Classification of Cryptosporidium species from patients with sporadic cryptosporidiosis by use of sequence-based multilocus analysis following mutation scanning

First report of Cryptosporidium andersoni and risk factors associated with the occurrence of Cryptosporidium spp. in pre-weaned native Korean calves with diarrhea

Cryptosporidium spp. are important enteric protozoan parasites that infect humans and other animals throughout the world. Cryptosporidium infection in cattle industry leads to substantial economic losses due to diarrhea, growth retardation, weight loss, and possibly death. Most studies have focused on C. parvum, and studies on other Cryptosporidium spp. and calf diarrhea are limited. Therefore, this study aimed to investigate the occurrence of Cryptosporidium spp. in pre-weaned calves, to determine the risk factors for Cryptosporidium spp. infection such as age and season, and to identify subtypes of C. parvum circulating in the Republic of Korea (ROK). A total of 510 fecal samples were collected from calves with diarrhea and divided by age and season. Cryptosporidium spp. were first screened using PCR targeting the small subunit (SSU) rRNA gene and further the 60-kDa glycoprotein gene for subtyping of C. parvum. Out of 510 fecal samples, 71 (13.9%) were positive for Cryptosporidium spp. in pre-weaned calves with diarrhea. C. andersoni (2.8%), C. bovis (30.9%), C. parvum (29.6%), and C. ryanae (36.6%) were identified. C. ryanae was the most predominant in calves in the ROK. Calf age was a significant risk factor for C. bovis (χ² = 13.83, P = 0.001), C. parvum (χ² = 7.57, P = 0.023), and C. ryanae (χ² = 20.18, P = 0.000) occurrence. Additionally, C. parvum was detected 3.1-fold more frequently in pre-weaned calves with diarrhea in fall (95% CI: 1.23-7.81; P = 0.016) than in spring, whereas C. ryanae was 8.9-fold more frequently detected in summer (95% CI: 1.65-48.68; P = 0.011) than in spring. Three subtypes (IIaA17G4R1, IIaA18G3R1, and IIaA20G3R1) of C. parvum were identified. Of them, IIaA17G4R1 was the most common, whereas IIaA20G3R1 was not previously detected in calves in the ROK. To our knowledge, this is the first report of C. andersoni in pre-weaned calves in the ROK. The occurrence of Cryptosporidium spp. appears to be age-dependent in calves. Season had a significant effect on the occurrence of C. parvum and C. ryanae. Taken together, C. bovis and C. ryanae along with C. parvum are detected in pre-weaned calves with diarrhea and these two pathogens should not be overlooked in the diagnosis of calf diarrhea.

Review of generic screening level assumptions for quantitative microbial risk assessment (QMRA) for estimating public health risks from Australian drinking water sources contaminated with Cryptosporidium by recreational activities

As urban communities continue to grow, demand for recreational access (including swimming) in drinking water sources have increased, yet relatively little is understood about the public health implications this poses for drinking water consumers. Preventative risk-based approaches to catchment management, informed by quantitative microbial risk assessment (QMRA), requires accurate input data to effectively model risks. A sound understanding of the knowledge gaps is also important to comprehend levels of uncertainty and help prioritise research needs. Cryptosporidium is one of the most important causes of waterborne outbreaks of gastroenteritis globally due to its resistance to chlorine. This review was undertaken by Water Research Australia to provide the most up-to-date information on current Cryptosporidium epidemiological data and underlying assumptions for exposure assessment, dose response and risk assessment for generic components of QMRA for Cryptosporidium and highlights priorities for common research. Key interim recommendations and guidelines for numerical values for relatively simple screening level QMRA modelling are provided to help support prospective studies of risks to drinking water consumers from Cryptosporidium due to body-contact recreation in source water. The review does not cover site-specific considerations, such as the levels of activity in the source water, the influence of dilution and inactivation in reservoirs, or water treatment. Although the focus is Australia, the recommendations and numerical values developed in this review, and the highlighted research priorities, are broadly applicable across all drinking source water sources that allow recreational activities.

Increased diversity and novel subtypes among clinical Cryptosporidium parvum and Cryptosporidium hominis isolates in Southern Ireland

Reported incidence rates of cryptosporidiosis in Ireland are consistently among the highest in Europe. Despite the national prevalence of this enteric parasite and the compulsory nature of incidence surveillance and reporting, in-depth analyses seeking to genotype clinical isolates of Cryptosporidium on an intra-species level are rarely undertaken in Ireland. This molecular epidemiology study of 163 clinical Cryptosporidium isolates was conducted in Southern Ireland, from 2015 to 2018, in order to ascertain population subtype heterogeneity. Analysis was conducted via real-time PCR amplification and gp60 gene sequencing, which successfully determined the subtype designation of 149 of the 163 (91.4%) tested isolates. Overall, 12 C. parvum and five C. hominis subtypes were identified, with the incidence of the regionally predominant C. parvum species found to primarily occur during springtime months, while C. hominis incidence was largely confined to late summer and autumnal months. Additionally, one C. parvum and four C. hominis subtypes were newly reported by this study, having not been previously identified in clinical or livestock infection in Ireland. Overall, these data give insight into the diversification of the Cryptosporidium population and emergent subtypes, while also allowing comparisons to be made with clinical epidemiological profiles reported previously in Ireland and elsewhere.

Species and genotypes causing human cryptosporidiosis in New Zealand

Cryptosporidium is one of the most common causes of diarrhoea around the world. Successful management and prevention of this infectious disease requires knowledge of the diversity of species and subtypes causing human disease. We use sequence data from 2598 human faecal samples collected during an 11-year period (2009-2019) to better understand the impact of different species and subtypes on public health and to gain insights into the variation of human cryptosporidiosis in New Zealand. Human cryptosporidiosis in New Zealand is caused by a high diversity of species and subtypes. Six species cause human disease in New Zealand: C. hominis, C. parvum, C. cuniculus, C. erinacei, C. meleagridis and C. tyzzeri. Sequence analysis of the gp60 gene identified 16 subtype families and 101 subtypes. Cryptosporidium hominis IbA10G2 and C. parvum IIaA18G3R1 were the most frequent causes of human cryptosporidiosis with 27% and 29% of infections, respectively. Cryptosporidium hominis presented a peak of notified human cases during autumn (March-May) whereas most cases of human cryptosporidiosis caused by C. parvum are found during the calving and lambing season in spring (September-November). We also reported some subtypes that have been rarely detected in other countries such as IbA20G2 and IIoA13G1 and a low prevalence of the hypertransmissible and virulent IIaA15G2R1. This study provides insight into the variability of cryptosporidiosis in New Zealand essential for disease management and surveillance to prevent the introduction or spread of new species and subtypes in the country.

