Subtypes of Cryptosporidium spp. in mice and other small mammals

Critters and contamination: Zoonotic protozoans in urban rodents and water quality

Rodents represent the single largest group within mammals and host a diverse array of zoonotic pathogens. Urbanisation impacts wild mammals, including rodents, leading to habitat loss but also providing new resources. Urban-adapted (synanthropic) rodents, such as the brown rat (R. norvegicus), black rat (R. rattus), and house mouse (Mus musculus), have long successfully adapted to living close to humans and are known carriers of zoonotic pathogens. Two important enteric, zoonotic protozoan parasites, carried by rodents, include Cryptosporidium and Giardia. Their environmental stages (oocysts/cysts), released in faeces, can contaminate surface and wastewaters, are resistant to common drinking water disinfectants and can cause water-borne related gastritis outbreaks. At least 48 species of Cryptosporidium have been described, with C. hominis and C. parvum responsible for the majority of human infections, while Giardia duodenalis assemblages A and B are the main human-infectious assemblages. Molecular characterisation is crucial to assess the public health risk linked to rodent-related water contamination due to morphological overlap between species. This review explores the global molecular diversity of these parasites in rodents, with a focus on evaluating the zoonotic risk from contamination of water and wasterwater with Cryptosporidium and Giardia oocysts/cysts from synanthropic rodents. Analysis indicates that while zoonotic Cryptosporidium and Giardia are prevalent in farmed and pet rodents, host-specific Cryptosporidium and Giardia species dominate in urban adapted rodents, and therefore the risks posed by these rodents in the transmission of zoonotic Cryptosporidium and Giardia are relatively low. Many knowledge gaps remain however, and therefore understanding the intricate dynamics of these parasites in rodent populations is essential for managing their impact on human health and water quality. This knowledge can inform strategies to reduce disease transmission and ensure safe drinking water in urban and peri‑urban areas.

Subtyping of Nonhuman Primate-Adapted Cryptosporidium hominis in Macaca Fascicularis and Macaca mulatta in Yunnan Province, Southwestern China

Background: Cryptosporidium spp. are a type of protozoan parasite responsible for causing diarrheal illness worldwide. They infect a broad range of vertebrate hosts, including both non-human primates (NHPs) and humans. In fact, zoonotic transmission of cryptosporidiosis from NHPs to humans is frequently facilitated by direct contact between the two groups. However, there is a need to enhance the information available on the subtyping of Cryptosporidium spp. in NHPs in the Yunnan province of China. Materials and Methods: Thus, the study investigated the molecular prevalence and species of Cryptosporidium spp. from 392 stool samples of Macaca fascicularis (n = 335) and Macaca mulatta (n = 57) by using nested PCR targeting the large subunit of nuclear ribosomal RNA (LSU) gene. Of the 392 samples, 42 (10.71%) were tested Cryptosporidium-positive. Results: All the samples were identified as Cryptosporidium hominis. Further, the statistical analysis revealed that age is a risk factor for the infection of C. hominis. The probability of detecting C. hominis was found to be higher (odds ratio = 6.23, 95% confidence interval 1.73-22.38) in NHPs aged between 2 and 3 years, as compared with those younger than 2 years. Sequence analysis of the 60 kDa glycoprotein (gp60) identified six (IbA9 n = 4, IiA17 n = 5, InA23 n = 1, InA24 n = 2, InA25 n = 3, and InA26 n = 18) C. hominis subtypes with "TCA" repeats. Among these subtypes, it has been previously reported that the Ib family subtypes are also capable of infecting humans. Conclusion: The findings of this study highlight the genetic diversity of C. hominis infection among M. fascicularis and M. mulatta in Yunnan province. Further, the results confirm that both these NHPs are susceptible to C. hominis infection, posing a potential threat to humans.

