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From culture to metagenomics: A paradigm shift in diagnosing infective endocarditis

Mahmoud ElHefnawi1, Dina H Amin2, Asmaa M Elfiky3

  • 1Biomedical Informatics and Chemoinformatic Group, Informatics and Systems Department, National Research Centre, Cairo, Egypt.

Diagnostic Microbiology and Infectious Disease
|May 5, 2026
PubMed

Insights

Infective endocarditis (IE) diagnosis faces challenges with traditional blood cultures. Metagenomic sequencing, particularly cell-free metagenomic DNA (cf-mDNA), shows promise for detecting difficult-to-culture organisms and improving IE management.

Area of Science:

  • Cardiology
  • Infectious Diseases
  • Microbiology

Background:

  • Infective endocarditis (IE) is a severe heart valve infection with high mortality.
  • IE complications include heart failure, embolic events, and stroke.
  • Traditional diagnostic methods like blood cultures have limitations.

Purpose of the Study:

  • To review the clinical burden and microbial causes of IE.
  • To examine diagnostic challenges, focusing on blood culture limitations.
  • To explore the potential of metagenomic approaches in IE diagnosis.

Main Methods:

  • Comprehensive literature review on IE diagnostic methods.
  • Analysis of blood cultures, molecular assays, and metagenomic sequencing.
  • Exploration of bacterial biofilms' role in treatment failure.

Main Results:

  • Blood cultures struggle with culture-negative and fastidious organisms.
  • Metagenomic sequencing, especially cf-mDNA, offers a promising non-invasive diagnostic alternative.
  • Bacterial biofilms contribute to treatment failure and antibiotic resistance.

Conclusions:

  • Metagenomics can overcome limitations of culture-based IE diagnostics.
  • Standardized protocols and prospective studies are essential for clinical validation.
  • Metagenomic approaches may enhance IE diagnosis and patient management.
Keywords:
Culture-negativeDiagnosticsInfective endocarditis, Clinical metagenomicsNext-generation sequencingPathogens

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