Been reading about EC and found this link very informative, and have put some quotes below covering a few important points. But I sum it up as most rabbits have it but do not suffer any symptoms unless they have compromised immune systems. Its very difficult for humans to catch it, would need to have aids, be on chemo or other immune suppressant drugs and then ingest it. And they shed the spores before the symptoms not after. Here's the quotes.
"The true incidence of clinical disease is unknown". (B609.2.w2)
Most rabbits are asymptomatic. (B609.2.w2)
Up to 80% of rabbits tested serologically positive for Encephalitozoon cuniculi in Europe and the United States. (B609.2.w2)
In the UK, this disease is widespread in the domestic rabbit population - in clinically healthy pet rabbits the seroprevalence is thought to be around 52 %. (B601.11.w11, B603.4.w4)"
"Rabbits that are showing clinical signs of this disease are no longer shedding spores as the spores are only shed for three weeks after infection. (B609.2.w2)"
"Human Health Considerations
Zoonotic potential particularly in immunosuppressed humans.*(B601.11.w11, B603.4.w4, B609.2.w2)*
Primarily people with AIDs. (B603.4.w4, B614.10.w10)
Encephalitozoonisis can cause diarrhoea, keratoconjunctivitis and renal disease.*(B600.16.w16, B603.4.w4)
It has also been associated with peritonitis. (B614.10.w10)
Human susceptibility and mode of transmission is not clear. (B609.2.w2)
Resistance is T-lymphocyte dependent so humans with CD4 T-lymphocyte deficiences are reported to be particularly susceptible to microsporidian infections as are patients who are on immunosuppressive drugs. (B602.20.w20)
Infections in humans is thought to be mainly through environmental spore contamination, for example, via contaminated water sources. (B601.11.w11)
There have been no reports or evidence of direct transmission of this disease from rabbits to humans (B601.11.w11, B614.10.w10) "although infections in humans have been shown to be the same strain that infects rabbits". (B601.11.w11)
It has been shown that human strains may be transferred to rabbits. (B601.11.w11)
Yep, but the spores remain viable for up to 30 days outside of the host. So transmission from Rabbit to Rabbit can readily happen given that shedding of spores happens BEFORE obvious signs of illness present.