Cryptosporidium species in humans and animals: current understanding and research needs

Prevalence of Cryptosporidium species and subtypes in paediatric oncology and non-oncology patients with diarrhoea in Jordan

Cryptosporidiosis is a protozoan parasitic disease which affects human and animals worldwide. In adult immunocompetent individuals, cryptosporidiosis usually results in acute and self-limited diarrhoea; however, it can cause life threatening diarrhoea in children and immunocompromised individuals. In the present study, we compared the prevalence of Cryptosporidium species and gp60 subtypes amongst paediatric oncology patients with diarrhoea (n=160) from King Hussein Medical Centre for Cancer in Jordan, and non-oncology paediatric patients with diarrhoea (n=137) from Al-Mafraq paediatric hospital. Microscopy results using modified acid fast staining identified a significantly (p≤0.05) higher prevalence of Cryptosporidium in paediatric oncology patients with diarrhoea (14.4% - 23/160), compared to non-oncology paediatric patients with diarrhoea only (5.1% - 7/137). With the exception of one sample, all microscopy-positive samples (n=29) and an additional 3/30 microscopy-negative controls were typed to species and subtype level at the 18S and gp60 loci, respectively. All Cryptosporidium positives were typed as C. parvum. Of the 22 typed Cryptosporidium positives from the paediatric oncology patients, 21 were subtyped as IIaA17G2R1 and one as IIaA16G2R1 C. parvum subtypes. The 7 typed positives from the paediatric patients from Al-Mafraq hospital were subtyped as IIaA17G2R1 (n=5) and IIaA16G2R1 (n=2). The 3 additional positives from the 30 microscopy negative control samples were subtyped as IIaA17G2R1. The high prevalence of the IIaA17G2R1 subtype, particularly amongst oncology patients, suggests that an outbreak of cryptosporidiosis may have been occurring in oncology patients during the collection period (April to December, 2016). New therapies for cryptosporidiosis in immunocompromised patients are urgently required.

Preliminary Characterization of MEDLE-2, a Protein Potentially Involved in the Invasion of Cryptosporidium parvum

Cryptosporidium spp. are important causes of diarrhea in humans, ruminants, and other mammals. Comparative genomic analysis indicated that genetically related and host-adapted Cryptosporidium species have different numbers of subtelomeric genes encoding the Cryptosporidium-specific MEDLE family of secreted proteins, which could contribute to differences in host specificity. In this study, a Cryptosporidium parvum-specific member of the protein family MEDLE-2 encoded by cgd5_4590 was cloned and expressed in Escherichia coli. Immunofluorescent staining with antibodies generated from the recombinant protein showed the expression of the protein in sporozoites and development stages. In vitro neutralization assay with the antibodies partially blocked the invasion of sporozoites. These results support the potential involvement of MEDLE-2 in the invasion of host cells.

Subtype analysis of zoonotic pathogen Cryptosporidium skunk genotype

Cryptosporidium skunk genotype is a zoonotic pathogen commonly identified in surface water. Thus far, no subtyping tool exists for characterizing its transmission in humans and animals and transport in environment. In this study, a subtyping tool based on the 60kDa glycoprotein (gp60) gene previously developed for Cryptosporidium chipmunk genotype I was used in the characterization of Cryptosporidium skunk genotype in animal and storm runoff samples from a watershed in New York. Altogether, 17 positive samples from this watershed and 5 human and animal specimens from other areas were analyzed. We identified 14 subtypes of Cryptosporidium skunk genotype, 11 of which were seen in the watershed. In phylogenetic analysis, these subtypes belonged to 4 subtype families (XVIa, XVIb, XVIc, and XVId). No host-adapted subtypes were identified and the two subtypes in humans were genetically similar to some in raccoons, otters, and storm runoff samples from the watershed. The characteristics of gp60 protein sequences of the Cryptosporidium skunk genotype are similar to those of other Cryptosporidium species, but only its XVIb subtype family has a putative furin cleavage site. This subtyping tool might be useful in characterizing Cryptosporidium skunk genotype in clinical and environmental samples.

Giardia duodenalis and Cryptosporidium spp. as contaminant protozoa of the main rivers of western Romania: genetic characterization and public health potential of the isolates

The objective of this study was to establish the prevalence, contamination level, and public health significance of Giardia duodenalis and Cryptosporidium spp. in the primary rivers of western Romania. A total of 53 sampling points in the 24 most important western Romanian rivers in four counties (Arad, Bihor, Caraș-Severin, and Timiș) were investigated from March to September 2016. Surface water samples were collected by microfiber filtration. Cryptosporidium and Giardia (oo)cysts were isolated using immunomagnetic separation (IMS) according to the USEPA 1623 method and, after staining with fluorescently labeled (FITC) monoclonal antibodies, were identified and counted under a microscope. The Cryptosporidium and Giardia (oo)cysts were identified to species and assemblage/sub-assemblage level through the nested PCR-RFLP procedure targeting the 18S ribosomal RNA and gdh genes, respectively. PCR-based techniques were utilized for all water samples. Overall, 22 samples (41.5%) were determined to be positive for Giardia cysts (ranging from 0.05 to 300 cysts per liter), and four samples (7.5%) tested positive for Cryptosporidium oocysts (0.17-48 oocysts/l). G. duodenalis was molecularly identified in 13 water samples (24.5%), indicating the presence of the sub-assemblage A-II (n = 12) and assemblage E (n = 1). PCR-RFLP showed that two samples (3.8%) contained Cryptosporidium DNA, and the identified species were Cryptosporidium parvum and Cryptosporidium canis. All positive results were successfully confirmed by DNA sequencing. Subtyping of the zoonotic C. parvum isolate based on sequence analysis of the GP60 gene revealed the occurrence of the IIaA16G1R1 subtype. The results of this study highlight considerable contamination of river waters with pathogenic Giardia spp. and Cryptosporidium spp., suggesting a potential risk for the public and animal health. This report presents the first extended published description of the presence of Giardia spp. and Cryptosporidium spp. in the aquatic environment in Romania.

Environmental Transport of Emerging Human-Pathogenic Cryptosporidium Species and Subtypes through Combined Sewer Overflow and Wastewater

The environmental transport of Cryptosporidium spp. through combined sewer overflow (CSO) and the occurrence of several emerging human-pathogenic Cryptosporidium species in developing countries remain unclear. In this study, we collected 40 CSO samples and 40 raw wastewater samples from Shanghai, China, and examined them by PCR and DNA sequencing for Cryptosporidium species (targeting the small subunit rRNA gene) and Giardia duodenalis (targeting the triosephosphate isomerase, β-giardin, and glutamate dehydrogenase genes) and Enterocytozoon bieneusi (targeting the ribosomal internal transcribed spacer) genotypes. Human-pathogenic Cryptosporidium species were further subtyped by sequence analysis of the 60-kDa glycoprotein gene, with additional multilocus sequence typing on the emerging zoonotic pathogen Cryptosporidium ubiquitum. Cryptosporidium spp., G. duodenalis, and E. bieneusi were detected in 12 and 15, 33 and 32, and 37 and 40 CSO and wastewater samples, respectively, including 10 Cryptosporidium species, 3 G. duodenalis assemblages, and 8 E. bieneusi genotypes. In addition to Cryptosporidium hominis and Cryptosporidium parvum, two new pathogens identified in industrialized nations, C. ubiquitum and Cryptosporidium viatorum, were frequently detected. The two novel C. ubiquitum subtype families identified appeared to be genetic recombinants of known subtype families. Similarly, the dominant group 1 E. bieneusi genotypes and G. duodenalis subassemblage AII are known human pathogens. The similar distribution of human-pathogenic Cryptosporidium species and E. bieneusi and G. duodenalis genotypes between wastewater and CSO samples reaffirms that storm overflow is potentially a significant contamination source of pathogens in surface water. The frequent identification of C. ubiquitum and C. viatorum in urban wastewater suggests that these newly identified human pathogens may be endemic in China.IMPORTANCECryptosporidium spp., Giardia duodenalis, and Enterocytozoon bieneusi are major waterborne pathogens. Their transport into surface water through combined sewer overflow, which remains largely untreated in developing countries, has not been examined. In addition, the identification of these pathogens to genotypes and subtypes in urban storm overflow and wastewater is necessary for rapid and accurate assessment of pathogen transmission in humans and transport in the environment. Data from this study suggest that, like untreated urban wastewater, combined sewer overflow is commonly contaminated with human-pathogenic Cryptosporidium, G. duodenalis, and E. bieneusi genotypes and subtypes, and urban storm overflow potentially plays a significant role in the contamination of drinking source water and recreational water with human pathogens. They also indicate that Cryptosporidium ubiquitum and Cryptosporidium viatorum, two newly identified human pathogens, may be common in China, and genetic recombination can lead to the emergence of novel C. ubiquitum subtype families.

