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Background   Cryptosporidium  is a protozoan parasite that causes diarrheal illness in a wide range of hosts including humans. Two species,  C. parvum  and  C. hominis  are of primary public health relevance. Genome sequences of these two species are available and show only 3-5% sequence divergence. We investigated this sequence variability, which could correspond either to sequence gaps in the published genome sequences or to the presence of species-specific genes. Comparative genomic tools were used to identify putative species-specific genes and a subset of these genes was tested by PCR in a collection of  Cryptosporidium  clinical isolates and reference strains.    Results  The majority of the putative species-specific genes examined were in fact common to  C. parvum  and  C. hominis . PCR product sequence analysis revealed interesting SNPs, the majority of which were species-specific. These genetic loci allowed us to construct a robust and multi-locus analysis. The Neighbour-Joining phylogenetic tree constructed clearly discriminated the previously described lineages of  Cryptosporidium  species and subtypes.    Conclusions  Most of the genes identified as being species specific during bioinformatics in  Cryptosporidium  sp. are in fact present in multiple species and only appear species specific because of gaps in published genome sequences. Nevertheless SNPs may offer a promising approach to studying the taxonomy of closely related species of Cryptosporidia.

Multi-locus analysis of human infective Cryptosporidium species and subtypes using ten novel genetic loci