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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 / DNA-based pathogen tests support microbiologists and infectious disease specialists in providing early indications of sepsis-causing pathogens directly from whole blood and other sample matrices.

This is particularly relevant for microorganisms that grow slowly or not at all in the provided growth media or which are already weakened by antimicrobial treatment.

Molecular Microbiology
Why it matters

Early results - optimised therapy

Earlier to result

Comprehensive pathogen ID directly from whole blood and other sample matrices in less than 3 hours — no culturing required.

Additional results

Additional results from DNA-based detection of pathogens that are difficult to culture (fungi, fastidious bacteria, anaerobes) or for patients who have already undergone treatment.

Versatile multiplexing

Sepsis, other severe infections (pneumonia, etc.), or general 16S/28S amplicon sequencing—the same platform, the same products, multiple applications.

Intended uses

Four applications, one system

Sepsis diagnosis · culture-free, from whole blood
82–87microorganisms & resistance genes
View the test panel
Time to result
3 hours
Sample
0.5 mL EDTA blood
Sample prep
Enrichment of microbes
DNA extraction
Columns or magnetic beads

In suspected sepsis, the test gives a very early indication of the causative microorganisms — directly from 0.5 mL of fresh EDTA whole blood. In the GINA process most human cells are separated before the microbial DNA is purified, amplified by PCR and identified on the hybcell.

  • Up to 98% yield of microbial DNA
  • Sensitive, parallel identification of bacteria, fungi and resistance genes
  • Detection of multiple pathogens / mixed infections
  • Optional internal process control (IPC) to validate negative results
  • Clinical sensitivity: 74%
  • Specificity: 98%
  • Limit of detection: 20 CFU/mL
  1. 01

    Sample preparation

    • GINA 500
  2. 02

    DNA extraction & detection

    ~1.75 h
    • GINA DNA Purification
    • 3rd party DNA extraction
    • PCR-Box Bacteria
    • PCR-Box Fungi
  3. 03

    Identification

    < 3 h total
    • hybcell Bacteria DNA xB
    • hybcell Fungi DNA xB
Pneumonia diagnosis · extraction-free, from BAL
31microorganisms
View the test panel
Time to result
2 hours
Sample
BAL, a few µl
Sample prep
Homogenised in LINA buffer
No DNA extraction

BAL is tested directly without DNA extraction: a few µl are homogenised in the ready-to-use LINA modulation buffer and used immediately in PCR. The same products (PCR and hybcell) as for sepsis testing are used; a software option restricts the output to the CE-IVD-certified pneumonia panel.

  • No DNA extraction, few manual steps
  • Sensitive, parallel identification of bacteria and fungi
  • Detection of mixed infections
  • CE-IVD-certified pneumonia panel via software option
  1. 01

    Sample preparation

    • LINA
  2. 02

    PCR detection

    • PCR-Box Bacteria
    • PCR-Box Fungi
  3. 03

    Identification

    2 h total
    • hybcell Bacteria DNA xB
    • hybcell Fungi DNA xB
Microbial identification · directly from positive blood culture
95microorganisms & resistance genes
View the test panel
Time to result
2 hours
Hands-on
~1 min
Sample
Positive blood culture, a few µl
Sample prep
Added directly to LINA buffer
No DNA extraction

Fast DNA-based identification of pathogens grown in blood cultures — with no further sub-culture. A few µl are added directly to the LINA buffer with about one minute of hands-on time, transferred to PCR and identified on the hybcell. Also suitable as a backup to MALDI-TOF-based identification.

  • No DNA extraction, no sub-culture
  • Even slow-growing pathogens alongside the dominant organism
  • Detection of mixed infections
  • Result in under 2 hours
  • Bacteria: 56 species + 11 genera
  • Fungi: 19 species + 5 genera
  • Resistance genes: 4
  1. 01

    Sample preparation

    • LINA
  2. 02

    PCR detection

    • PCR-Box Bacteria
    • PCR-Box Fungi
  3. 03

    Identification

    < 2 h total
    • hybcell Bacteria DNA xB
    • hybcell Fungi DNA xB
For research use · broad molecular fungal test RUO
66fungal targets · 16 genera, 50 species
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Time to result
2.5 hours

Extensive DNA-based identification of fungi from a wide range of samples — from whole blood through BAL, urine, CSF and tissue to skin, nails and hair. The GINA sample prep also shortens time to result significantly for difficult samples.

  • Testing of highly varied sample matrices
  • Automated workflow with few manual steps
  • Detection of multiple pathogens / mixed infections

Research Use Only (RUO).

  1. 01

    Sample preparation

    • GINA
  2. 02

    DNA extraction & detection

    • GINA DNA Purification
    • 3rd party DNA extraction
    • PCR-Box Fungi
  3. 03

    Identification

    2.5 h total
    • hybcell Fungi DNA xB

Running your own 16S or 28S sequencing? GINA and PCR-Box prepare the sample and the amplicons. 16S & 28S sequencing

Evidence

Molecular Microbiology — literature

The technology has been evaluated in independent studies. A selection of available literature:

  1. 2016Sensitive Molecular Identification of Pathogens causing Implant and Tissue Infections (ITI)
  2. 2020Molecular pathogen identification and resistance gene detection from positive blood cultures
  3. 2020Presence and distribution of fungal species and dermatophytes in nail and skin samples
  4. 2021SMARTDIAGNOS – next generation molecular sepsis diagnosis technology for whole blood samples
  5. 2022Extraction-free Molecular Identification of Bacteria/Fungi Directly from BAL Samples
  6. 2023Comparison of two molecular assays and MALDI-TOF MS Sepsityper for the rapid identification of pathogens from positive blood cultures
  7. 2023Detection of bacterial pneumonia pathogens in patients with COVID-19
  8. 2023Diagnostic value of blood culture independent molecular tests for the diagnosis of bloodstream infections in neutropenic patients with fever
  9. 2026Performance comparison to in-house PCR and 16S sequencing
  10. 2026Infective endocarditis: an alternative molecular diagnostic approach to improve laboratory analysis of heart valve tissue
  11. 2026Rapid molecular detection directly from whole blood for the early diagnosis of paediatric bloodstream infections using the cube dx system

Molecular microbiology is at the heart of cube dx diagnostics: a single, end-to-end system covers sepsis, pneumonia, identification from positive blood culture and the broad molecular fungal test — fast, sensitive and directly from the sample.

Interested?

Let's discuss your application

We'll show you the system in your lab environment and discuss the right panel configuration.

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Christoph Reschreiter, Management, cube dx