Hiya - I was pregnant last year and at my booking in appointment with the midwife, when she asked if I had any pets and I said we had two guinea pigs, she didn't say anything about risks of infection from them. However, I do understand how scary any risk is when you're pregnant.
I think its only cats or birds that could be a problem. My hubbie cleaned out our cats tray while I was carrying. If year concerned in anyway, just wear gloves while cleaning out. I shouldnt think there will be a problem.