Potential utility of metagenomic sequencing for improving etiologic diagnosis of infective endocarditis.

To explore potential utility of metagenomic sequencing for improving etiologic diagnosis of infective endocarditis (IE) caused by fastidious bacteria. Plasma and heart valves of two patients, who were diagnosed with IE caused by and species, were sequenced by using Illumina MiSeq and Nanopore MinION. For patient 1, was detected in the plasma pool collected 4 days before valvular replacement surgery. For patient 2, sp. oral taxon 193 was detected in the plasma sample collected on hospital day 1. Nearly complete bacterial genomes (>98%) were retrieved from resected heart valves of both patients, enabling detection of antibiotic resistance-associated features. Real-time sequencing of heart valves identified both pathogens within the first 16 min of sequencing runs. Metagenomic sequencing may be a helpful supplement to IE diagnostic workflow, especially when conventional tests fail to yield a diagnosis.