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Open Access Research article

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

Maha Bouzid1, Kevin M Tyler1, Richard Christen2, Rachel M Chalmers3, Kristin Elwin3 and Paul R Hunter1*

Author Affiliations

1 Biomedical Research Centre, School of Medicine, Health Policy and Practice, University of East Anglia, Norwich NR4 7TJ, UK

2 CNRS UMR 6543. Institute of Signalling, Developmental Biology and Cancer Centre de Biochimie, Faculté des Sciences, 06108 Nice cedex 2, France

3 UK Cryptosporidium Reference Unit, Public Health Wales, Microbiology ABM, Singleton Hospital, Swansea SA2 8QA, UK

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BMC Microbiology 2010, 10:213  doi:10.1186/1471-2180-10-213

Published: 9 August 2010



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.


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.


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.