Metagenomic analysis of cell-free DNA from whole blood specimens of patients with suspected infections: performance and therapeutic impact in clinical routine

Background: Sensitivity of blood culture analysis is limited especially in cases of existing antibiotic therapy and some pathogens, like Aspergillus spp., do not grow in blood cultures at all. Metagenomic analysis of cell-free DNA (cfDNA) from whole blood has the potential to compensate for the disadvantages of blood culture diagnostics.

Methods: The study was conducted over 3 months at the University Hospital Erlangen. Adult and pediatric patients with suspected infections were included. cfDNA from whole blood was analysed by metagenomic next-generation sequencing with an Illumina NextSeq instrument. Sequences were analysed with the DISQVER^® platform (Noscendo GmbH, Germany), comprising a CE-IVD-labelled software algorithm and a curated database. In parallel, a minimum of two blood cultures were analysed.

Results: 203 samples of 156 patients (25 pediatric, 131 adult) were analysed. 12 samples (5.9%) were excluded from metagenomic analysis due to technical reasons. Mean time from sampling to result of metagenomic analysis (including logistics) was 3 days. A total of 160 pathogens were detected (1-10 pathogens per sample, mean 2). The positivity rate was 42.4%. Detected pathogens were 103 bacteria, 51 viruses, 4 fungi and 2 parasites. The most common bacteria were Enterobacteriaceae (n=31), Enterococci (n=16) and Staphylococci (n=11). The most common viruses were Epstein-Barr-virus (n=15), Herpesvirus-6B (n=10) and Cytomegalovirus (n=9). Mycobacterium avium, Legionella pneumophila, Tropheryma whipplei, Rhizomucor pusillus, and Leishmania infantum were detected in one sample each. Parallel blood cultures were positive in 11.2%. However, 62% of patients received antibiotic therapy at the time of blood culture sampling. The bacterial pathogens detected by metagenomic analysis were confirmed by classical microbiological diagnostics in 47% of cases. The analysis of the clinical data and the impact of the metagenomic analysis on anti-infective therapy are currently being investigated.

Conclusions: Metagenomic analysis of cfDNA with the DISQVER^® platform found a pathogen in a significant number of samples in which classical microbiological diagnostics were negative.