High applicability of a novel method for gp60-based subtyping of Cryptosporidium meleagridis

Detection and characterization of Cryptosporidium species and genotypes in three chicken production systems in Brazil using different molecular diagnosis protocols

The objective of this study was to determine the occurrence of Cryptosporidium spp. in domestic chickens raised in different chicken production systems in Brazil using three nested PCR protocols. The purification and concentration of oocysts present in 190 fecal samples from chickens raised in extensive, semi-intensive and intensive production systems were accomplished by centrifugal flotation in Sheather's solution and were followed by the extraction of genomic DNA. The detection and molecular characterization of Cryptosporidium species and genotypes were performed using three nested polymerase chain reaction (nested PCR) protocols targeting the 18S rRNA gene followed by sequencing of the amplified fragments. Subgenotyping of C. meleagridis was performed using a nested PCR reaction targeting the gp60 gene. Sample identified as Cryptosporidium sp. genetically similar to Cryptosporidium xiaoi and Cryptosporidium bovis by 18S rRNA gene sequencing were further analyzed by nested PCR targeting the actin gene and subsequent sequencing of the amplified fragment. Positive amplification for Cryptosporidium spp. was observed in 12.6% (24/190) of the samples, including C. baileyi (9.8%; 18/190), C. meleagridis (0.5%, 1/190), C. parvum (2.1%; 4/190) and Cryptosporidium sp. (0.5%; 1/190). Subgenotyping of C. meleagridis revealed the presence of the zoonotic subtype IIIgA23G3R1. Sequencing of the 18S rRNA gene and the actin gene fragments revealed a Cryptosporidium genotype in an extensive poultry system genetically related to C. xiaoi and C. bovis. There was no significant difference in the frequency of positive results obtained by the three nested PCR protocols (p > 0.05); additionally, the agreement obtained by Kappa index ranged from substantial (0.70) to almost perfect (0.9).

Cryptosporidium viatorum from the native Australian swamp rat Rattus lutreolus - An emerging zoonotic pathogen?

Cryptosporidium viatorum is a globally distributed pathogenic species of Cryptosporidium that has only ever been recorded from humans, until now. For the first time, we molecularly characterised a novel subtype of C. viatorum (subtype XVbA2G1) from the endemic Australian swamp rat (Rattus lutreolus) using the small subunit of nuclear ribosomal RNA (SSU) gene and then subtyped it using the 60-kilodalton glycoprotein (gp60) gene. In total, faecal samples from 21 swamp rats (three were positive for C. viatorum), three broad toothed rats (Mastacomys fuscus) and two bush rats (Rattus fuscipes) were tested for Cryptosporidium. The long-term, isolated nature of the swamp rat population in Melbourne's drinking water catchment system (where public access is prohibited), the lack of C. viatorum from other mammals and birds living within the vicinity of this system and its genetic distinctiveness in both the SSU and gp60 gene sequences from other species of Cryptosporidium collectively suggest that C. viatorum might be endemic to native rats in Australia. The current state of knowledge of epidemiological surveys of Cryptosporidium of rats and the zoonotic potential are further discussed in light of the finding of C. viatorum. Long-term studies, with the capacity to repetitively sample a variety of hosts in multiple localities, in different seasons and years, will allow for greater insight into the epidemiological patterns and zoonotic potential of rare Cryptosporidium species such as C. viatorum.

Genetic diversity of Cryptosporidium isolates from human populations in an urban area of Northern Tunisia

