OK. I did a little poking around, and nothing is conclusive, but it fits the symptoms, and circumstances. There may be co-infections with these conditions as well. The red worms in the nasal sample may have been colonies.
The suspect: psittacosis
* fever,
* chills,
* cough,
* weakness or fatigue,
* muscle and chest pain,
* loss of appetite,
* nausea,
* vomiting,
* diarrhea,
* headache,
* sweating,
* abnormal intolerance to light.
This is a type of chlamydia transferred from exotic birds to humans.
It fits with chronic unexplained respiratory difficulties.
Hope that helps. You will have to investigate how the diagnostics are done, and treatment options.
Shroom