# 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. ## One workflow, three steps PCR screening for bacteria (16S) and fungi (28S) followed by identification on the hybcell is what we call compact sequencing. Test components and workflow are the same across all intended uses — only sample preparation differs by sample type. 01. **Sample prep & DNA purification** — Whole blood: human DNA is removed with the GINA kit. BAL and positive blood cultures: no extraction — the LINA modulation buffer is enough. 02. **pan-bacterial / pan-fungal PCR** — The enriched microbial DNA is amplified with the PCR master mixes — pan-bacterial (16S), pan-fungal (28S) and optionally for resistance genes. 03. **Identification on the hybcell** — Positive samples are identified on the hybcell; results are summarised automatically in a compact report. ## Four applications, one system ### Sepsis diagnosis · culture-free, from whole blood **82–87** microorganisms & resistance genes · 3 hours 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. - Sample: 0.5 mL EDTA blood - Preparation: Enrichment of microbes - Preparation: DNA extraction - Preparation: Columns or magnetic beads - 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 Workflow: 01. Sample preparation: GINA 500 02. DNA extraction & detection (~1.75 h): GINA DNA Purification, 3rd party DNA extraction, PCR-Box Bacteria, PCR-Box Fungi 03. Identification (< 3 h total): hybcell Bacteria DNA xB, hybcell Fungi DNA xB ### Pneumonia diagnosis · extraction-free, from BAL **31** microorganisms · 2 hours 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. - Sample: BAL, a few µl - Preparation: Homogenised in LINA buffer - Preparation: No DNA extraction - 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 Workflow: 01. Sample preparation: LINA 02. PCR detection: PCR-Box Bacteria, PCR-Box Fungi 03. Identification (2 h total): hybcell Bacteria DNA xB, hybcell Fungi DNA xB ### Microbial identification · directly from positive blood culture **95** microorganisms & resistance genes · 2 hours 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. - Hands-on: ~1 min - Sample: Positive blood culture, a few µl - Preparation: Added directly to LINA buffer - Preparation: No DNA extraction - 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 Workflow: 01. Sample preparation: LINA 02. PCR detection: PCR-Box Bacteria, PCR-Box Fungi 03. Identification (< 2 h total): hybcell Bacteria DNA xB, hybcell Fungi DNA xB ### For research use · broad molecular fungal test **66** fungal targets · 16 genera, 50 species · 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 Workflow: 01. Sample preparation: GINA 02. DNA extraction & detection: GINA DNA Purification, 3rd party DNA extraction, PCR-Box Fungi 03. Identification (2.5 h total): hybcell Fungi DNA xB ## Molecular Microbiology — literature The technology has been evaluated in independent studies. A selection of available literature: - 2016: [Sensitive Molecular Identification of Pathogens causing Implant and Tissue Infections (ITI)](https://www.cubedx.com/literature/2016KHWELSComparisonCultureTissue.pdf) - 2020: [Molecular pathogen identification and resistance gene detection from positive blood cultures](https://www.cubedx.com/literature/2020ECCMIDAbstract-LINApositiveBC.pdf) - 2020: [Presence and distribution of fungal species and dermatophytes in nail and skin samples](https://www.cubedx.com/literature/2020ECCMIDAbstract-Dermatophytes.pdf) - 2021: [SMARTDIAGNOS – next generation molecular sepsis diagnosis technology for whole blood samples](https://www.cubedx.com/literature/2021ECCMIDPoster-SMARTDIAGNOSSepsis.pdf) - 2022: [Extraction-free Molecular Identification of Bacteria/Fungi Directly from BAL Samples](https://www.cubedx.com/literature/2022CDXAppNoteLINABAL.pdf) - 2023: [Comparison of two molecular assays and MALDI-TOF MS Sepsityper for the rapid identification of pathogens from positive blood cultures](https://www.cubedx.com/literature/2023ECCMIDPoster-LINAvsSepsityperMUV.pdf) - 2023: [Detection of bacterial pneumonia pathogens in patients with COVID-19](https://www.cubedx.com/literature/2023ECCMIDPoster-LINAwithBALMUE.pdf) - 2023: [Diagnostic value of blood culture independent molecular tests for the diagnosis of bloodstream infections in neutropenic patients with fever](https://www.cubedx.com/literature/2023ECCMIDPoster-NeutropfeverComparisonbloodtestMUV.pdf) - 2026: [Performance comparison to in-house PCR and 16S sequencing](https://www.cubedx.com/literature/ESCMID2026POSTER-ComparisonPCR16SHAUKELANDUNIVERSITY.pdf) - 2026: [Infective endocarditis: an alternative molecular diagnostic approach to improve laboratory analysis of heart valve tissue](https://www.cubedx.com/literature/ESCMID2026POSTER-EndocarditsHOSPITALVERONA.pdf) - 2026: [Rapid molecular detection directly from whole blood for the early diagnosis of paediatric bloodstream infections using the cube dx system](https://www.cubedx.com/literature/ESCMID2026POSTER-BSITestingChildrenBAMBINOGESU.pdf) 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.