Validation of fragment analysis by capillary electrophoresis to resolve mixed infections by Cryptosporidium parvum subpopulations

Multilocus Sequence Typing as a Useful Tool for the Study of the Genetic Diversity and Population Structure of Cryptosporidium Spp

One of the most important aquatic parasites in industrialized countries, Cryptosporidium spp., is a major cause of diarrheal disease in humans and animals worldwide. The contingent evolution of cryptosporidia with hosts, host adaptation, and geographic variation contributed to the creation of species subtypes, thereby shaping their population genetic structures. Multilocus typing tools for population genetic characterizations of transmission dynamics and delineation of mechanisms for the emergence of virulent subtypes have played an important role in improving our understanding of the transmission of this parasite. However, to better understand the significance of different subtypes with clinical disease manifestations and transmission risks, a large number of samples and preferably from different geographical areas need to be analyzed. This review provides an analysis of genetic variation through multilocus sequence typing, provides an overview of subtypes, typing gene markers for Cryptosporidium parvum, Cryptosporidium hominis, Cryptosporidium muris and Cryptosporidium andersoni genotypes and an overview of the hosts of these parasites.

Multilocus Sequence Typing helps understand the genetic diversity of Cryptosporidium hominis and Cryptosporidium parvum isolated from Colombian patients

Multilocus Sequence Typing has become a useful tool for the study of the genetic diversity and population structure of different organisms. In this study, a MLST approach with seven loci (CP47, MS5, MS9, MSC6-7, TP14, and gp60) was used to analyze the genetic diversity of Cryptosporidium hominis and Cryptosporidium parvum isolated from 28 Colombian patients. Five Cryptosporidium species were identified: C. hominis, C. parvum, Cryptosporidium felis, Cryptosporidium meleagridis, and Cryptosporidium suis. Unilocus gp60 analysis identified four allelic families for C. hominis (Ia, Ib, Id, and Ie) and two for C. parvum (IIa and IIc). There was polymorphic behavior of all markers evaluated for both C. hominis and C. parvum, particularly with the CP47, MS5, and gp60 markers. Phylogenetic analysis with consensus sequences (CS) of the markers showed a taxonomic agreement with the results obtained with the 18S rRNA and gp60 gene. Additionally, two monophyletic clades that clustered the species C. hominis and C. parvum were detected, with a higher number of subclades within the monophyletic groups compared to those with the gp60 gene. Thirteen MLG were identified for C. hominis and eight for C. parvum. Haplotypic and nucleotide diversity were detected, but only the latter was affected by the gp60 exclusion from the CS analysis. The gene fixation index showed an evolutionary closeness between the C. hominis samples and a less evolutionary closeness and greater sequence divergence in the C. parvum samples. Data obtained in this work support the implementation of MLST analysis in the study of the genetic diversity of Cryptosporidium, considering the more detailed information that it provides, which may explain some genetic events that with an unilocus approach could not be established. This is the first multilocus analysis of the intra-specific variability of Cryptosporidium from humans in South America.

Microsatellite Analysis of Geographically Close Isolates of Cystoisospora suis

Microsatellites are short repetitive DNA sequences of 2–6 repeats interspersed in the genome that display a rapid mutation rate and consequently show high variation between individuals or populations. They have been used to characterize population diversity and structure and the level of variation between different isolates of a number of different organisms, including apicomplexan protozoa. Currently nothing is known about the genetic variability and population structure of Cystoisospora suis (Apicomplexa: Coccidia), the causative agent of piglet coccidiosis, and we made use of the recently available genome of C. suis (strain Wien-I) to amplify microsatellite regions (ca. 300–550 bp) and evaluate the applicability of fluorescence-labeled primers to investigate amplicon length variation at high resolution using capillary electrophoresis (CE). Two phenotypically characterized isolates (Wien-I, toltrazuril susceptible; Holl 1 toltrazuril resistant) and six field isolates from Europe were compared by conventional PCR followed by agar-gel electrophoresis, Sanger sequencing, and CE (fluorescence labeling and fragment length analysis) to evaluate the applicability of the method. Four primer pairs could be identified that amplified bands of the expected size and were labeled for CE analysis. High resolution CE for size determination of PCR amplicons proved to be a reliable and simple method. It revealed high diversity of the analyzed strains, with marked differences even between two strains from neighboring swine farms. In follow-up studies, adaptation of the PCR assay to multiplexing and amplification of small DNA quantities will provide a cost-effective tool to analyse field strains to reveal geographic diversity that could be mapped to phenotypic traits.

