PSI and Ethox researchers Dr Tess Johnson, Dr Zeb Jamrozik, and Dr Stephanie Johnson, with University of Melbourne colleague Dr Prashanth Ramachandran, have this week published a paper that highlights ethical questions raised by emerging uses of metagenomics for clinicians, microbiologists, policymakers and ethicists.
Metagenomics is a pathogen-agnostic sequencing method that can be more efficient and informative than traditional microbiological testing to diagnose patients with infections in healthcare settings. The team uses three case studies built on real-world examples to show how certain issues may complicate clinicians’ decisions to use metagenomics for diagnosis, including those related to uncertain or incidental findings or diagnoses of untreatable disease.
Existing microbiological methods such as culture and PCR can, for instance, identify the pathogen likely causing illness, or inform clinicians about its susceptibility to drugs.
Metagenomics has the potential to reshape patient diagnosis in cases where many agents may be causing disease, where culturing would take too long, or where there may be an outbreak of a novel or re-emerging pathogen.
Metagenomics methods are already being used to diagnose respiratory or neurological infections in patients admitted to intensive care units, for determining best treatment for drug-resistant infections and for identifying causes of new or unexpected disease outbreaks.
While the technology is being developed and implemented fast, there has been minimal ethical guidance so far. Clinicians, microbiologists, and others need answers to questions such as:
- Should clinicians share incidental findings with patients, e.g. microbes detected by metagenomics that are not likely related to the current disease episode? Under what circumstances?
- What is the benefit to patients of diagnosing infections with no specific treatments?
- How should clinicians and microbiologists avoid deterministic ideas about infection, e.g. that all microbes detected by metagenomics are likely to cause harm and/or require treatment?
This paper takes an essential step in outlining these questions and indicating areas that may provide answers.
Much potentially useful ethical guidance can be found in the area of human genomics. Still, there is considerable work to be done to formulate ethical positions and relate them to the most pressing questions that clinicians face when considering the use of metagenomics and other genomic methods for diagnosing infectious diseases.
Dr Tess Johnson, GLIDE Postdoctoral Researcher in the Ethics of Pandemic Preparedness, Surveillance and Response at PSI, and lead author on the paper, said: ‘What I think is really useful and important about this paper is that we aimed to make it relevant for clinicians. We have thought about real-world cases where metagenomics is already being used, and real-world dilemmas that are raised, first for microbiologists about analysing, interpreting, and reporting data to clinicians, second for clinicians about making sure that patients are giving adequately informed consent, where required, for testing, that clinicians are sharing relevant data with patients, and that the information is informing their care in appropriate ways. We want to provide a practical, approachable ethical exploration of this topic, which will lead to further development of ethics guidance in future work.’
The full paper is available to read on the Journal of Medical Microbiology website: https://www.microbiologyresearch.org/content/journal/jmm/10.1099/jmm.0.001967