Molecular characterisation of Cryptosporidium isolates from rivers, water treatment plants and abattoirs in Ibadan, Nigeria

•Occurrence of Cryptosporidium in water in Ibadan, Nigeria.•First genetic characterization of Cryptosporidium in water in Nigeria.•Rivers used for household purposes are potential reservoirs and infection sources of Cryptosporidium species for humans and livestock. 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.