Intra-Species Diversity and Panmictic Structure of Cryptosporidium parvum Populations in Cattle Farms in Northern Spain

The intra-herd and intra-host genetic variability of 123 Cryptosporidium parvum isolates was investigated using a multilocus fragment typing approach with eleven variable-number tandem-repeat (VNTR) loci and the GP60 gene. Isolates were collected from intensively farmed diarrheic pre-weaned calves originating from 31 dairy farms in three adjoining regions in northern Spain (País Vasco, Cantabria and Asturias). The multilocus tool demonstrated an acceptable typeability, with 104/123 samples amplifying at all twelve loci. The ML2, TP14, GP60 and the previously un-described minisatellite at locus cgd2_3850 were the most discriminatory markers, while others may be dismissed as monomorphic (MSB) or less informative (CP47, ML1 and the novel minisatellites at loci Cgd1_3670 and Cgd6_3940). The 12-satellite typing tool provided a Hunter-Gaston index (HGDI) of 0.987 (95% CI, 0.982-0.992), and differentiated a total of 70 multilocus subtypes (MLTs). The inclusion of only the four most discriminatory markers dramatically reduced the number of MLTs (n: 44) but hardly reduced the HGDI value. A total of 54 MLTs were distinctive for individual farms, indicating that cryptosporidiosis is an endemic condition on most cattle farms. However, a high rate of mixed infections was detected, suggesting frequent meiotic recombination. Namely, multiple MLTs were seen in most farms where several specimens were analyzed (90.5%), with up to 9 MLTs being found on one farm, and individual specimens with mixed populations being reported on 11/29 farms. Bayesian Structure analysis showed that over 35% of isolates had mixed ancestry and analysis of evolutionary descent using the eBURST algorithm detected a high rate (21.4%) of MLTs appearing as singletons, indicating a high degree of genetic divergence. Linkage analysis found evidence of linkage equilibrium and an overall panmictic structure within the C. parvum population in this discrete geographical area.

Multiple Cryptosporidium parvum subtypes detected in a unique isolate of a Chilean neonatal calf with diarrhea

To further understand the composition of population of parasite in a single host, we analyzed the GP60 gene of Cryptosporidium parvum amplified from DNA of a randomly selected isolate found in the feces of a diarrheic calf from a dairy farm in Central Chile. Direct sequencing of the amplicon yield the IIaA17G4R1 C. parvum subtype. The same amplicon was cloned in Escherichia coli (22 clones) and sequenced, yielding three different GP60 subtypes, IIaA17G4R1 (16/22), IIaA16G4R1 (1/22), and IIaA15G4R1 (1/22), and four sequences with nucleotide substitutions in the serine repeats, which subtype would be otherwise IIaA17G4R1. It is thus possible to determine allelic polymorphism using Sanger sequencing with an additional step of bacterial cloning. The results also indicate the necessity to further characterize parasite populations in a single host to better understand the dynamics of Cryptosporidium epidemiology.

Optimization of a fragment size analysis tool for identification of Cryptosporidium species and Gp60 alleles infecting domestic ruminants

A capillary electrophoresis (CE)-based DNA fragment analysis tool was optimized to identify in a single capillary the most common Cryptosporidium species and Cryptosporidium parvum GP60 alleles infecting domestic ruminants. For this purpose, a panel of genomic DNA samples including six Cryptosporidium species (C. parvum, C. bovis, C. ryanae, C. andersoni, C. ubiquitum, and C. hominis) and 18 C. parvum GP60 subtypes belonging to the subtype families IIa and IId was used. All these samples had been characterized previously by sequencing of SSU rRNA and GP60 genes. Isolates were re-amplified by PCR at these loci using sets of newly designed primers and subjected to CE. Fragment sizes were adjusted after comparison with sizes obtained by sequence analysis. The optimized CE-based approach provided fragments of different size for most Cryptosporidium species, but did not differentiate C. bovis and C. ryanae. Many of the GP60 subtypes (11/18) were also readily differentiated by CE, although overlapping in fragment sizes between IIa and IId subtypes was noticed. The CE-based tool was subsequently used to analyze Cryptosporidium isolates from naturally infected calves (n: 123) and lambs (n: 113) from farms in northern Spain. All isolates provided fragments typical of C. parvum. Fragment analysis at the GP60 locus differentiated a total of 10 alleles within isolates from calves (6 alleles) and lambs (8 alleles), with all but three alleles being host-associated. These findings support the validity of the optimized CE approach as a discriminatory and time- and cost-saving alternative to sequencing for identification of Cryptosporidium species and GP60 alleles in domestic ruminants.