Global Cryptosporidium Loads from Livestock Manure

Understanding the environmental pathways of Cryptosporidium is essential for effective management of human and animal cryptosporidiosis. In this paper we aim to quantify livestock Cryptosporidium spp. loads to land on a global scale using spatially explicit process-based modeling, and to explore the effect of manure storage and treatment on oocyst loads using scenario analysis. Our model GloWPa-Crypto L1 calculates a total global Cryptosporidium spp. load from livestock manure of 3.2 × 10²³ oocysts per year. Cattle, especially calves, are the largest contributors, followed by chickens and pigs. Spatial differences are linked to animal spatial distributions. North America, Europe, and Oceania together account for nearly a quarter of the total oocyst load, meaning that the developing world accounts for the largest share. GloWPa-Crypto L1 is most sensitive to oocyst excretion rates, due to large variation reported in literature. We compared the current situation to four alternative management scenarios. We find that although manure storage halves oocyst loads, manure treatment, especially of cattle manure and particularly at elevated temperatures, has a larger load reduction potential than manure storage (up to 4.6 log units). Regions with high reduction potential include India, Bangladesh, western Europe, China, several countries in Africa, and New Zealand.

Local and global genetic diversity of protozoan parasites: Spatial distribution of Cryptosporidium and Giardia genotypes

Cryptosporidiosis and giardiasis are recognized as significant enteric diseases due to their long-term health effects in humans and their economic impact in agriculture and medical care. Molecular analysis is essential to identify species and genotypes causing these infectious diseases and provides a potential tool for monitoring. This study uses information on species and genetic variants to gain insights into the geographical distribution and spatial patterns of Cryptosporidium and Giardia parasites. Here, we describe the population heterogeneity of genotypic groups within Cryptosporidium and Giardia present in New Zealand using gp60 and gdh markers to compare the observed variation with other countries around the globe. Four species of Cryptosporidium (C. hominis, C. parvum, C. cuniculus and C. erinacei) and one species of Giardia (G. intestinalis) were identified. These species have been reported worldwide and there are not unique Cryptosporidium gp60 subtype families and Giardiagdh assemblages in New Zealand, most likely due to high gene flow of historical and current human activity (travel and trade) and persistence of large host population sizes. The global analysis revealed that genetic variants of these pathogens are widely distributed. However, genetic variation is underestimated by data biases (e.g. neglected submission of sequences to genetic databases) and low sampling. New genotypes are likely to be discovered as sampling efforts increase according to accumulation prediction analyses, especially for C. parvum. Our study highlights the need for greater sampling and archiving of genotypes globally to allow comparative analyses that help understand the population dynamics of these protozoan parasites. Overall our study represents a comprehensive overview for exploring local and global protozoan genotype diversity and advances our understanding of the importance for surveillance and potential risk associated with these infectious diseases.

Infectious diseases threaten the health and well-being of wildlife, livestock and human populations and contribute to significant economic impact in agriculture and medical care. Cryptosporidium and Giardia are enteric protozoan pathogens that cause diarrhea and nutritional disorders on a global level. Using molecular analysis and a review framework we showed that species and genetic variants within genera Cryptosporidium and Giardia (including two species recently infecting humans) found in an island system are not different from other parts of the world. This similarity is likely due to high gene flow of historical and current human activity (travel and trade) and persistence of large host population sizes, such as cattle and people. We also show that, although species and genotypes are widely distributed, new variants will arise when sampling effort increase and their dispersal will be facilitated by human activity. These findings suggest that geographical distribution of species and genotypes within Cryptosporidium and Giardia parasites may yield important clues for designing effective surveillance strategies and identification of factors driving within and cross species transmission.

Molecular diversity and frequency of the diarrheagenic enteric protozoan Giardia duodenalis and Cryptosporidium spp. in a hospital setting in Northern Spain

Background

Human giardiosis and cryptosporidiosis are caused by the enteric protozoan parasites Giardia duodenalis and Cryptosporidium spp. Both pathogens are major contributors to the global burden of diarrhoeal disease, affecting primarily children and immunodebilitated individuals in resource-poor settings. Giardiosis and cryptosporidiosis also represent an important, often underestimate, public health threat in developed countries. In Spain only limited information is currently available on the epidemiology of these infections. Molecular data on the diversity, frequency, geographical distribution, and seasonality of G. duodenalis assemblages/sub-assemblages and Cryptosporidium species/sub-genotypes are particularly scarce.

Methods

A longitudinal molecular epidemiological survey was conducted between July 2015 to September 2016 in patients referred to or attended at the Hospital San Pedro (La Rioja, Northern Spain) that tested positive for G. duodenalis (N = 106) or Cryptosporidium spp. (N = 103) by direct microscopy and/or a rapid lateral flow immunochromatographic assay. G. duodenalis infections were subsequently confirmed by real-time PCR and positive isolates assessed by multi-locus sequence genotyping of the glutamate dehydrogenase and β-giardin genes of the parasite. Cryptosporidium species and sub-genotypes were investigated at the 60 kDa glycoprotein or the small subunit ribosomal RNA genes of the parasite. Sociodemographic and clinical parameters of infected patients were also gathered and analysed.

Principal findings

Out of 90 G. duodenalis-positive isolates by real-time PCR a total of 16 isolates were successfully typed. AII (44%, 7/16) was the most prevalent sub-assemblage found, followed by BIV (31%, 5/16) and BIII (19%, 3/16). A discordant genotype result AII/AIII was identified in an additional (6%, 1/16) isolate. No mixed infections A+B were detected. Similarly, a total of 81 Cryptosporidium spp. isolates were successfully typed, revealing the presence of C. hominis (81%, 66/81) and C. parvum (19%, 15/81). Obtained GP60 sequences were assigned to sub-type families Ib (73%, 59/81) within C. hominis, and IIa (7%, 6/81) and IId (2%, 2/81) within C. parvum. A marked inter-annual variation in Cryptosporidium cases was observed.

Conclusions

Human giardiasis and cryptosporidiosis are commonly identified in patients seeking medical care in Northern Spain and represent a more important health concern than initially thought. Assemblage A within G. duodenalis and sub-genotype IbA10G2 within C. hominis were the genetic variants of these parasite species more frequently found circulating in the population under study. Molecular data presented here seem to suggest that G. duodenalis and Cryptosporidium infections arise through anthroponotic rather than zoonotic transmission in this Spanish region.

Association between enteric protozoan parasites and gastrointestinal illness among HIV- and tuberculosis-infected individuals in the Chowke district, southern Mozambique

Human immune deficiency virus (HIV) and tuberculosis (TB) infections remain major public health issues globally, particularly in sub-Saharan Africa. Impairment of both cell-mediated and humoral immunity by HIV and/or TB infections may limit the host's defences against other pathogens, including the diarrheagenic protozoan Cryptosporidium spp., Giardia intestinalis, and Entamoeba histolytica. During September-December 2015 a cross-sectional study was conducted to assess the prevalence and molecular diversity of these enteric parasites among HIV- and/or TB-infected patients at a medical reference centre in Chowke district, southern Mozambique. A total of 99 stool specimens were initially screened by direct microscopy and further confirmed and characterised by molecular methods. DNA sequence analyses of the genes encoding the small subunit ribosomal RNA and the 60-kDa glycoprotein were used for the typing and sub-typing of Cryptosporidium isolates, respectively. G. intestinalis-positive isolates by real-time PCR were subsequently typed at the glutamate dehydrogenase locus. Differential diagnosis of E. histolytica/dispar was achieved by real-time PCR. G. intestinalis (8.1%) was the enteric protozoan more frequently detected, followed by Cryptosporidium spp. (7.1%), and Entamoeba histolytica/dispar (6.1%). Two HIV-infected (but not TB-infected) patients harbour G. intestinalis and Cryptosporidium spp. co-infections. Two (29%) G. intestinalis isolates were successfully characterised, revealing the presence of known AII and novel BIV genotypes. Four (57%) Cryptosporidium isolates were unmistakeable assigned to C. hominis, identifying two (IbA10G2 and IdA22) sub-types. Cryptosporidium infections were not associated to diarrhoea in HIV-positive patients, probably because improved immune function in the affected individuals due to antiretroviral therapy. G. intestinalis was considered a non-opportunistic pathogen, whereas the presence of E. histolytica could not be confirmed by molecular methods. Based on their common presence in the studied clinical population, we recommend the effective diagnosis and treatment of these enteropathogens for improving the management of HIV and TB patients.

