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

Microbial cell-free DNA (mcfDNA) enables rapid and sensitive pathogen detection via direct plasma-sequencing. Here, we present a fast, cost-effective mcfDNA multiplex workflow to complement or improve the sensitivity of microbiological diagnostics for systemic and focal infections which can be challenged by prior antibiotic treatment or non-culturable pathogens. In an explorative study of 18 patients, mcfDNA sequencing matched the clinical diagnosis in 16 cases (89%), was detected up to 16 days after starting targeted antibiotic therapy and identified Staphylococcus aureus in two cases of culture-negative endocarditis. By providing an open-access protocol, we aim to promote broader accessibility and globally available application.