing services based on Rep-PCR and MLST.


MLST typing offers the advantage that the sequence data are unambiguous and the MLST profiles can easily be compared with a large central database. We can help you to determine the optimal typing method, quality level and delivery time and help you solve your contamination problem.


Rep-PCR is a universal method for both fungi and bacteria. In addition, we offer the possibility to do Multi-Locus Sequence Typing (MLST) on bacterial and some fungal species.

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BaseClear Microbiology services

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