No molecular epidemiological evidence supporting household transmission of zoonotic Giardia duodenalis and Cryptosporidium spp. from pet dogs and cats in the province of Álava, Northern Spain

The role of pet dogs and cats as suitable source of human infections by the diarrheagenic protozoan parasites Giardia duodenalis and Cryptosporidium spp. has been a topic of intense debate for long time and still remains a largely unsolved problem. In this cross-sectional molecular epidemiological survey we attempted to investigate whether zoonotic (or zooanthroponotic) disease transmission was occurring among humans and domestic dogs and cats sharing the same spatial and temporal setting in both rural and urban areas of the province of Álava, Northern Spain. A total of 268 (including 179 human, 55 canine, and 34 feline) individual faecal specimens were obtained from 63 family households during February-March and November-December 2014. Detection of G. duodenalis cysts and Cryptosporidium spp. oocysts was achieved by direct fluorescence microscopy (DFAT) and PCR-based methods targeting the small subunit (SSU) ribosomal RNA gene of the parasites. Giardia-positive isolates were subsequently sub-genotyped at the glutamate dehydrogenase (GDH) and β-giardin (BG) genes. Overall, G. duodenalis infections were identified in 3.4% (6/179) of humans, 29% (16/55) of dogs, and 5.9% (2/34) of cats, respectively. Cryptosporidium spp. infections were detected in 1.1% (2/179) of humans, 5.5% (3/55) of dogs, and 8.8% (3/34) of cats, respectively. Simultaneous infections in human and canine/feline hosts by G. duodenalis or Cryptosporidium spp. were only demonstrated in a single household in which a cat and its owner tested positive for Cryptosporidium by DFAT, but this result could not be confirmed by SSU-PCR. Infections were homogeneously distributed among the studied human or animal populations irrespectively of their sex, age group, or geographical region of origin. Inadequate washing of raw vegetables and fruits was the only risk factor significantly associated to a higher likelihood of having human giardiosis/cryptosporidiosis. Molecular characterization of G. duodenalis isolates revealed the presence of sub-assemblage BIV in a single human isolate. All dog (n=3) and cat (n=2) isolates successfully genotyped were assigned to canine- and feline-specific assemblages C and F, respectively. No mixed assemblage or sub-assemblage infections could be demonstrated. Regarding Cryptosporidium, C. canis was found infecting dogs (n=2), and C. felis a single cat. Attempts to amplify and characterize Cryptosporidium human isolates failed repeatedly. Our results suggest that pet dogs and cats do not seem to play a significant role as suitable reservoirs of human giardiosis or cryptosporidiosis in the province of Álava. We conclude, therefore, that zoonotic transmission of giardiosis or cryptosporidiosis among pet dogs and cats and their owners in this geographical region is very likely a rare event.

First molecular investigation of Cryptosporidium spp. in young calves in Algeria

To date, no information is available on the prevalence and genetic identity of Cryptosporidium spp. in cattle in Algeria. In this study, 17 dairy farms in the province of Batna, located in the northeast of the country, were visited to collect 132 fecal samples from young calves (< 8 weeks old). Samples were examined microscopically using the modified Ziehl-Neelsen acid-fast staining method, and at least one sample per farm was submitted for molecular analysis. Amplification of a fragment of the small subunit ribosomal RNA gene was positive for 24 of the 61 samples (40%), and sequence analysis identified three species, namely Cryptosporidium bovis (n = 14), C. ryanae (n = 6), and C. parvum (n = 4). The C. parvum IIaA13G2R1 subtype, an uncommon zoonotic subtype, was identified in two isolates from a single farm by sequencing a fragment of the GP60 gene. This is the first report about genotyping and subtyping of Cryptosporidium in calves in Algeria.

Occurrence and removal of Giardia spp. cysts and Cryptosporidium spp. oocysts from a municipal wastewater treatment plant in Brazil

Sewage and sewage sludge have been recognized as potential sources of two important waterborne pathogenic protozoa: Giardia spp. and Cryptosporidium spp. Due to the lack of studies about the occurrence of these pathogens in sewage and sludge in Brazil, an investigation was conducted at various stages of a municipal wastewater treatment plant (WWTP) aiming to assess the occurrence of Giardia spp. cysts and Cryptosporidium spp. oocysts, their removal by the treatment processes, which are upflow anaerobic sludge blanket (UASB) reactor and dissolved air flotation process, and also the correlations between protozoa and indicator microorganisms. Significant quantities of cysts were detected in 100% of the analyzed wastewater samples, while oocysts were detected only in 39.0% of all wastewater samples. The overall removal of Giardia spp. cysts from the WWTP was on average 2.03 log, and the UASB reactor was more efficient than flotation. The sludge samples presented high quantities of (oo)cysts, implying the risks of contamination in the case of sludge reuse or inadequate disposal. Giardiasis prevalence was estimated between 2.21% and 6.7% for the population served by the WWTP, while cryptosporidiosis prevalence was much lower. Significant positive correlation was obtained only between cysts and Clostridium spores in anaerobic effluent.

Cryptosporidium and Giardia in Africa: current and future challenges

Cryptosporidium and Giardia are important causes of diarrhoeal illness. Adequate knowledge of the molecular diversity and geographical distribution of these parasites and the environmental and climatic variables that influence their prevalence is important for effective control of infection in at-risk populations, yet relatively little is known about the epidemiology of these parasites in Africa. Cryptosporidium is associated with moderate to severe diarrhoea and increased mortality in African countries and both parasites negatively affect child growth and development. Malnutrition and HIV status are also important contributors to the prevalence of Cryptosporidium and Giardia in African countries. Molecular typing of both parasites in humans, domestic animals and wildlife to date indicates a complex picture of both anthroponotic, zoonotic and spill-back transmission cycles that requires further investigation. For Cryptosporidium, the only available drug (nitazoxanide) is ineffective in HIV and malnourished individuals and therefore more effective drugs are a high priority. Several classes of drugs with good efficacy exist for Giardia, but dosing regimens are suboptimal and emerging resistance threatens clinical utility. Climate change and population growth are also predicted to increase both malnutrition and the prevalence of these parasites in water sources. Dedicated and co-ordinated commitments from African governments involving "One Health" initiatives with multidisciplinary teams of veterinarians, medical workers, relevant government authorities, and public health specialists working together are essential to control and prevent the burden of disease caused by these parasites.

