Just saw this story and thought people might be interested in it.
Source: Brain-Invading Tapeworm That Eluded Doctors Spotted by New DNA Test – Scientific American
The article discusses a new test to be offered by UCSF as well as some other tests from other places that all involve some type of metagenomic sequencing to identify the possible causes of mysterious infections. The science here does not sound too complex but they do not provide a lot of details. It certainly seems like metagenomics could provide a useful alternative method for looking at mysterious infections.