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

Moragues-Solanas, Lluís, Scotti, Riccardo and O'Grady, Justin (2021) Rapid metagenomics for diagnosis of bloodstream and respiratory tract nosocomial infections: current status and future prospects. Expert Review of Molecular Diagnostics, 21 (4). pp. 371-380. ISSN 1473-7159

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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.

Item Type: Article
Additional Information: Funding Information: L Moragues-Solanas is funded by the MRC Doctoral Antimicrobial Research Training (DART) Industrial CASE Programme. R Scotti is funded by Innovative UK grant number TS/S00887X/1. The authors gratefully acknowledge the support of the Biotechnology and Biological Sciences Research Council (BBSRC)); this research was funded by the BBSRC Institute Strategic Programme Microbes in the Food Chain BB/R012504/1 and its constituent projects BBS/E/F/000PR10348, BBS/E/F/000PR10349, BBS/E/F/000PR10351.
Uncontrolled Keywords: antimicrobial resistance (amr),infection,blood stream infection,clinical metagenomics (cmg),diagnosis,mngs,respiratory tract infection,sepsis,sequencing,pathology and forensic medicine,molecular medicine,molecular biology,genetics ,/dk/atira/pure/subjectarea/asjc/2700/2734
Faculty \ School: Faculty of Medicine and Health Sciences > Norwich Medical School
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Depositing User: LivePure Connector
Date Deposited: 16 Oct 2021 00:53
Last Modified: 30 Jan 2024 02:46
URI: https://ueaeprints.uea.ac.uk/id/eprint/81743
DOI: 10.1080/14737159.2021.1906652


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