title: A comparison of sequence and length polymorphism for genotyping Cryptosporidium isolates.
abstract: Simple sequence repeat markers have played an important role in elucidating the epidemiology of human and animal cryptosporidiosis. The drawback of sequence length polymorphisms is that nucleotide substitutions remain undetected. As some laboratories have opted for using length polymorphisms, while others have relied on sequencing, there is a need to compare both methods. We used a diversified set of unique length polymorphisms and matching nucleotide sequences to assess the ability of each genotyping protocol to discern clusters of related Cryptosporidium parvum isolates. We found a weak correlation between the two distance measures for individual markers. This analysis was extended to four-locus genotypes based on sequence length data or concatenated sequences from the same loci. We interrogated these data to assess whether one would reach the same conclusions regardless of the genotyping method. Clusters of isolates generated with the concatenated sequences were not observed with amplicon length, indicating that inferences on the structure of a Cryptosporidium population depend on the genotyping method. Moreover, isolate clusters derived from concatenated sequences were dependent on the algorithm used to calculate distances. These results emphasize the need for harmonizing genotyping tools, not only by selecting informative markers, but also by standardizing the entire genotyping method.
authors.affiliation: Department of Infectious Disease and Global Health,Cummings School of Veterinary Medicine at Tufts University,North Grafton,Massachusetts,USA.
authors.forename: G
authors.initials: G
authors.lastname: Widmer
authors.affiliation: Department of Infectious,Parasitic and Immunomediated Diseases,Istituto Superiore di Sanità,Rome,Italy.
authors.forename: S M
authors.initials: SM
authors.lastname: Cacciò
mesh_terms: D001483:Base Sequence; D003457:Cryptosporidiosis / Q000453:epidemiology / Q000469:parasitology*; D003458:Cryptosporidium / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D016054:DNA, Protozoan / Q000235:genetics; D005838:Genotype; D060005:Genotyping Techniques / Q000379:methods* / Q000592:standards; D018895:Microsatellite Repeats / Q000235:genetics; D008969:Molecular Sequence Data; D011110:Polymorphism, Genetic / Q000235:genetics*; D017422:Sequence Analysis, DNA
chemical_list: D016054:DNA, Protozoan
keywords: Cryptosporidium; Mantel test; principal coordinate analysis; sequence polymorphism; simple sequence repeat