When I became pregnant my husband really took charge of caring for our chickens, mostly because he wanted to be helpful and allow me to rest as much as possible. Before helping him clean the coop to prepare it for the winter season, I wanted to make sure it would be safe for my pregnancy to be in such a dusty, cobwebbed, poop-covered environment.
For the most part, it seems safe to continue regular chicken-keeping duties while pregnant, however there was little information on the internet and in my chicken-keeping library regarding the topic. The number one thing I did find was that when pregnant, one should make sure they wash their hands thoroughly when handling chickens, eggs, or after providing water or feed; this should be done ALL the time, but is even more important while pregnant. Proper hand washing can help one avoid salmonella. Additionally, cleaning the coop or even raking pine shavings should be avoided as there is a risk of contracting histoplasmosis through the chicken poop, dust, and dander. If having someone else do these chores is not an option, a mask should be worn.
For further reading:
Chicken Keeping Secrets: Keeping Chickens Whilst Pregnant