Cryptosporidium is an enteric parasite infecting a wide range of hosts. It has emerged as an important cause of chronic life-threatening diarrhea in humans worldwide. Several subtypes of Cryptosporidium sp. have been described to be responsible for several large outbreaks related to water contamination in developed countries. However, there is a lack of information in the genetic diversity of Cryptosporidium among human population especially in developing countries. The present study aimed to update and report the genetic diversity of human Cryptosporidium spp. at the subtype level in an urban area of Tunisia using the 18S rRNA and gp60 gene. Genotyping of 42 Cryptosporidium positive isolates from different human populations at the 18S rRNA locus has identified three Cryptosporidium species: C. hominis (n = 20), C. parvum (n = 19), C. meleagridis (n = 2) and a co-infection C. hominis/C. meleagridis (n = 1). The sub-genotyping of these isolates at the 60-kda glycoprotein (gp60) locus was possible in 40 cases. It showed the presence of three subtype families (IIa, IIb and IIc) within C. parvum, a single subtype family within C. hominis and C. meleagridis isolates (Ia and IIIb respectively). Several subtypes were implicated in different human populations with the dominance of IaA26G1R1, IIaA15G2R1, IIdA16G1R1, IIdA22G2R1 and IIIbA26G1R1 variant respectively for C. hominis, C. parvum and C. meleagridis. The distribution of Cryptosporidium isolates in urban area of Northern Tunisia was dominated by the anthroponotic transmission via C. hominis species and the IIc subtype of C. parvum. However, zoonotic transmission is still possible in this region via zoonotic subtypes of C. parvum (IIa and IId) and C. meleagridis (IIIb). Subtype diversity was higher in this area.

Identification of pig-specific Cryptosporidium species in mixed infections using Illumina sequencing technology

Nowadays molecular methods are widely used in epidemiological studies of Cryptosporidium infections in humans and animals. However to gain better understanding of parasite species or genotypes, especially when mixed infections are noticed, highly sensitive tools with adequate resolution power need to be employed. In this article, we report an application of the next generation sequencing method (NGS) for detection and characterisation of Cryptosporidium species concurrently present in pig faeces. A mixture of Cryptosporidium DNA obtained from two faecal samples was amplified at the 18 SSU rRNA gene locus and the resulting amplicons were subsequently used for MiSeq sequencing. Although initial molecular analyses indicated the possible presence of another Cryptosporidium species other than Cryptosporidium scrofarum and Cryptosporidium suis, deep sequencing only confirmed the presence of pig-specific Cryptosporidium.

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

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

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.

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.

Cryptosporidium meleagridis and C. baileyi (Apicomplexa) in domestic and wild birds in Algeria

A total of 345 faecal samples were collected from domestic, captive and wild birds in rural areas, urban areas and a Zoo in Algeria. Samples were screened for the presence of parasites belonging to the genus Cryptosporidium Tyzzer, 1910 by microscopy and PCR analysis of the small-subunit rRNA (SSU), actin and 60-kDa glycoprotein (gp60) genes. Cryptosporidium spp. were detected in 31 samples. Sequence analysis of SSU and actin genes revealed the presence of C. baileyi Current, Upton et Haynes, 1986 in domestic chicken broilers (n = 12), captive ostriches (n = 4) and a wild mallard (n = 1), and C. meleagridis Slavin, 1955 in a graylag goose (n = 1), chickens (n = 11) and turkeys (n = 2). Twenty-three chicken and two turkey broilers from five farms were positive for cryptosporidia, with an overall prevalence of 2% and 6%, respectively. Both C. meleagridis and C. baileyi were detected in farmed chicken broilers, with a prevalence ranging from 9% to 69%. Farmed turkeys broilers were positive only for C. meleagridis, with a 13% prevalence at the animal level. Subtyping of C. meleagridis isolates at the gp60 locus showed the presence of subtype IIIgA22G3R1 in graylag goose and chicken broilers and IIIgA23G2R1 in chicken and turkey broilers. Infection with cryptosporidia was not associated with any clinical diseases. The results of the present study, which provides the first data on the prevalence of Cryptosporidium spp. in wild birds in Africa, demonstrate the presence of human pathogenic C. meleagridis in both domestic and wild birds in Algeria.

First survey of Cryptosporidium, Giardia and Enterocytozoon in diarrhoeic children from Wuhan, China

Intestinal protozoan pathogens cause significant diarrhoeal diseases in children. However, to date, there has been limited genetic study of the intestinal pathogens Cryptosporidium, Giardia and Enterocytozoon in humans in China, with the exception of research in a small number of cities/provinces. In the present study, PCR-based tools were used to detect and characterise these protistan parasites from 500 children with a history of diarrhoea in Wuhan and environs, Hubei province, China. Genomic DNAs from faecal samples were screened for the particular protists by PCR utilising regions in the small subunit (SSU) of the nuclear ribosomal RNA, the 60kDa glycoprotein (gp60), the internal transcribed spacer of nuclear ribosomal DNA (ITS) and/or the triose phosphate isomerase (tpi) genes as markers. Cryptosporidium meleagridis subtype IIIb (10/500, 2.0%), Giardia duodenalis assemblage A (7/500, 1.4%) and Enterocytozoon bieneusi genotype D (1/500, 0.2%) were identified in small percentages of the 500 samples. No significant gender- or age-associated differences in the prevalence of Cryptosporidium and Giardia infections were found. Future studies might focus on the occurrence of these protists in children as well as animals, with an emphasis on Cryptosporidium meleagridis in pets and agriculturally important birds, in different parts of Hubei province.

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.

Human infective potential of Cryptosporidium spp., Giardia duodenalis and Enterocytozoon bieneusi in urban wastewater treatment plant effluents

Cryptosporidiosis, giardiasis, and microsporidiosis are important waterborne diseases. In the standard for wastewater treatment plant (WWTP) effluents in China and other countries, the fecal coliform count is the only microbial indicator, raising concerns about the potential for pathogen transmission through WWTP effluent reuse. In this study, we collected 50 effluent samples (30 L/sample) from three municipal WWTPs in Shanghai, China, and analyzed for Cryptosporidium spp., Giardia duodenalis and Enterocytozoon bieneusi by microscopy and/or polymerase chain reaction (PCR). Moreover, propidium monoazide (PMA)-PCR was used to assess the viability of oocysts/cysts. The microscopy and PCR-positive rates for Cryptosporidium spp. were 62% and 40%, respectively. The occurrence rates of G. duodenalis were 96% by microscopy and 92-100% by PCR analysis of three genetic loci. Furthermore, E. bieneusi was detected in 70% (35/50) of samples by PCR. Altogether, 10 Cryptosporidium species or genotypes, two G. duodenalis genotypes, and 11 E. bieneusi genotypes were found, most of which were human-pathogenic. The chlorine dioxide disinfection employed in WWTP1 and WWTP3 failed to inactivate the residual pathogens; 93% of the samples from WWTP1 and 83% from WWTP3 did not meet the national standard on fecal coliform levels. Thus, urban WWTP effluents often contain residual waterborne human pathogens.

Public health significance of zoonotic Cryptosporidium species in wildlife: Critical insights into better drinking water management

Cryptosporidium is an enteric parasite that is transmitted via the faecal-oral route, water and food. Humans, wildlife and domestic livestock all potentially contribute Cryptosporidium to surface waters. Human encroachment into natural ecosystems has led to an increase in interactions between humans, domestic animals and wildlife populations. Increasing numbers of zoonotic diseases and spill over/back of zoonotic pathogens is a consequence of this anthropogenic disturbance. Drinking water catchments and water reservoir areas have been at the front line of this conflict as they can be easily contaminated by zoonotic waterborne pathogens. Therefore, the epidemiology of zoonotic species of Cryptosporidium in free-ranging and captive wildlife is of increasing importance. This review focuses on zoonotic Cryptosporidium species reported in global wildlife populations to date, and highlights their significance for public health and the water industry.

