Sensitive genotyping of Cryptosporidium parvum by PCR-RFLP analysis of the 70-kilodalton heat shock protein (HSP70) gene

Polymorphism of 16s rRNA Gene: Any Effect on the Biomolecular Quantitation of the Honey Bee (Apis mellifera L., 1758) Pathogen Nosema ceranae?

The microsporidian Nosema ceranae is a severe threat to the western honey bee Apis mellifera, as it is responsible for nosemosis type C, which leads the colonies to dwindle and collapse. Infection quantification is essential to clinical and research aims. Assessment is made often with molecular assays based on rRNA genes, which are present in the N. ceranae genome as multiple and polymorphic copies. This study aims to compare two different methods of Real-Time PCR (qPCR), respectively relying on the 16S rRNA and Hsp70 genes, the first of which is described as a multiple and polymorphic gene. Young worker bees, hatched in the laboratory and artificially inoculated with N. ceranae spores, were incubated at 33 °C and subject to different treatment regimens. Samples were taken post-infection and analyzed with both qPCR methods. Compared to Hsp70, the 16S rRNA method systematically detected higher abundance. Straightforward conversion between the two methods is made impossible by erratic 16s rRNA/Hsp70 ratios. The 16s rRNA polymorphism showed an increase around the inoculated dose, where a higher prevalence of ungerminated spores was expected due to the treatment effects. The possible genetic background of that irregular distribution is discussed in detail. The polymorphic nature of 16S rRNA showed to be a limit in the infection quantification. More reliably, the N. ceranae abundance can be assessed in honey bee samples with methods based on the single-copy gene Hsp70.

Genomics and molecular epidemiology of Cryptosporidium species

Cryptosporidium is one of the most widespread protozoan parasites that infects domestic and wild animals and is considered the second major cause of diarrhea and death in children after rotavirus. So far, around 20 distinct species are known to cause severe to moderate infections in humans, of which Cryptosporidium hominis and Cryptosporidium parvum are the major causative agents. Currently, ssurRNA and gp60 are used as the optimal markers for differentiating species and subtypes respectively. Over the last decade, diagnostic tools to detect and differentiate Cryptosporidium species at the genotype and subtype level have improved, but our understanding of the zoonotic and anthroponotic transmission potential of each species is less clear, largely because of the paucity of high resolution whole genome sequencing data for the different species. Defining which species possess an anthroponotic vs. zoonotic transmission cycle is critical if we are to limit the spread of disease between animals and humans. Likewise, it is unclear to what extent genetic hybridization impacts disease potential or the emergence of outbreak strains. The development of high resolution genetic markers and whole genome sequencing of different species should provide new insights into these knowledge gaps. The aim of this review is to outline currently available molecular epidemiology and genomics data for different species of Cryptosporidium.

Methods for the detection of Cryptosporidium and Giardia: From microscopy to nucleic acid based tools in clinical and environmental regimes

The detection and characterization of genotypes and sub genotypes of Cryptosporidium and Giardia is essential for their enumeration, surveillance, prevention, and control. Different diagnostic methods are available for the analysis of Cryptosporidium and Giardia including conventional phenotypic tools that face major limitations in the specific diagnosis of these protozoan parasites. The substantial advancement in the development of genetic signature based molecular tools for the quantification, diagnosis and genetic variation analysis has increased the understanding of the epidemiology and preventive measures of related infections. The conventional methods such as microscopy, antibody and enzyme based approaches, offer better detection results when combined with advanced molecular methods. Gene based approaches increase the precision of identification, for example, many signatures detected in environmental matrices represent species/genotype that are not infectious to humans. This review summarizes the available methods and the advantages and limitations of advance detection techniques like nucleic acid-based approaches for the detection of viable oocysts and cysts of Cryptosporidium and Giardia along with the conventional and widely accepted detection techniques like microscopy, antibody and enzyme based ones. This technical article also encourages the wide application of molecular methods in genetic characterization of distinct species of Cryptosporidium and Giardia, to adopt necessary preventive measures with reliable identification and mapping the source of contamination.

