Strain typing

To control unwanted bacteria you need to know what the contaminating organism is and how it entered your environment. For this ProBase Pharma offers a microbial strain typing service using rep-PCR in combination with 16S sequencing. These techniques use 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. Quality control labs in for instance pharmaceutical, biotechnological, food, medical device and health care industries use these strain typing techniques to track and trend microbial contaminations and environmental monitoring isolates.


Repetitive element sequence-based PCR (rep-PCR) is a strain typing method that enables the generation of DNA fingerprints that discriminates different samples. Eukaryotic and prokaryotic DNA contains so-called repetitive DNA elements distributed more or less randomly over the genome.

Rep-PCR uses primers complementary to interspersed repetitive consensus sequences that enable amplification of diverse-sized DNA fragments consisting of sequences between the repetitive elements. The PCR-products are separated by a microfluidics-based platform for sizing and a species (sometimes strain)-specific pattern is obtained. Isolates with similar patterns (i.e. belonging to the same species) will cluster together.

Examples of these repetitive elements are the repetitive extragenic palindromic (REP) sequences, the enterobacterial repetitive intergenic consensus (ERIC) sequences, the BOX sequences, and the polytrinucleotide (GTG)5 sequence.