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.

87 microorganisms / resistance genes - in 3 hours

DIAGNOSING SEPSIS – WITHOUT CULTURING / FROM BLOOD

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.

31 microorganisms - in 2 hours

DIAGNOSING PNEUMONIA – WITHOUT EXTRACTION / FROM BAL

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.

100 microorganisms / resistance genes - in 2 hours

MICROBIAL IDENTIFICATION – DIRECTLY FROM POSITIVE HEMOCULTURE

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.

16 fungal genera / 50 fungal species - in 2.5 hours

FOR RESEARCH PURPOSES - WIDE MOLECULAR FUNGUS TEST

Cube Dx offers fast and comprehensive DNA-based identification of fungi from different samples for research purposes. By using our GINA sample preparation, the overall time to result for ‘difficult’ samples such as skin or nail scales can also be drastically reduced.

For example, 0.5 mL of fresh EDTA blood can be used as a sample, which is prepared using the GINA sample preparation system. However, any other sample - from BAL to urine, CSF, tissue, skin, nails or hair - can also be used. The sample DNA contained in the eluate serves as the input material for the test.
The microbial DNA is amplified with the PCR master mix and positive samples are transferred to the hybcell cartridges and the fungi are identified by compact sequencing. The results are automatically summarised in a compact report.

Molecular microbiology - Literature

Available literature