Using Cryptosporidium genomics for investigating outbreaks and disease transmission

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Cryptosporidiosis is a significant diarrhoeal disease globally, caused by several species of the apicomplexan Cryptosporidium. As a zoonosis, Cryptosporidium has a wide host range, including livestock. The project will involve close work with the National Cryptosporidium Reference Unit (CRU) for England and Wales. The aim is to improve the detection of outbreaks, for instance by identifying more linked cases, and to ensure that the CRU is using the most appropriate tools e.g. for investigating disease transmission, improving monitoring and managing zoonotic risk, and preparing for future outbreaks. To address this, we hypothesise that (a) whole genome sequencing (WGS) for the discrimination of Cryptosporidium subtypes is better than (b) multiple loci variable number of tandem repeats analysis (MLVA) for elucidating population structure; and hence also for case clustering and outbreak identification