Metagenomic next-generation sequencing of cell-free microbial DNA (mcfDNA) for pathogen identification

The University Hospital Basel now offers metagenomic next-generation sequencing (mNGS) of cell-free microbial DNA (cfDNA) using the DISQVER platform, which enables culture-independent detection of bacterial, viral, parasitic, and fungal DNA in plasma and is used in particular for complex or culture-negative infections. An expansion to bronchoalveolar lavage (BAL) and synovial fluid is currently undergoing validation.

2026-04-21, 12:02

The test involves the isolation of cell-free DNA, sequencing (in collaboration between the Department of Pathology and the Department of Clinical Microbiology), followed by data transfer to Noscendo GmbH (Duisburg, Germany) and bioinformatic analysis through comparison with a validated, IVDR-compliant reference database (DISQVER).

 

The available evidence1-5 demonstrates the additional diagnostic value of cfDNA-based mNGS, particularly for culture-negative and previously treated infections. The underlying platform is described in a recent WHO analysis as the only commercial clinically available NGS-based diagnostic solution for invasive fungal infections6.

 

For preanalytical processing, samples must be submitted in cfDNA-stabilizing tubes (e.g., Streck Cell-Free DNA BCT, Streck, USA). Requests are submitted externally via the submission form for Molecular Infectious Pathology and internally via the “Molecular Diagnostics (Microbiology)” tab within the laboratory medical analyses.

 

Indications:

 

  • Fever of unknown origin (FUO)
  • Culture-negative endocarditis
  • Suspected invasive fungal infection with negative routine diagnostics
  • Complex immunocompromised cases
  • Travel history and suspicion of rare pathogens
  • Suspicion of zoonoses
  • Deep abscesses without the possibility of invasive sample collection
  • Prosthesis- or device-associated infections with negative cultures
  • Antibiotic pretreatment, limited culture detectability
  • Other diagnostically challenging infectious disease scenarios

 

Due to its centralized, once-weekly processing, the method is not suitable for acute diagnostics.

 

References:

1Blauwkamp, T.A., Thair, S., Rosen, M.J. et al. Analytical and clinical validation of a microbial cell-free DNA sequencing test for infectious disease. Nat Microbiol 4, 663–674 (2019).

 

2Park SY, Chang EJ, Ledeboer N et al.. 2023. Plasma Microbial Cell-Free DNA Sequencing from over 15,000 Patients Identified a Broad Spectrum of Pathogens. J Clin Microbiol 61:e01855-22.

 

3Wolf, Joshua, Kathryn P. Goggin et al. "Predicting bloodstream infection by plasma cell-free metagenomic sequencing: a prospective cohort study." The Lancet Microbe (2026).

 

4Esse, J., Träger, J., Steininger et al. , 2025. Metagenomic analysis of microbial cell-free DNA from plasma of patients with suspected infections: performance and therapeutic impact in clinical routine. Clinical Microbiology and Infection, 31(6), pp.1018-1025.

 

5Neidhöfer, C., Klein, N., Yürüktümen, A et al., 2025. Retrospective analysis of 300 microbial cell-free DNA sequencing results in routine blood stream infection diagnostics. Frontiers in cellular and infection microbiology, 15, p.1504262.

 

6Landscape analysis of commercially available diagnostics for fungal priority pathogens.Genf: WHO, 2023. https://www.who.int/publications/i/item/9789240105539