Microbial cell-free DNA for rapid pathogen identification in clinical diagnostics: a proof of concept study

Area of Science:

• Clinical Microbiology
• Genomics
• Infectious Diseases

Background:

• Microbial cell-free DNA (mcfDNA) sequencing is a promising tool for pathogen detection.
• Current microbiological diagnostics can be limited by factors like prior antibiotic use or non-culturable pathogens.

Purpose of the Study:

• To develop and present a fast, cost-effective mcfDNA multiplex workflow.
• To enhance the sensitivity of microbiological diagnostics for systemic and focal infections.

Main Methods:

• Explorative study involving 18 patients.
• Direct plasma-mcfDNA sequencing.
• Development of a multiplex workflow.

Main Results:

• mcfDNA sequencing matched clinical diagnosis in 16 out of 18 patients (89%).
• mcfDNA was detected up to 16 days after initiating antibiotic therapy.
• Identified Staphylococcus aureus in two culture-negative endocarditis cases.

Conclusions:

• The mcfDNA multiplex workflow is effective for pathogen detection in challenging cases.
• This approach can improve microbiological diagnostics, especially when culture methods fail or are compromised.
• An open-access protocol is provided to promote global accessibility.