How to identify the culprit of an infection

When someone has a serious infection, it is often necessary to work out exactly which microbe is responsible for causing the disease.

The process starts in the doctor’s surgery or hospital, where a patient’s symptoms can provide clues as to what the microbe is likely to be. Samples are taken (eg urine, blood, throat swab, skin scraping) and given to a pathology lab. Clinical microbiologists will then determine if the pathogen is a bacterium, fungus, protist or virus (no archaea have been found to cause disease) and produce a pure culture (if this is possible; as you explored in Week 2 – not all microbes can be cultured).

There are a range of techniques that can be used to identify precisely which microbe is responsible for causing an infection. This information can help doctors to select the best treatment, and health agencies to prevent the spread of the infectious disease to other people in the community.

In the video, Harriet and Jordan identify three pathogens using a variety of culture-based methods. In many hospitals, such traditional culture-based tests are being predominately replaced by automated machines. These include a technique called MALDI-TOF that identifies bacteria based on the proteins they contain (their proteome). You can watch a video of what’s involved in the MALDI-TOF process here. Other sensitive molecular techniques can be performed on clinical samples without needing to culture the pathogens in the laboratory. These include PCR (the key technology behind SARS-CoV-2 tests) and nucleic acid (DNA/RNA) sequencing. Continued development of molecular techniques ensures not only rapid, sensitive and accurate results, but can also substantially reduce costs.