Pathogen Detection in Infective Endocarditis Using Targeted Metagenomics on Whole Blood and Plasma: a Prospective Pilot Study

J Clin Microbiol. 2022 Sep 21;60(9):e0062122. doi: 10.1128/jcm.00621-22. Epub 2022 Aug 30.


Initial microbiologic diagnosis of infective endocarditis (IE) relies on blood cultures and Bartonella and Coxiella burnetii serology. Small case series and one prospective study have preliminarily reported application of metagenomic sequencing on blood or plasma for IE diagnosis. Here, results of a prospective pilot study evaluating targeted metagenomic sequencing (tMGS) for blood-based early pathogen detection and identification in IE are reported. Subjects diagnosed with possible or definite IE at a single institution were prospectively enrolled with informed consent from October 2020 to July 2021. Blood was drawn and separated into whole blood and plasma. Both specimen types were subjected to nucleic acid extraction and PCR targeting the V1-V3 region of the 16S ribosomal RNA gene, followed by next-generation sequencing on an Illumina MiSeqTM platform. 35 subjects, 28 (80%) with definite and 7 (20%) with possible IE were enrolled, including 6 (17%) with blood culture-negative endocarditis (BCNE). Overall, 20 whole blood (59%) and 16 plasma (47%) samples tested positive (P = 0.47). When results of whole blood and plasma testing were combined, a positive tMGS result was found in 23 subjects (66%). tMGS identified a potential pathogen in 5 of 6 culture-negative IE cases. Although further study is needed, the results of this pilot study suggest that blood-based tMGS may provide pathogen identification in subjects with IE, including in culture-negative cases.

Keywords: 16S rRNA PCR; 16S ribosomal RNA gene; endocarditis; next generation sequencing; targeted metagenomics.

MeSH terms

  • Endocarditis* / diagnosis
  • Endocarditis* / microbiology
  • Endocarditis, Bacterial* / diagnosis
  • Endocarditis, Bacterial* / microbiology
  • Humans
  • Metagenomics
  • Pilot Projects
  • Prospective Studies
  • RNA, Ribosomal, 16S / genetics


  • RNA, Ribosomal, 16S