Next-Generation Sequencing for the Diagnosis of Challenging Culture-Negative Endocarditis

Abstract

Diagnosis of culture-negative infective endocarditis usually implies indirect pathogen identification by serologic or molecular techniques. Clinical metagenomics, relying on next-generation sequencing (NGS) is an emerging approach that allows pathogen identification in challenging situations, as evidenced by a clinical case. We sequenced the DNA extracted from the surgically-removed frozen valve tissue from a patient with suspected infective endocarditis with negative blood and valve cultures. Mapping of the sequence reads against reference genomic sequences, a 16S rRNA gene database and clade-specific marker genes suggested an infection caused by Cardiobacterium hominis.

Keywords: Cardiobacterium hominis; clinical metagenomics; culture-negative endocarditis; diagnosis; next-generation sequencing.

Figure 1

Relative abundance of prokaryotic taxa determined by classification of genome fragment sequences (CLARK), classification of 16S rRNA gene fragments (mothur/Wang) and read mapping to clade markers (MetaPhlAn2). All taxa with relative abundance <1% were summed up and represented as “others.” For simplicity, in the mothur/Wang approach, only results obtained with forward sequence reads are presented. n, number of hits obtained for each sample and method used.