饮用水和农业水源水中寄生原生动物的存在越来越令人担忧。虽然临床样本（粪便、血液和组织）中有许多可用于鉴定这些生物体的方案，但这些方法并不容易，也不总是成功地转化为环境水样。作者致力于开发一种分子方法来鉴定环境水体中的环孢菌。从这项工作中，我们发现了两个可能继续困扰水微生物学家的重要问题。其中一个众所周知的现象是腐殖酸等抑制物质的存在。 另一个研究较少的问题是，环境水体中存在非人类致病微生物，尽管基因相似。鉴于隐孢子虫和环孢菌（最近出现的三种水传播原生动物病原体中的两种）都有致病性和非致病性物种，这种区分致病性和非致病性物种的困难很可能在未来再次出现。包括22个参考文献、表格和图表。

The presence of parasitic protozoa in source water used for drinking andagriculture is a growing concern. While there are numerous protocols available for the identification of these organisms in clinical samples (feces, blood and tissues), these methods are not easily nor always successfully translated to environmental water samples. The authors have focused on developing a molecular method to identify Cyclospora cayetanensis in environmental waters. From this work, two important issues that are likely to continue to be troublesome for water microbiologists have been identified. One, well recognized, is the presence of inhibitory substances such as humic acids. Another, less studied, is the presence of non-human pathogenic microorganisms, though genetically similar, in environmental waters. Given that there are pathogenic and non-pathogenic species of both Cryptosporidium and Cyclospora, two of the three most recently emerged waterborne protozoan pathogens, it is more than likely that this difficulty in distinguishing pathogenic and non-pathogenic species will reoccur in the future. Includes 22 references, tables, figures.