Microbial strain typing

For root cause analysis of microbial contaminants or epidemiological purposes, BaseClear offers microbial strain typing services. Strain typing provides information in regards to the familiarity of strains. For this purpose BaseClear offers strain typing services using our validated Multi-locus sequencing typing (MLST) and/or repetitive element palindromic PCR (rep-PCR). Our rep-PCR is also available as GMP certified service. In addition, BaseClear can also offer strain typing service based on whole genome sequencing (WGS).

Quality control laboratories in the 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 addition, we offer GMP Microbial strain typing services through our GMP brand ProBase Pharma.

Strain typing using Whole Genome Sequencing

Whole genome sequencing (WGS) of microbial contaminants has become an effective method for investigating the information contained in the genome sequence. In addition, its highly discriminative power enables the comparison of genetic relatedness between bacteria and fungi even on a sub-species level. For this reason, WGS is being implemented worldwide and across sectors (pharma, biotech, food, veterinary and environment) for root cause analysis, the investigation of outbreaks, source attribution, and improved risk characterization models. In order to extract relevant information from the large quantity and complex data produced by WGS, BaseClear developed bioinformatics tools, allowing to analyse and interpret the data, starting from simple gene-searches to complex phylogenetic studies.

Our GMP certified servicesRequest quotation

Multi-locus sequence typing (MLST)

Our MLST is an unambiguous procedure for characterizing isolates of bacterial species using the sequences of internal fragments of (usually) 6 to 8 house-keeping genes. Approximately 450-500 bp internal fragments of each gene are used, as these can be accurately sequenced on both strands. For each of these housekeeping genes, the different sequences are assigned as alleles and the alleles at the loci provide an allelic profile or sequence type (ST). A series of profiles can then be the identification marker for strain typing.

The great advantage of MLST is that sequence data are unambiguous and the allelic profiles of isolates can easily be compared to those in a large central database via the internet. A further advantage of MLST is that the profiles can be obtained from clinical material directly from CSF or blood. Thus isolates can be precisely characterized even when they cannot be cultured from clinical material. The common microorganisms tested in our laboratory include Cronobacter spp, Bacillus cereus, Bacillus licheniformis, Escherichia coli, Listeria monocytogenes, Propionibacterium acnes, Salmonella enterica and Staphylococcos aureus.

Get in touch!

  • * Required fields

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.

Get in touch