Encephalitozoon cuniculi infects a wide range of mammalian hosts. Three genotypes based on the number of GTTT repeats in the internal transcribed spacer (ITS) of the rRNA have been described, of which genotypes I and III have been identified in humans. In this study, the genetic diversity of E. cuniculi was examined at the polar tube protein (PTP) and spore wall protein I (SWP-1) loci. Nucleotide sequence analysis of the PTP gene divided 11 E. cuniculi isolates into three genotypes in congruence with the result of analysis of the ITS of the rRNA gene. The three PTP genotypes differed from one another by the copy number of the 78-bp central repeat as well as point mutations. These E. cuniculi isolates also differed from one another in the number of 15-and 36-bp repeats in the SWP-1 gene. In addition, some E. cuniculi isolates had heterogeneous copies of the SWP-1 gene with various numbers of repeats. Intragenotypic variation was also observed at the SWP-1 locus. Based on the length polymorphism and sequence diversities of the PTP and SWP-1 genes, two simple PCR tests were developed to differentiate E. cuniculi in clinical samples.Encephalitozoon cuniculi is a common microsporidian parasite that infects various mammals, such as rabbits, rats, mice, horses, foxes, cats, dogs, muskrats, leopards, baboons, and humans (7, 13). Recent characterization of the internal transcribed spacer (ITS) of the rRNA gene has identified three genotypes of E. cuniculi based on the number of GTTT repeats present: a genotype or strain I from rabbits containing three repeats, a genotype or strain II from mice containing two repeats, and a genotype or strain III from dogs containing four repeats (9). Thus far, both genotype or strain I and genotype or strain III genotypes of E. cuniculi have been found in humans, indicating that human E. cuniculi infection can be of zoonotic origin (6,8,18,20,21). The number of human E. cuniculi isolates characterized so far, however, is very small (13).Currently, genotyping of E. cuniculi involves mostly DNA sequencing of ITS, which is not practical in most diagnostic laboratories because of the technical demands and high cost. Thus, there is a need for the development of simpler genotyping tools that are more cost-effective and can be performed in most diagnostic laboratories. This will allow the genotyping of E. cuniculi in large numbers of laboratories and better characterization of the epidemiology of human E. cuniculi infection. Recently, genes coding for the polar tube protein (PTP) and spore wall protein I (SWP-1) of E. cuniculi were reported (2, 5). Because the gene has long central repeats of 78 bp in PTP and 15 and 36 bp in SWP-1 and the number of repeats in repetitive proteins tends to vary in other parasites such as Plasmodium spp., we examined the sequence diversity of PTP and SWP-1 genes among various isolates of E. cuniculi. This study has led to the development of two simple PCR-based molecular diagnostic tests.
MATERIALS AND METHODSParasite isolates. The E. cuniculi isolates used in thi...