Possible zoonotic transmission of Cryptosporidium felis in a household

In humans, the risk of contracting cryptosporidiosis caused by Cryptosporidium felis is considered to be relatively low, and most of the confirmed cases have been observed in immunocompromised patients. Both anthroponotic and zoonotic transmission routes have been suggested. Here, we report a case of suspected zoonotic transmission of C. felis from a cat to a human. The cat developed diarrhea several months before such symptoms were displayed by its owner, a 37-year-old immunocompetent woman. The presence of identical C. felis SSU rRNA, HSP70, and COWP gene sequences was verified in both hosts. In conclusion, it is highly probable that the cat was the initial source of infection and not the opposite. Our results show that Cryptosporidium infection can be transmitted from pets to humans and that molecular analysis is needed to confirm the identity of the oocysts.

Cryptosporidium infections in birds - a review

Cryptosporidiosis is one of the main protozoan infections in birds. It manifests as either a respiratory or a digestive illness, and it affects a very large number of avian species across several continents. The aim of this review is to report on the main results of studies on cryptosporidiosis among birds and the importance of these results to veterinary medicine and public health.

Development and Application of a gp60-Based Typing Assay for Cryptosporidium viatorum

The apicomplexan intestinal parasites of the genus Cryptosporidium take a major toll on human and animal health and are frequent causes of waterborne outbreaks. Several species and genotypes can infect humans, including Cryptosporidium viatorum, which, to date, has only been found in humans. Molecular characterization of Cryptosporidium spp., critical to epidemiological analyses, is commonly based on gp60 gene analysis, which appears to require bespoke species- or group-specific PCR primers due to extensive genetic diversity across the genus. In this study, we amplified, sequenced, and characterized the gp60 gene of C. viatorum for the first time. Moreover, we developed and validated a gp60 typing assay for this species and applied it to 27 isolates originating from Asia, Africa, and Central America. A single subtype family, XVa, was identified containing multiple alleles.

First finding of spontaneous infections with Cryptosporidium baileyi and C. meleagridis in the red-legged partridge Alectoris rufa from an aviary in the Czech Republic

This paper represents the first report of spontaneous infection with Cryptosporidium baileyi and Cryptosporidium meleagridis in the red-legged partridge (Alectoris rufa), as well as the percentage of positive samples and age-associated dynamics of cryptosporidial infections in an aviary in the Czech Republic. The entire infection process was monitored over two semesters (July-December 2012 and 2013) until release of birds for hunting purposes. Coprological examination of 663 pooled fecal samples and 89 post-mortem examinations of red-legged partridges were carried out. Our results indicated that infections with C. baileyi only occurred in 5-7 week-old birds during 2013 (percentage of positivity, 1%) and those with C. meleagridis in 18-22 week (17%) and 17-21 week-old birds (24%) during 2012 and 2013, respectively. Molecular characterization of isolates of C. baileyi and C. meleagridis heat shock protein 70 and actin genes were analyzed in order to support our coprological results. DNA sequence analysis of the 60kDa glycoprotein gene was used to subtype C. meleagridis. Our findings extend the host range for C. baileyi.

Subtyping novel zoonotic pathogen Cryptosporidium chipmunk genotype I

Cryptosporidium chipmunk genotype I is an emerging zoonotic pathogen in humans. The lack of subtyping tools makes it impossible to determine the role of zoonotic transmission in epidemiology. To identify potential subtyping markers, we sequenced the genome of a human chipmunk genotype I isolate. Altogether, 9,509,783 bp of assembled sequences in 853 contigs were obtained, with an N50 of 117,886 bp and >200-fold coverage. Based on the whole-genome sequence data, two genetic markers encoding the 60-kDa glycoprotein (gp60) and a mucin protein (ortholog of cgd1_470) were selected for the development of a subtyping tool. The tool was used for characterizing chipmunk genotype I in 25 human specimens from four U.S. states and Sweden, one specimen each from an eastern gray squirrel, a chipmunk, and a deer mouse, and 4 water samples from New York. At the gp60 locus, although different subtypes were seen among the animals, water, and humans, the 15 subtypes identified differed mostly in the numbers of trinucleotide repeats (TCA, TCG, or TCT) in the serine repeat region, with only two single nucleotide polymorphisms in the nonrepeat region. Some geographic differences were found in the subtype distribution of chipmunk genotype I from humans. In contrast, only two subtypes were found at the mucin locus, which differed from each other in the numbers of a 30-bp minisatellite repeat. Thus, Cryptosporidium chipmunk genotype I isolates from humans and wildlife are genetically similar, and zoonotic transmission might play a potential role in human infections.

