To understand the molecular characteristics of Cryptosporidium species contaminating rivers, water treatment plants and abattoirs in Ibadan Nigeria, water samples were obtained from ten rivers used for household and agricultural purposes, three major functional water treatment plants and three major abattoirs located within Ibadan metropolis during dry and rainy seasons between November, 2016 to October, 2017. Obtained samples were examined for Cryptosporidium oocysts using microscopy after using modified formalin–ether concentration method and modified acid-fast staining. Cryptosporidium oocysts were detected in samples from five rivers with mean oocyst count/field ranging from 7.70 ± 0.57–1.34 ± 0.57, oocysts were also detected in samples from two abattoirs with mean oocyst count/field ranging from 4.60 ± 0.33–2.50 ± 0.33. Genomic DNA were extracted from microscopy positive river and abattoir samples using sucrose gradient purification method and genotypes and subtypes of parasites were detected by nested PCR amplification and nucleotide sequence analysis of both 18S rRNA and 60-kDa glycoprotein (gp60) genes. Cryptosporidium parvum, C. muris and C. fragile were the only genotypes detected in some river samples, while gp60 gene sequence analysis showed that the C. parvum strain detected was subtype IIa. This study provides evidence that rivers used for household and agricultural purposes in studied area may be potential reservoirs and infection sources for Cryptosporidium species and zoonotic subtypes of public health importance.

为了了解尼日利亚伊巴丹河中隐孢子虫种的分子特征，这些污染物来自河流，水处理厂和屠宰场，在干旱期间，从十个用于家庭和农业目的的河流，三座主要功能性水处理厂和三座主要屠场获得了水样。 2016年11月至2017年10月之间的雨季和雨季。使用改良的福尔马林-乙醚浓度法和改良的耐酸染色后，使用显微镜检查获得的样本中的隐孢子虫卵囊。隐孢子虫在五个河流的样品中检测到卵囊，平均卵囊计数/视野范围为7.70±0.57–1.34±0.57，在两个屠宰场的样品中也检测到卵囊，平均卵囊计数/视野范围为4.60±0.33-2.50±0.33。使用蔗糖梯度纯化法从显微镜阳性河和屠宰场样品中提取基因组DNA，并通过嵌套PCR扩增和18S rRNA和60-kDa糖蛋白（gp60）基因的核苷酸序列分析，检测了寄生虫的基因型和亚型。在一些河流样本中仅检测到隐孢子虫，鼠隐孢子虫和脆弱隐孢子虫的基因型，而gp60基因序列分析表明，隐孢子虫检测到的菌株为IIa亚型。这项研究提供了证据，表明研究区域中用于家庭和农业目的的河流可能是隐孢子虫物种和具有公共卫生重要性的人畜共患病亚型的潜在水库和感染源。