Retrospective analysis of Cryptosporidium species in Western Australian human populations (2015-2018), and emergence of the C. hominis IfA12G1R5 subtype

Cryptosporidium species are a major cause of diarrhoea worldwide. In the present study, a retrospective analysis of 109 microscopically Cryptosporidium-positive faecal specimens from Western Australian patients, collected between 2015 and 2018 was conducted. Sequence analysis of the 18S rRNA and the 60 kDa glycoprotein (gp60) gene loci identified four Cryptosporidium species: C. hominis (86.2%, 94/109), C. parvum (11.0%, 12/109), C. meleagridis (1.8%, 2/109) and C. viatorum (0.9%, 1/109). Subtyping at the gp60 locus identified a total of 11 subtypes including the emergence of the previously rare C. hominis IfA12G1R5 subtype in 2017 as the dominant subtype (46.7%, 21/45). This subtype has also recently emerged as the dominant subtype in the United States but the reasons for its emergence are unknown. This is also the first report of C. viatorum in humans in Australia and a novel subtype (XVaA3g) was identified in the one positive patient.

Anthroponotic transmission of Cryptosporidium parvum predominates in countries with poorer sanitation: a systematic review and meta-analysis

Background

Globally cryptosporidiosis is one of the commonest causes of mortality in children under 24 months old and may be associated with important longterm health effects. Whilst most strains of Cryptosporidium parvum are zoonotic, C. parvum IIc is almost certainly anthroponotic. The global distribution of this potentially important emerging infection is not clear.

Methods

We conducted a systematic review of papers identifying the subtype distribution of C. parvum infections globally. We searched PubMed and Scopus using the following key terms Cryptospor* AND parvum AND (genotyp* OR subtyp* OR gp60). Studies were eligible for inclusion if they had found C. parvum within their human study population and had subtyped some or all of these samples using standard gp60 subtyping. Pooled analyses of the proportion of strains being of the IIc subtype were determined using StatsDirect. Meta-regression analyses were run to determine any association between the relative prevalence of IIc and Gross Domestic Product, proportion of the population with access to improved drinking water and improved sanitation.

Results

From an initial 843 studies, 85 were included in further analysis. Cryptosporidium parvum IIc was found in 43 of these 85 studies. Across all studies the pooled estimate of relative prevalence of IIc was 19.0% (95% CI: 12.9–25.9%), but there was substantial heterogeneity. In a meta-regression analysis, the relative proportion of all C. parvum infections being IIc decreased as the percentage of the population with access to improved sanitation increased and was some 3.4 times higher in those studies focussing on HIV-positive indivduals.

Conclusions

The anthroponotic C. parvum IIc predominates primarily in lower-income countries with poor sanitation and in HIV-positive individuals. Given the apparent enhanced post-infectious virulence of the other main anthroponotic species of Cryptosporidium (C. hominis), it is important to learn about the impact of this subtype on human health.

Electronic supplementary material

The online version of this article (10.1186/s13071-018-3263-0) contains supplementary material, which is available to authorized users.

Comparison of current methods used to detect Cryptosporidium oocysts in stools

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

Zoonotic Cryptosporidium Species in Animals Inhabiting Sydney Water Catchments

Cryptosporidium is one of the most common zoonotic waterborne parasitic diseases worldwide and represents a major public health concern of water utilities in developed nations. As animals in catchments can shed human-infectious Cryptosporidium oocysts, determining the potential role of animals in dissemination of zoonotic Cryptosporidium to drinking water sources is crucial. In the present study, a total of 952 animal faecal samples from four dominant species (kangaroos, rabbits, cattle and sheep) inhabiting Sydney's drinking water catchments were screened for the presence of Cryptosporidium using a quantitative PCR (qPCR) and positives sequenced at multiple loci. Cryptosporidium species were detected in 3.6% (21/576) of kangaroos, 7.0% (10/142) of cattle, 2.3% (3/128) of sheep and 13.2% (14/106) of rabbit samples screened. Sequence analysis of a region of the 18S rRNA locus identified C. macropodum and C. hominis in 4 and 17 isolates from kangaroos respectively, C. hominis and C. parvum in 6 and 4 isolates respectively each from cattle, C. ubiquitum in 3 isolates from sheep and C. cuniculus in 14 isolates from rabbits. All the Cryptosporidium species identified were zoonotic species with the exception of C. macropodum. Subtyping using the 5' half of gp60 identified C. hominis IbA10G2 (n = 12) and IdA15G1 (n = 2) in kangaroo faecal samples; C. hominis IbA10G2 (n = 4) and C. parvum IIaA18G3R1 (n = 4) in cattle faecal samples, C. ubiquitum subtype XIIa (n = 1) in sheep and C. cuniculus VbA23 (n = 9) in rabbits. Additional analysis of a subset of samples using primers targeting conserved regions of the MIC1 gene and the 3' end of gp60 suggests that the C. hominis detected in these animals represent substantial variants that failed to amplify as expected. The significance of this finding requires further investigation but might be reflective of the ability of this C. hominis variant to infect animals. The finding of zoonotic Cryptosporidium species in these animals may have important implications for the management of drinking water catchments to minimize risk to public health.

Mussels (Perna perna) as bioindicator of environmental contamination by Cryptosporidium species with zoonotic potential

Sources of contamination such as animal feces runoff, organic fertilizer application, and the release of partially treated or untreated sewage can lead to the contamination of aquatic environments by Cryptosporidium spp. The quality of mussels as food is closely related to the sanitary conditions of the marine environment where these bivalves are found. Marine mollusks are filter feeders that are able to retain Cryptosporidium oocysts in their tissue, thus functioning as bioindicators. A total of 72 pooled mussel samples of the species Perna perna were collected at two sites (A and B) in the municipality of Mangaratiba, Rio de Janeiro State, Brazil. Sampling involved removal of 30 mussels, from each collection site every month for one year. The 30 mussels from each sampling were then allocated into three groups of 10. Two Cryptosporidium spp. genes (18S and GP60) were targeted for DNA amplification from the samples obtained. After purification, all of the products obtained were sequenced and phylogenetic analyses were performed. Of the 72 samples analyzed using the nested-PCR for the 18S gene target, 29.2% were positive for the presence of Cryptosporidium spp. Of these samples, 52.4% were collected at site A (ie 11/21) and 47.6% at site B (ie 10/21). The 18S genes of all the samples considered positive for Cryptosporidium spp. were sequenced, and the following three species were identified: Cryptosporidium parvum, C. meleagridis, and C. andersoni. Three distinct C. parvum subtypes (IIaA19G2R2; IIaA20G2R2; IIaA20G3R2) were identified using the GP60 gene. More studies to evaluate the zoonotic potential of this species should be performed as both sampling locations contain human and/or animal fecal contaminants.

