Diagnosing endocarditis by metagenomics

We compared the diagnostic performance of metagenomic next-generation sequencing (mNGS) to standard clinical laboratory testing on operative specimens of cardiac valves from 19 patients with suspected infective endocarditis (IE). From each resected valve, we extracted DNA using two protocols for bacterial DNA enrichment, based on selective removal of host DNA. Metagenomic libraries were sequenced on an Illumina MiSeq instrument, providing on average 1,7 million quality filtered reads per sample. Identification of IE pathogens by mNGS was in agreement with results of blood culture. Inability to identify IE causative agents by mNGS when valves were resected at longer time after blood culture positivity was most likely due to pathogen clearing.