Using Cryptosporidium genomics for investigating outbreaks and disease transmission

隐孢子虫病是一种重要的全球腹泻疾病，由几种顶端复合体隐孢子虫引起。作为一种人畜共患病，隐孢子虫的宿主范围很广，包括牲畜。该项目将与英格兰和威尔士国家隐孢子虫参考股(CRU)密切合作。其目的是改进对疫情的检测，例如通过确定更多的关联病例，并确保CRU使用最适当的工具，例如调查疾病传播、改进监测和管理人畜共患病风险以及为未来的疫情做准备。为了解决这个问题，我们假设：(A)全基因组测序(WGS)用于区分隐孢子虫亚型优于(B)多位点可变数目串联重复序列分析(MLVA)，用于阐明种群结构；因此也用于病例聚集和暴发识别

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