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Different species of Cryptosporidium diagnosed in Perna perna mussels.

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C. parvum subtypes of IIa zoonotic subfamily diagnosed in P. perna mussels.

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First report of the zoonotic species C. meleagridis in Brazilian mollusk bivalves.

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Mollusks bivalves used as bioindicator of environmental pollution.

Molecular characterization and first report of Cryptosporidium genotypes in human population in the Slovak Republic

In our study, we examined 91 fecal samples from five different groups of people containing HIV patients, hemodialysis patients, kidney transplant recipients, immunocompetent humans without clinical signs, and humans with suspected cryptosporidiosis. The purpose of our study was to determine species and genotype composition of representatives of Cryptosporidium spp. using PCR analysis of small subunit ribosomal RNA gene and 60-kDa glycoprotein gene and examine their phylogenetic relationship. In HIV-positive/AIDS-infected group of patients and in hemodialysis patients, no presence of Cryptosporidium species was detected. In two kidney transplant recipients, we detected species/genotypes Cryptosporidium parvum IIaA13G1T1R1 (KT355488) and Cryptosporidium hominis IaA11G2R8 (KT355489) and in two immunocompetent patients with clinical symptoms, we identified Cryptosporidium muris and C. hominis IbA10G2T1 (KT355490). In the group of healthy immunocompetent individuals without clinical signs, we identified species/genotype C. hominis IbA11G2 (KT355491) in one sample.

Genetic analysis of Giardia and Cryptosporidium from people in Northern Australia using PCR-based tools

To date, there has been limited genetic study of the gastrointestinal pathogens Giardia and Cryptosporidium in northern parts of Australia. Here, PCR-based methods were used for the genetic characterization of Giardia and Cryptosporidium from 695 people with histories of gastrointestinal disorders from the tropical North of Australia. Genomic DNAs from fecal samples were subjected to PCR-based analyses of regions from the triose phosphate isomerase (tpi), small subunit (SSU) of the nuclear ribosomal RNA and/or the glycoprotein (gp60) genes. Giardia and Cryptosporidium were detected in 13 and four of the 695 samples, respectively. Giardia duodenalis assemblages A and B were found in 4 (31%) and 9 (69%) of the 13 samples in persons of <9 years of age. Cryptosporidium hominis (subgenotype IdA18), Cryptosporidium mink genotype (subgenotype IIA16R1) and C. felis were also identified in single patients of 11-21 years of age. Future studies might focus on a comparative study of these and other protists in rural communities in Northern Australia.

Cryptosporidium species and subtype analysis in diarrhoeic pre-weaned lambs and goat kids from north-western Spain

Faecal specimens from diarrhoeic pre-weaned lambs (n = 171) and goat kids (n = 118) were collected in 37 sheep and 23 goat flocks, respectively, from NW Spain and microscopically examined for the presence of Cryptosporidium oocysts. Positive specimens were selected for molecular characterization. Presence of Cryptosporidium oocysts were significantly higher in specimens from goat kids (62.7%) than from lambs (31.6%). PCR products of the SSU rRNA locus were obtained for 108 isolates, and three Cryptosporidium species were identified. Cryptosporidium parvum was the most common species identified from both lambs (74.4%) and goat kids (93.8%). The remaining PCR products from lambs (25.6%) and goat kids (7.7%) were identified as Cryptosporidium Ubiquitum and Cryptosporidium xiaoi, respectively. Five C. parvum subtypes were identified; IIaA13G1R1, IIaA14G2R1, IIaA15G2R1 and IIaA16G3R1 were found in both host species, and IIdA17G1 was only detected in goat kids. Subtype IIaA15G2R1 was the most common and widely distributed. The present study provides the first description of subtypes IIaA13G1R1 in both small ruminant species, IIaA14G2R1 in sheep and IIaA16G3R1 in goats. Our results also reveal that diarrhoeic pre-weaned lambs and goat kids must be considered important reservoirs of Cryptosporidium species with zoonotic potential, such as C. parvum and C. ubiquitum.

A perspective on Cryptosporidium and Giardia, with an emphasis on bovines and recent epidemiological findings

Cryptosporidium and Giardia are two common aetiological agents of infectious enteritis in humans and animals worldwide. These parasitic protists are usually transmitted by the faecal-oral route, following the ingestion of infective stages (oocysts or cysts). An essential component of the control of these parasitic infections, from a public health perspective, is an understanding of the sources and routes of transmission in different geographical regions. Bovines are considered potential sources of infection for humans, because species and genotypes of Cryptosporidium and Giardia infecting humans have also been isolated from cattle in molecular parasitological studies. However, species and genotypes of Cryptosporidium and Giardia of bovids, and the extent of zoonotic transmission in different geographical regions in the world, are still relatively poorly understood. The purpose of this article is to (1) provide a brief background on Cryptosporidium and Giardia, (2) review some key aspects of the molecular epidemiology of cryptosporidiosis and giardiasis in animals, with an emphasis on bovines, (3) summarize research of Cryptosporidium and Giardia from cattle and water buffaloes in parts of Australasia and Sri Lanka, considering public health aspects and (4) provide a perspective on future avenues of study. Recent studies reinforce that bovines harbour Cryptosporidium and Giardia that likely pose a human health risk and highlight the need for future investigations of the biology, population genetics and transmission dynamics of Cryptosporidium and Giardia in cattle, water buffaloes and other ruminants in different geographical regions, the fate and transport of infective stages following their release into the environment, as well as for improved strategies for the control and prevention of cryptosporidiosis and giardiasis, guided by molecular epidemiological studies.

Cryptosporidium suis infection in post-weaned and adult pigs in Shaanxi province, northwestern China

Cryptosporidium spp., ubiquitous enteric parasitic protozoa of vertebrates, recently emerged as an important cause of economic loss and zoonosis. The present study aimed to determine the distribution and species of Cryptosporidium in post-weaned and adult pigs in Shaanxi province, northwestern China. A total of 1,337 fresh fecal samples of post-weaned and adult pigs were collected by sterile disposable gloves from 8 areas of Shaanxi province. The samples were examined by Sheather's sugar flotation technique and microscopy at × 400 magnification for Cryptosporidium infection, and the species in positive samples was further identified by PCR amplification of the small subunit (SSU) rRNA gene. A total of 44 fecal samples were successfully amplified by the nested PCR of the partial SSU rRNA, with overall prevalence of 3.3%. The average prevalence of Cryptosporidium infection in each pig farms ranged from 0 to 14.4%. Species identification by sequencing of SSU rRNA gene revealed that 42 (3.1%) samples were Cryptosporidium suis and 2 (0.15%) were Cryptosporidium scrofarum. C. suis had the highest prevalence (7.5%) in growers and the lowest in breeding pigs (0.97%). C. suis was the predominant species in pre-weaned and adult pigs, while C. scrofarum infected pigs older than 3 months only. A season-related difference of C. suis was observed in this study, with the highest prevalence in autumn (5.5%) and the lowest (1.7%) in winter. The present study provided basic information for control of Cryptosporidium infection in pigs and assessment of zoonotic transmission of pigs in Shaanxi province, China.

