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Review
. 2022 Dec 11;11(12):1798.
doi: 10.3390/antibiotics11121798.

Utility of Metagenomic Next-Generation Sequencing in Infective Endocarditis: A Systematic Review

Sara F Haddad  1 , Daniel C DeSimone  1   2 , Supavit Chesdachai  1 , Danielle J Gerberi  3 , Larry M Baddour  1   2
Affiliations
Review

Utility of Metagenomic Next-Generation Sequencing in Infective Endocarditis: A Systematic Review

Sara F Haddad et al. Antibiotics (Basel). .

Abstract

Blood cultures have been the gold standard for identifying pathogens in infective endocarditis (IE). Blood culture-negative endocarditis (BCNE), however, occurs in 40% or more of IE cases with the bulk of them due to recent antibiotic exposure prior to obtaining blood cultures. Increasingly, molecular techniques are being used for pathogen identification in cases of BCNE and more recently has included metagenomic next-generation sequencing (mNGS). We therefore performed a literature search on August 31, 2022, that assessed the mNGS in IE and 13 publications were identified and included in a systematic review. Eight (61.5%) of them focused only on IE with mNGS performed on cardiac valve tissue in four studies, plasma in three studies and cardiac implantable electronic devices (CIED) in one study. Gram-positive cocci, including Staphylococcus aureus (n = 31, 8.9%), coagulase-negative staphylococci (n = 61, 17.6%), streptococci (n = 130, 37.5%), and Enterococcus faecalis (n = 23, 6.6%) were the predominant organisms identified by mNGS. Subsequent investigations are needed to further define the utility of mNGS in BCNE and its impact on patient outcomes. Despite some pitfalls, mNGS seems to be of value in pathogen identification in IE cases, particularly in those with BCNE. This study was registered and on the Open Science Framework platform.

Keywords: cardiovascular implantable electronic devices; device-related infections; diagnosis; infective endocarditis; metagenomic next-generation sequencing; molecular.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Search strategy flowchart.
Figure 2
Figure 2
A proposed multimodal laboratory strategy for pathogen identification in patients with blood culture-negative endocarditis. anti-B2GP1: anti-beta-2-glycoproteins; anti-dsDNA: anti-double-stranded DNA; ANA: anti-nuclear antibodies; ENA: extractable nuclear antigens; FISH: fluorescence in situ hybridization; NAAT: Nucleic acid amplification test; NBTE: Nonbacterial thrombotic endocarditis; PCR: polymerase chain reaction; RF: rheumatoid factor; 16S rRNA: 16S ribosomal RNA.
See this image and copyright information in PMC

References

    1. Miller J.M., Binnicker M.J., Campbell S., Carroll K.C., Chapin K.C., Gilligan P.H., Gonzalez M.D., Jerris R.C., Kehl S.C., Patel R., et al. A Guide to Utilization of the Microbiology Laboratory for Diagnosis of Infectious Diseases: 2018 Update by the Infectious Diseases Society of America and the American Society for Microbiology. Clin. Infect. Dis. 2018;67:813–816. doi: 10.1093/cid/ciy584. - DOI - PubMed
    1. Baddour L.M., Wilson W.R., Bayer A.S., Fowler V.G., Jr., Tleyjeh I.M., Rybak M.J., Barsic B., Lockhart P.B., Gewitz M.H., Levison M.E., et al. Infective Endocarditis in Adults: Diagnosis, Antimicrobial Therapy, and Management of Complications: A Scientific Statement for Healthcare Professionals From the American Heart Association. Circulation. 2015;132:1435–1486. doi: 10.1161/CIR.0000000000000296. - DOI - PubMed
    1. Lamas C.C., Fournier P.E., Zappa M., Brandão T.J., Januário-da-Silva C.A., Correia M.G., Barbosa G.I., Golebiovski W.F., Weksler C., Lepidi H., et al. Diagnosis of blood culture-negative endocarditis and clinical comparison between blood culture-negative and blood culture-positive cases. Infection. 2016;44:459–466. doi: 10.1007/s15010-015-0863-x. - DOI - PubMed
    1. Topan A., Carstina D., Slavcovici A., Rancea R., Capalneanu R., Lupse M. Assesment of the Duke criteria for the diagnosis of infective endocarditis after twenty-years. An analysis of 241 cases. Clujul. Med. 2015;88:321–326. doi: 10.15386/cjmed-469. - DOI - PMC - PubMed
    1. Fournier P.E., Gouriet F., Casalta J.P., Lepidi H., Chaudet H., Thuny F., Collart F., Habib G., Raoult D. Blood culture-negative endocarditis: Improving the diagnostic yield using new diagnostic tools. Medicine (Baltimore) 2017;96:e8392. doi: 10.1097/MD.0000000000008392. - DOI - PMC - PubMed

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