Cryptosporidium is one of the most common causes of diarrhoea around the world. Successful management and prevention of this infectious disease requires knowledge of the diversity of species and subtypes causing human disease. We use sequence data from 2598 human faecal samples collected during an 11-year period (2009–2019) to better understand the impact of different species and subtypes on public health and to gain insights into the variation of human cryptosporidiosis in New Zealand. Human cryptosporidiosis in New Zealand is caused by a high diversity of species and subtypes. Six species cause human disease in New Zealand: C. hominis, C. parvum, C. cuniculus, C. erinacei, C. meleagridis and C. tyzzeri. Sequence analysis of the gp60 gene identified 16 subtype families and 101 subtypes. Cryptosporidium hominis IbA10G2 and C. parvum IIaA18G3R1 were the most frequent causes of human cryptosporidiosis with 27% and 29% of infections, respectively. Cryptosporidium hominis presented a peak of notified human cases during autumn (March–May) whereas most cases of human cryptosporidiosis caused by C. parvum are found during the calving and lambing season in spring (September–November). We also reported some subtypes that have been rarely detected in other countries such as IbA20G2 and IIoA13G1 and a low prevalence of the hypertransmissible and virulent IIaA15G2R1. This study provides insight into the variability of cryptosporidiosis in New Zealand essential for disease management and surveillance to prevent the introduction or spread of new species and subtypes in the country.

隐孢子虫是全世界腹泻的最常见原因之一。成功控制和预防这种传染病需要了解引起人类疾病的物种和亚型的多样性。我们使用在11年期间（2009-2019年）收集的2598份人类粪便样本的序列数据，以更好地了解不同物种和亚型对公共卫生的影响，并深入了解新西兰人类隐孢子虫病的变化。新西兰的人类隐孢子虫病是由物种和亚型的高度多样性引起的。六种导致人类疾病在新西兰：C.人型支原体，小隐孢子虫，C. cuniculus，C. erinacei，C.火鸡和C. tyzzeri。gp60基因的序列分析确定了16个亚型家族和101个亚型。人隐孢子虫IbA10G2和细小隐孢子虫IIaA18G3R1是人类隐孢子虫病的最常见原因，分别占感染的27％和29％。人型隐孢子虫秋季（三月至五月）期间提出的通报人感染病例的峰值，而人为造成的隐孢子虫病大多数情况下，小隐孢子虫在春季（9月至11月）的产犊和羔羊季节发现。我们还报告了在其他国家很少发现的一些亚型，例如IbA20G2和IIoA13G1，以及高传播性和高毒性IIaA15G2R1的低患病率。这项研究深入了解了新西兰隐孢子虫病的变异性，这对于疾病管理和监测至关重要，以防止在该国引入或传播新物种和亚型。