Molecular characterization of Cryptosporidium spp. in pre-weaned calves in Shaanxi Province, north-western China

Cryptosporidium, a worldwide protozoan parasite, is one of the most common causes of diarrhoea in humans and animals. The aim of the present study was to determine Cryptosporidium species/genotypes in pre-weaned calves in Shaanxi Province using PCR and sequencing based on the small subunit rRNA gene. A total of 258 faecal samples were collected from pre-weaned calves in 19 different farms from six areas in Shaanxi Province, north-western China. Cryptosporidium infection was detected in 14 of 19 farms (73.7 %), with a total prevalence of 20.2 % (52/258). Both dairy and Qinchuan (beef) cattle were found with Cryptosporidium infection. Three Cryptosporidium species, namely Cryptosporidium bovis (n = 26), Cryptosporidium andersoni (n = 14) and Cryptosporidium ryanae (n = 12), were detected in pre-weaned calves in Shaanxi Province, with C. bovis (in 12 farms) identified as the most common species on cattle farms. Two additional and previously unknown C. ryanae genotypes, CRTypes III and IV, were observed in the present study. However, the zoonotic species, Cryptosporidium parvum, was not detected in this study, which suggested a low zoonotic potential in Cryptosporidium-infected pre-weaned calves in this province.

First genetic analysis of Cryptosporidium from humans from Tasmania, and identification of a new genotype from a traveller to Bali

Little is known about the molecular composition of Cryptosporidium species from humans living in the insular state of Tasmania, Australia. In the present study, we genetically characterized 82 samples of Cryptosporidium from humans following conventional coproscopic testing in a routine, diagnostic laboratory. Using a PCR-coupled single-strand conformation polymorphism (SSCP) technique, targeting portions of the small subunit rRNA (SSU), and 60 kDa glycoprotein (gp60) loci, we identified two species of Cryptosporidium, including C. hominis (subgenotypes IbA10G2, IdA16, IeA12G3T3, and IfA19G1) and C. parvum (IIaA16G1R1 and IIaA18G3), and a new operational taxonomic unit (OTU) that genetically closely resembled C. wrairi. This OTU was further characterized using markers in the actin, Cryptosporidium oocyst wall protein (COWP), and 70 kDa heat shock protein (hsp70) genes. This study provides the first characterization of species and genotypes of Cryptosporidium from Tasmania, and presents clear genetic evidence, using five independent genetic loci, for a new genotype or species of Cryptosporidium in a Tasmanian person with a recent history of travelling to Bali, Indonesia. It would be interesting to undertake detailed molecular-based studies of Cryptosporidium in Indonesia and neighbouring countries, in conjunction with morphological and experimental investigations of new genotypes.

Cryptosporidiosis in Iranian Farm Workers and Their Household Members: A Hypothesis about Possible Zoonotic Transmission

Objectives. The prevalence of Cryptosporidium and the risk factors of zoonotic transmission in Najafabad, Isfahan, Iran dairy farms were examined. Methods. One fecal sample was collected from all calves less than 6 months old in eight dairy farms around Najafabad (Isfahan province, Central Iran) as well as individuals working in these farms and their household members. A two-step nested PCR protocol was used to amplify the 18S rRNA gene (830 bp). Results. Cryptosporidium was identified in the stool of 36 (prevalence 8.5%) of 96 farm workers and 326 household members. Furthermore, 31 (14.2%) of 218 calf samples were positive. Cryptosporidium parvum was identified in 15 (72%) of the positive farm workers and 10 (65%) of the positive household members. Of the positive calves, 20 (64.5%) were infected with C. parvum, indicating possible zoonotic transmission in these farms. Contact with calves (P < 0.0001) was the most significant risk factor of C. parvum infection. A considerable negative association was observed between C. parvum infection and cleaning of shoes/boots after daily work (P = 0.004), hand washing (P = 0.013), and use of piped water (P < 0.006). In the multivariate analysis with logistic regression, only contact with calves was significant. Conclusion. Zoonotic transmission of C. parvum due to contact with calves is predominant among farm workers and their household members of this region and appropriate health measures must be applied to control the infection and decrease of zoonotic transmission of this parasite.

Molecular characterization of Cryptosporidium spp. in children from Mexico

Cryptosporidiosis is a parasitic disease caused by Cryptosporidium spp. In immunocompetent individuals, it usually causes an acute and self-limited diarrhea; in infants, infection with Cryptosporidium spp. can cause malnutrition and growth retardation, and declined cognitive ability. In this study, we described for the first time the distribution of C. parvum and C. hominis subtypes in 12 children in Mexico by sequence characterization of the 60-kDa glycoprotein (GP60) gene of Cryptosporidium. Altogether, 7 subtypes belonging to 4 subtype families of C. hominis (Ia, Ib, Id and Ie) and 1 subtype family of C. parvum (IIa) were detected, including IaA14R3, IaA15R3, IbA10G2, IdA17, IeA11G3T3, IIaA15G2R1 and IIaA16G1R1. The frequency of the subtype families and subtypes in the samples analyzed in this study differed from what was observed in other countries.

Genetic characterization of selected parasites from people with histories of gastrointestinal disorders using a mutation scanning-coupled approach

A SSCP analysis and targeted sequencing approach was used for the genetic characterization of some major pathogens from a cohort of 227 people with histories of gastrointestinal disorders. Genomic DNAs from fecal samples were subjected to PCR-amplification of regions in the glycoprotein (gp60) or triose phosphate isomerase (tpi) gene, or the second internal transcribed spacer of nuclear ribosomal DNA (ITS-2). Cryptosporidium, Giardia, and strongylid nematodes were detected in 94, 132 and 12 samples. Cryptosporidium hominis subgenotypes IbA10G2, IdA15G1, IgA17, IgA18, and IfA13G1 were identified in 74.6, 16.9, 5.6, 1.4, and 1.4% of 71 samples, respectively. For Cryptosporidium parvum, subgenotypes IIaA17G2R1 (47.6%) and IIaA18G3R1 (23.8%) were identified in 23 samples. Giardia duodenalis assemblage B (78%) was more common than assemblage A (22%). In addition, DNA of the nematodes Ancylostoma ceylanicum (n = 2), Ancylostoma duodenale (4), Necator americanus (5), and Haemonchus contortus (1) was specifically detected. This is the first report of A. ceylanicum in two persons in Australia and, we provide molecular evidence of H. contortus in a child. This SSCP-based approach should provide a useful diagnostic and analytical tool for a wide range of pathogens.