Cryptosporidium spp. and Giardia spp. in feces and water and the associated exposure factors on dairy farms

The aims of this study were to verify the prevalence of Cryptosporidium spp. and Giardia spp. in animal feces and drinking water on dairy farms and to identify a possible relation between the exposure factors and the presence of these parasites. Fecal samples from cattle and humans and water samples were collected on dairy farms in Paraná, Brazil. Analysis of (oo)cysts in the feces was performed by the modified Ziehl-Neelsen staining and centrifugal flotation in zinc sulfate. Test-positive samples were subjected to nested PCR amplification of the 18SSU ribosomal RNA gene for identification of Cryptosporidium and Giardia and of the gp60 gene for subtyping of Cryptosporidium. Microbiological analysis of water was carried out by the multiple-tube method and by means of a chromogenic substrate, and parasitological analysis was performed on 31 samples by direct immunofluorescence and nested PCR of the genes mentioned above. Identification of the species of Cryptosporidium was performed by sequencing and PCR with analysis of restriction fragment length polymorphisms. The prevalence of Giardia and Cryptosporidium was higher in calves than in adults. Among the samples of cattle feces, Cryptosporidium parvum was identified in 41 (64%), C. ryanae in eight (12.5%), C. bovis in four (6.3%), C. andersoni in five (7.8%), and a mixed infection in 20 samples (31.3%). These parasites were not identified in the samples of human feces. Thermotolerant coliform bacteria were identified in 25 samples of water (45.5%). Giardia duodenalis and C. parvum were identified in three water samples. The gp60 gene analysis of C. parvum isolates revealed the presence of two strains (IIaA20G1R1 and IIaA17G2R2) in the fecal samples and one (IIaA17G2R1) in the water samples. The presence of coliforms was associated with the water source, structure and degradation of springs, rain, and turbidity. The prevalence of protozoa was higher in calves up to six months of age. C. parvum and G. duodenalis were identified in the water of dairy farms, as were thermotolerant coliforms; these findings point to the need for guidance on handling of animals, preservation of water sources, and water treatment.

Pathogenic Mechanisms of Cryptosporidium and Giardia

Intestinal protozoa are important etiological agents of diarrhea, particularly in children, yet the public health risk they pose is often neglected. Results from the Global Enteric Multicenter Study (GEMS) showed that Cryptosporidium is among the leading causes of moderate to severe diarrhea in children under 2 years. Likewise, Giardia infects approximately 200 million individuals worldwide, and causes acute diarrhea in children under 5 years. Despite this recognized role as pathogens, the question is why and how these parasites cause disease in some individuals but not in others. This review focuses on known pathogenic mechanisms of Cryptosporidium and Giardia, and infection progress towards disease.

Occurrence and Genetic Characteristics of Cryptosporidium hominis and Cryptosporidium andersoni in Horses from Southwestern China

A total of 333 fecal specimens from horses in southwestern China were genotyped based on analysis of the small subunit rRNA (SSUrRNA) gene. Cryptosporidium hominis and Cryptosporidium andersoni were identified in 2 and 4 stool specimens, respectively. The identification of C. hominis was confirmed by sequence analysis of the 70‐kDa heat shock protein (HSP70) and oocyst wall protein (COWP) genes. Subtyping analysis of the 60‐kDa glycoprotein (GP60) gene sequence of C. hominis revealed a new rare subtype Id, named IdA15; only three Id isolates have been reported in humans to date. Multilocus sequence typing (MLST) analysis indicated that the C. andersoni subtype was A6, A5, A2, and A1 at the four minisatellite loci (MS1, MS2, MS3, and MS16, respectively). This is the first report to identify the presence of C. andersoni and C. hominis in horses in southwestern China and the first to identify a rare zoonotic subtype Id of C. hominis in horses. These findings suggest that infected horses may act as potential reservoirs of Cryptosporidium to transmit infections to humans.

Report of fatal mixed infection with Cryptosporidium parvum and Giardia intestinalis in neonatal calves

In the production and management of beef and dairy cattle, controlling diarrhea is one of the important concerns. Pathogenic agents of the disease, protozoan parasites including Cryptosporidium spp., are difficult to control, making prevention, diagnoses, and treatment of diarrhea. In the present study, we investigated a farm with a history of calf deaths over a period of 10 years in order to determine the cause of disease and to clarify the detailed distribution of the pathogens. In four examined calves that were reared in calf pens, all were positive with Cryptosporidium and/or Giardia, while the other breeding stock and adult cattle were negative. Molecular analyses revealed that the isolates from calves were C. parvum subtype IIaA15G2R1 as a zoonotic and G. intestinalis assemblage E. Other pathogenic bacteria and diarrhea-causing viruses were not detected. After treating the calf pens with boiling water and milk of lime (Ca[OH]2), oocysts of C. parvum and cysts of G. intestinalis were not found and no additional calves died. This is the first report to describe the mixed infection of both parasites in Japan.

Molecular characterization of zoonotic pathogens Cryptosporidium spp., Giardia duodenalis and Enterocytozoon bieneusi in calves in Algeria

Little is known on the identity and public health potential of Cryptosporidium spp., Giardia duodenalis and Enterocytozoon bieneusi in farm animals in Algeria. In this study, 102 fecal specimens from pre-weaned dairy calves with or without diarrhea were collected from 19 dairy farms located in 6 provinces. PCR-restriction fragment length polymorphism analysis of the small subunit rRNA gene was used to detect and differentiate Cryptosporidium spp., whereas PCR-sequence analysis of the triosephosphate isomerase gene and ribosomal internal transcribed spacer were used to detect and genotype G. duodenalis and E. bieneusi, respectively. Cryptosporidium was found in 14 specimens, among which 7 had C. parvum, 4 had C. bovis, and 3 had mixed infection of C. parvum and C. bovis or C. bovis and C. andersoni. Subtyping of C. parvum by PCR-sequence analysis of the 60kDa glycoprotein gene identified two zoonotic subtypes IIaA16G2R1 and IIaA17G3R1. G. duodenalis was found in 28 specimens, with 6 having the host-specific assemblage E, 14 having the zoonotic assemblage A (all belonging to A2 subtype), and 8 having mixed assemblages. Six known genotypes of E. bieneusi belonging to Group 2, including I, J, BEB3, BEB4, BEB6 and PtEb XI, were identified in 11 specimens. Diarrhea was mostly associated with the occurrence of C. parvum. Data from this study suggest that human-pathogenic C. parvum subtypes and G. duodenalis and E. bieneusi genotypes are common on dairy farms in Algeria.

Comparative genomic analysis of the IId subtype family of Cryptosporidium parvum

Host adaptation is known to occur in Cryptosporidium parvum, with IIa and IId subtype families preferentially infecting calves and lambs, respectively. To improve our understanding of the genetic basis of host adaptation in Cryptosporidium parvum, we sequenced the genomes of two IId specimens and one IIa specimen from China and Egypt using the Illumina technique and compared them with the published IIa IOWA genome. Sequence data were obtained for >99.3% of the expected genome. Comparative genomic analysis identified differences in numbers of three subtelomeric gene families between sequenced genomes and the reference genome, including those encoding SKSR secretory proteins, the MEDLE family of secretory proteins, and insulinase-like proteases. These gene gains and losses compared with the reference genome were confirmed by PCR analysis. Altogether, 5,191-5,766 single nucleotide variants were seen between genomes sequenced in this study and the reference genome, with most SNVs occurring in subtelomeric regions of chromosomes 1, 4, and 6. The most highly polymorphic genes between IIa and IId encode mainly invasion-associated and immunodominant mucin proteins, and other families of secretory proteins. Further studies are needed to verify the biological significance of these genomic differences.

Prevalence and risk factors for cryptosporidiosis: a global, emerging, neglected zoonosis

Background

Cryptosporidiosis is a zoonotic disease caused by the important parasitic diarrheal agent Cryptosporidium spp. Cryptosporidiosis occurs in all classes of animals and man with a rapidly expanding host range and increased importance since the occurrence of human immunodeficiency virus/acquired immunodeficiency syndrome in man.

Objectives

To review the global picture of cryptosporidiosis in man and animals with emphasis on prevalence and risk factors.

Methods

Current relevant literature on cryptosporidiosis was reviewed.

Results

Cryptosporidiosis is widely distributed and the risk factors vary from one region to another with hygiene and immune status as important risk factors.

Conclusions

Cryptosporidium spp. associated mortality has not only been reported in immune-compromised patients, but also in immune-competent patients. Yet in many countries not much attention is paid to the control and prevention of this infection in animals and man. The neglect of this disease despite the serious threat it poses to animals, their husbandry, and humans, has led the World Health Organization to list it among globally neglected diseases. To control and prevent this infection more effort needs to be directed at controlling the risk factors of the infection in man and animals.

Abundance, zoonotic potential and risk factors of intestinal parasitism amongst dog and cat populations: The scenario of Crete, Greece

Background

The objectives of this study were to evaluate the prevalence and infection intensity of intestinal parasites in different dog and cat populations in Crete, Greece, estimate the zoonotic risk and identify risk factors.

