Morris Arthur, Robinson Guy, Swain Martin T, Chalmers Rachel M
Institute of Biological, Environmental & Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom.
Cryptosporidium Reference Unit, Public Health Wales Microbiology, Singleton Hospital, Swansea, United Kingdom.
Front Public Health. 2019 Dec 11;7:360. doi: 10.3389/fpubh.2019.00360. eCollection 2019.
The protozoan parasite is an important cause of diarrheal disease (cryptosporidiosis) in humans and animals, with significant morbidity and mortality especially in severely immunocompromised people and in young children in low-resource settings. Due to the sexual life cycle of the parasite, transmission is complex. There are no restrictions on sexual recombination between sub-populations, meaning that large-scale genetic recombination may occur within a host, potentially confounding epidemiological analysis. To clarify the relationships between infections in different hosts, it is first necessary to correctly identify species and genotypes, but these differentiations are not made by standard diagnostic tests and more sophisticated molecular methods have been developed. For instance, multilocus genotyping has been utilized to differentiate isolates within the major human pathogens, and . This has allowed mixed populations with multiple alleles to be identified: recombination events are considered to be the driving force of increased variation and the emergence of new subtypes. As yet, whole genome sequencing (WGS) is having limited impact on public health investigations, due in part to insufficient numbers of oocysts and purity of DNA derived from clinical samples. Moreover, because public health agencies have not prioritized parasites, validation has not been performed on user-friendly data analysis pipelines suitable for public health practitioners. Nonetheless, since the first whole genome assembly in 2004 there are now numerous genomes of human and animal-derived cryptosporidia publically available, spanning nine species. It has also been demonstrated that WGS from very low numbers of oocysts is possible, through the use of amplification procedures. These data and approaches are providing new insights into host-adapted infectivity, the presence and frequency of multiple sub-populations of spp. within single clinical samples, and transmission of infection. Analyses show that although whole genome sequences do indeed contain many alleles, they are invariably dominated by a single highly abundant allele. These insights are helping to better understand population structures within hosts, which will be important to develop novel prevention strategies in the fight against cryptosporidiosis.
这种原生动物寄生虫是人类和动物腹泻疾病（隐孢子虫病）的重要病因，尤其在资源匮乏地区的严重免疫功能低下人群和幼儿中，会导致显著的发病率和死亡率。由于该寄生虫的有性生活周期，其传播较为复杂。亚群体之间的有性重组没有限制，这意味着在宿主体内可能发生大规模的基因重组，从而可能混淆流行病学分析。为了阐明不同宿主感染之间的关系，首先需要正确识别物种和基因型，但这些区分并非通过标准诊断测试完成，因此已开发出更复杂的分子方法。例如，多位点基因分型已被用于区分主要人类病原体中的分离株，如 和 。这使得能够识别具有多个等位基因的混合群体：重组事件被认为是变异增加和新亚型出现的驱动力。到目前为止，全基因组测序（WGS）对公共卫生调查的影响有限，部分原因是临床样本中卵囊数量不足以及DNA纯度问题。此外，由于公共卫生机构未将寄生虫作为优先事项，尚未对适合公共卫生从业者的用户友好型数据分析流程进行验证。尽管如此，自2004年首次进行全基因组组装以来，现在有许多来自人类和动物的隐孢子虫基因组公开可用，涵盖九个物种。通过使用扩增程序，也已证明从极少量卵囊中进行WGS是可行的。这些数据和方法为宿主适应性感染性、单个临床样本中 物种多个亚群体的存在和频率以及感染传播提供了新见解。分析表明，虽然全基因组序列确实包含许多等位基因，但它们总是由单个高度丰富的等位基因主导。这些见解有助于更好地理解宿主体内的种群结构，这对于制定对抗隐孢子虫病的新型预防策略至关重要。