Genetic characterisation of Cryptosporidium and Giardia from dairy calves: discovery of species/genotypes consistent with those found in humans

Cryptosporidium and Giardia are important genera of parasitic protists that can cause significant diarrhoeal diseases in humans and other animals. Depending on the species/genotype of parasite, human infection may be acquired via anthroponotic or zoonotic transmission routes. Here, we undertook a molecular epidemiological investigation of these two genera of parasites in pre- and post-weaned calves from eight locations in Canterbury, New Zealand, by PCR-coupled sequencing and phylogenetic analysis of sequence data for regions in the 60 kDa glycoprotein (pgp60) gene of Cryptosporidium and/or the triose-phosphate isomerase (ptpi) gene of Giardia. The pgp60 and ptpi regions were specifically amplified from 15 (8.3%) and 11 (6.1%) of the 180 individual faecal samples, respectively. The sequences derived from all of the amplicons were aligned with homologous reference sequences and subjected to phylogenetic analysis by Bayesian inference. For Cryptosporidium, three samples contained Cryptosporidium parvum genotype IIa, subgenotypes IIaA15G3R1, IIaA19G3R1 and IIaA23G4. Twelve samples contained Cryptosporidium hominis genotype Ib, subgenotype IbA10G2R2. While subgenotypes IIaA15G3R1 and IIaA23G4 are new records, IIaA19G3R1 and IbA10G2R2 are commonly found in humans in various countries. For Giardia, two samples contained Giardia duodenalis assemblage A, also common in humans. In contrast, nine samples contained G. duodenalis assemblage E, which is the first report of this assemblage in cattle in New Zealand. Therefore, the present results indicate that dairy calves on the South Island of New Zealand harbour 'zoonotic' genotypes of Cryptosporidium and Giardia, which is likely to have significant public health implications.

Cryptosporidium species in Australian wildlife and domestic animals

Cryptosporidium is an important enteric parasite that is transmitted via the fecal-oral route, water and food. Humans, wildlife and domestic livestock all potentially contribute Cryptosporidium to surface waters. Most species of Cryptosporidium are morphologically indistinguishable and can only be identified using molecular tools. Over 24 species have been identified and of these, 7 Cryptosporidium species/genotypes are responsible for most human cryptosporidiosis cases. In Australia, relatively few genotyping studies have been conducted. Six Cryptosporidium species (C. hominis, C. parvum, C. meleagridis, C. fayeri, C. andersoni and C. bovis) have been identified in humans in Australia. However, little is known about the contribution of animal hosts to human pathogenic strains of Cryptosporidium in drinking water catchments. In this review, we focus on the available genotyping data for native, feral and domestic animals inhabiting drinking water catchments in Australia to provide an improved understanding of the public health implications and to identify key research gaps.

Molecular epidemiology and clinical manifestations of human cryptosporidiosis in Sweden

This study describes the epidemiology and symptoms in 271 cryptosporidiosis patients in Stockholm County, Sweden. Species/genotypes were determined by polymerase chain reaction–restriction fragment-length polymorphism (PCR–RFLP) of theCryptosporidiumoocyst wall protein (COWP) and 18S rRNA genes. Species wereC. parvum(n=111),C. hominis(n=65),C. meleagridis(n=11),C. felis(n=2),Cryptosporidiumchipmunk genotype 1 (n=2), and a recently described species,C. viatorum(n=2). Analysis of the Gp60 gene revealed fiveC. hominisallele families (Ia, Ib, Id, Ie, If), and fourC. parvumallele families (IIa, IIc, IId, IIe). MostC. parvumcases (51%) were infected in Sweden, as opposed toC. hominiscases (26%). Clinical manifestations differed slightly by species. Diarrhoea lasted longer inC. parvumcases compared toC. hominisandC. meleagridiscases. At follow-up 25–36 months after disease onset, 15% of the patients still reported intermittent diarrhoea. In four outbreaks and 13 family clusters, a single subtype was identified, indicating a common infection source, which emphasizes the value of genotyping for epidemiological investigations.

Prevalence of Cryptosporidium species in recreational versus non-recreational water sources

Cryptosporidiosis, caused by the protozoan parasite Cryptosporidium, represents the major public health concern of water utilities in developed nations due to its small size, resistance to disinfection and ability to be shed in large numbers in faeces. In Australia, recreational access is not allowed on direct supply sources, however, in Western Australia, limited recreational access to drinking water catchments has been allowed, although only in the outer catchment. Recreational activities within 2 km of the drinking water body is prohibited. The present study compared the amount, prevalence and species of Cryptosporidium in recreational versus non-recreational water catchments in the south west of Western Australia (WA). Recreational water catchments, which allowed swimming and camping had a higher prevalence of Cryptosporidium and the majority of samples were the human-associated C. hominis. Non-recreational catchments had a lower prevalence and all the samples genotyped were C. parvum. Risk analysis identified increasing population as strongly correlated with an increase in the prevalence of Cryptosporidium in recreational catchments. This suggests that recreational access to drinking water catchments is a serious public health risk and government policy limiting activities to the outer catchment should be supported.

Advances in diagnosis of protozoan diseases

Microscopy still remains the gold standard procedure for the diagnosis of many protozoan infections in animals, but the specific identification requires skilled and experienced personnel. Immunoassays, detecting antibodies or specific protozoan antigens, have been developed but often lack sensitivity and specificity due to close relationship between many protozoa. Recent research has focussed almost exclusively on molecular based techniques for the identification and quantification of parasite DNA in samples. Opinion differ on most appropriate targets to use and there are very few diagnostic kits available making comparison between laboratories difficult. Future research needs to focus on robust, cheap field diagnostic assays.

