Please refer to the following suggestions...
Usually, outbreaks of such infectious diseases such as Cryptosporidiosis
and Cyclospora have the same clinical feature as : diarrhea
(including of serious type as in your setting case).
It is true that the real diagnosis is done through microscopical examination of feces for ova/parasites where the oocysts/cysts of Cyclospora and the Cryptosporidium
Other tests include ELISA
or molecular testing for respective parasites.
Usually, Cryposporidium outbreaks are noticed in various care settings where proper hygiene and sanitary measures are not followed. Cryptosporidium itself is very resistant to chlorine or other sanitizers which makes the outbreaks very easily to develop and difficult to manage.
I am currently working at the Public Health sector in my country, and the very first thing to do in such cases is to take the emergency measures by putting our patients' life safe.
The second thing (at the same time too) is to take samples and further investigate to come out with the final report. Feces, water, foods, etc. are taken as sample for further investigation.
For both diseases, contaminated water and food could be to blame although the real transmission chain is not established yet for cyclospora infection.
We also evaluate if the cases were in a caring settings as yours or sporadic cases or more. We also evaluate the medical history and recent travelling of the patients.
At the end, to my knowledge, CDC is being in touch with the public health officials of each states together with FDA with regards to managing and confirmatory testing for such infectious diseases.
Could be that both infections had happened at the same time, but without any lab report, cannot tell for sure.
Hope it answered to your questions!
p.s. if you have more questions, do not hesitate to write me back!