Molecular microbiology

Molecular Microbiology

Sepsis and other severe infections are mainly caused by bacteria or fungi. Early identification of the causative pathogen is crucial for effective and successful treatment with antibiotics, antimycotics, supporting medication, and other treatments. Cube Dx molecular pathogen tests support microbiologists and infectious disease specialists in providing early indications of sepsis-causing pathogens in whole blood and other sample matrices. 


This is particularly relevant for microorganisms that have been weakened by antimicrobial treatment or which demonstrate slow growth in or on microbiological nutrient media. The broad spectrum of the Cube Dx molecular microbiology test is ideally suited to test for pathogens causing sepsis and other severe infections.

The test is based on three steps: sample preparation and DNA purification, PCR and identification with the hybcell.


The PCR screening for bacteria (16S rDNA) and fungi (28S rDNA) and the follow up identification process on the hybcell are termed compact sequencing, and the test components (PCR mixes and hybcells) and processes are the same for all intended uses. The treatment of the different sample matrices differs strongly between analysing whole blood for sepsis diagnostics or BAL / positive blood cultures for diagnosing pneumonia and other infections.


Whereas analysing whole blood requires the removal of human DNA using the GINA kit, BAL or positive blood cultures require no DNA extraction process whatsoever and use the modulation buffer LINA instead.

87 microorganisms / resistance genes - in 3 hours


CubeDx supports clinicians by providing a very early indication of sepsis-causing microorganisms directly in whole blood. Testing whole blood reduces the time to result to just 3 hours! Our multiplex technology allows for identification of 87 targets (microorganisms and resistance genes) in parallel. 

Fresh EDTA blood (0.5ml) serves as a sample. To validate a negative result, an Internal Process Control (IPC) can optionally be introduced into the sample.

During the GINA process, most cells of human origin are depleted before DNA is purified.

The enriched microbial DNA is amplified using a choice of PCR master-mixes: pan-bacterial PCR, pan-fungal PCR or PCR to screen for several resistance genes.

Positive samples are transferred into the hybcell cartridges, and the microorganisms and resistance genes are identified by the hybcell and its compact sequencing process, with the results subsequently presented in a comprehensive report.

Features / Advantages:

  • Results in just 3 hours!

  • Yield of up to 98% of microbial DNA

  • Limit of detection (whole blood): 20 CFU/mL

  • Clinical sensitivity: 74% and specificity: 98%

  • Early and comprehensive results from 0.5 mL whole blood

  • Sensitive and parallel identification of bacteria, fungi, and resistance genes

  • Identification of multiple pathogens/mixed infections

  • Simple handling, an optimized workflow with 24/7 availability and immediate results

31 microorganisms - in 2 hours


Cube Dx’s highly sensitive PCR mixes can test BAL without the need for prior DNA extraction. A simple modulation buffer – LINA – is used to modulate and homogenize BAL. Using the extraction-free protocol shortens the time to result to only 2 hours.

The LINA modulation buffer is used for samples with a relatively high concentration of pathogens, for example BAL. Only a few µL of BAL are added to the ready-to-use LINA tube and the solution is mixed. The mixture is directly used for the follow-up PCR. The test (PCR and hybcell) is the same product as used for testing for sepsis – a software option limits the output to the CE-IVD certified panel for pneumonia.


The LINA transfer and modulation buffer shorten the time for molecular identification to 2 hours – as it eliminates the DNA extraction process.

Features / Advantages:

  • No DNA extraction

  • Identification of pathogens in less than 2 hours

  • Simple and fast

  • Sensitive and parallel identification of bacteria and fungi

  • Identification of multiple pathogens/mixed infections

100 microorganisms / resistance genes - in 2 hours


CubeDx offers fast DNA-based identification of microorganisms grown in blood cultures. No further pure culture is needed, and even slow growers can be identified in parallel to the dominating microorganism. This test can, at the very least, serve as a backup system to identification with MALDI-TOF. 

The LINA buffer offers a simple, fast and efficient path to identifying disease-causing pathogens with only 1 minute actual hands-on time. A few µL of positive blood culture can be directly added to the LINA buffer without the need for pure cultures. The mixture is transferred into the PCR module, and identification with hybcell follows with the result being delivered in 2 hours.

Features / Advantages:

  • Bacteria: 56 species + 11 genera

  • Fungi: 19 species + 5 genera

  • 9 antibiotic resistance genes

  • Results for mixed infections

  • No DNA extraction

  • Identification of pathogens in less than 2 hours

  • Simple and fast

  • Identification of multiple pathogens/mixed infections

Molecular microbiology - Literature

Available literature