Cryptic parasite revealed improved prospects for treatment and control of human cryptosporidiosis through advanced technologies

Cryptosporidium is an important genus of parasitic protozoa of humans and other vertebrates and is a major cause of intestinal disease globally. Unlike many common causes of infectious enteritis, there are no widely available, effective vaccine or drug-based intervention strategies for Cryptosporidium, and control is focused mainly on prevention. This approach is particularly deficient for infections of severely immunocompromised and/or suppressed, the elderly or malnourished people. However, cryptosporidiosis also presents a significant burden on immunocompetent individuals, and can, for example have lasting effects on the physical and mental development of children infected at an early age. In the last few decades, our understanding of Cryptosporidium has expanded significantly in numerous areas, including the parasite life-cycle, the processes of excystation, cellular invasion and reproduction, and the interplay between parasite and host. Nonetheless, despite extensive research, many aspects of the biology of Cryptosporidium remain unknown, and treatment and control are challenging. Here, we review the current state of knowledge of Cryptosporidium, with a focus on major advances arising from the recently completed genome sequences of the two species of greatest relevance in humans, namely Cryptosporidium hominis and Cryptosporidium parvum. In addition, we discuss the potential of next-generation sequencing technologies, new advances in in silico analyses and progress in in vitro culturing systems to bridge these gaps and to lead toward effective treatment and control of cryptosporidiosis.

High diversity of Cryptosporidium subgenotypes identified in Malaysian HIV/AIDS individuals targeting gp60 gene

Background

Currently, there is a lack of vital information in the genetic makeup of Cryptosporidium especially in developing countries. The present study aimed at determining the genotypes and subgenotypes of Cryptosporidium in hospitalized Malaysian human immunodeficiency virus (HIV) positive patients.

Methodology/Principal Findings

In this study, 346 faecal samples collected from Malaysian HIV positive patients were genetically analysed via PCR targeting the 60 kDa glycoprotein (gp60) gene. Eighteen (5.2% of 346) isolates were determined as Cryptosporidium positive with 72.2% (of 18) identified as Cryptosporidium parvum whilst 27.7% as Cryptosporidium hominis. Further gp60 analysis revealed C. parvum belonging to subgenotypes IIaA13G1R1 (2 isolates), IIaA13G2R1 (2 isolates), IIaA14G2R1 (3 isolates), IIaA15G2R1 (5 isolates) and IIdA15G1R1 (1 isolate). C. hominis was represented by subgenotypes IaA14R1 (2 isolates), IaA18R1 (1 isolate) and IbA10G2R2 (2 isolates).

Conclusions/Significance

These findings highlighted the presence of high diversity of Cryptosporidium subgenotypes among Malaysian HIV infected individuals. The predominance of the C. parvum subgenotypes signified the possibility of zoonotic as well as anthroponotic transmissions of cryptosporidiosis in HIV infected individuals.

Evidence of Cryptosporidium transmission between cattle and humans in northern New South Wales

Cryptosporidium is an enteric parasite of public health significance that causes diarrhoeal illness through faecal oral contamination and via water. Zoonotic transmission is difficult to determine as most species of Cryptosporidium are morphologically identical and can only be differentiated by molecular means. Transmission dynamics of Cryptosporidium in rural populations were investigated through the collection of 196 faecal samples from diarrheic (scouring) calves on 20 farms and 63 faecal samples from humans on 14 of these farms. The overall prevalence of Cryptosporidium in cattle and humans by PCR and sequence analysis of the 18S rRNA was 73.5% (144/196) and 23.8% (15/63), respectively. Three species were identified in cattle; Cryptosporidium parvum, Cryptosporidium bovis and Cryptosporidium ryanae, and from humans, C. parvum and C. bovis. This is only the second report of C. bovis in humans. Subtype analysis at the gp60 locus identified C. parvum subtype IIaA18G3R1 as the most common subtype in calves. Of the seven human C. parvum isolates successfully subtyped, five were IIaA18G3R1, one was IIdA18G2 and one isolate had a mix of IIaA18G3R1 and IIdA19G2. These findings suggest that zoonotic transmission may have occurred but more studies involving extensive sampling of both calves and farm workers are needed for a better understanding of the sources of Cryptosporidium infections in humans from rural areas of Australia.

Molecular epidemiology and spatial distribution of a waterborne cryptosporidiosis outbreak in Australia

Cryptosporidiosis is one of the most common waterborne diseases reported worldwide. Outbreaks of this gastrointestinal disease, which is caused by the Cryptosporidium parasite, are often attributed to public swimming pools and municipal water supplies. Between the months of January and April in 2009, New South Wales, Australia, experienced the largest waterborne cryptosporidiosis outbreak reported in Australia to date. Through the course of the contamination event, 1,141 individuals became infected with Cryptosporidium. Health authorities in New South Wales indicated that public swimming pool use was a contributing factor in the outbreak. To identify the Cryptosporidium species responsible for the outbreak, fecal samples from infected patients were collected from hospitals and pathology companies throughout New South Wales for genetic analyses. Genetic characterization of Cryptosporidium oocysts from the fecal samples identified the anthroponotic Cryptosporidium hominis IbA10G2 subtype as the causative parasite. Equal proportions of infections were found in males and females, and an increased susceptibility was observed in the 0- to 4-year age group. Spatiotemporal analysis indicated that the outbreak was primarily confined to the densely populated coastal cities of Sydney and Newcastle.

Molecular epidemiology, spatiotemporal analysis, and ecology of sporadic human cryptosporidiosis in Australia

Parasites from the Cryptosporidium genus are the most common cause of waterborne disease around the world. Successful management and prevention of this emerging disease requires knowledge of the diversity of species causing human disease and their zoonotic sources. This study employed a spatiotemporal approach to investigate sporadic human cryptosporidiosis in New South Wales, Australia, between January 2008 and December 2010. Analysis of 261 human fecal samples showed that sporadic human cryptosporidiosis is caused by four species; C. hominis, C. parvum, C. andersoni, and C. fayeri. Sequence analysis of the gp60 gene identified 5 subtype families and 31 subtypes. Cryptosporidium hominis IbA10G2 and C. parvum IIaA18G3R1 were the most frequent causes of human cryptosporidiosis in New South Wales, with 59% and 16% of infections, respectively, attributed to them. The results showed that infections were most prevalent in 0- to 4-year-olds. No gender bias or regional segregation was observed between the distribution of C. hominis and C. parvum infections. To determine the role of cattle in sporadic human infections in New South Wales, 205 cattle fecal samples were analyzed. Four Cryptosporidium species were identified, C. hominis, C. parvum, C. bovis, and C. ryanae. C. parvum subtype IIaA18G3R1 was the most common cause of cryptosporidiosis in cattle, with 47% of infections attributed to it. C. hominis subtype IbA10G2 was also identified in cattle isolates.

