Rapid metagenomics for diagnosis of bloodstream and respiratory tract nosocomial infections: current status and future prospects

Lluís Moragues-Solanas, Riccardo Scotti, Justin O'Grady

Research output: Contribution to journalArticlepeer-review

11 Citations (Scopus)
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Introduction: Nosocomial infections represent a major problem for the health-care systems worldwide. Currently, diagnosis relies on microbiological culture, which is slow and has poor sensitivity. While waiting for a diagnosis, patients are treated with empiric broad spectrum antimicrobials, which are often inappropriate for the infecting pathogen. This results in poor patient outcomes, poor antimicrobial stewardship and increased costs for health-care systems. Areas covered: Clinical metagenomics (CMg), the application of metagenomic sequencing for the diagnosis of infection, has the potential to become a viable alternative to culture that can offer rapid results with high accuracy. In this article, we review current CMg methods for the diagnosis of nosocomial bloodstream (BSI) and lower respiratory-tract infections (LRTI). Expert opinion: CMg approaches are more accurate in LRTI compared to BSI. This is because BSIs are caused by low pathogen numbers in a high background of human cells. To overcome this, most approaches focus on cell-free DNA, but, to date, these tests are not accurate enough yet to replace blood culture. The higher pathogen numbers in LRTI samples make this a more suitable for CMg and accurate approaches have been developed, which are likely to be implemented in hospitals within the next 2–5 years.

Original languageEnglish
Pages (from-to)371-380
Number of pages10
JournalExpert Review of Molecular Diagnostics
Issue number4
Publication statusPublished - 29 Apr 2021


  • Antimicrobial resistance (AMR)
  • Infection
  • blood stream infection
  • clinical metagenomics (CMg)
  • diagnosis
  • mNGS
  • respiratory tract infection
  • sepsis
  • sequencing

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