Methods

Faecal samples from shelter, household and shepherd dogs and shelter and household cats were analyzed using sedimentation/flotation techniques. Giardia and Cryptosporidium were detected by a quantitative direct immunofluorescence assay (IFA). PCR and sequencing was performed to evaluate the zoonotic potential of Giardia and Cryptosporidium positive samples.

Results

Totals of 879 dog and 264 cat faecal samples were examined. In dogs, the overall prevalence was 25.2% (CI: 22.4–28.1) for Giardia spp.; 9.2% (CI: 7.3–11.1) for Ancylostoma/Uncinaria spp.; 7.6% (CI: 5.9–9.4) for Toxocara spp.; 5.9% (CI: 4.4–7.5) for Cryptosporidium spp.; 4.6% (CI: 3.2–5.9) for Cystoisospora spp.; 2.7% (CI: 1.7–3.8) for Toxascaris leonina; 1.7% (CI: 0.9–2.6) for Capillaria spp.; 0.8% (CI: 0.2–1.4) for taeniid eggs; 0.2% (CI: 0–0.5) for Dipylidium caninum; and 0.1% (CI: 0–0.3) for Strongyloides stercoralis. In cats, the prevalence was 20.5% (CI: 15.6–25.3) for Giardia spp.; 9.5% (CI: 5.9–13.0) for Cystoisospora spp.; 8.3% (CI: 5.0–11.7) for Toxocara spp.; 7.6% (CI: 4.4–10.8) for Ancylostoma/Uncinaria spp.; 6.8% (CI: 3.8–9.9) for Cryptosporidium spp.; 4.2% (CI: 1.8–6.6) for Capillaria spp.; 0.8% (CI: 0–1.8) for taeniid eggs; and 0.4% (CI: 0–1.1) for Hammondia/Toxoplasma. Concerning the risk factors evaluated, there was a negative association between age and Giardia infection and between age and T. leonina infection intensity for dogs. Sequencing results revealed the presence of mainly animal-specific G. duodenalis assemblages C and D in dogs and assemblages F, C and BIV-like in cats, with only a limited number of (co-)infections with assemblage A. As for Cryptosporidium, the dog-specific C. canis and the pig-specific C. scrofarum were detected in dogs and the cat-specific C. felis was detected in cats.

Conclusions

High levels of parasitism in both dogs and cats were recorded. Giardia was the most prevalent parasite in all dog and cat populations except for shepherd dogs. Genotyping results suggest a limited zoonotic risk of Giardia and Cryptosporidium infections from dogs and cats in Crete. Taeniid eggs were more prevalent in shepherd dogs suggesting access to carcasses and posing a threat for cystic echinococcosis transmission. Infection rates of Toxocara spp. in both dogs and cats show that companion animals could be a significant source of infection to humans.

Electronic supplementary material

The online version of this article (doi:10.1186/s13071-017-1989-8) contains supplementary material, which is available to authorized users.

Occurrence and molecular genotyping of Giardia duodenalis and Cryptosporidium spp. in wild mesocarnivores in Spain

There is a surprisingly scarce amount of epidemiological and molecular data on the prevalence, frequency, and diversity of the intestinal protozoan parasites Giardia duodenalis and Cryptosporidium spp. in wildlife in general and mesocarnivore species in particular. Consequently, the extent of the cyst/oocyst environmental contamination attributable to these wild host species and their potential implications for public veterinary health remain largely unknown. In this molecular epidemiological survey a total of 193 individual faecal samples from badgers (Meles meles, n=70), ferrets (Mustela putorius furo, n=2), genets (Genetta genetta, n=6), Iberian lynxes (Lynx pardinus, n=6), beech martens (Martes foina, n=8), mongooses (Herpestes ichneumon, n=2), otters (Lutra lutra, n=2), polecats (Mustela putorius, n=2), red foxes (Vulpes vulpes, n=87), wildcats (Felis silvestris, n=2), and wolves (Canis lupus, n=6) were obtained from road-killed, hunted, and accidentally found carcasses, and from camera-trap surveys or animals entering rescue shelters, during the period December 2003-April 2016. Investigated specimens were collected in five Spanish autonomous regions including Andalusia (n=1), Asturias (n=69), Basque Country (n=49), Castile-La Mancha (n=38), and Extremadura (n=36). The presence of cysts/oocysts was confirmed by PCR-based methods targeting the small subunit (ssu) ribosomal RNA gene of these parasite species. Genotyping of the obtained isolates were attempted at appropriate markers including the glutamate dehydrogenase (G. duodenalis) and the 60-kDa glycoprotein (C. parvum and C. ubiquitum) loci. Overall, G. duodenalis was detected in 8% (7/87) of red foxes, a single beech marten, and a single wolf, respectively. Cryptosporidium was identified in 3% (2/70) of badgers, 8% (7/87) of red foxes, a single genet, and a single mongoose, respectively. None of the nine G. duodenalis isolates generated could be genotyped at the assemblage/sub-assemblage level. Out of the nine Cryptosporidium isolates successfully characterized, three were identified as C. canis (one in a mongoose and two in red foxes), and three as C. parvum (one in a badger and three in red foxes). The remaining three isolates were assigned to C. felis (in a red fox), C. hominis (in a badger), and C. ubiquitum (in a red fox), respectively. Two additional Cryptosporidium isolates infecting a badger and a genet, respectively, were untypable. The red fox was confirmed as a suitable host of potentially zoonotic Cryptosporidium species, mainly C. parvum and C. ubiquitum. The high mobility and wide home range of red foxes, together with their increasing presence in urban and peri-urban settings, may led to the overlapping of sylvatic and domestic cycles of the parasite, and consequently, to an increased risk of cryptosporidiosis in production animals and humans. The detection of C. hominis oocysts in a badger raises the question of whether this finding represents a true infection or a sporadic event of mechanical passage of C. hominis oocyst of anthroponotic origin.

Epidemiology of Cryptosporidium infection in cattle in China: a review

The present review discusses the findings of cryptosporidiosis research conducted in cattle in China and highlights the currently available information on Cryptosporidium epidemiology, genetic diversity, and distribution in China, which is critical to understanding the economic and public health importance of cryptosporidiosis transmission in cattle. To date, 10 Cryptosporidium species have been detected in cattle in China, with an overall infection rate of 11.9%. The highest rate of infection (19.5%) was observed in preweaned calves, followed by that in juveniles (10.69%), postweaned juveniles (9.0%), and adult cattle (4.94%). The dominant species were C. parvum in preweaned calves and C. andersoni in postweaned, juvenile, and adult cattle. Zoonotic Cryptosporidium species (C. parvum and C. hominis) were found in cattle, indicating the possibility of transmission between humans and cattle. Different cattle breeds had significant differences in the prevalence rate and species of Cryptosporidium. This review demonstrates an age-associated, breed-associated, and geographic-related occurrence of Cryptosporidium and provides references for further understanding of the epidemiological characteristics, and for preventing and controlling the disease.

Community Laboratory Testing for Cryptosporidium: Multicenter Study Retesting Public Health Surveillance Stool Samples Positive for Cryptosporidium by Rapid Cartridge Assay with Direct Fluorescent Antibody Testing

Cryptosporidium is a common cause of sporadic diarrheal disease and outbreaks in the United States. Increasingly, immunochromatography-based rapid cartridge assays (RCAs) are providing community laboratories with a quick cryptosporidiosis diagnostic method. In the current study, the Centers for Disease Control and Prevention (CDC), the Association of Public Health Laboratories (APHL), and four state health departments evaluated RCA-positive samples obtained during routine Cryptosporidium testing. All samples underwent “head to head” re-testing using both RCA and direct fluorescence assay (DFA). Community level results from three sites indicated that 54.4% (166/305) of Meridian ImmunoCard STAT! positives and 87.0% (67/77) of Remel Xpect positives were confirmed by DFA. When samples were retested by RCA at state laboratories and compared with DFA, 83.3% (155/186) of Meridian ImmunoCard STAT! positives and 95.2% (60/63) of Remel Xpect positives were confirmed. The percentage of confirmed community results varied by site: Minnesota, 39.0%; New York, 63.9%; and Wisconsin, 72.1%. The percentage of confirmed community results decreased with patient age; 12.5% of community positive tests could be confirmed by DFA for patients 60 years of age or older. The percentage of confirmed results did not differ significantly by sex, storage temperature, time between sample collection and testing, or season. Findings from this study demonstrate a lower confirmation rate of community RCA positives when compared to RCA positives identified at state laboratories. Elucidating the causes of decreased test performance in order to improve overall community laboratory performance of these tests is critical for understanding the epidemiology of cryptosporidiosis in the United States (US).