Cases of cryptosporidiosis co-infections in AIDS patients: a correlation between clinical presentation and GP60 subgenotype lineages from aged formalin-fixed stool samples

Nine cases of cryptosporidiosis co-infections in AIDS patients were clinically categorised into severe (patients 1, 3, 8 and 9), moderate (patients 4 and 5) and mild (patients 2, 6 and 7). Formalin-fixed faecal specimens from these patients were treated to obtain high quality DNA competent for amplification and sequencing of the 60-kDa glycoprotein (GP60) gene. Sequence analysis revealed that one patient was infected with Cryptosporidium hominis whereas the remaining eight patients were infected with C. parvum. Interestingly, the patients showing severe cryptosporidiosis harboured two subtypes within the C. parvum allelic family IIc (IIcA5G3 and IIcA5G3R2), whereas patients with moderate or mild infections showed various subtypes of the C. parvum allelic family IIa (IIaA14G2R1, IIaA15G2R1, IIaA17G3R1 and IIaA18G3R1). DNA extraction and genotyping of Cryptosporidium spp. is a challenging task on formalin-fixed stool samples, whose diagnostic outcome is age-dependent. The method herein reported represents a step forward routine diagnosis and improves epidemiology of HIV-related clinical cases. Due to the need to elucidate genetic richness of Cryptosporidium human isolates, this approach represents a useful tool to correlate individual differences in symptoms to subgenotyping lineages.

First genetic classification of Cryptosporidium and Giardia from HIV/AIDS patients in Malaysia

Given the HIV epidemic in Malaysia, genetic information on opportunistic pathogens, such as Cryptosporidium and Giardia, in HIV/AIDS patients is pivotal to enhance our understanding of epidemiology, patient care, management and disease surveillance. In the present study, 122 faecal samples from HIV/AIDS patients were examined for the presence of Cryptosporidium oocysts and Giardia cysts using a conventional coproscopic approach. Such oocysts and cysts were detected in 22.1% and 5.7% of the 122 faecal samples, respectively. Genomic DNAs from selected samples were tested in a nested-PCR, targeting regions of the small subunit (SSU) of nuclear ribosomal RNA and the 60kDa glycoprotein (gp60) genes (for Cryptosporidium), and the triose-phosphate isomerase (tpi) gene (for Giardia), followed by direct sequencing. The sequencing of amplicons derived from SSU revealed that Cryptosporidium parvum was the most frequently detected species (64% of 25 samples tested), followed by C. hominis (24%), C. meleagridis (8%) and C. felis (4%). Sequencing of a region of gp60 identified C. parvum subgenotype IIdA15G2R1 and C. hominis subgenotypes IaA14R1, IbA10G2R2, IdA15R2, IeA11G2T3R1 and IfA11G1R2. Sequencing of amplicons derived from tpi revealed G. duodenalis assemblage A, which is of zoonotic importance. This is the first report of C. hominis, C. meleagridis and C. felis from Malaysian HIV/AIDS patients. Future work should focus on an extensive analysis of Cryptosporidium and Giardia in such patients as well as in domestic and wild animals, in order to improve the understanding of transmission patterns and dynamics in Malaysia. It would also be particularly interesting to establish the relationship among clinical manifestation, CD4 cell counts and genotypes/subgenotypes of Cryptosporidium and Giardia in HIV/AIDS patients. Such insights would assist in a better management of clinical disease in immuno-deficient patients as well as improved preventive and control strategies.

Longitudinal and spatial distribution of GP60 subtypes in human cryptosporidiosis cases in Ireland

Within Europe, Ireland has one of the highest reported infection rates with the diarrhoeal protozoan pathogen Cryptosporidium. In this study 249 Cryptosporidium parvum isolates collected from Irish patients between 2000 and 2009 were subtyped by sequence analysis of the GP60 locus. A subsample of 127 isolates was also typed at the MS1 and ML1 loci. GP60 subtype IIaA18G3R1 was the predominant subtype in every year and every season throughout the country. Over the 10-year period there was no evidence that host immunity to the predominant subtype caused a shift in its prevalence. Length frequency distributions of the GP60 TCA/TCG repeats compiled from published data, showed distinct patterns for countries with predominantly zoonotic or anthroponotic transmission cycles, respectively. Although considered to be mostly affected by zoonotic cryptosporidiosis, the GP60 fragment length of Irish C. parvum isolates mirrored that of countries with predominantly human-to-human transmission, indicating more complex routes of infection between livestock and humans. Due to their homogeneity, ML1 and MS1 were not considered useful loci for subtyping C. parvum strains in Ireland.

Molecular detection of Cryptosporidium cuniculus in rabbits in Australia

In the United Kingdom, rabbits have been reported to harbour genotypes of Cryptosporidium (now recognized as C. cuniculus) identical to those from human patients exhibiting symptoms of cryptosporidiosis. The high density of rabbits in many regions of Australia, including both rural and urban as well as natural water catchments areas, and the absence of any information on Cryptosporidium from lagomorphs in this country stimulated the present study. We undertook an epidemiological study that genetically characterized Cryptosporidium from rabbits from four locations in Victoria by PCR-coupled sequencing and phylogenetic analysis of sequence data for loci within the small subunit of nuclear ribosomal RNA (SSU; for specific identification) and the 60kDa glycoprotein gene (gp60; for genotypic/subgenotypic identification). Cryptosporidium was detected in 12 (6.8%) of 176 individual faecal samples. For SSU, all 12 sequences were identical to each other and to that of C. cuniculus. For pgp60, all corresponding sequences matched the known genotype Vb, and were classified as subgenotype VbA23R3 (n=11) and VbA26R4 (n=1), which are both new records. Present evidence indicates that genotype Vb is limited to rabbits; however, it would be premature to conclude that this genotype is not zoonotic. Future studies should focus on the zoonotic potential of C. cuniculus from rabbits and a wide range of yet unstudied animals. (Nucleotide sequences reported in this paper are available in the GenBank database under accession nos. HM852431-HM852433).

Global distribution, public health and clinical impact of the protozoan pathogen cryptosporidium

Cryptosporidium spp. are coccidians, oocysts-forming apicomplexan protozoa, which complete their life cycle both in humans and animals, through zoonotic and anthroponotic transmission, causing cryptosporidiosis. The global burden of this disease is still underascertained, due to a conundrum transmission modality, only partially unveiled, and on a plethora of detection systems still inadequate or only partially applied for worldwide surveillance. In children, cryptosporidiosis encumber is even less recorded and often misidentified due to physiological reasons such as early-age unpaired immunological response. Furthermore, malnutrition in underdeveloped countries or clinical underestimation of protozoan etiology in developed countries contribute to the underestimation of the worldwide burden. Principal key indicators of the parasite distribution were associated to environmental (e.g., geographic and temporal clusters, etc.) and host determinants of the infection (e.g., age, immunological status, travels, community behaviours). The distribution was geographically mapped to provide an updated picture of the global parasite ecosystems. The present paper aims to provide, by a critical analysis of existing literature, a link between observational epidemiological records and new insights on public health, and diagnostic and clinical impact of cryptosporidiosis.

