Fungal infection research catches up with virology

Fungal infections are a growing problem for human health and for food security, and yet research on them still lags behind work on other infectious diseases. That gap translates directly into diagnostics and treatment: fewer tools, fewer molecular targets, fewer tests. A review published in Communications Biology describes what one particular technique changes about that situation.

Single-cell RNA sequencing, scRNA-seq, reads gene activity separately in each cell of a sample instead of averaging it across a tissue. The method has been standard for years in work on viral and bacterial infection, where it reveals differences between immune cells that an averaged measurement merges into one. In fungal infection research it is only now coming into use.

The gain is resolution. The response to a fungal infection is not uniform: some macrophages kill the pathogen, some die, some stay passive, and the fungus in the same tissue can be at different stages. Averaging those states produces a result that exists in no single cell. Separating them makes it possible to ask what distinguishes a cell that copes from one that does not.

The authors do not hide the limitations. A fungal cell wall makes it hard to obtain a clean single-cell suspension, material from infected tissue is often scarce, and telling host transcripts from pathogen transcripts requires separate bioinformatic work. Cost is added to that, and in an underfunded field cost is often decisive.

For this site the review is useful as context. Every report on the mechanisms of fungal infection that we publish rests on the toolkit such papers describe — and the pace at which that toolkit develops sets the pace of the whole field.

The scale of the neglect can be measured, and is worth naming. Fungal disease accounts for millions of deaths a year, and there are only a handful of antifungal drug classes — fewer than the classes of antibacterial antibiotics developed in a single decade of the twentieth century. The WHO priority pathogen list published in 2022 exists precisely to name that disproportion and steer funding.

It should be said plainly what this publication is. It is a review rather than a new experimental result: it summarises what single-cell methods have established so far and points at directions. We publish entries of this kind because they describe the state of the tools rather than a discovery — and that is how they should be read.

For mycology outside medicine the same technique has an application the review mentions in passing: it allows the variation between cells within a single mycelium to be studied. A hypha growing inside a root and the same mycelium in soil can have different expression profiles, and an averaged reading will never show it.

Source status — 29 August 2026

Published on 29 May 2026, this is a peer-reviewed Review article, not a new experiment or a clinical diagnostic trial. The authors survey existing single-cell RNA-sequencing work in fungal infections of humans, animals and plants, together with technical barriers: dissociating cells, penetrating fungal walls, low amounts of pathogen RNA and the need to read host and fungus at once. The method reveals differences hidden by tissue-wide averages, but it is expensive and vulnerable to sample-preparation artefacts. Its present value is in asking sharper questions and identifying candidates for validation, not in providing a ready test for patients.