Beyond research: a primer for considerations on using viral metagenomics in the field and clinic

Infectious diseases often remain undiagnosed because the pathogen is unknown, or not expected in a given patient. In such cases, the only option may be to use metagenomics, an approach that identifies all the micro-organisms in a sample at once, by using a combination of modern high-throughput DNA sequencing technologies, and advanced bioinformatics. Metagenomics is potentially a very powerful diagnostic tool, and hospitals, agricultural companies, and public health agencies are about to start using it.

But before it takes off, there are several important issues that need to be discussed in a public debate. In a new article in Frontiers in Microbiology, Hall and collaborators provide a primer for this debate. Two examples of important points that need to be addressed are:

  1. Unexpected information.

If someone is tested to diagnose a cough, but happens to be HIV positive – what do you do? Metagenomics is so powerful that it may give you more information than you bargained for – probably sensitive, and possibly even damaging information. Health specialists should be aware of this possibility for incidental findings, and have clear protocols in place to best help the patient.

  1. Patient privacy.

When metagenomic samples are derived from humans (e.g. faeces or saliva), bioinformatic techniques are now so sensitive that they can identify an individual. Clearly, this leads to a potential privacy breach when the data would be publicly available. Normally, human genomic data are protected by special regulations but these do not yet exist for clinical metagenomics.

Metagenomics has the potential to become a powerful diagnostic tool in the field and the clinic. However, before implementation, several important outstanding issues need to be broadly discussed. Then, researchers and policy makers must unite their efforts and produce guidelines to help and protect patients while providing them with the advantages of metagenomic diagnosis.



Hall, Draper, Nielsen, and Dutilh (2015) “Beyond research: a primer for considerations on using viral metagenomics in the field and clinic”, Frontiers in Microbiology: