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Journal of Medical Microbiology logo Journal of Medical Microbiology

Volume 74, Issue 2

Clinical metagenomics: ethical issues Open Access

This article is part of the Pathogen Genomics in Clinical Practice collection. 

Abstract

Metagenomics is increasingly used for diagnosis in hospital settings. It is useful particularly in cases of unknown aetiology, where novel or difficult-to-diagnose pathogens are suspected, and/or following unexplained disease outbreaks. In this paper, we present three use cases that draw on existing reports: one involving a patient in intensive care with encephalitis of unknown aetiology; a second case with likely infection with drug-resistant and an incidental finding of unknown relevance; and a third case situated in an unexplained outbreak of acute hepatitis in children, with severe outcomes due to co-infection. We examine each case in turn, highlighting ethical questions arising in relation to clinical issues including: disclosure to patients of untreatable disease, cost-effectiveness, the value of resistance testing, sensitivity and specificity, uncertain or unexpected findings, patient consent and data sharing. We conclude by proposing recommendations for further research and developing particular pieces of guidance to improve clinical uses of metagenomics for diagnosis.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): clinical ethics , diagnostic , ELSI , metagenomics and next-generation sequencing
Funding
This study was supported by the:
  • National Health and Medical Research Council (Award Early Investigator)
    • Principle Award Recipient: PrashanthRamachandran
  • Wellcome Trust (Award 221038/Z/20/Z])
    • Principle Award Recipient: StephanieJohnson
  • Moh Family Foundation (Award Pandemic Sciences Institute Trust and Confidence Theme)
    • Principle Award Recipient: EuzebiuszJamrozik
  • Moh Family Foundation (Award Pandemic Sciences Institute Trust and Confidence Theme)
    • Principle Award Recipient: TessJohnson
  • Wellcome Trust (Award 221719)
    • Principle Award Recipient: EuzebiuszJamrozik
  • Wellcome Trust (Award 221719)
    • Principle Award Recipient: TessJohnson
  • Wellcome Trust (Award 203132)
    • Principle Award Recipient: EuzebiuszJamrozik
© 2025 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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2025-02-27
2025-04-20
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Clinical metagenomics: ethical issues
J. Med. Microbiol. 74, 001967 (2025); https://doi.org/10.1099/jmm.0.001967
/content/journal/jmm/10.1099/jmm.0.001967
/content/journal/jmm/10.1099/jmm.0.001967
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