Comparison of current methods used to detect Cryptosporidium oocysts in stools

In this review all of the methods that are currently in use for the investigation of Cryptosporidium in stool material are highlighted and critically discussed. It appears that more qualifications and background knowledge in this field regarding the diagnosis of the Cryptosporidium parasite is required. Furthermore, there is no standardization for the protocols that are commonly used to either detect oocysts in faeces or to diagnose the Cryptosporidium infection. It is therefore necessary to initiate further education and research that will assist in improving the accuracy of the diagnosis of Cryptosporidium oocysts in the faecal micro-cosmos. Where ambient concentrations of oocysts are low in stool material, detection becomes a formidable task. Procedures for ring tests and the standardization of multi-laboratory testing are recommended. It is also necessary to enhance the routine surveillance capacity of cryptosporidiosis and to improve the safety against it, considering the fact that this disease is under diagnosed and under reported. This review is intended to stimulate research that could lead to future improvements and further developments in monitoring the diagnostic methodologies that will assist in harmonizing Cryptosporidium oocysts in stool diagnosis.

Biotin- and Glycoprotein-Coated Microspheres as Surrogates for Studying Filtration Removal of Cryptosporidium parvum in a Granular Limestone Aquifer Medium

Members of the genus Cryptosporidium are waterborne protozoa of great health concern. Many studies have attempted to find appropriate surrogates for assessing Cryptosporidium filtration removal in porous media. In this study, we evaluated the filtration of Cryptosporidium parvum in granular limestone medium by the use of biotin- and glycoprotein-coated carboxylated polystyrene microspheres (CPMs) as surrogates. Column experiments were carried out with core material taken from a managed aquifer recharge site in Adelaide, Australia. For the experiments with injection of a single type of particle, we observed the total removal of the oocysts and glycoprotein-coated CPMs, a 4.6- to 6.3-log10 reduction of biotin-coated CPMs, and a 2.6-log10 reduction of unmodified CPMs. When two different types of particles were simultaneously injected, glycoprotein-coated CPMs showed a 5.3-log10 reduction, while the uncoated CPMs displayed a 3.7-log10 reduction, probably due to particle-particle interactions. Our results confirm that glycoprotein-coated CPMs are the most accurate surrogates for C. parvum; biotin-coated CPMs are slightly more conservative, while unmodified CPMs are markedly overly conservative for predicting C. parvum removal in granular limestone medium. The total removal of C. parvum observed in our study suggests that granular limestone medium is very effective for the filtration removal of C. parvum and could potentially be used for the pretreatment of drinking water and aquifer storage recovery of recycled water.

Multi-locus analysis of human infective Cryptosporidium species and subtypes using ten novel genetic loci

Background

Cryptosporidium is a protozoan parasite that causes diarrheal illness in a wide range of hosts including humans. Two species, C. parvum and C. hominis are of primary public health relevance. Genome sequences of these two species are available and show only 3-5% sequence divergence. We investigated this sequence variability, which could correspond either to sequence gaps in the published genome sequences or to the presence of species-specific genes. Comparative genomic tools were used to identify putative species-specific genes and a subset of these genes was tested by PCR in a collection of Cryptosporidium clinical isolates and reference strains.

Results

The majority of the putative species-specific genes examined were in fact common to C. parvum and C. hominis. PCR product sequence analysis revealed interesting SNPs, the majority of which were species-specific. These genetic loci allowed us to construct a robust and multi-locus analysis. The Neighbour-Joining phylogenetic tree constructed clearly discriminated the previously described lineages of Cryptosporidium species and subtypes.

Conclusions

Most of the genes identified as being species specific during bioinformatics in Cryptosporidium sp. are in fact present in multiple species and only appear species specific because of gaps in published genome sequences. Nevertheless SNPs may offer a promising approach to studying the taxonomy of closely related species of Cryptosporidia.

