Comparison of single- and multilocus genetic diversity in the protozoan parasites Cryptosporidium parvum and C. hominis

Abstract

The genotyping of numerous isolates of Cryptosporidium parasites has led to the definition of new species and a better understanding of the epidemiology of cryptosporidiosis. A single-locus genotyping method based on the partial sequence of a polymorphic sporozoite surface glycoprotein gene (GP60) has been favored by many for surveying Cryptosporidium parvum and C. hominis populations. Since genetically distinct Cryptosporidium parasites recombine in nature, it is unclear whether single-locus classifications can adequately represent intraspecies diversity. To address this question, we investigated whether multilocus genotypes of C. parvum and C. hominis cluster according to the GP60 genotype. C. hominis multilocus genotypes did not segregate according to this marker, indicating that for this species the GP60 sequence is not a valid surrogate for multilocus typing methods. In contrast, in C. parvum the previously described "anthroponotic" genotype was confirmed as a genetically distinct subspecies cluster characterized by a diagnostic GP60 allele. However, as in C. hominis, several C. parvum GP60 alleles did not correlate with distinct subpopulations. Given the rarity of some C. parvum GP60 alleles in our sample, the existence of additional C. parvum subgroups with unique GP60 alleles cannot be ruled out. We conclude that with the exception of genotypically distinct C. parvum subgroups, multilocus genotyping methods are needed to characterize C. parvum and C. hominis populations. Unless parasite virulence is controlled at the GP60 locus, attempts to find associations within species or subspecies between GP60 and phenotype are unlikely to be successful.

FIG. 1.

PCoA of 60 unique C. parvum and C. hominis MLGs. GP60 alleles are colored according to species: white, C. parvum; black, C. hominis. Symbols represent alleles as indicated in the embedded legend. The C. hominis MLG with a IIc allele is shown with a black star and an asterisk in the legend. PCoA is based on SSR genetic distance (left) and Hamming distance (right). The percentages variation explained by the 1st and 2nd axes are indicated.

FIG. 2.

C. hominis PCoA. The symbols represent different GP60 genotypes, as shown in the symbol legend. PCoA is based on SSR genetic distance (left) and Hamming distance (right). Note the overlapping distribution of MLGs with different GP60 genotypes. See the legend to Fig. 1 for additional details.

FIG. 3.

C. parvum PCoA. As in Fig. 1 and 2, PCoA is based on SSR genetic distance (left) and Hamming distance (right). Note the tight cluster of MLGs with the IIc GP60 allele but no apparent segregation of other MLGs. See the legend to Fig. 1 for details.

FIG. 4.

Pairwise linkage analysis. Pairs of markers in LD are represented with white squares and +. Linkage equilibrium is indicated with a shaded field and −. Column totals in the bottom row show for each marker the number of markers in linkage equilibrium. The chromosome location of each marker is shown at the top. Two pairs of markers are located on chromosome I and VI. The distance between MSA and MSB is more than 400,000 bp and between MSG and GP60 is over 140,000 bp. Left, C. parvum excluding IIc MLGs (n = 22); right, C. hominis (n = 30).