Diversity of Cryptosporidium in brush-tailed rock-wallabies (Petrogale penicillata) managed within a species recovery programme

•

Cryptosporidium diversity was investigated in a BTRW as part of a recovery programme.

•

Faecal samples from captive bred, supplemented and wild wallabies were screened.

•

Cryptosporidium isolates were identified at three gene loci using PCR.

•

Diverse species of Cryptosporidium were identified across populations.

•

Both specific, C. fayeri, and broad host species, C. meleagridis, were identified.

Host–parasite relationships are likely to be impacted by conservation management practices, potentially increasing the susceptibility of wildlife to emerging disease. Cryptosporidium, a parasitic protozoan genus comprising host-adapted and host-specific species, was used as an indicator of parasite movement between populations of a threatened marsupial, the brush-tailed rock-wallaby (Petrogale penicillata). PCR screening of faecal samples (n = 324) from seven wallaby populations across New South Wales, identified Cryptosporidium in 7.1% of samples. The sampled populations were characterised as captive, supplemented and wild populations. No significant difference was found in Cryptosporidium detection between each of the three population categories. The positive samples, detected using 18S rRNA screening, were amplified using the actin and gp60 loci. Multi-locus sequence analysis revealed the presence of Cryptosporidium fayeri, a marsupial-specific species, and C. meleagridis, which has a broad host range, in samples from the three population categories. Cryptosporidium meleagridis has not been previously reported in marsupials and hence the pathogenicity of this species to brush-tailed rock-wallabies is unknown. Based on these findings, we recommend further study into Cryptosporidium in animals undergoing conservation management, as well as surveying wild animals in release areas, to further understand the diversity and epidemiology of this parasite in threatened wildlife.

Occurrence, source, and human infection potential of Cryptosporidium and Enterocytozoon bieneusi in drinking source water in Shanghai, China, during a pig carcass disposal incident

In March 2013, thousands of domestic pig carcasses were found floating in the Huangpu River, a drinking source water in Shanghai, China. To investigate the impact of the pig carcass incident on microbial water quality, 178 river water samples were collected from the upper Huangpu River from March 2013 to March 2014. Samples were concentrated by calcium carbonate flocculation and examined for host-adapted Cryptosporidium and Enterocytozoon bieneusi by ploymerase chain reaction (PCR). Positive PCR products were sequenced to determine Cryptosporidium species and E. bieneusi genotypes. A total of 67 (37.6%) and 56 (31.5%) samples were PCR-positive for Cryptosporidium and E. bieneusi, respectively. The occurrence rates of Cryptosporidium and E. bieneusi in March 2013 (83.3%; 41.7%) and May 2013 (73.5%; 44.1%) were significantly higher than rates in later sampling times. Among the 13 Cryptosporidium species/genotypes identified, C. andersoni and C. suis were the most common species, being found in 38 and 27 samples, respectively. Seventeen E. bieneusi genotypes were found, belonging to 11 established genotypes (EbpC, EbpA, D, CS-8, PtEb IX, Peru 8, Peru 11, PigEBITS4, EbpB, G, O) and six new ones (RWSH1 to RWSH6), most of which belonged to pig-adapted Groups 1d and 1e. EbpC was the most common genotype, being found in 37 samples. The distribution of Cryptosporidium species and E. bieneusi genotypes suggest that dead pigs contributed significantly to Cryptosporidium and E. bieneusi contamination in the Huangpu River. Although most Cryptosporidium species found in river water were not major human pathogens, the majority of E. bieneusi genotypes detected were endemic in China. Data from this study should be useful in the development of strategies in addressing future contamination events in drinking water supplies.