Multilocus genetic analysis of Cryptosporidium parvum from Egypt

Cryptosporidium parvum is a ubiquitous zonootic parasite causing enteritis in man and animals. Cryptosporidium infection was confirmed microscopically in neonatal calves (less than 6 weeks of age) at Kafr El Sheikh Province, Egypt. Multilocus analysis using a wide array of genetic markers was carried out to assess genetic diversity of C. parvum isolates. PCR amplification and partial sequence analysis of 70 kDa heat shock protein, dihydrofolate reductase, alpha-tubulin, elongation factor 1 alpha as well as thrombospondin-related anonymous protein of Cryptosporidium-1, and thrombospondin-related anonymous protein of Cryptosporidium-2 gene markers were achieved. Data indicated that the analyzed isolates belong to C. parvum genotype II with obvious sequence heterogeneity compared with counterparts deposited in Genebank.

Longitudinal multi-locus molecular characterisation of sporadic Australian human clinical cases of cryptosporidiosis from 2005 to 2008

Cryptosporidium is a gastrointestinal parasite that is recognised as a significant cause of non-viral diarrhea in both developing and industrialised countries. In the present study, a longitudinal analysis of 248 faecal specimens from Australian humans with gastrointestinal symptoms from 2005 to 2008 was conducted. Sequence analysis of the 18S rRNA gene locus and the 60kDa glycoprotein (gp60) gene locus revealed that 195 (78.6%) of the cases were due to infection with Cryptosporidium hominis, 49 (19.8%) with Cryptosporidium parvum and four (1.6%) with Cryptosporidium meleagridis. A total of eight gp60 subtype families were identified; five C. hominis subtype families (Ib, Id, Ie, If and Ig), and two C. parvum subtype families (IIa and IId). The Id subtype family was the most common C. hominis subtype family identified in 45.7% of isolates, followed by the Ig subtype family (30.3%) and the Ib subtype family (20%). The most common C. parvum subtype was IIaA18G3R1, identified in 65.3% of isolates. The more rare zoonotic IId A15G1 subtype was identified in one isolate. Statistical analysis showed that the Id subtype was associated with abdominal pain (p<0.05) and that in sporadic cryptosporidiosis, children aged 5 and below were 1.91 times and 1.88 times more likely to be infected with subtype Id (RR 1.91; 95% CI, 1.7-2.89; p<0.05) and Ig (RR 1.88; 95% CI, 1.10-3.24; p<0.05) compared to children aged 5 and above. A subset of isolates were also analysed at the variable CP47 and MSC6-7 gene loci. Findings from this study suggest that anthroponotic transmission of Cryptosporidium plays a major role in the epidemiology of cryptosporidiosis in Western Australian humans.

Molecular characterisation of Cryptosporidium outbreaks in Western and South Australia

Molecular typing at the 18S rRNA and Gp60 loci was conducted on Cryptosporidium-positive stool samples from cases collected during 2007 Western Australian and South Australian outbreaks of cryptosporidiosis. Analysis of 48 Western Australian samples identified that all isolates were C. hominis and were from five different Gp60C. hominis subtype families. The IbA10G2 subtype was most common across all age groups (37/48). In South Australia, analysis of 24 outbreak samples, identified 21 C. hominis isolates, two C. parvum isolates and one sample with both C. hominis and C. parvum. All C. hominis isolates were identified as the IbA10G2 subtype.

Genetic richness and diversity in Cryptosporidium hominis and C. parvum reveals major knowledge gaps and a need for the application of "next generation" technologies--research review

Cryptosporidium species (apicomplexan protists) are a major cause of diarrhoeal disease (= cryptosporidiosis) in humans worldwide. The impact of cryptosporidiosis is also compounded by the spread of HIV/AIDS and a lack of cost-effective anti-cryptosporidial chemotherapeutics or vaccines. Mitigation of the impact of cryptosporidiosis in humans needs to focus on prevention and control strategies, built on a sound understanding of the epidemiology of Cryptosporidium species. Refined epidemiological studies rely on the use of molecular tools employing informative genetic markers. Currently, the 60-kDa glycoprotein gene (gp60) is the most suitable and widely used genetic marker for Cryptosporidium species infecting humans. Here, we undertake an analysis of all publicly-available gp60 sequence data and associated literature for C. hominis and C. parvum, and yield useful insights into the richness, diversity and distribution of genetic variants, and link these variants to human cryptosporidiosis. This global analysis reveals that, despite high genetic richness in Cryptosporidium isolates from humans, there is a surprisingly low diversity. It also highlights limited knowledge about the genetics of cryptosporidiosis in developing nations and in many animals that might act as infection sources. Clearly, there is a major need for more comprehensive studies of Cryptosporidium infecting humans and other animals in Africa and Asia. As molecular technologies improve and become affordable, future studies should utilize "next generation" sequencing and bioinformatic platforms to conduct comparative 'genome sequence surveys' to test the validity of current genetic classifications based on gp60 data. Complemented by in vitro and in vivo investigations, these biotechnological advances will also assist significantly in the search for new intervention strategies against human cryptosporidiosis.

Genetic characterization of Cryptosporidium parvum from calves by mutation scanning and targeted sequencing--zoonotic implications

This study explored the genetic make-up of Cryptosporidium in fecal samples from 268 individual calves on pasture-based dairy farms in three regions of Victoria, Australia. An integrated approach, using PCR-coupled single-strand conformation polymorphism, targeted sequencing and phylogenetic analysis, was employed to classify the genetic variants (i.e. genotypes and subgenotypes) of Cryptosporidium parvum present in 124 (46.3%) samples and to infer their zoonotic potential. Genotypic and subgenotypic classification was achieved using a portion of the 60 kDa glycoprotein gene (designated pgp60); specific identity was verified using a region within the small subunit of the nuclear ribosomal RNA (pSSU). Twelve sequence types representing ten distinct subgenotypes were defined within genotype IIa, namely IIaA16G3R1 (n=7), IIaA17G2R1 (1), IIaA18G2R1a (2), IIaA18G2R1b (1), IIaA18G4R1 (1), IIaA19G3R1a (80), IIaA19G3R1b (1), IIaA20G2R1 (9), IIaA20G3R1 (1), IIaA20G4R1 (9), IIaA21G3R1 (1) and IIaA23G3R1 (9), of which IIaA18G2R1b, IIaA18G4R1 and IIaA19G3R1b are new records. All of the subgenotypes, except IIaA16G3R1, IIaA18G4R1 and IIaA20G4R1, have been detected previously in humans and are thus considered to be of zoonotic relevance. (Nucleotide sequences reported in this paper are available in the GenBank database under accession numbers FJ825018-FJ825029).