Presence of zoonotic Cryptosporidium scrofarum, Giardia duodenalis assemblage A and Enterocytozoon bieneusi genotypes in captive Eurasian wild boars (Sus scrofa) in China: potential for zoonotic transmission

Background

Cryptosporidium spp., Giardia duodenalis and Enterocytozoon bieneusi are the main causal pathogens of gastrointestinal disease. However, there are limited reports about the prevalence of these organisms in captive Eurasian wild boars worldwide. Therefore, we examined the occurrence and identified the species/assemblages/genotypes of these pathogens in captive Eurasian wild boars, and estimated the zoonotic potential.

Findings

Of 357 fecal samples collected from captive Eurasian wild boars in China, 155 (43.4%) were infected with Cryptosporidium, G. duodenalis and/or E. bieneusi. The infection rates significantly differed in different areas, but did not differ between wild boars kept indoors and outdoors. Three (0.8%), 11 (3.1%) and 147 (41.2%) fecal samples were positive for Cryptosporidium, G. duodenalis and E. bieneusi, respectively. Sequence analysis of SSU rRNA gene revealed that all of the Cryptosporidium strains belonged to C. scrofarum. Based on the sequence analysis of the β-giardia gene of G. duodenalis, assemblages E and A were characterized. Fourteen E. bieneusi genotypes comprising five novel (WildBoar 7–11) and eight known (EbpC, F, CHG19, CHC5, PigEBITS5, D, RWSH4, SC02) genotypes were identified by ITS sequencing. EbpC was the most frequent genotype, detected in 85 specimens. Phylogenetic analysis revealed that all 14 genotypes belonged to Group 1.

Conclusions

This first report on the occurrence of Cryptosporidium, G. duodenalis and E. bieneusi in captive wild boars in China indicates that the presence of zoonotic species/assemblages/genotypes poses a threat to public health. The findings suggest that wild boars could be a significant source of human infection and water pollution.

Real-time nucleic acid sequence-based amplification (NASBA) assay targeting MIC1 for detection of Cryptosporidium parvum and Cryptosporidium hominis oocysts

Both Cryptosporidium parvum and Cryptosporidium hominis are often associated with cryptosporidiosis in humans, but whereas humans are the main host for C. hominis, C. parvum is zoonotic and able to infect a variety of species. The oocyst transmission stages of both species of parasites are morphologically identical and molecular techniques, usually polymerase chain reaction (PCR), are required to distinguish between oocysts detected by standard methods in environmental samples, such as water. In this study, we developed two primer sets for real-time nucleic acid sequence-based amplification (NASBA), targeting the MIC1 transcript in C. parvum (CpMIC1) and C. hominis (ChMIC1). Using these primer sets, we were not only able to detect low numbers of C. parvum and C. hominis oocysts (down to 5 oocysts in 10 μl, and down to 1 oocyst using diluted RNA samples), but also distinguish between them. One of the primer sets targeted an exon only occurring in CpMIC1, thereby providing a tool for distinguishing C. parvum from other Cryptosporidium species. Although mRNA has been suggested as a tool for assessing viability of Cryptosporidium oocysts, as it is short-lived and may have high transcription, this NASBA assay detected MIC1 mRNA in inactivated oocysts. RNA within the oocysts seems to be protected from degradation, even when the oocysts have been killed by heating or freeze-thawing. Thus, our approach detects both viable and non-viable oocysts, and RNA does not seem to be a suitable marker for assessing oocyst viability.

Pseudo-Second-Order Calcium-Mediated Cryptosporidium parvum Oocyst Attachment to Environmental Biofilms

Cryptosporidium parvum oocysts are able to infect a wide range of mammals, including humans, via fecal-oral transmission. The remobilization of biofilm-associated C. parvum oocysts back into the water column by biofilm sloughing or bulk erosion poses a threat to public health and may be responsible for waterborne outbreaks; thus, the investigation of C. parvum attachment mechanisms to biofilms, particularly the physical and chemical factors controlling oocyst attachment to biofilms, is essential to predict the behavior of oocysts in the environment. In our study, biofilms were grown in rotating annular bioreactors using prefiltered stream water (0.2-μm retention) and rock biofilms (6-μm retention) until the mean biofilm thickness reached steady state. Oocyst deposition followed a calcium-mediated pseudo-second-order kinetic model. Kinetic parameters (i.e., initial oocyst deposition rate constant and total number of oocysts adhered to biofilms at equilibrium) from the model were then used to evaluate the impact of water conductivity on the attachment of oocysts to biofilms. Oocyst deposition was independent of solution ionic strength; instead, the presence of calcium enhanced oocyst attachment, as demonstrated by deposition tests. Calcium was identified as the predominant factor that bridges the carboxylic functional groups on biofilm and oocyst surfaces to cause attachment. The pseudo-second-order kinetic profile fit all experimental conditions, regardless of water chemistry and/or lighting conditions.

IMPORTANCE

The cation bridging model in our study provides new insights into the impact of calcium on the attachment of C. parvum oocysts to environmental biofilms. The kinetic parameters derived from the model could be further analyzed to elucidate the behavior of oocysts in commonly encountered complex aquatic systems, which will enable future innovations in parasite detection and treatment technologies to protect public health.

Evolution of mitosome metabolism and invasion-related proteins in Cryptosporidium

Background

The switch from photosynthetic or predatory to parasitic life strategies by apicomplexans is accompanied with a reductive evolution of genomes and losses of metabolic capabilities. Cryptosporidium is an extreme example of reductive evolution among apicomplexans, with losses of both the mitosome genome and many metabolic pathways. Previous observations on reductive evolution were largely based on comparative studies of various groups of apicomplexans. In this study, we sequenced two divergent Cryptosporidium species and conducted a comparative genomic analysis to infer the reductive evolution of metabolic pathways and differential evolution of invasion-related proteins within the Cryptosporidium lineage.

Results

In energy metabolism, Cryptosporidium species differ from each other mostly in mitosome metabolic pathways. Compared with C. parvum and C. hominis, C. andersoni possesses more aerobic metabolism and a conventional electron transport chain, whereas C. ubiquitum has further reductions in ubiquinone and polyisprenoid biosynthesis and has lost both the conventional and alternative electron transport systems. For invasion-associated proteins, similar to C. hominis, a reduction in the number of genes encoding secreted MEDLE and insulinase-like proteins in the subtelomeric regions of chromosomes 5 and 6 was also observed in C. ubiquitum and C. andersoni, whereas mucin-type glycoproteins are highly divergent between the gastric C. andersoni and intestinal Cryptosporidium species.

Conclusions

Results of the study suggest that rapidly evolving mitosome metabolism and secreted invasion-related proteins could be involved in tissue tropism and host specificity in Cryptosporidium spp. The finding of progressive reduction in mitosome metabolism among Cryptosporidium species improves our knowledge of organelle evolution within apicomplexans.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-3343-5) contains supplementary material, which is available to authorized users.

