There's a lab at UCSF[1] that actually specializes in doing genome sequencing of cerebrospinal fluid specifically for cases like this. They're talked about pretty extensively in Adam Savage's "Still Untitled" podcast[2] and all the crazy weird things they managed to diagnose this way.

We all have the impression that medicine is a solved problem, but we've still got a way to go. We're still making progress though.

[1] https://nextgendiagnostics.ucsf.edu/

[2] https://www.tested.com/podcasts/adam-savage-project/854328-s...