Identification of fungi and ameba from human wound genomic sequencing

Hypothesis-free detection of pathogens directly in sample material from patients with infectious diseases of unknown origin using next generation sequencing (NGS) is an important goal of diagnostic research. However, NGS is highly susceptible to contamination, which complicates the interpretation of diagnostic results from samples with (poly-)microbial contamination. The potential of NGS for hypothesis-free diagnostic approaches of such difficult sample material is examined in the study presented here, using the example of formalin-fixed, paraffin embedded tissue samples from patients with invasive fungal infections and invasive amebiasis.