Comparison of Single- and Multilocus Genetic Diversity in the Protozoan Parasites Cryptosporidium parvum and C. hominis

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.The lack of variable morphological traits to identify oocysts from different Cryptosporidium species has driven the development of numerous genotyping methods to survey the diversity in this genus. Genetic markers such as single-nucleotide polymorphisms (24), restriction fragment length polymorphisms (7, 34), random amplification methods (17, 20), conformational polymorphisms (11), simple sequence repeats (3, 10), and DNA sequence polymorphisms (6, 36) have been used to type Cryptosporidium oocysts excreted by humans and animals and oocysts recovered from the environment. This effort has led to a deeper understanding of the taxonomy of the genus Cryptosporidium and the epidemiology of cryptosporidiosis in humans and livestock. As a result of this work, two species responsible for a majority of human infections, Cryptosporidium parvum and C. hominis, were identified (21) and our understanding of the taxonomy of the genus was refined (35).The application of genetic markers to define species, i.e., reproductively isolated populations, is straightforward. At this taxonomic level, all genotypes cosegregate and the choice of marker will have little impact on the outcome, provided that the marker, or combination thereof, is sufficiently polymorphic. The classical example is the variable region of the small-subunit rRNA gene which has been used, as in other taxa, to define many Cryptosporidium species. For studying intraspecies polymorphism, the choice of genotyping methods needs to take into consideration the potential for genetic recombination. This is clearly the case for species such as those belonging to the genus Cryptosporidium, which are known to undergo an obligatory sexual cycle during which genetically dissimilar haplotypes can recombine (28).Among the many markers that have been applied in epidemiological surveys of C. parvum and C. hominis, a variable fragment of the gene encoding a sporozoite surface glycoprotein (8, 26) has been particularly popular. As a result of the widespread adoption of this marker, variously named GP60, cpgp40/15, or gp40, numerous alleles have been identified and deposited in GenBank. The analysis of this continuously growing collection of GP60 sequences has led to the identification of groups of related sequences (18, 27, 32, 33). In an attempt to simplify the comparison of GP60 genotypes among different laboratories, a GP60 nomenclature distinguishing the main groups of alleles has been created (26) and later refined (27).The desire to streamline the genotyping of large numbers of Cryptosporidium isolates collected during surveys has led to the widespread adoption of the GP60 genotype as the only marker for defining intraspecies groups. Since this approach is not compatible with the reassortment of unlinked loci, the classification of isolates on the basis of the GP60 genotype, or any other single marker, needs to be evaluated. Within a recombining population, no single genetic marker can a priori be expected to serve as a surrogate for other loci or multilocus genotypes (MLGs), and any apparent clustering of isolates is dependent on the marker. To investigate the validity of the GP60 genotyping method as commonly applied to the classification of C. parvum and C. hominis isolates, the GP60 genotype was added to a previously described 9-locus genotype (29) and a diversified collection of 10-locus genotypes was examined for intraspecies clusters. We show that, with the exception of some GP60 alleles apparently restricted to human C. parvum, neither C. parvum nor C. hominis GP60 alleles define subspecies genotypes. These results are discussed in the context of ongoing research to better understand the population structure of these parasites and identify genotypes associated with virulence traits.