Quantification and Identification of Microorganisms in Beverages, Food and Water

 HybriScan® Rapid Microbial Test System

Our HybriScan® molecular screening system uses sandwich hybridization to provide fast and accurate detection, identification and quantification of spoilage and pathogenic microorganisms in beverages, water and food.  It is ideal for the comprehensive and reliable routine control of raw materials and concentrates in all production steps up to the quality check of finished goods.

The HybriScan® system can reduce your time to result by 2-14 days, depending on the target organism, while keeping costs low. Results are visible within 2 hours after the enrichment without the need for expensive instruments—the test can be performed with standard laboratory equipment and minimal training.

 20-minute talk: in situ hybridization

Our expert, Jvo Siegrist, explains the technology of in situ hybridization on the example of the HybriScan® test system. Watch the presentation to learn about the advantages, disadvantages and costs of this rapid method compared to common methods.



HybriScan® system screening workflow with analysis time of approx. 2–2.5 hours

Figure 1. HybriScan® system screening workflow with analysis time of approx. 2–2.5 hours


 Rapid Microbiological Method: Sandwich Hybridization

The method simply needs a centrifuge, a thermal mixer and an optional a microplate reader. The complete analysis can be achieved in 2 hours for the HybriScan®D kit (quantitative kits) and about 1 hour for HybriScan®I kit (identification kits). Qualitative results can be determined by eye or, for quantitative measurement, use with a microplate reader.

 Sensitivity, Specificity and Flexibility of Sandwich Hybridization

Sandwich hybridization is very sensitive and can detect attomoles of the target rRNA molecules in yeast or bacteria.1-3 These types of cells contain a large number of rRNA-containing ribosomes; a single cell therefore contains several thousand copies of rRNA but only one DNA copy. Sandwich hybridization provides sensitivity in crude biological samples because it is not susceptible to matrix interference. By using specific probes, the HybriScan® system allows both genus or species-specific detection and it is therefore applicable to many analytical fields, including monitoring the microbial content of beer, wine, non-alcoholic beverages, drinking water, a wide variety of foods and wastewater.

  • Detects viable microorganisms only—minimizes false-positive results from dead bacteria
  • Not sensitive to sample matrix
  • Genus- and species-specific detection
  • Results in just 2 hours after enrichment
  • Broad application range: beer, wine, non-alcoholic beverages, drinking water, food and wastewater

 Advantages of HybriScan® technology over other microbial detection techniques


Detection Technology Advantage Disadvantage
HybriScan® system
  • Detects only living cells 
  • Minimal interference by sample matrix
  • High specificity
  • Low cross-reactivity
  • Easy handling
  • Cost-efficient read-out
  • Quantitative and qualitative
  • High sample throughput (96-microwell plates)
  • Detects of non-culturable microbes
  • No differentiation of serotypes or subspecies
  • Limited probe design (rRNA target)
  • High sample throughput
  • Sensitive
  • Quantitative
  • No live/dead cell differentiation
  • Sensitive to matrix interference (high extraction effort)
  • Susceptible to polymerase inhibition
  • Differentiation of serotypes or subspecies
  • High sample throughput (96-microwell plates)
  • Quantitative and qualitative
  • Low sensitivity
  • Low specificity, higher cross-reactivity
  • Slow and expensive assay development
Conventional cultivation-based methods
  • Relatively inexpensive
  • Simple
  • Specific
  • Widely accepted method
  • Time-consuming (up to 10 days)
  • No detection of non-culturable microbes
  • Low sample throughput
  • Laborious

 HybriScan® Waste Water Bacterial Count Calculator

For our Wastewater Kits (04447 HybriScan® D Waste Water Microthrix parvicella, 78436 HybriScan® D Waste Water Total Bacterial Count), we provide an excel sheet for calculation of total bacterial count, Microthrix count and ratio of Microthrix : Total Bacterial Count.

To download the file please click on the links below:

Hybriscan Waste Water Calculator English

Excel Sheet 28KB

Waste Water Calculator English
Hybriscan Waste Water Calculator Deutsch

Excel Sheet 56KB

Waste Water Calculator Deutsch





  1. Huhtamella, S.; Leinonen, M.; Nieminen, T.; Fahnert, B.; Myllykoski, L.; Breitenstein, A.; Neubauer, P. RNA-based sandwich hybridisation method for detection of lactic acid bacteria in brewery samples. J. Microbiol. Methods 2007, 68(3), 543-53.
  2. Leskela, T.; Tilsala-Timisjarvi, A.; Kusnetsov, J.; Neubauer, P.; Breitenstein, A. Sensitive genus-specific detection of Legionella by a 16S rRNA based sandwich hybridization assay. J. Microbiol. Methods 2005, 62(2), 167-79.
  3. Rautio, J.; Barken, KB.; Lahdenpera, J.; Breitenstein, A.; Molin, S.; Neubauer, P. Sandwich hybridisation assay for quantitative detection of yeast RNAs in crude cell lysates. Microb. Cell Fact. 2003, 2(1), 4-12.