Metagenomic analysis of microbial cell-free DNA from plasma of patients with suspected infections: performance and therapeutic impact in clinical routine.

Abstract

Objectives: The sensitivity of blood cultures (BC) is limited, especially when antimicrobial therapy already has been administered or when non-culturable pathogens are causing the disease. Metagenomic next-generation sequencing (mNGS) of cell-free DNA (cfDNA) from plasma has the potential to compensate for the disadvantages of BC diagnostics.

Methods: We conducted a retrospective study in patients with suspected infections over a period of 3 months. cfDNA from plasma was analysed by mNGS (Illumina NextSeq, 25 million reads per sample, read length 75 base pairs) and sequences were analysed with DISQVER®, a CE-IVDD-labelled software algorithm and curated database. The data were compared to findings obtained with simultaneously taken BC and other microbiological results (+/- 7 days).

Results: DISQVER® analysis was performed on 190 samples from 147 patients (124 adult, 23 pediatric). The median time-to-result including transport was two days (IQR 2-3; range 2-8). DISQVER® detected 158 pathogens (103 bacteria, 49 viruses, four fungi, one parasite) in 80 plasma samples (positivity rate 42.1%). The median number of pathogens per positive sample was one (IQR 1-2; range 1-10). The most common bacteria were Enterobacterales (30.1%; 31/103), anaerobic bacteria (18.4%; 19/103) and Enterococcus spp. (15.5%; 16/103), the most frequent viruses were Epstein-Barr virus (28.6%; 14/49), human herpesvirus 6B (18.4%; 9/49) and human cytomegalovirus (18.4%; 9/49). Mycobacterium avium, Legionella pneumophila, Tropheryma whipplei, Rhizomucor pusillus and Leishmania infantum were detected in one sample each. Simultaneous BC were positive in only 10.2% (18/176) of the samples, but were mostly (68.2%; 120/176) collected under antibiotic therapy. DISQVER® analysis resulted in 24 treatment changes in 20 patients (13.6%; 20/147; 9 start/escalation, 10 stop/de-escalation, 2 catheter replacements, 3 other).

Conclusions: DISQVER® significantly increased the detection rate of pathogens, led to the diagnosis of serious infections that otherwise would have been missed, and possibly improved the treatment of more than 10% of patients.