Forward Genetics in Cryptosporidium Enabled by Complete in Vitro Development in Stem Cell-Derived Intestinal Epithelium

Despite being a frequent cause of severe diarrheal disease in infants and an opportunistic infection in immunocompromised patients, Cryptosporidium research has lagged due to a lack of facile culture methods. Here, we describe a platform for complete life cycle development and long-term growth of C. parvum in vitro using “air-liquid interface” (ALI) cultures derived from intestinal epithelial stem cells. Transcriptomic profiling revealed that differentiating epithelial cells grown under ALI conditions undergo profound changes in metabolism and development that enable complete development of the parasite life cycle in vitro. ALI cultures supported parasite expansion >100-fold and led to the production of viable oocysts that were transmissible in vitro and to mice. Transgenic parasite lines created using CRISPR/Cas9 were used to complete a genetic cross in vitro, demonstrating conventional meiosis and Mendelian segregation. ALI culture provides an accessible model that will enable innovative studies into Cryptosporidium biology and host interactions.