Antigenic differences within the Cryptosporidium hominis and Cryptosporidium parvum surface proteins P23 and GP900 defined by monoclonal antibody reactivity

The biological basis for the specificity of host infectivity patterns of Cryptosporidium spp., in particular C. hominis and C. parvum, has yet to be fully elucidated. Comparison of the C. parvum and C. hominis P23 and GP900 predicted amino acid sequences revealed 3 differences in P23 and 4 and 17 differences in GP900 domains 1 and 5, respectively. Using monoclonal antibodies developed against the surface (glyco)proteins P23 and GP900 of the C. parvum Iowa isolate, solubilized glycoprotein from three C. hominis isolates was screened for reactivity using Western immunoblots. One of ten P23 MAbs and three of 21 GP900 MAbs were not reactive with any of the three C. hominis isolates. The non-reactive P23 MAb binds to a peptide epitope, while the non-reactive GP900 MAbs bind to either carbohydrate/carbohydrate-dependent or peptide epitopes of C. parvum. These results demonstrate phenotypic differences between C. hominis and C. parvum within two (glyco)proteins that are involved in parasite gliding motility and attachment/invasion.

Cryptosporidium--biotechnological advances in the detection, diagnosis and analysis of genetic variation

Cryptosporidiosis is predominantly a gastrointestinal disease of humans and other animals, caused by various species of protozoan parasites representing the genus Cryptosporidium. This disease, transmitted mainly via the faecal-oral route (in water or food), is of major socioeconomic importance worldwide. The diagnosis and genetic characterization of the different species and population variants (usually recognised as "genotypes" or "subgenotypes") of Cryptosporidium is central to the prevention, surveillance and control of cryptosporidiosis, particularly given that there is presently no broadly applicable treatment regimen for this disease. Although traditional phenotypic techniques have had major limitations in the specific diagnosis of cryptosporidiosis, there have been major advances in the development of molecular analytical and diagnostic tools. This article provides a concise account of Cryptosporidium and cryptosporidiosis, and focuses mainly on recent advances in nucleic acid-based approaches for the diagnosis of cryptosporidiosis and analysis of genetic variation within and among species of Cryptosporidium. These advances represent a significant step toward an improved understanding of the epidemiology as well as the prevention and control of cryptosporidiosis.

An evaluation of primers amplifying DNA targets for the detection of Cryptosporidium spp. using C. parvum HNJ-1 Japanese isolate in water samples

The performance of polymerase chain reaction (PCR) procedures for the detection of Cryptosporidium parvum HNJ-1 strain (genotype II) oocysts purified from mice using published protocols was evaluated. Oocysts were concentrated from fecal samples of infected severe combined immunodeficiency (SCID) mice by sucrose flotation and were then purified by immunomagnetic separation method. The genotype of C. parvum was established as type II by restriction fragment length polymorphism (RFLP) analysis. Water samples were spiked with different numbers of oocysts, determined by limiting dilution. Genomic DNA was extracted and used for PCR assays targeting various Cryptosporidium species genes (Beta-Tubulin, COWP, 70 kDa HSP, SSU rRNA, ITS1, TRAP-C1 and TRAP-C2 gene). DNA from oocyst numbers of more than 1 x 10(4) was detected using each of the primers. However, when using lower oocyst numbers, the tools based on 9 of the 16 different primer assays gave sufficient results. Assays using the remaining seven primers gave less than satisfactory results. A new primer set, named VKSS-F1/2 and VKSS-R1/2, that target the 18 SSU rRNA gene of C. parvum was constructed and applied. The VKSS-F1/2 and VKSS-R1/2 assays amplified DNA isolated from spiked samples in 206 of 211 trials (97.6%). This illustrates the difficulty of detecting low numbers of Cryptosporidium spp. oocysts by molecular methods when working with environmental samples.

Cryptosporidium

This review discusses characteristics of the genus Cryptosporidium and addresses the pathogenesis, reservoirs, public health significance and current applications for the detection and typing of this important pathogen. By increasing knowledge in key areas of Cryptosporidium research such as aetiology, epidemiology, transmission and host interactions, the numbers of cases of human cryptosporidiosis should be reduced.

Detection ofCryptosporidium parvum oocysts using a microfluidic device equipped with the SUS micromesh and FITC-labeled antibody

Development of a microfluidic device equipped with micromesh for detection of Cryptosporidium parvum oocyst was reported. A micromesh consisting of 10 x 10 cavities was microfabricated on the stainless steel plate by laser ablation. Each cavity size, approximately 2.7 microm in diameter, was adopted to capture a single C. parvum oocyst. Under negative pressure operation, suspensions containing microbeads or C. parvum oocysts flowed into the microchannel. Due to strong non-specific adsorption of microbeads onto the PDMS microchannel surface during sample injection, the surface was treated with air plasma, followed by treatment with 1% sodium dodecyl sulfate (SDS) solution. This process reduced the non-specific adsorption of microbeads on the microchannel to 10% or less in comparison to a non-treated microchannel. This microfluidic device equipped with the SUS micromesh was further applied for the capture of C. parvum oocysts. Trapped C. parvum oocysts were visualized by staining with FITC-labeled anti-C. parvum oocyst antibody on a micromesh and counted under fluoroscopic observation. The result obtained by our method was consistent with that obtained by direct immunofluorescence assay coupled with immunomagnetic separation (DFA-IMS) method, indicating that the SUS micromesh is useful for counting of C. parvum oocysts. The newly designed microfluidic device exploits a geometry that allowed for the entrapment of oocysts on the micromesh while providing the rapid introduction of a series of reagents and washes through the microfluidic structure. Our data indicate that this microfluidic device is useful for high-throughput counting of C. parvum oocysts from tap water sample.

First record of Cryptosporidium infection in a raccoon dog (Nyctereutes procyonoides viverrinus)

Cryptosporidium species have been found in more than 150 species of mammals, but there has been no report in raccoon dogs. Here we found the Cryptosporidium organism in a raccoon dog, Nyctereutes procyonoides viverrinus, and identified this isolate using PCR-based diagnostic methods. Cryptosporidium diagnostic fragments of the 18S ribosomal RNA, Cryptosporidium oocyst wall protein and 70-kDa heat shock protein genes were amplified from the isolate and sequenced to reveal the phylogenetic relationships between it and other Cryptosporidium species or genotypes reported previously. The results showed that the raccoon dog isolate represented the C. parvum cattle genotype which could be a causative agent in human cryptosporidiosis.

Molecular characterization of a Cryptosporidium isolate from a banded mongoose Mungos mungo

Cryptosporidium spp. has been found in more than 150 species of mammals, but there has been no report in mongooses. In this study, we report the isolation of Cryptosporidium sp. in a banded mongoose Mungos mungo, which was brought from Tanzania to Japan; the isolate was analyzed genetically to validate the occurrence of a new, host-adapted genotype. Cryptosporidium diagnostic fragments of 18S ribosomal RNA and 70-kDa heat shock protein genes were amplified from this isolate and compared with the other Cryptosporidium species and genotypes reported previously. Analyses showed that the mongoose isolate represents a new genotype, closely related to that of bears.

Cryptosporidium taxonomy: recent advances and implications for public health

There has been an explosion of descriptions of new species of Cryptosporidium during the last two decades. This has been accompanied by confusion regarding the criteria for species designation, largely because of the lack of distinct morphologic differences and strict host specificity among Cryptosporidium spp. A review of the biologic species concept, the International Code of Zoological Nomenclature (ICZN), and current practices for Cryptosporidium species designation calls for the establishment of guidelines for naming Cryptosporidium species. All reports of new Cryptosporidium species should include at least four basic components: oocyst morphology, natural host specificity, genetic characterizations, and compliance with the ICZN. Altogether, 13 Cryptosporidium spp. are currently recognized: C. muris, C. andersoni, C. parvum, C. hominis, C. wrairi, C. felis, and C. cannis in mammals; C. baïleyi, C. meleagridis, and C. galli in birds; C. serpentis and C. saurophilum in reptiles; and C. molnari in fish. With the establishment of a framework for naming Cryptosporidium species and the availability of new taxonomic tools, there should be less confusion associated with the taxonomy of the genus Cryptosporidium. The clarification of Cryptosporidium taxonomy is also useful for understanding the biology of Cryptosporidium spp., assessing the public health significance of Cryptosporidium spp. in animals and the environment, characterizing transmission dynamics, and tracking infection and contamination sources.

Survey of Cryptosporidium parvum genotypes in humans from the UK by mutation scanning analysis of a heat shock protein gene region

A mutation scanning-selective sequencing approach was employed for the genotypic identification and differentiation of Cryptosporidium parvum isolates. Genomic DNA samples (n=158) from Cryptosporidium oocysts from humans with clinical cryptosporidiosis (following recent foreign travel or during different outbreaks) in the UK were subjected to PCR-based single-strand conformation polymorphism (SSCP) analysis of a heat shock protein 70 gene region (p-hsp70; 448 bp). Samples representing different SSCP profiles were then subjected to sequencing. The analysis allowed the classification of 149 of the 158 samples as type-1 ( approximately 49%) or type-2 ( approximately 46%); amplicons from the remaining nine samples were consistent in size with p-hsp70 but represented non-specific, faecal contaminants. The percentages reflected those of a previous study in the UK for autochtonous, sporadic cases of cryptosporidiosis ( approximately 49% for type-1 and approximately 47% for type-2; n approximately 4000), but contrasted another survey of sporadic cases where type-2 dominated ( approximately 62%; n approximately 1000). The ability of the present SSCP-sequencing approach to accurately screen for C. parvum genotypes and to reliably discern erroneous amplicons has significant implications for the accurate diagnosis and monitoring of cryptosporidiosis and for population genetic studies.

Intraspecies polymorphism of Cryptosporidium parvum revealed by PCR-restriction fragment length polymorphism (RFLP) and RFLP-single-strand conformational polymorphism analyses

A glycoprotein (Cpgp40/15)-encoding gene of Cryptosporidium parvum was analyzed to reveal intraspecies polymorphism within C. parvum isolates. Forty-one isolates were collected from different geographical origins (Japan, Italy, and Nepal) and hosts (humans, calves, and a goat). These isolates were characterized by means of DNA sequencing, PCR-restriction fragment length polymorphism (PCR-RFLP), and RFLP-single-strand conformational polymorphism (RFLP-SSCP) analyses of the gene for Cpgp40/15. The sequence analysis indicated that there was DNA polymorphism between genotype I and II, as well as within genotype I, isolates. The DNA and amino acid sequence identities between genotypes I and II differed, depending on the isolates, ranging from 73.3 to 82.9% and 62.4 to 80.1%, respectively. Those among genotype I isolates differed, depending on the isolates, ranging from 69.0 to 85.4% and 54.8 to 79.2%, respectively. Because of the high resolution generated by PCR-RFLP and RFLP-SSCP, the isolates of genotype I could be subtyped as genotypes Ia1, Ia2, Ib, and Ie. The isolates of genotype II could be subtyped as genotypes IIa, IIb, and IIc. The isolates from calves, a goat, and one Japanese human were identified as genotype II. Within genotype II, the isolates from Japan were identified as genotype IIa, those from calves in Italy were identified as genotype IIb, and the goat isolate was identified as genotype IIc. All of the genotype I isolates were from humans. The Japanese isolate (code no. HJ3) and all of the Nepalese isolates were identified as genotypes Ia1 and Ia2, respectively. The Italian isolates were identified as genotype Ib, and the Japanese isolate (code no. HJ2) was identified as genotype Ie. Thus, the PCR-RFLP-SSCP analysis of this glycoprotein Cpgp40/15 gene generated a high resolution that has not been achieved by previous methods of genotypic differentiation of C. parvum.

Identification of genotypes of Cryptosporidium parvum isolates from ferrets in Japan

Recent molecular studies show that Cryptosporidium parvum is composed of at least eight genotypes including zoonotic genotypes. Therefore, it is important to screen the genotypes of the isolates harbored in animals for the control of human cryptosporidiosis. The ferret is a popular pet, but also a reservoir of Cryptosporidium. Since the infectivity of zoonotic genotypes in ferrets remains unclear, there is a possibility these hosts harbor zoonotic genotypes. In the present study, we examined the genotypes of C. parvum isolates from ferrets in Japan using polymerase chain reaction direct sequencing. The sequences of the isolates examined clustered with the ferret-adapted genotype (ferret genotype). Our study suggests that ferrets harbor the ferret genotype which is conserved across geographical areas. Further study is required to determine whether ferrets are a significant reservoir for human cryptosporidiosis.

Utility of the Cryptosporidium oocyst wall protein (COWP) gene in a nested PCR approach for detection infection in cattle

A preliminary molecular epidemiological study was carried out to investigate the utility of the Cryptosporidium oocyst wall protein (COWP) gene in the detection of Cryptosporidium oocysts in fecal samples. A nested polymerase chain reaction (PCR) approach using COWP gene primers was adopted for this purpose. Fecal samples were spiked with each of 1, 10, and 100 oocysts of C. parvum, four samples for each number, and the DNA was extracted from each sample using a glassbead method. The presence of oocysts was determined using the nested PCR with COWP gene primers, and the limit of detection of oocysts by the PCR was determined. The limit of detection was 100 oocysts spiked in 1 ml of fecal material (50% sold material) (four positives/four samples tested). Seventy-five percent of DNA extracted samples spiked with 1 and 10 oocysts was positive by the PCR (three positives/four samples tested). Based on this, small sample size using the COWP gene primers with a nested PCR analysis could reliably identify infected animals rather conveniently and accurately.

Cryptosporidium hominis n. sp. (Apicomplexa: Cryptosporidiidae) from Homo sapiens

The structure and infectivity of the oocysts of a new species of Cryptosporidium from the feces of humans are described. Oocysts are structurally indistinguishable from those of Cryptosporidium parvum. Oocysts of the new species are passed fully sporulated, lack sporocysts. and measure 4.4-5.4 microm (mean = 4.86) x 4.4-5.9 microm (mean = 5.2 microm) with a length to width ratio 1.0-1.09 (mean 1.07) (n = 100). Oocysts were not infectious for ARC Swiss mice, nude mice. Wistar rat pups, puppies, kittens or calves, but were infectious to neonatal gnotobiotic pigs. Pathogenicity studies in the gnotobiotic pig model revealed significant differences in parasite-associated lesion distribution (P = 0.005 to P = 0.02) and intensity of infection (P = 0.04) between C. parvum and this newly described species from humans. In vitro cultivation studies have also revealed growth differences between the two species. Multi-locus analysis of numerous unlinked loci, including a preliminary sequence scan of the entire genome demonstrated this species to be distinct from C. parvum and also demonstrated a lack of recombination, providing further support for its species status. Based on biological and molecular data, this Cryptosporidium infecting the intestine of humans is proposed to be a new species Cryptosporidium hominis n. sp.

Direct detection of Cryptosporidium parvum oocysts by immunomagnetic separation-polymerase chain reaction in raw milk

Cryptosporidium parvum is an emerging protozoan parasite responsible for several serious outbreaks of cryptosporidiosis, an enteric infection characterized by severe intestinal distress. This parasite can be transmitted through contaminated water and raw food in the oocyst form, which is resistant to many environmental stresses and food processes. C. parvum is also commonly found on dairy farms and could be transmitted to humans through contaminated raw milk and dairy products. Thus, an immunomagnetic separation-polymerase chain reaction assay for direct detection of C. parvum oocysts in milk was developed. The procedure was able to detect < 10 C. parvum oocysts. Thus, it could be used for monitoring milk samples.

Detection and differentiation of Cryptosporidium parasites that are pathogenic for humans by real-time PCR

Cryptosporidiosis is a significant cause of food-borne and waterborne outbreaks of diarrheal diseases. To better understand the route of transmission of Cryptosporidium parasites, a number of genotyping techniques have been developed, based on PCR-restriction fragment length polymorphism or sequencing analysis of antigen, structural, and housekeeping genes. In this study, a real-time assay for the detection of Cryptosporidium oocysts is described. This technique had a detection limit of five oocysts. By melting curve analysis of PCR products with fluorescence-labeled hybridization probes, this technique was able to differentiate five common Cryptosporidium parasites that are pathogenic for humans in a single PCR. We evaluated and validated the test using samples from presently known Cryptosporidium parasites that are pathogenic for humans. This technique provides an alternative molecular tool in epidemiologic studies of human cryptosporidiosis.