In addition to routine screening for harmful pathogens, bacterial species identification and further strain differentiation play an important role in food safety and quality investigations. These methods can offer an immediate classification of an existing or new problem in a given facility. Additionally, the resulting data gives manufacturers the ability to track contamination strains and map the bacterial flora present within their facility in order to monitor raw materials, surfaces, finished product and overall sanitation effectiveness.

Over the past few decades, outbreak investigations involving contaminated food from pathogenic microorganisms have advanced through the use of Next Generation Sequencing (NGS) technology. However, there are many other cost-effective methods for identifying bacteria below the species level. One such technique for strain differentiation is ribotyping.

What is Ribotyping?

Living cells contain ribosomes, which are part of the cellular machinery responsible for creating proteins. A ribosome is composed of ribonucleic acid (RNA) that is folded and organized in a particular formation. This RNA is referred to as ribosomal RNA (rRNA). From organism to organism, the DNA genes that encode rRNA (rDNA genes) are very similar, even across different species. However, some regions of the rDNA are variable, even from one strain of bacteria to the next strain of the same species. These variable regions are detected, mapped and stored to create a precise fingerprint of the strain for comparison purposes.

How are the Variable Regions Detected?

Ribotyping utilizes restriction enzymes to scan the genome and detect specific DNA sequences. Upon encountering these sequences, and under the right conditions, these enzymes will make a very precise cut in the DNA. Thus, if a strain of bacteria has that specific sequence in its DNA, then the DNA will be cut at that location by the enzyme. If another strain of bacteria has a few different bases or even one base different in the same region, the enzyme will not recognize it and the DNA will not be cut. After restriction (“cutting”), the genome is now in pieces, and any pieces of DNA that contain part of the rDNA region (5S, 16S, 23S, and flanking regions) can be detected with a DNA probe. These rDNA-containing fragments of different sizes can be visualized, creating a ribotype pattern.

Mérieux NutriSciences is excited to announce that we will be offering a new microbial strain characterization service, Hygiena RiboPrinter® coming this fall. The RiboPrinter® system is a standardized, fully automated and reproducible genome-level restriction enzyme-based method that specifically targets the ribosomal DNA to generate a fingerprint pattern of a given microorganism for strain tracking purposes.

In some cases, it is desirable to conduct strain tracking analysis without identifying the species present, such as when testing product contact surfaces for Listeria species. This new offering allows strain tracking to be conducted without identifying the species of the organism and with no potential linkage to public health illness database.


Meet the Author

Seth Keller
Product Manager – Analytical Services, Mérieux NutriSciences

Seth Keller is the Product Manager for Analytical Services at Mérieux NutriSciences. His current focus is on the development of analytical offerings in GMO, in addition to reviewing and implementing new microbiological methods. Seth received a Bachelors degree in Molecular and Cellular Biology from the University of Illinois Urbana-Champaign in 2011. In his free time he enjoys playing golf, working out, cooking, spending time with his friends, and rooting for all Chicago teams, specifically the Cubs and Blackhawks.

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