What is Metagenomics?

Clinical metagenomics is a way of testing patient samples to find out which microbes are present.

Instead of trying to grow bacteria in the lab, which can take several days, metagenomics looks directly at all the genetic material (DNA and RNA) in a sample. It will also detect all types of viruses, without having to specify which virus you are looking for before testing. This means it can detect any pathogen in the sample.

Why it matters?

Many microbes are difficult or impossible to grow using standard laboratory methods. Metagenomics helps by:

Detecting all types of microbes including bacteria, viruses, fungi and parasites.
Providing rapid results, within one working day, quicker than agar culture.
Finding microbes that are slow or difficult to grow.
Identifying microbes without needing a specific targeted test (like PCR).
Detecting microbes even if the patient has already taken antibiotics.

What can metagenomics tell us?

Metagenomics can help identify:

Which microbes are present in a sample
The relative amount of each microbe
If there is enough data, it can predict resistance to some important antibiotics.

Common challenges

While powerful, metagenomics also has limitations:

Contamination from laboratory materials or the environment can affect results
Human DNA can sometimes overwhelm the microbial signal
If a microbe is not well represented in reference databases, it may be missed or misidentified
It cannot always tell the difference between harmless colonisation and true infection

The workflow

A clinical sample is taken from a patient with a suspected infection. This could be sputum (mucus from the lungs) or a sample collected from deep in the lungs using a bronchoscopy procedure.

Most of the patient’s own DNA is removed so that the microbial genetic material can be more easily detected.

DNA and RNA are carefully extracted from the sample.

Any RNA is converted into DNA so it can be analysed.

The microbial genetic material is copied to ensure there is enough to study.

A sequencing machine, known as a nanopore sequencer, reads the genetic code of the microbes.

The results are compared against large databases of known microbes to identify: