Emergence of distinct genotypes of Cryptosporidium parvum in structured host populations

Cryptosporidium parvum gp60 subtypes in diarrheic lambs and goat kids from Israel

Cryptosporidium parvum is the second-most prevalent Cryptosporidium species that infects humans worldwide. In European countries, it is the most prevalent species in sheep, suggesting that these animals are a source of zoonotic infection. Preweaned lambs and goats are particularly susceptible to infection by the parasite and may suffer from severe diarrhea whilst excreting large quantities of infectious oocysts. Fifty fecal samples from preweaned lambs and goats with diarrhea from 35 farms across Israel, found to be Cryptosporidium-positive by microscopy, were tested by PCR and sequence analyses to determine the infective species and subtypes. Cryptosporidium parvum DNA was detected in most samples from both lambs and goats (46/50). Cryptosporidium xiaoi DNA was detected in three samples from kids, with co-infection detected in a single sample. Eleven different C. parvum subtypes were found, 10 in lambs and 5 in goats. All subtypes were from the IIa and IId subtype families, with subtypes IIdA20G1 and IIaA15G2R1 being the most prevalent and widespread. These subtypes were previously found in calves and humans in Israel and are considered the most prevalent C. parvum subtypes in small ruminants globally. These results underline the zoonotic potential of C. parvum from small ruminants and the high subtype diversity compared to previous reports from other Middle Eastern countries. In addition, this is the first report of C. xiaoi in Israel.

Epidemiological and Molecular Study of Cryptosporidium in Preweaned Calves in Kuwait

Cryptosporidium is a worldwide enteric protozoan parasite that causes gastrointestinal infection in animals, including humans. The most notable species is Cryptosporidium parvum because of its zoonotic importance; it is also the leading cause of cryptosporidiosis in preweaned calves. A cross-sectional study was conducted to determine the prevalence of Cryptosporidium infection, investigate the potential risk factors, and use molecular diagnosis to identify the predominant Cryptosporidium spp. in preweaned calves in Kuwait. Of 175 preweaned calves, Cryptosporidium antigens were detected in 58 (33.1%) using rapid lateral immunochromatography assay (IC). Calves less than one month of age (OR = 4.32, p = 0.0001) and poor hygiene (OR = 2.85, p = 0.0075) were identified as significant risk factors associated with Cryptosporidium infection. Molecular identification revealed that C. parvum (62.8%) was the dominant species infecting preweaned calves in Kuwait. In contrast, C. bovis and C. andersoni were recorded at 5.7% and 2.9%, respectively. All C. parvum gp60 nucleotide sequences were subtype IIaA15G2R1. Calves could be a source of C. parvum infection due to the similarity of the subtypes recorded previously in Kuwaiti children and preweaned calves in this study. Therefore, more research is needed to understand the Cryptosporidium transmission cycle in Kuwait.

Cryptosporidium parvum subtypes from diarrheic dairy calves in Israel

Cryptosporidium are protozoan parasites with worldwide distribution, infecting a wide range of terrestrial and aquatic animals, as well as humans. Cryptosporidium parvum is the most important zoonotic species and is the primary cause of cryptosporidiosis in preweaned calves, a highly prevalent, economically important disease. Extensive subtyping of C. parvum from infected humans and animals has expanded current understanding of the parasites' epidemiology. Israel has a highly developed dairy sector with intensive, zero-grazing operations. While C. parvum has been found in dairy calves throughout the country, and subtype data from human patients have also been published, subtype data from animals, and in particular preweaned ruminants, are lacking. We carried out an initial study of Cryptosporidium species and subtypes from preweaned diarrheic calves. Cryptosporidium species were determined in 71 fecal samples from 43 different dairy farms using 18S rRNA PCR, and subtyping of C. parvum based on the 60-kDa glycoprotein (gp60) sequences was done on one sample per farm. C. parvum was the only species found, with eight different subtypes belonging to the zoonotic IIa and IId families. Subtype IIaA15G2R1 was the most prevalent and widespread, found in 50% of the farms over a wide geographical distribution. Our results confirm the presence of subtypes IIaA15G2R1 and IIdA20G1, which were previously found in human patients in Israel, also in Israeli calves. In addition, subtype IIaA12G1R1 is reported here for the first time in an animal. These findings demonstrate the value of monitoring C. parvum subtypes in animal samples, and suggest that the role of calves as well as other young ruminants in the transmission of zoonotic cryptosporidiosis in Israel should be further studied.

Challenges for Cryptosporidium Population Studies

Cryptosporidiosis is ranked sixth in the list of the most important food-borne parasites globally, and it is an important contributor to mortality in infants and the immunosuppressed. Recently, the number of genome sequences available for this parasite has increased drastically. The majority of the sequences are derived from population studies of Cryptosporidium parvum and Cryptosporidium hominis, the most important species causing disease in humans. Work with this parasite is challenging since it lacks an optimal, prolonged, in vitro culture system, which accurately reproduces the in vivo life cycle. This obstacle makes the cloning of isolates nearly impossible. Thus, patient isolates that are sequenced represent a population or, at times, mixed infections. Oocysts, the lifecycle stage currently used for sequencing, must be considered a population even if the sequence is derived from single-cell sequencing of a single oocyst because each oocyst contains four haploid meiotic progeny (sporozoites). Additionally, the community does not yet have a set of universal markers for strain typing that are distributed across all chromosomes. These variables pose challenges for population studies and require careful analyses to avoid biased interpretation. This review presents an overview of existing population studies, challenges, and potential solutions to facilitate future population analyses.

Development of a novel, high resolution melting analysis based genotyping method for Cryptosporidium parvum

This study employed the post-real-time PCR application, high resolution melting (HRM) analysis, in order to differentiate between characterised clinical and reference Cryptosporidium parvum samples obtained from Cork University Hospital (Cork, Ireland) and the Cryptosporidium Reference Unit (Swansea, Wales). A sample set composed of 18 distinct C. parvum gp60-subtypes of the IIa gp60-subtype family (an allele family accounting for over 80% of all cryptosporidiosis cases in Ireland) was employed. HRM analysis-based interrogation of the gp60, MM5 and MS9-Mallon tandem repeat loci was found to completely differentiate between 10 of the 18 studied gp60-subtypes. The remaining eight gp60-subtypes were differentiated into three distinct groupings, with the designations within these groupings resolved to two to three potential gp60-subtypes. The current study aimed to develop a novel, reproducible, real-time PCR based multi-locus genotyping method to distinguish between C. parvum gp60-subtypes. These preliminary results support the further expansion of the multi-locus panel in order to increase the discriminatory capabilities of this novel method.

Molecular analysis of cryptosporidiosis cases in Western Australia in 2019 and 2020 supports the occurrence of two swimming pool associated outbreaks and reveals the emergence of a rare C. hominis IbA12G3 subtype

Cryptosporidium is an important protozoan parasite and due to its resistance to chlorine is a major cause of swimming pool-associated gastroenteritis outbreaks. The present study combined contact tracing and molecular techniques to analyse cryptosporidiosis cases and outbreaks in Western Australia in 2019 and 2020. In the 2019 outbreak, subtyping at the 60 kDa glycoprotein (gp60) gene identified 89.0% (16/18) of samples were caused by the C. hominis IdA15G1 subtype. Amplicon next generation sequencing (NGS) at the gp60 locus identified five C. hominis IdA15G1 subtype samples that also had C. hominis IdA14 subtype DNA, while multi locus sequence typing (MLST) analysis on a subset (n = 14) of C. hominis samples identified three IdA15G1 samples with a 6 bp insertion at the end of the trinucleotide repeat region of the cp47 gene. In 2020, 88.0% (73/83) of samples typed were caused by the relatively rare C. hominis subtype IbA12G3. Four mixed infections were observed by NGS with three IdA15G1/ IdA14 mixtures and one C. parvum IIaA18G3R1 sample mixed with IIaA16G3R1. No genetic diversity using MLST was detected. Epidemiological and molecular data indicates that the outbreaks in 2019 and 2020 were each potentially from swimming pool point sources and a new C. hominis subtype IbA12G3 is emerging in Australia. The findings of the present study are important for understanding the introduction and transmission of rare Cryptosporidium subtypes to vulnerable populations.

Population structure and geographical segregation of Cryptosporidium parvum IId subtypes in cattle in China

Background

Cryptosporidium parvum is a zoonotic pathogen worldwide. Extensive genetic diversity and complex population structures exist in C. parvum in different geographical regions and hosts. Unlike the IIa subtype family, which is responsible for most zoonotic C. parvum infections in industrialized countries, IId is identified as the dominant subtype family in farm animals, rodents and humans in China. Thus far, the population genetic characteristics of IId subtypes in calves in China are not clear.

Methods

In the present study, 46 C. parvum isolates from dairy and beef cattle in six provinces and regions in China were characterized using sequence analysis of eight genetic loci, including msc6-7, rpgr, msc6-5, dz-hrgp, chom3t, hsp70, mucin1 and gp60. They belonged to three IId subtypes in the gp60 gene, including IIdA20G1 (n = 17), IIdA19G1 (n = 24) and IIdA15G1 (n = 5). The data generated were analyzed for population genetic structures of C. parvum using DnaSP and LIAN and subpopulation structures using STRUCTURE, RAxML, Arlequin, GENALEX and Network.

Results

Seventeen multilocus genotypes were identified. The results of linkage disequilibrium analysis indicated the presence of an epidemic genetic structure in the C. parvum IId population. When isolates of various geographical areas were treated as individual subpopulations, maximum likelihood inference of phylogeny, pairwise genetic distance analysis, substructure analysis, principal components analysis and network analysis all provided evidence for geographical segregation of subpopulations in Heilongjiang, Hebei and Xinjiang. In contrast, isolates from Guangdong, Shanghai and Jiangsu were genetically similar to each other.

Conclusions

Data from the multilocus analysis have revealed a much higher genetic diversity of C. parvum than gp60 sequence analysis. Despite an epidemic population structure, there is an apparent geographical segregation in C. parvum subpopulations within China.

Molecular detection of genotypes and subtypes of Cryptosporidium infection in diarrheic calves, lambs, and goat kids from Turkey

The studies on Cryptosporidium infections of animals in Turkey mostly rely on microscopic observation. Few data are available regarding the prevalence of Cryptosporidium genotypes and subtypes infection. The aim of this study is to analyse the detection of Cryptosporidium genotypes and subtypes from young ruminants. A total of 415 diarrheic fecal specimens from young ruminants were examined for the Cryptosporidium detection by use of nested PCR of the small subunit ribosomal RNA (SSU rRNA) gene and the highly polymorphic 60 kDa glycoprotein (gp60) gene followed by sequence analyses. The results of this study revealed that 25.6% (106 of 415) of the specimens were positive for Cryptosporidium spp. infection. We identified 27.4% (91/333), 19.4% (13/67), and 13.4% (2/15) of positivity in calves, lambs and goat kids, respectively. Genotyping of the SSU rRNA indicated that almost all positive specimens were of C. parvum, except for one calf which was of C. bovis. Sequence analysis of the gp60 gene revealed the most common zoonotic subtypes (IIa and IId) of C. parvum. We detected 11 subtypes (IIaA11G2R1, IIaA11G3R1, IIaA12G3R1, IIaA13G2R1, IIaA13G4R1, IIaA14G1R1, IIaA14G3R1, IIaA15G2R1, IIdA16G1, IIdA18G1, IIdA22G1); three of them (IIaA12G3R1, IIaA11G3R1 and IIaA13G4R1) was novel subtypes found in calves and lambs. Additionally, three subtypes (IIaA11G2R1, IIaA14G3R1, and IIdA16G1) were detected in young ruminants for the first time in Turkey. These results indicate the high infection of Cryptosporidium in Turkey and propose that young ruminants are likely a major reservoir of C. parvum and a potential source of zoonotic transmission.

Cryptosporidium infections in terrestrial ungulates with focus on livestock: a systematic review and meta-analysis

Background

Cryptosporidium spp. are causative agents of gastrointestinal diseases in a wide variety of vertebrate hosts. Mortality resulting from the disease is low in livestock, although severe cryptosporidiosis has been associated with fatality in young animals.

Methods

The goal of this systematic review and meta-analysis was to review the prevalence and molecular data on Cryptosporidium infections in selected terrestrial domestic and wild ungulates of the families Bovidae (bison, buffalo, cattle, goat, impala, mouflon sheep, sheep, yak), Cervidae (red deer, roe deer, white-tailed deer), Camelidae (alpaca, camel), Suidae (boar, pig), Giraffidae (giraffes) and Equidae (horses). Data collection was carried out using PubMed, Scopus, Science Direct and Cochran databases, with 429 papers being included in this systematic analysis.

Results

The results show that overall 18.9% of ungulates from the investigated species were infected with Cryptosporidium spp. Considering livestock species (cattle, sheep, goats, pigs, horses and buffaloes), analysis revealed higher Cryptosporidium infection prevalence in ungulates of the Cetartiodactyla than in those of the Perissodactyla, with cattle (29%) being the most commonly infected farm animal.

Conclusions

Overall, the investigated domestic ungulates are considered potential sources of Cryptosporidium contamination in the environment. Control measures should be developed to reduce the occurrence of Cryptosporidium infection in these animals. Furthermore, literature on wild populations of the named ungulate species revealed a widespread presence and potential reservoir function of wildlife.

Prevalence and Population Genetics Analysis of Enterocytozoon bieneusi in Dairy Cattle in China

Enterocytozoon bieneusi, an obligate intracellular pathogen, can infect various hosts. In this study, 3527 dairy cattle fecal specimens were collected from different geographic locations in China (including 673 from Shandong province, 1,440 from Guangdong province and 1,414 from Gansu province) and examined for the presence of E. bieneusi using polymerase chain reactions targeting the ribosomal internal transcribed spacer (ITS). The dominant genotypes identified were further subtyped by multilocus sequence typing. The overall prevalence of E. bieneusi was 14.2% (501/3527), with a significant difference in prevalence among the different geographical locations (P < 0.001). Our logistic regression analysis showed that all four variables (farming model, location, age, and clinical manifestations) had strong effects on the risk of contracting E. bieneusi. Sequence analysis revealed 11 genotypes: eight known genotypes (J, I, BEB4, BEB10, D, EbpC, CM19, and CM21) and three novel genotypes (named here as CGC1, CGC2, and CGC3). Genotypes J and I, the commonest, were found on all farms across the three provinces. Our linkage disequilibrium analysis showed a clonal population structure in the E. bieneusi dairy cattle population but the ITS genotypes had different population structures. Phylogenetic and haplotype network analysis showed the absence of geographical segregation in the E. bieneusi dairy cattle populations. Instead, they revealed the presence of host adaptation to the E. bieneusi populations in various animals. Our findings augment the current understanding of E. bieneusi transmission dynamics.

Molecular epidemiologic tools for waterborne pathogens Cryptosporidium spp. and Giardia duodenalis

Molecular diagnostic tools have played an important role in improving our understanding of the transmission of Cryptosporidium spp. and Giardia duodenalis, which are two of the most important waterborne parasites in industrialized nations. Genotyping tools are frequently used in the identification of host-adapted Cryptosporidium species and G. duodenalis assemblages, allowing the assessment of infection sources in humans and public health potential of parasites found in animals and the environment. In contrast, subtyping tools are more often used in case linkages, advanced tracking of infections sources, and assessment of disease burdens attributable to anthroponotic and zoonotic transmission. More recently, multilocus typing tools have been developed for population genetic characterizations of transmission dynamics and delineation of mechanisms for the emergence of virulent subtypes. With the recent development in next generation sequencing techniques, whole genome sequencing and comparative genomic analysis are increasingly used in characterizing Cryptosporidium spp. and G. duodenalis. The use of these tools in epidemiologic studies has identified significant differences in the transmission of Cryptosporidium spp. in humans between developing countries and industrialized nations, especially the role of zoonotic transmission in human infection. Geographic differences are also present in the distribution of G. duodenalis assemblages A and B in humans. In contrast, there is little evidence for widespread zoonotic transmission of giardiasis in both developing and industrialized countries. Differences in virulence have been identified among Cryptosporidium species and subtypes, and possibly between G. duodenalis assemblages A and B, and genetic recombination has been identified as one mechanism for the emergence of virulent C. hominis subtypes. These recent advances are providing insight into the epidemiology of waterborne protozoan parasites in both developing and developed countries.

Multilocus sequence typing and clonal population genetic structure of Cyclospora cayetanensis in humans

To investigate the prevalence of Cyclospora cayetanensis in a longitudinal study and to conduct a population genetic analysis, fecal specimens from 6579 patients were collected during the cyclosporiasis - prevalent seasons in two urban areas of central China in 2011-2015. The overall incidence of C. cayetanensis infection was 1·2% (76/6579): 1·6% (50/3173) in Zhengzhou and 0·8% (26/3406) in Kaifeng (P 0·05). All the isolates clustered in the C. cayetanensis clade based on the small subunit ribosomal RNA gene sequence phylogenetic analysis. There were 45 specimens positive for all the five C. cayetanensis microsatellite loci, and formed 29 multilocus genotypes (MLGs). The phylogenetic relationships of 54 distinct MLGs (including 25 known reference MLGs), based on the concatenated multilocus sequences, formed three main clusters. A population structure analysis showed that the 79 isolates (including 34 known reference isolates) of C. cayetanensis produced three distinct subpopulations based on allelic profile data. In conclusion, we determined the frequency of C. cayetanensis infection in humans in Henan Province. The clonal population structure of the human C. cayetanensis isolates showed linkage disequilibrium and three distinct subpopulations.

Cryptosporidium species and Cryptosporidium parvum subtypes in dairy calves and goat kids reared under traditional farming systems in Turkey

Molecular characterizations of Cryptosporidium spp. in ruminants reared under traditional animal management systems are scarce and studies conducted thus far have revealed largely an absence of the pathogenic and zoonotic species Cryptosporidium parvum in pre-weaned animals. In this study, we examined Cryptosporidium species and subtype distribution in free-range pre-weaned dairy calves and goat kids with diarrhea. Cryptosporidium-positive specimens from pre-weaned calves on 10 farms and goat kids on 4 farms in Ankara, Balikesir, Corum, Kirikkale, and Kirsehir Provinces, Turkey were genotyped by PCR-restriction length polymorphism analysis of the small subunit rRNA gene, which identified C. parvum in 27 calves and 9 goat kids and Cryptosporidium ryanae in 1 calf. Among the C. parvum isolates successfully subtyped by DNA sequence analysis of the 60 kDa glycoprotein gene, three subtypes were detected in calves, including IIaA13G2R1 (20/23), IIdA18G1 (2/23), and IIdA20G1b (1/23), and four subtypes were detected in goat kids, including IIaA13G2R1 (3/8), IIaA15G1R1 (2/8), IIdA22G1 (2/8), and IIdA18G1 (1/8). Data of the study suggest that dairy calves reared in a traditional cow-calf system in Turkey are mainly infected with a C. parvum subtype rarely seen elsewhere, whereas goat kids are infected with diverse subtypes. As all five C. parvum subtypes found in this study are known human pathogens, pre-weaned farm animals could play a potential role in the transmission of human cryptosporidiosis.

Intra-Species Genetic Diversity and Clonal Structure of Cryptosporidium parvum in Sheep Farms in a Confined Geographical Area in Northeastern Spain

A multilocus fragment typing approach including eleven variable-number tandem-repeat (VNTR) loci and the GP60 gene was used to investigate the intra-farm and intra-host genetic diversity of Cryptosporidium parvum in sheep farms in a confined area in northeastern Spain. Genomic DNA samples of 113 C. parvum isolates from diarrheic pre-weaned lambs collected in 49 meat-type sheep farms were analyzed. Loci exhibited various degrees of polymorphism, the finding of 7–9 alleles in the four most variable and discriminatory markers (ML2, Cgd6_5400, Cgd6_3940, and GP60) being remarkable. The combination of alleles at the twelve loci identified a total of 74 multilocus subtypes (MLTs) and provided a Hunter-Gaston discriminatory index of 0.988 (95% CI, 0.979−0.996). The finding that most MLTs (n = 64) were unique to individual farms evidenced that cryptosporidial infection is mainly transmitted within sheep flocks, with herd-to-herd transmission playing a secondary role. Limited intra- host variability was found, since only five isolates were genotypically mixed. In contrast, a significant intra-farm genetic diversity was seen, with the presence of multiple MLTs on more than a half of the farms (28/46), suggesting frequent mutations or genetic exchange through recombination. Comparison with a previous study in calves in northern Spain using the same 12-loci typing approach showed differences in the identity of major alleles at most loci, with a single MLT being shared between lambs and calves. Analysis of evolutionary descent by the algorithm eBURST indicated a high degree of genetic divergence, with over 41% MLTs appearing as singletons along with a high number of clonal complexes, most of them linking only two MLTs. Bayesian Structure analysis and F statistics also revealed the genetic remoteness of most C. parvum isolates and no ancestral population size was chosen. Linkage analysis evidenced a prevalent pattern of clonality within the parasite population.

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.

Suitability of loci for multiple-locus variable-number of tandem-repeats analysis of Cryptosporidium parvum for inter-laboratory surveillance and outbreak investigations

Cryptosporidium parvum is the major cause of livestock and zoonotically-acquired human cryptosporidiosis. The ability to track sources of contamination and routes of transmission by further differentiation of isolates would assist risk assessment and outbreak investigations. Multiple-locus variable-number of tandem-repeats (VNTR) analysis provides a means for rapid characterization by fragment sizing and estimation of copy numbers, but structured, harmonized development has been lacking for Cryptosporidium spp. To investigate potential for application in C. parvum surveillance and outbreak investigations, we studied nine commonly used VNTR loci (MSA, MSD, MSF, MM5, MM18, MM19, MS9-Mallon, GP60 and TP14) for chromosome distribution, repeat unit length and heterogeneity, and flanking region proximity and conservation. To investigate performance in vitro, we compared these loci in 14 C. parvum samples by capillary electrophoresis in three laboratories. We found that many loci did not contain simple repeat units but were more complex, hindering calculations of repeat unit copy number for standardized reporting nomenclature. However, sequenced reference DNA enabled reproducible fragment sizing and inter-laboratory allele assignation based on size normalized to that of the sequenced fragments by both single round and nested polymerase chain reactions. Additional Cryptosporidium loci need to be identified and validated for robust inter-laboratory surveillance and outbreak investigations.

Development of a framework for genotyping bovine-derived Cryptosporidium parvum, using a multilocus fragment typing tool

Background

There is a need for an integrated genotyping approach for C. parvum; no sufficiently discriminatory scheme to date has been fully validated or widely adopted by veterinary or public health researchers. Multilocus fragment typing (MLFT) can provide good differentiation and is relatively quick and cheap to perform. A MLFT tool was assessed in terms of its typeability, specificity, precision (repeatability and reproducibility), accuracy and ability to genotypically discriminate bovine-derived Cryptosporidium parvum.

Methods

With the aim of working towards a consensus, six markers were selected for inclusion based on their successful application in previous studies: MM5, MM18, MM19, TP14, MS1 and MS9. Alleles were assigned according to the fragment sizes of repeat regions amplified, as determined by capillary electrophoresis. In addition, a region of the GP60 gene was amplified and sequenced to determine gp60 subtype and this was added to the allelic profiles of the 6 markers to determine the multilocus genotype (MLG). The MLFT tool was applied to 140 C. parvum samples collected in two cross-sectional studies of UK calves, conducted in Cheshire in 2004 (principally dairy animals) and Aberdeenshire/Caithness in 2011 (beef animals).

Results

Typeability was 84 %. The primers did not amplify tested non-parvum species frequently detected in cattle. In terms of repeatability, within- and between-run fragment sizes showed little variability. Between laboratories, fragment sizes differed but allele calling was reproducible. The MLFT had good discriminatory ability (Simpson’s Index of Diversity, SID, was 0.92), compared to gp60 sequencing alone (SID 0.44). Some markers were more informative than others, with MS1 and MS9 proving monoallelic in tested samples.

Conclusions

Further inter-laboratory trials are now warranted with the inclusion of human-derived C. parvum samples, allowing progress towards an integrated, standardised typing scheme to enable source attribution and to determine the role of livestock in future outbreaks of human C. parvum.

Geographical segregation of Cryptosporidium parvum multilocus genotypes in Europe

Cryptosporidium parvum is a common enteric protozoan pathogen of humans and livestock. Multilocus genotyping based on simple sequence repeat polymorphisms has been used extensively to identify transmission cycles and to investigate the structure of C. parvum populations and of the related pathogen Cryptosporidiumhominis. Using such methods, the zoonotic transmission of C. parvum has been shown to be epidemiologically important. Because different genetic markers have been used in different surveys, the comparison of Cryptosporidium genotypes across different laboratories is often not feasible. Therefore, few comparisons of Cryptosporidium populations across wide geographical areas have been published and our understanding of the epidemiology of cryptosporidiosis is fragmented. Here we report on the genotypic analysis of a large collection of 692 C. parvum isolates originating primarily from cattle and other ruminants from Italy, Ireland and Scotland. Because the same genotypic markers were used in these surveys, it was possible to merge the data. We found significant geographical segregation and a correlation between genetic and geographic distance, consistent with a model of isolation by distance. The presence of strong LD and positive IA(S) values in the combined MLG dataset suggest departure from panmixia, with different population structures of the parasite prevailing in each country.

Population structure of natural and propagated isolates of Cryptosporidium parvum, C. hominis and C. meleagridis

The three protozoan species Cryptosporidium parvum, C. meleagridis and C. hominis (phylum Apicomplexa) are enteric pathogens of humans. The former two species are zoonotic and the latter is thought to infect only humans. To better characterize the structure and transmission of natural and laboratory-propagated isolates, we analyzed a collection of archived human and animal isolates of these three species by deep-sequencing polymerase chain reaction products amplified from a polymorphic sequence on chromosome 1. Thousands of screened 200-nucleotide sequences were analyzed to compare the diversity among samples, to assess the impact of laboratory propagation on population complexity and to identify taxonomically mixed isolates. Contrary to our expectation, repeated propagation in animals did not reduce intra-isolate diversity nor was diversity associated with host species. Significantly, in most samples, sequences characteristic of a different species were identified. The presence of C. hominis alleles in C. parvum and C. meleagridis isolates confirms earlier reports of mixed isolates and raises the possibility that the host range of C. hominis is broader than typically assumed. In a genetically divergent isolate of C. parvum, a majority of sequences was found to be recombinant, suggesting that this genotype originated from a C. parvum × C. hominis recombination event.

Host association of Cryptosporidium parvum populations infecting domestic ruminants in Spain

A stock of 148 Cryptosporidium parvum DNA extracts from lambs and goat kids selected from a previous study examining the occurrence of Cryptosporidium species and GP60 subtypes in diarrheic lambs and goat kids in northeastern Spain was further characterized by a multilocus fragment typing approach with six mini- and microsatellite loci. Various degrees of polymorphism were seen at all but the MS5 locus, although all markers exhibited two major alleles accounting for more than 75% of isolates. A total of 56 multilocus subtypes (MLTs) from lambs (48 MLTs) and goat kids (11 MLTs) were identified. Individual isolates with mixed MLTs were detected on more than 25% of the farms, but most MLTs (33) were distinctive for individual farms, revealing the endemicity of cryptosporidial infections on sheep and goat farms. Comparison with a previous study in calves in northern Spain using the same six-locus subtyping scheme showed the presence of host-associated alleles, differences in the identity of major alleles, and very little overlap in MLTs between C. parvum isolates from lambs and those from calves (1 MLT) or isolates from lambs and those from goat kids (3 MLTs). The Hunter-Gaston index of the multilocus technique was 0.976 (95% confidence interval [CI], 0.970 to 0.982), which supports its high discriminatory power for strain typing and epidemiological tracking. Population analyses revealed the presence of two host-associated subpopulations showing epidemic clonality among the C. parvum isolates infecting calves and lambs/goat kids, respectively, although evidence of genetic flow between the two subpopulations was also detected.

Panmictic structure of the Cryptosporidium parvum population in Irish calves: influence of prevalence and host movement

In total, 245 Cryptosporidium parvum specimens obtained from calves in 205 Irish herds between 2003 and 2005 were subtyped by sequencing the glycoprotein gene gp60 and performing multilocus analysis of seven markers. The transmission dynamics of C. parvum and the influence of temporal, spatial, parasitic, and host-related factors on the parasite (sub)populations were studied. The relationship of those factors to the risk of cryptosporidiosis was also investigated using results from 1,368 fecal specimens submitted to the veterinary laboratories for routine diagnosis during 2005. The prevalence was greatest in the northwest and midwest of the country and on farms that bought in calves. The panmixia (random mating) detected in the C. parvum population may relate to its high prevalence, the cattle density, and the frequent movement of cattle. However, local variations in these factors were reflected in the C. parvum subpopulations. This study demonstrated the importance of biosecurity in the control of bovine cryptosporidiosis (e.g., isolation and testing of calves before introduction into a herd). Furthermore, the zoonotic risk of C. parvum was confirmed, as most specimens possessed GP60 and MS1 subtypes previously described in humans.

Assessment of polymorphic genetic markers for multi-locus typing of Cryptosporidium parvum and Cryptosporidium hominis

The use of high resolution molecular tools to study Cryptosporidium parvum and Cryptosporidium hominis intra-species variation is becoming common practice, but there is currently no consensus in the methods used. The most commonly applied tool is partial gp60 gene sequence analysis. However, multi-locus schemes are acknowledged to improve resolution over analysis of a single locus, which neglects potential re-assortment of genes during the sexual phase of the Cryptosporidium life-cycle. Multi-locus markers have been investigated in isolates from a variety of sampling frames, in varying combinations and using different assays and methods of analysis. To identify the most informative markers as candidates for the development of a standardised multi-locus fragment size-based typing (MLFT) scheme to integrate with epidemiological analyses, we examined the published literature. A total of 31 MLFT studies were found, employing 55 markers of which 45 were applied to both C. parvum and C. hominis. Of the studies, 11 had sufficient raw data, from three or more markers, and a sampling frame containing at least 50 samples, for meaningful in-depth analysis using assessment criteria based on the sampling frame, study size, number of markers investigated in each study, marker characteristics (>2 nucleotide repeats) and the combinations of markers generating all possible multi-locus genotypes. Markers investigated differed between C. hominis and C. parvum. When each scheme was analysed for the fewest markers required to identify 95% of all MLFTs, some redundancy was identified in all schemes; an average redundancy of 40% for C. hominis and 27% for C. parvum. Ranking markers, based on the most productive combinations, identified two different sets of potentially most informative candidate markers, one for each species. These will be subjected to technical evaluation including typability (percentage of samples generating a complete multi-locus type) and discriminatory power by direct fragment size analysis and analysed for correlation with epidemiological data in suitable sampling frames. The establishment of a group of users and agreed subtyping scheme for improved epidemiological and public health investigations of C. parvum and C. hominis will facilitate further developments and consideration of technological advances in a harmonised manner.

Evidence of host-associated populations of Cryptosporidium parvum in Italy

Recent studies have revealed extensive genetic variation among isolates of Cryptosporidium parvum, an Apicomplexan parasite that causes gastroenteritis in both humans and animals worldwide. The parasite's population structure is influenced by the intensity of transmission, the host-parasite interaction, and husbandry practices. As a result, C. parvum populations can be panmictic, clonal, or even epidemic on both a local scale and a larger geographical scale. To extend the study of C. parvum populations to an unexplored region, 173 isolates of C. parvum collected in Italy from humans and livestock (calf, sheep, and goat) over a 10-year period were genotyped using a multilocus scheme based on 7 mini- and microsatellite loci. In agreement with other studies, extensive polymorphism was observed, with 102 distinct multilocus genotypes (MLGs) identified among 173 isolates. The presence of linkage disequilibrium, the confinement of MLGs to individual farms, and the relationship of many MLGs inferred using network analysis (eBURST) suggest a predominantly clonal population structure, but there is also evidence that part of the diversity can be explained by genetic exchange. MLGs from goats were found to differ from bovine and sheep MLGs, supporting the existence of C. parvum subpopulations. Finally, MLGs from isolates collected between 1997 and 1999 were also identified as a distinct subgroup in principal-component analysis and eBURST analysis, suggesting a continuous introduction of novel genotypes in the parasite population.

Genomics and population biology of Cryptosporidium species

We describe recent advances in the genomics and population biology of Cryptosporidium parvum and C. hominis, the causative agents of cryptosporidiosis in humans and animals. Many basic aspects of the biology of Cryptosporidium species remain to be investigated and effective drugs to control cryptosporidiosis are not available. Sequencing and annotation of the genome of C. parvum and C. hominis has uncovered unique features of the metabolism of these species. The recently sequenced genome of the gastric species C. muris is providing new insights into the evolution of the genus. Cryptosporidian sequence information has facilitated the identification of polymorphic genetic markers. Genotyping of oocysts excreted by human and animal hosts using such markers has revealed many new species and genotypes, and is leading to a better understanding of the epidemiology of cryptosporidiosis.

Assessment of three methods for multilocus fragment typing of Cryptosporidium parvum from domestic ruminants in north west Spain

The performance of three different methods, capillary electrophoresis (CE), high resolution slab-gel electrophoresis and sequencing, for PCR fragment size analysis of two Cryptosporidium parvum microsatellite regions, ML1 and ML2, was investigated by analysing 27 isolates from calves and 14 from lambs. To assess genetic variability of this protozoan in domestic ruminants in north west Spain, results were combined with sequence analysis of the 60 kDa glycoprotein (GP60) gene creating a multilocus type and analysed by farm and host species. CE showed greater overall typability (T), discriminatory power and ease of use than slab-gel electrophoresis and sequencing which were both affected by PCR stutter, especially at ML2. CE fragment sizes were consistently 4 bp longer compared to sequencing which is considered the gold standard for allele sizing but which gave the lowest typability; CE sizes were therefore adjusted. Only three alleles were identified at the ML1 locus (ML1-238, ML1-229 and ML1-226). The ML2 locus was more polymorphic and eight alleles were found (ML2-235, ML2-233, ML2-231, ML2-229, ML2-227, ML2-225, ML2-201 and ML2-176). Adjusted ML1 and ML2 CE fragment sizes were combined with GP60 subtype for 37 of the 41 C. parvum isolates which were typable at all three loci (T=0.90): nine multilocus types (MLTs) were identified. The discriminatory power of the 3-locus typing method was 0.83. Greater genetic variability was observed in calf isolates (7 MLTs) than in those from lambs (4 MLTs) although more calf isolates were studied. The most common MLT in cattle was MLT1 (ML1-238, ML2-231, GP60 subtype IIaA15G2R1), while MLT3 (ML1-238, ML2-227, GP60 IIaA16G3R1) was predominant in lambs. Our findings demonstrate that high discrimination can be achieved by means of multilocus typing. CE appears to be an economic and rapid option for performing microsatellite fragment size analysis offering good typability, discrimination and ease of use but may require calibration to sequenced standards.

Multilocus fragment typing and genetic structure of Cryptosporidium parvum Isolates from diarrheic preweaned calves in Spain

A collection of 140 Cryptosporidium parvum isolates previously analyzed by PCR-restriction fragment length polymorphism (PCR-RFLP) and sequence analyses of the small-subunit (SSU) rRNA and 60-kDa glycoprotein (GP60) genes was further characterized by multilocus fragment typing of six minisatellite (MSB and MS5) and microsatellite (ML1, ML2, TP14, and 5B12) loci. Isolates were collected from diarrheic preweaned calves originating from 61 dairy cattle farms in northern Spain. A capillary electrophoresis-based tool combining three different fluorescent tags was used to analyze all six satellites in one capillary. Fragment sizes were adjusted after comparison with sizes obtained by sequence analysis of a selection of isolates for every allele. Size discrepancies at all but the 5B12 locus were found for those isolates that were typed by both techniques, although identical size differences were reported for every allele within each locus. A total of eight alleles were seen at the ML2 marker, which contributed the most to the discriminatory power of the multilocus approach. Multilocus fragment typing clearly improved the discriminatory power of GP60 sequencing, since a total of 59 multilocus subtypes were identified based on the combination of alleles at the six satellite loci, in contrast to the 7 GP60 subtypes previously reported. The majority of farms (38) displayed a unique multilocus subtype, and individual isolates with mixed multilocus subtypes were seen at 22 farms. Bayesian structure analysis based on combined data for both satellite and GP60 loci suggested the presence of two major clusters among the C. parvum isolates from cattle farms in this geographical area.

Population genetic analysis and sub-structuring in Babesia bovis

The tick-borne protozoan parasite, Babesia bovis is one of the causes of bovine babesiosis, an economically important disease of cattle in tropical and sub-tropical countries. Using the recently published genome sequence of the parasite, we developed a panel of eight mini- and micro-satellite markers and used these to investigate the role of genetic exchange in the population structure and diversity of the parasite using isolates from Zambia and Turkey. This population genetic analysis showed that genetic exchange occurs and that there are high levels of genetic diversity, with geographical sub-structuring quantified using Wright's F Index. Linkage disequilibrium was observed when isolates from both countries were treated as one population, but when isolates from Zambia were analysed separately linkage equilibrium was observed. The Turkish isolates were sub-structured, containing two genetically distinct sub-groups, both of which appeared to be in linkage equilibrium. The results of the Zambian study suggest that a sub-set of the parasite population is responsible for the westward spread of babesiosis into the previously disease-free central region of the country. The Zambian isolates had a significantly higher number of genotypes per sample than those from Turkey and age was found to be a significant predictor of the multiplicity of infection. The high levels of diversity seen in the Zambian and Turkish B. bovis populations have implications in the development of subunit vaccines against the disease and the spread of drug resistance.

Cryptosporidium parvum causes gastroenteritis epidemics in the Nablus region of Palestine

A total of 30 faecal samples collected from individuals admitted to a local hospital in Nablus city in Palestine with gastroenteritis symptoms, plus five faecal samples from healthy individuals living in the same area were screened for the presence of Cryptosporidium spp. by microscopic analysis using malachite green negative staining. Molecular techniques were used to confirm the microscopic identification. All 30 samples from individuals with gastroenteritis symptoms were positive by both techniques. No other parasites were found in the faecal material of patients or healthy individuals. To explore the source of the outbreak, water was collected from various reservoirs and springs that supply the city with drinking water. Al-Qaryoon water spring was found to be contaminated with Cryptosporidium using both microscopic and molecular analysis. No other water resources were found to be contaminated. Genotyping analysis of Cryptosporidium oocysts using PCR-RFLP technique identified the parasite as C. parvum.

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.

Meta-analysis of a polymorphic surface glycoprotein of the parasitic protozoa Cryptosporidium parvum and Cryptosporidium hominis

Due to its extensive polymorphism, a partial sequence of the Cryptosporidium surface glycoprotein gene gp60 has been frequently used as a genetic marker. I explored the global diversity of this protein, and compared its sequence diversity in Cryptosporidium parvum and Cryptosporidium hominis. In marked contrast to the geographical partition of C. parvum and C. hominis multi-locus genotypes, gp60 allelic groups showed no evidence of segregating in space, or of differing with respect to geographical diversity. Globally, genetic diversity of C. hominis gp60 exceeded that of C. parvum. Within C. parvum, gp60 alleles originating from human isolates were more diverse than those infecting ruminants. Phylogenetic analysis grouped gp60 sequences into a small number of relatively homogenous allelic groups, with only a small number of alleles having evolved independently. With the notable exception of a group of alleles restricted to humans, C. parvum alleles are found in ruminants and humans.

Cryptosporidium parvum DNA replication in cell-free culture

The lack of robust methods for culturing Cryptosporidium parasites remains a major challenge and is hampering efforts to screen for anti-cryptosporidial drugs. In existing culture methods, monolayers of mammalian epithelial cells are inoculated with oocysts. The system supports an initial phase of asexual proliferation of the parasite. For reasons that are not clear, development rapidly declines within 2-3 days. The unexpected report of Cryptosporidium parvum culture in the absence of host cells, and the failure of others to reproduce the method, prompted us to apply quantitative PCR to measure changes in C. parvum DNA levels in cell-free cultures, and parasite-specific antibodies to identify different life cycle stages. Based on this approach, which has not been applied previously to analyze C. parvum growth in cell-free culture, we found that the concentration of C. parvum DNA increased by about 5-fold over 5 days of culture. Immuno-labeling of cultured organisms revealed morphologically distinct stages, only some of which reacted with Cryptosporidium-specific monoclonal antibodies. These observations are indicative of a modest proliferation of C. parvum in cell-free culture.

Molecular epidemiology of cryptosporidiosis: an update

Molecular tools have been developed to detect and differentiate Cryptosporidium at the species/genotype and subtype levels. These tools have been increasingly used in characterizing the transmission of Cryptosporidium spp. in humans and animals. Results of these molecular epidemiologic studies have led to better appreciation of the public health importance of Cryptosporidium species/genotypes in various animals and improved understanding of infection sources in humans. Geographic, seasonal and socioeconomic differences in the distribution of Cryptosporidium spp. in humans have been identified, and have been attributed to differences in infection sources and transmission routes. The transmission of C. parvum in humans is mostly anthroponotic in developing countries, with zoonotic infections play an important role in developed countries. Species of Cryptosporidium and subtype families of C. hominis have been shown to induce different clinical manifestations and have different potential to cause outbreaks. The wide use of a new generation of genotyping and subtyping tools in well designed epidemiologic studies should lead to a more in-depth understanding of the epidemiology of cryptosporidiosis in humans and animals.

Cryptosporidiumspecies and subtype analysis from dairy calves in Spain

Faecal specimens from 287 diarrhoeic calves younger than 21 days, collected over a 2-year period (2006–2007) from 82 dairy cattle farms in 14 provinces across the north of Spain, were examined for the presence ofCryptosporidiumoocysts. Overall, 63 farms (76·8%) and 166 calves (57·8%) tested positive by microscopy. In order to elucidate the genetic diversity, selected positive specimens from 149 calves originating from 61 farms in the 14 provinces were examined by genotyping and subtyping techniques.Cryptosporidium parvumwas the only species identified by PCR-RFLP of SSU rDNA from all 149 isolates and sequencing of a subset of 50 isolates, except for 2 specimens that were identified asC. bovis. Sequence analyses of the glycoprotein (GP60) gene revealed that mostC. parvumisolates (98%) belonged to the subtype family IIa and 2 isolates were identified as the novel subtype IIdA23G1. Subtype IIaA15G2R1 was the most common and widely distributed (80·3% of the 61 farms), followed by subtype IIaA16G3R1 (14·7%), whereas the remaining IIa subtypes (IIaA16G2R1, IIaA17G2R1, IIaA18G3R1, IIaA19G3R1) were restricted to 1–3 farms. All theseC. parvumIIa subtypes have previously been described in human patients, indicating that most isolates from diarrhoeic calves in northern Spain have zoonotic potential.

Inferences about the global population structures of Cryptosporidium parvum and Cryptosporidium hominis

Cryptosporidium parvum and Cryptosporidium hominis are two related species of apicomplexan protozoa responsible for the majority of human cases of cryptosporidiosis. In spite of their considerable public health impact, little is known about the population structures of these species. In this study, a battery of C. parvum and C. hominis isolates from seven countries was genotyped using a nine-locus DNA subtyping scheme. To assess the existence of geographical partitions, the multilocus genotype data were mined using a cluster analysis based on the nearest-neighbor principle. Within each country, the population genetic structures were explored by combining diversity statistical tests, linkage disequilibrium, and eBURST analysis. For both parasite species, a quasi-complete phylogenetic segregation was observed among the countries. Cluster analysis accurately identified recently introduced isolates. Rather than conforming to a strict paradigm of either a clonal or a panmictic population structure, data are consistent with a flexible reproductive strategy characterized by the cooccurrence of both propagation patterns. The relative contribution of each pattern appears to vary between the regions, perhaps dependent on the prevailing ecological determinants of transmission.

Prevalence and molecular characterization of human and bovine Cryptosporidium isolates in Thailand

This study was performed to determine the prevalence and genotypes of Cryptosporidium species among HIV patients and cattle in Thailand. Stool specimens were collected from 46 HIV patients from Prabat Nampu Temple, Lop Buri Province in central Thailand. Two hundred fecal samples from dairy cattle were collected from seven farms in Chon Buri Province, the eastern part of Thailand. Each sample was concentrated by Sheather's sucrose flotation technique and stained by acid fast stain (AFS) for the identification of oocysts by microscopy. All HIV stool samples and 83 fecal specimens from cattle were further tested using nested polymerase chain reaction (PCR) targeting the 18S SSUrRNA gene to characterize the detected species. In HIV patient samples, the detection rate was 28.7% by AFS and 4.35% by nested PCR. In cattle samples, the detection rate was 13% by AFS and 9.63% by nested PCR. After DNA sequencing results, we identified the genotypes of the Cryptosporidium from seven of the PCR positive samples. All were found to be C. parvum. The findings presented here represent the first genetic identification of Cryptosporidium species in cattle in Thailand.

Cryptosporidium genotypes and subtypes in lambs and goat kids in Spain

To provide information on the transmission dynamics of cryptosporidial infections in domestic small ruminants and the potential role of sheep and goats as a source for human cryptosporidiosis, Cryptosporidium-positive isolates from 137 diarrheic lambs and 17 goat kids younger than 21 days of age were examined by using genotyping and subtyping techniques. Fecal specimens were collected between 2004 and 2006 from 71 sheep and 7 goat farms distributed throughout Aragón (northeastern Spain). Cryptosporidium parvum was the only species identified by restriction analyses of PCR products from small-subunit rRNA genes from all 154 microscopy-positive isolates and the sequencing of a subset of 50 isolates. Sequence analyses of the glycoprotein (GP60) gene revealed extensive genetic diversity within the C. parvum strains in a limited geographical area, in which the isolates from lambs exhibited 11 subtypes in two subtype families (IId and IIa) and those from goat kids displayed four subtypes within the family IId. Most isolates (98%) belonged to the subtype family IId, whereas only three isolates belonged to the most widely distributed family, IIa. Three of the four most prevalent subtypes (IIdA17G1a, IIdA19G1, and IIdA18G1) were previously identified in humans, and five subtypes (IIdA14G1, IIdA15G1, IIdA24G1, IIdA25G1, and IIdA26G1) were novel subtypes. All IId subtypes were identical to each other in the nonrepeat region, except for subtypes IIdA17G1b and IIdA22G1, which differed by a single nucleotide polymorphism downstream of the trinucleotide repeats. These findings suggest that lambs and goat kids are an important reservoir of the zoonotic C. parvum subtype family IId for humans.

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.

Molecular epidemiology of Cryptosporidium subtypes in cattle in England

Samples of Cryptosporidium spp., collected in a cross-sectional study of calves (median age 26 days) from 41 farms in Cheshire, UK, underwent molecular typing. The aim was to determine naturally occurring species/genotypes and to investigate transmission pathways within a local area. Of 60 positive samples, 54 were sequenced at an 18S rRNA locus and 51 were typed at a GP60 locus. C. parvum was identified in 50 samples, three cases were C. bovis and one was Cryptosporidium deer-like genotype. Six GP60 subgenotypes were identified. One subgenotype (IIaA15G2R1) was highly prevalent throughout the study area. A single subgenotype was identified on 20/22 farms. Two subgenotypes were found on 2/22 farms. The spatial scan statistic detected a cluster of subgenotype IIaA15G2R1 comprising seven farms. This suggests local transmission of the parasite between farms. As most of the isolates detected were the potentially zoonotic C. parvum allele IIa, intervention strategies should be considered to reduce the threat to public health. Biosecurity measures may reduce transmission between farms and result in lower levels of environmental contamination.

Cryptosporidium parvum, a potential cause of colic adenocarcinoma

Background

Cryptosporidiosis represents a major public health problem. This infection has been reported worldwide as a frequent cause of diarrhoea. Particularly, it remains a clinically significant opportunistic infection among immunocompromised patients, causing potentially life-threatening diarrhoea in HIV-infected persons. However, the understanding about different aspects of this infection such as invasion, transmission and pathogenesis is problematic. Additionally, it has been difficult to find suitable animal models for propagation of this parasite. Efforts are needed to develop reproducible animal models allowing both the routine passage of different species and approaching unclear aspects of Cryptosporidium infection, especially in the pathophysiology field.

Results

We developed a model using adult severe combined immunodeficiency (SCID) mice inoculated with Cryptosporidium parvum or Cryptosporidium muris while treated or not with Dexamethasone (Dex) in order to investigate divergences in prepatent period, oocyst shedding or clinical and histopathological manifestations. C. muris-infected mice showed high levels of oocysts excretion, whatever the chemical immunosuppression status. Pre-patent periods were 11 days and 9.7 days in average in Dex treated and untreated mice, respectively. Parasite infection was restricted to the stomach, and had a clear preferential colonization for fundic area in both groups. Among C. parvum-infected mice, Dex-treated SCID mice became chronic shedders with a prepatent period of 6.2 days in average. C. parvum-inoculated mice treated with Dex developed glandular cystic polyps with areas of intraepithelial neoplasia, and also with the presence of intramucosal adenocarcinoma.

Conclusion

For the first time C. parvum is associated with the formation of polyps and adenocarcinoma lesions in the gut of Dex-treated SCID mice. Additionally, we have developed a model to compare chronic muris and parvum cryptosporidiosis using SCID mice treated with corticoids. This reproducible model has facilitated the evaluation of clinical signs, oocyst shedding, location of the infection, pathogenicity, and histopathological changes in the gastrointestinal tract, indicating divergent effects of Dex according to Cryptosporidium species causing infection.

The population structure of the Cryptosporidium parvum population in Scotland: a complex picture

We genotyped 297 Scottish C. parvum samples using micro- and minisatellites. Treated as a single population, the population structure was epidemic. When regional populations were analysed, there was evidence of sub-population structure variations. This was dependent upon excluding sub-groups exhibiting significant genetic distance from the main population, implying genetic sub-structuring. We tested the hypothesis that these sub-groups originated outside the UK and demonstrated that one sub-group clustered with Peruvian samples. A geographically comprehensive panel of isolates would fully confirm this result. These data indicate limited sub-structuring within a small geographical area, but substantial sub-structuring over larger geographical distances. Host movement influences parasite diversity and population structure, evidenced by strong correlation (r² = 0.9686) between cattle movements and parasite diversity. Thus, the population structure of C. parvum is complex, with sub-populations differing in structure and being influenced by host movements, including the introduction of novel multilocus genotypes from geographically distinct regions.

Genotypic characterization and phylogenetic analysis of Cryptosporidium sp. from domestic animals in Brazil

The purpose of the present study was the genetic characterization, sequencing and phylogenetic analysis of 18S rDNA sequences of Cryptosporidium isolates obtained from different animal hosts in Brazil. Fecal samples containing Cryptosporidium oocysts were obtained from chickens, ducks, quails, guinea pigs, dairy calves, dogs and cats. For amplification of 18S rDNA sequences the Secondary-PCR product of the extracted DNA from fecal suspension of each studied animal was utilized. The primary genetic characterization of Cryptosporidium sp. was performed using RFLP with the enzymes SspI and VspI. DNA samples were sequenced and subjected to phylogenetic analysis. The results showed C. baileyi infecting two ducks and one quail and C. melagridis infecting one chicken. The sequences obtained from Cryptosporidium sp. infecting guinea pigs were not identified within groups of known Cryptosporidium species. The isolates found parasitizing cats and one dog were diagnosed as C. felis and C. canis, respectively. One isolate of calf origin was identified as C. parvum. The phylogenetic analysis showed clear distribution of isolates between two Cryptosporidium sp. groups according to their gastric or intestinal parasitism. A great genetic distance was observed between C. felis and C. canis from Brazil when compared to the reference sequences obtained from GenBank. The results obtained during this study constitute the first report of rDNA sequences from C. baileyi, C. meleagridis, C. felis, C. canis and C. parvum isolated in Brazil.

Host-shaped segregation of the Cryptosporidium parvum multilocus genotype repertoire

Cattle are among the major reservoirs of Cryptosporidium parvum in nature. However, the relative contribution of C. parvum oocysts originating from cattle to human disease burden is difficult to assess, as various transmission pathways -- including the human to human route -- can co-occur. In this study, multilocus genotype richness of representative samples of human and bovine C. parvum are compared statistically using analytical rarefaction and non-parametric taxonomic richness estimators. Results suggest that in the time and space frames underlying the analysed data, humans were infected with significantly wider spectra of C. parvum genotypes than cattle, and consequently, a significant fraction of human infections may not have originated from the regional bovine reservoirs. This study provides statistical support to the emerging idea of the existence of distinct anthroponotic C. parvum cycles that do not involve cattle.

Prevalence of Cryptosporidium species and genotypes in mature dairy cattle on farms in eastern United States compared with younger cattle from the same locations

Feces collected from 541 milking cows on two dairy farms each in Vermont, New York, Pennsylvania, Maryland, Virginia, North Carolina, and Florida were examined for the presence of Cryptosporidium oocysts. Oocysts were concentrated from 15 g of feces from each cow and DNA was extracted. A two-step nested PCR protocol was used to amplify an 830 base pair fragment of the SSUrRNA gene. PCR-positive products were purified and sequenced. PCR-positive findings were obtained from cows in all seven states and from 11 of 14 farms. Cryptosporidium parvum, Cryptosporidium bovis, and Cryptosporidium andersoni were found on 2, 6, and 8 farms, and infected 0.4, 1.7, and 3.7% of the 541 cows, respectively. The overall lower prevalence of Cryptosporidium in these cows was very highly significant (p< or =0.0001) compared with younger cattle and the relative prevalence of each species of Cryptosporidium also differed when compared with younger cattle previously examined on most of these same farms. The very low level of infection with C. parvum, the major species pathogenic to both cattle and humans, suggests that mature dairy cattle are a relatively low risk source of infection for humans.

Genotypes and subtypes of Cryptosporidium spp. in neonatal calves in Northern Ireland

Cryptosporidium spp. in diarrheic calves less than 30 days old from farms across Northern Ireland were examined over a year period by microscopic, genotyping, and subtyping techniques to characterize the transmission dynamics. Cryptosporidium oocysts were detected in 291 of 779 (37.4%) animals. The prevalence rates of rotavirus, coronavirus, and Escherichia coli K99+ were lower as seen in 242 of 806 (30.0%), 46/806 (5.7%), and 16/421 (3.8%) of animals, respectively. Of the 224 Cryptosporidium-positive specimens available for molecular analysis, Cryptosporidium parvum was identified in 213 (95.1%) specimens, Cryptosporidium bovis in eight (3.6%), and Cryptosporidium deer-like genotype in three (1.3%). Sequence analysis of the 60-kDa glycoprotein gene identified 16 IIa subtypes and a new subtype family, with 120 of the 216 (55.6%) positive specimens having the subtype IIaA18G3R1. Eight of the IIa subtypes were previously seen in humans in Northern Ireland. Several subtypes were temporally or geographically unique. The genetic diversity in calves in Northern Ireland was much greater than that reported from other areas. This work demonstrates the utility of genotyping and subtyping tools in characterizing the transmission of Cryptosporidium spp. in calves and humans.

Distribution of Cryptosporidium parvum subtypes in calves in eastern United States

Cryptosporidium parvum DNA from 175 neonatal calves on 16 farms in eight eastern states in the United States was subtyped by sequence analysis of the 60-kDa glycoprotein gene to determinate the parasite genetic diversity. Six subtypes of the IIa subtype family were found. Subtype IIaA15G2R1, which is the predominant C. parvum subtype in calves in many parts of the world, was identified in 77% of the C. parvum DNA from calves. Several farms had more than one C. parvum subtype and a few calves had infections with mixed subtypes. Distribution of subtypes differed geographically. Diversity of C. parvum in calves in eastern United States was lower than that previously seen in Michigan and southern Ontario. The high prevalence of one subtype in calves worldwide and frequent detection of this subtype in humans suggests that parasite fitness probably plays an important role in transmission of cryptosporidiosis among cattle and in zoonotic infections.