Zoonotic Cryptosporidium and Giardia shedding by captured rangeland goats

Faecal shedding of Cryptosporidium and Giardia by captured rangeland goats was investigated using a longitudinal study with four faecal samples collected from 125 male goats once monthly for four months, commencing immediately after capture and transport to a commercial goat depot (feedlot). Goats were composite breed and aged approximately 9-12months on arrival. Faecal samples were screened for Cryptosporidium and Giardia presence and concentration using quantitative PCR and sequencing at the 18S ribosomal RNA locus (Cryptosporidium), and glutamate dehydrogenase and β-giardin loci (Giardia). Longitudinal prevalence for Cryptosporidium was 27.2% (point prevalence range 3-14%) with 3 species identified: C. xiaoi (longitudinal prevalence 13.6%), C. ubiquitum (6.4%) and C. parvum (3.2%). Sub-typing at the gp60 locus identified C. ubiquitum XIIa, C. parvum IIaA17G2R1 and C. parvum IIaA17G4R1. This is the first report of the zoonotic C. parvum subtype IIaA17G4R1 in goats. The pattern of genotypes shed in faeces changed over the duration of study with C. ubiquitum identified only at the first and second samplings, and C. parvum identified only at the fourth sampling. Longitudinal prevalence for Giardia duodenalis was 29.6% (point prevalence range 4-12%) with all positives sub-typed as assemblage E. Only 2/125 goats were identified to be shedding Cryptosporidium or Giardia on more than one occasion. This is the first report of Cryptosporidium and Giardia genotypes in captured rangeland goats. Faecal shedding of zoonotic Cryptosporidium spp. and potentially zoonotic G.duodenalis has implications for food safety and effluent management. Keywords: Cryptosporidium; Giardia; Rangeland goats; zoonotic.

Subtyping of Cryptosporidium cuniculus and genotyping of Enterocytozoon bieneusi in rabbits in two farms in Heilongjiang Province, China

Cryptosporidium spp. and Enterocytozoon bieneusi are two prevalent opportunistic pathogens in humans and animals. Currently, few data are available on genetic characterization of both pathogens in rabbits in China. The aim of the present study was to understand prevalence and genetic characterization of Cryptosporidium spp. and E. bieneusi in rabbits. We collected 215 fecal samples from 150 Rex rabbits and 65 New Zealand White rabbits on two different farms in Heilongjiang Province, China. Cryptosporidium spp. and E. bieneusi were tested by polymerase chain reaction (PCR) and sequencing the partial small subunit of ribosomal DNA (SSU rDNA) and the internal transcribed spacer (ITS) region of rDNA, respectively. Cryptosporidium was detected in 3.3% (5/150) of Rex rabbits and 29.2% (19/65) of New Zealand White rabbits. All the 24 Cryptosporidium isolates were identified as C. cuniculus. Enterocytozoon bieneusi was only found in 14.7% (22/150) of Rex rabbits. Five known genotypes: CHN-RD1 (n = 12), D (n = 3), Type IV (n = 2), Peru6 (n = 1), and I (n = 1), and three novel ones CHN-RR1 to CHN-RR3 (one each) were detected. By analyzing the 60-kDa glycoprotein (gp60) gene sequences of C. cuniculus isolates, three subtypes were obtained: VbA28 (n = 2), VbA29 (n = 16), and VbA32 (n = 3). All these three C. cuniculus subtypes were reported previously in humans. Four known E. bieneusi genotypes have been found to be present in humans. The three novel ones fell into zoonotic group 1. The results suggest zoonotic potential of C. cuniculus and E. bieneusi isolates in rabbits.

Towards a more accurate quantitative assessment of seasonal Cryptosporidium infection risks in surface waters using species and genotype information

Many Cryptosporidium species/genotypes are not considered infectious to humans, and more realistic estimations of seasonal infection risks could be made using human infectious species/genotype information to inform quantitative microbial risk assessments (QMRA). Cryptosporidium oocyst concentration and species/genotype data were collected from three surface water surveillance programs in two river basins [South Nation River, SN (2004-09) and Grand River, GR (2005-13)] in Ontario, Canada to evaluate seasonal infection risks. Main river stems, tributaries, agricultural drainage streams, water treatment plant intakes, and waste water treatment plant effluent impacted sites were sampled. The QMRA employed two sets of exposure data to compute risk: one assuming all observed oocysts were infectious to humans, and the other based on the fraction of oocysts that were C. hominis and/or C. parvum (dominant human infectious forms of the parasite). Viability was not considered and relative infection risk was evaluated using a single hypothetical recreational exposure. Many sample site groupings for both river systems, had significant seasonality in Cryptosporidium occurrence and concentrations (p ≤ 0.05); occurrence and concentrations were generally highest in autumn for SN, and autumn and summer for GR. Mean risk values (probability of infection per exposure) for all sites combined, for each river system, were roughly an order of magnitude lower (avg. of SN and GR 5.3 × 10^-5) when considering just C. parvum and C. hominis oocysts, in relation to mean infection risk (per exposure) assuming all oocysts were infectious to humans (5.5 × 10^-4). Seasonality in mean risk (targeted human infectious oocysts only) was most strongly evident in SN (e.g., 7.9 × 10^-6 in spring and 8.1 × 10^-5 in summer). Such differences are important if QMRA is used to quantify effects of water safety/quality management practices where inputs from a vast array of fecal pollution sources can readily occur. Cryptosporidium seasonality in water appears to match the seasonality of human infections from Cryptosporidium in the study regions. This study highlights the importance of Cryptosporidium species/genotype data to help determine surface water pollution sources and seasonality, as well as to help more accurately quantify human infection risks by the parasite.

Molecular identification of Enterocytozoon bieneusi, Cryptosporidium, and Giardia in Brazilian captive birds

A total of 85 fecal samples from captive birds collected from October 2013 to September 2014 in Uberlândia and Belo Horizonte in the state of Minas Gerais (Brazil) were evaluated for the presence of Enterocytozoon bieneusi, Cryptosporidium, and Giardia by PCR. Of these, three birds were found positive for E. bieneusi (3.5%), two for Cryptosporidium (2.3%), and one for Giardia (1.2%). Two genotypes of E. bieneusi were detected by nucleotide sequence analysis of the ITS region, genotypes D and Peru 6 in a swan goose and in two rock pigeons, respectively. For Cryptosporidium and Giardia, nucleotide sequence analysis of the SSU rRNA identified Cryptosporidium baileyi and Duck genotype in a swan goose and a mandarin duck, respectively, and Giardia duodenalis assemblage A in a toco toucon. Our results demonstrate that human-pathogenic E. bieneusi genotypes D and Peru6 and G. duodenalis assemblage A are present in captive birds in Brazil, corroborating their potential role as a source of human infection and environmental contamination.

Cryptosporidium Infection Risk: Results of New Dose-Response Modeling

Cryptosporidium human dose-response data from seven species/isolates are used to investigate six models of varying complexity that estimate infection probability as a function of dose. Previous models attempt to explicitly account for virulence differences among C. parvum isolates, using three or six species/isolates. Four (two new) models assume species/isolate differences are insignificant and three of these (all but exponential) allow for variable human susceptibility. These three human-focused models (fractional Poisson, exponential with immunity and beta-Poisson) are relatively simple yet fit the data significantly better than the more complex isolate-focused models. Among these three, the one-parameter fractional Poisson model is the simplest but assumes that all Cryptosporidium oocysts used in the studies were capable of initiating infection. The exponential with immunity model does not require such an assumption and includes the fractional Poisson as a special case. The fractional Poisson model is an upper bound of the exponential with immunity model and applies when all oocysts are capable of initiating infection. The beta Poisson model does not allow an immune human subpopulation; thus infection probability approaches 100% as dose becomes huge. All three of these models predict significantly (>10x) greater risk at the low doses that consumers might receive if exposed through drinking water or other environmental exposure (e.g., 72% vs. 4% infection probability for a one oocyst dose) than previously predicted. This new insight into Cryptosporidium risk suggests additional inactivation and removal via treatment may be needed to meet any specified risk target, such as a suggested 10^-4 annual risk of Cryptosporidium infection.

Multilocus typing of Cryptosporidium spp. in young calves with diarrhea in Korea

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Cryptosporidium spp. were detected using PCR and ELISA in diarrheal feces from calves.

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PCR and ELISA data showed good agreement in detecting C. parvum.

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Multilocus typing with 18S rRNA, gp60, and hsp70 genes of C. parvum was performed.

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Subtyping of C. parvum gp60 gene first revealed IIaA18G3R1 and IIaA16G3R1 in Asia.

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PCR and sequencing of hsp70 gene clearly differentiated C. bovis and C. ryanae.

