While the article reporting the incident isn't exactly a medical journal article it does present a sufficient argument to accept that the player's infection almost certainly was a fungus and its source most likely was his instrument.

It would have been helpful if it had described how the instrument was "sterilized." Many kinds of fungi withstand most of the methods of sterilization commonly used for common "bugs," and quite a few of the common methods would be extremely destructive to an instrument like a clarinet (or lots of others). Alcohol in particular may kill most bacteria, but is almost useless for molds (although I've never heard whether drunken mushrooms exhibit self-destructive behaviours).

Most keyed instruments can be at least partially disassembled so that parts with different materials/constructions could be separately treated, but this isn't a good thing to do on a frequent basis. (Reseating a used pad on a key that's been removed and put back is about like trying to put the bottle cap back on the Coca Cola. It's very likely to leak.)

Separate methods for routine/daily cleaning and for more serious periodic sanitizing might be a good idea(?).

About the only likely method that comes immediately to my mind would be a chlorine bleach solution, which is generally effective against most fungal types although some might require more than brief exposure. The chlorine content would not necessarily have to be much higher than what is used in many public water supplies at the point where the supply goes into the distribution plumbing (although perhaps a little higher than expected when it comes out at the taps). (????)

A swab dampened with a chlorine solution should be effective for daily use, and many clarinet players routinely use one anyway just on the pretense that it helps dry the slobbers out of the innards.

Anyone else got some better ideas? And ideas about which instruments different ones would work on?

John