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Health and Taxonomy

Pathology

The TV show House has popularized medical mysteries, like the following story that relies on taxonomy for the proper treatment of patients.

A pathologist is a doctor who specializes in figuring out what is making someone sick. This might entail looking at biopsies to determine if a tumor is benign or malignant, or testing blood and tissue samples for the presence of genes that would identify which viruses, bacteria, protozoa, or fungi are infecting a patient.

A new patient comes in who is suffering from damage to his lungs from some sort of invader (or a pathogen). A tissue sample is taken and sent to the pathology lab to start unfolding the mystery.

A quick look under the microscope shows a filamentous fungus. That's already bad because, since fungi's cells are more similar to our cells than bacterial cells. It's harder to kill them without also killing the human cells that they are invading. The pathologist's first thought is that it is Paecilomyces variotii. Then she remembers reading a paper published in 2011 that reported that P. variotii can easily be mistaken for Geosmithia argillacea. She decides to use genetic sequencing to identify the fungus, knowing that correct treatment relies on correct identification.

The sequence data comes back showing that the fungus in the patient's lungs is definitely G. argillacea. That means that it is an aggressive infection that may be able to cross into other tissues. It will probably be resistant to most oral antifungal medicines and surgery might be the patient's best option. Unfortunately, a really effective drug isn't known. As more patients are correctly diagnosed with G. argillacea, instead of P. variotii, a clearer picture will develop. In the meantime, at least patients won't be given false hope.

See P. variotii here.

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