We assessed the prevalence and performed molecular analysis of Cryptosporidium spp. in diarrheal feces of calves in Korea. Diarrheal fecal samples were collected from 951 young calves (<3 months) on 425 farms. Cryptosporidium prevalence was assessed by PCR and ELISA, and molecular characterization was performed by targeting the 18S rRNA, heat-shock protein 70 (hsp70), and glycoprotein 60 (gp60) genes. Data were analyzed according to the sex, type of cattle, region, season, and type of diarrhea. PCR analysis revealed Cryptosporidium spp. in 9.9% (94/951) of diarrheal fecal samples. C. parvum and C. bovis/ryanae were present in 6.1% (58/951) and 4.1% (39/951) of diarrheal fecal samples, respectively. In addition, ELISA showed positive results for C. parvum in 9.7% (92/951) samples. Statistical analysis of the PCR and ELISA results revealed a lower prevalence of C. parvum in the hemorrhagic diarrheal samples (P < 0.05). For C. bovis/ryanae, seasonality and high prevalence in hemorrhagic diarrhea were observed (P < 0.05). Of the 951 samples tested for C. parvum, 903 samples showed agreement with a κ value of 0.65, indicating good agreement between the two tests. Although C. bovis and C. ryanae share highly similar 18S rRNA sequences, PCR based on hsp70 successfully distinguished C. bovis from C. ryanae. Sequence analysis of gp60 revealed that C. parvum belonged to the IIa families and was further subtyped as IIaA18G3R1 and IIaA16G3R1, which have not been previously reported in Asia. These findings indicate that Cryptosporidium spp. play an important role in diarrhea in young calves in Korea. Considering the zoonotic significance of C. parvum IIa subtype and dense rearing system of cattle in Korea, prevention and continuous monitoring of Cryptosporidium are required.

Annotated draft genome sequences of three species of Cryptosporidium: Cryptosporidium meleagridis isolate UKMEL1, C. baileyi isolate TAMU-09Q1 and C. hominis isolates TU502_2012 and UKH1

Human cryptosporidiosis is caused primarily by Cryptosporidium hominis, C. parvum and C. meleagridis. To accelerate research on parasites in the genus Cryptosporidium, we generated annotated, draft genome sequences of human C. hominis isolates TU502_2012 and UKH1, C. meleagridis UKMEL1, also isolated from a human patient, and the avian parasite C. baileyi TAMU-09Q1. The annotation of the genome sequences relied in part on RNAseq data generated from the oocyst stage of both C. hominis and C. baileyi. The genome assembly of C. hominis is significantly more complete and less fragmented than that available previously, which enabled the generation of a much-improved gene set for this species, with an increase in average gene length of 500 bp relative to the protein-encoding genes in the 2004 C. hominis annotation. Our results reveal that the genomes of C. hominis and C. parvum are very similar in both gene density and average gene length. These data should prove a valuable resource for the Cryptosporidium research community.

The release of the draft genome sequence, and corresponding annotation, of Cryptosporidium baileyi, C. hominis isolates TU502_2012 and UKH1, and C. meleagridis, will accelerate research on Cryptosporidium parasites.

Genetic diversity of Cryptosporidium identified in clinical samples from cities in Brazil and Argentina

The identification and characterisation of Cryptosporidiumgenotypes and subtypes are fundamental to the study of cryptosporidiosis epidemiology, aiding in prevention and control strategies. The objective was to determine the genetic diversity ofCryptosporidium in samples obtained from hospitals of Rio de Janeiro, Brazil, and Buenos Aires, Argentina. Samples were analysed by microscopy and TaqMan polymerase chain reaction (PCR) assays forCryptosporidium detection, genotyped by nested-PCR-restriction fragment length polymorphism (RFLP) analysis of the 18S rRNA gene and subtyped by DNA sequencing of the gp60 gene. Among the 89 samples from Rio de Janeiro, Cryptosporidium spp were detected in 26 by microscopy/TaqMan PCR. In samples from Buenos Aires,Cryptosporidium was diagnosed in 15 patients of the 132 studied. The TaqMan PCR and the nested-PCR-RFLP detected Cryptosporidium parvum, Cryptosporidium hominis, and co-infections of both species. In Brazilian samples, the subtypes IbA10G2 and IIcA5G3 were observed. The subtypes found in Argentinean samples were IbA10G2, IaA10G1R4, IaA11G1R4, and IeA11G3T3, and mixed subtypes of Ia and IIa families were detected in the co-infections. C. hominis was the species more frequently detected, and subtype family Ib was reported in both countries. Subtype diversity was higher in Buenos Aires than in Rio de Janeiro and two new subtypes were described for the first time.

Prevalence and Genetic Diversity of Giardia duodenalis and Cryptosporidium spp. among School Children in a Rural Area of the Amhara Region, North-West Ethiopia

Backgroud

Giardia duodenalis and Cryptosporidium spp. are enteric protozoan causing gastrointestinal illness in humans and animals. Giardiasis and cryptosporidiosis are not formally considered as neglected tropical diseases, but belong to the group of poverty-related infectious diseases that impair the development and socio-economic potential of infected individuals in developing countries.

Methods

We report here the prevalence and genetic diversity of G. duodenalis and Cryptosporidium spp. in children attending rural primary schools in the Bahir Dar district of the Amhara Region, Ethiopia. Stool samples were collected from 393 children and analysed by molecular methods. G. duodenalis was detected by real-time PCR, and the assemblages and sub-assemblages were determined by multilocus sequence-based genotyping of the glutamate dehydrogenase and β-giardin genes of the parasite. Detection and identification of Cryptosporidium species was carried out by sequencing of a partial fragment of the small-subunit ribosomal RNA gene.

Principal Findings

The PCR-based prevalences of G. duodenalis and Cryptosporidium spp. were 55.0% (216/393) and 4.6% (18/393), respectively. A total of 78 G. duodenalis isolates were successfully characterized, revealing the presence of sub-assemblages AII (10.3%), BIII (28.2%), and BIV (32.0%). Discordant typing results AII/AIII and BIII/BIV were identified in 7.7% and 15.4% of the isolates, respectively. An additional five (6.4%) isolates were assigned to assemblage B. No mixed infections of assemblages A+B were found. Extensive genetic variation at the nucleotide level was observed within assemblage B (but no within assemblage A), resulting in the identification of a large number of sub-types. Cryptosporidium diversity was demonstrated by the occurrence of C. hominis, C. parvum, and C. viatorum in the population under study.

Conclusions

Our data suggest an epidemiological scenario with an elevated transmission intensity of a wide range of G. duodenalis genetic variants. Importantly, the elevated degree of genetic diversity observed within assemblage B is consistent with the occurrence of intra-assemblage recombination in G. duodenalis.

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.

Cryptosporidium as a testbed for single cell genome characterization of unicellular eukaryotes

Background

Infectious disease involving multiple genetically distinct populations of pathogens is frequently concurrent, but difficult to detect or describe with current routine methodology. Cryptosporidium sp. is a widespread gastrointestinal protozoan of global significance in both animals and humans.

It cannot be easily maintained in culture and infections of multiple strains have been reported.

To explore the potential use of single cell genomics methodology for revealing genome-level variation in clinical samples from Cryptosporidium-infected hosts, we sorted individual oocysts for subsequent genome amplification and full-genome sequencing.

Results

Cells were identified with fluorescent antibodies with an 80 % success rate for the entire single cell genomics workflow, demonstrating that the methodology can be applied directly to purified fecal samples. Ten amplified genomes from sorted single cells were selected for genome sequencing and compared both to the original population and a reference genome in order to evaluate the accuracy and performance of the method. Single cell genome coverage was on average 81 % even with a moderate sequencing effort and by combining the 10 single cell genomes, the full genome was accounted for. By a comparison to the original sample, biological variation could be distinguished and separated from noise introduced in the amplification.

Conclusions

As a proof of principle, we have demonstrated the power of applying single cell genomics to dissect infectious disease caused by closely related parasite species or subtypes. The workflow can easily be expanded and adapted to target other protozoans, and potential applications include mapping genome-encoded traits, virulence, pathogenicity, host specificity and resistance at the level of cells as truly meaningful biological units.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2815-y) contains supplementary material, which is available to authorized users.