Detection and molecular characterization of Cryptosporidium spp. in pet hairless guinea pigs (Cavia Porcellus) from China

Cryptosporidium spp. are common protozoan parasites that can infect humans and animals worldwide. Recently, the hairless guinea pigs (also called Skinny pigs) were introduced into China as pets. However, Cryptosporidium species and their prevalence in these exotic animals were not studied. In this study, fecal samples were collected from a total of 324 hairless guinea pigs from a pet market and four breeding facilities in four provinces of China. The infection rate of Cryptosporidium was 6.8% (22/324). Three Cryptosporidium species were identified, including Cryptosporidium homai (n = 16), Cryptosporidium wrairi (n = 5), and Cryptosporidium hominis plus C. homai (n = 1). Sequence analysis of the small subunit (SSU) rRNA gene showed that the C. hominis isolate was a C. hominis variant, which mostly infects equine animals. However, the identification of C. hominis was not supported by the analysis of other genetic loci. The C. hominis isolate was characterized as C. homai at both 70-kDa heat shock protein (hsp70) and actin genes, indicating a mixed infection. At the 60-kDa glycoprotein (gp60) gene, subtyping of the C. hominis isolate was not successful. Five C. wrairi isolates were identified as subtype VIIaA13T1, which was previously reported in a guinea pig in the USA. The Cryptosporidium spp. identified in this study have no or low zoonotic potential.

Dominance of the zoonotic pathogen Cryptosporidium meleagridis in broiler chickens in Guangdong, China, reveals evidence of cross-transmission

Background

Cryptosporidium is one of the most prevalent parasites infecting both birds and mammals. To examine the prevalence of Cryptosporidium species and evaluate the public health significance of domestic chickens in Guangdong Province, southern China, we analyzed 1001 fecal samples from 43 intensive broiler chicken farms across six distinct geographical regions.

Methods

Individual DNA samples were subjected to nested PCR-based amplification and sequencing of the small subunit of the nuclear ribosomal RNA gene (SSU rRNA). Analysis of the 60 kDa glycoprotein gene (gp60) was performed to characterize the subtypes of C. meleagridis.

Results

The overall prevalence of Cryptosporidium was 13.2% (95% CI 11.1–15.3) (24 of 43 farms), with C. meleagridis (7.8%), C. baileyi (4.8%) and mixed infections (0.6%). Using the gp60 gene, three subtype families, IIIb, IIIe and IIIg, were identified, including six subtypes: one novel (IIIgA25G3R1a) and five previously reported (IIIbA23G1R1c, IIIbA24G1R1, IIIbA21G1R1a, IIIeA17G2R1 and IIIeA26G2R1). Within these subtypes, five known subtypes were genetically identical to those identified in humans.

Conclusions

This is the first report of C. meleagridis in chickens from Guangdong. The frequent occurrence of C. meleagridis in domestic chickens and the common C. meleagridis subtypes identified in both humans and chickens is of public health significance. Our study indicates that broiler chickens represent a potential zoonotic risk for the transmission of Cryptosporidium in this region.

Graphical Abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s13071-022-05267-x.

An Update on Zoonotic Cryptosporidium Species and Genotypes in Humans

The enteric parasite, Cryptosporidium is a major cause of diarrhoeal illness in humans and animals worldwide. No effective therapeutics or vaccines are available and therefore control is dependent on understanding transmission dynamics. The development of molecular detection and typing tools has resulted in the identification of a large number of cryptic species and genotypes and facilitated our understanding of their potential for zoonotic transmission. Of the 44 recognised Cryptosporidium species and >120 genotypes, 19 species, and four genotypes have been reported in humans with C. hominis, C. parvum, C. meleagridis, C. canis and C. felis being the most prevalent. The development of typing tools that are still lacking some zoonotic species and genotypes and more extensive molecular epidemiological studies in countries where the potential for transmission is highest are required to further our understanding of this important zoonotic pathogen. Similarly, whole-genome sequencing (WGS) and amplicon next-generation sequencing (NGS) are important for more accurately tracking transmission and understanding the mechanisms behind host specificity.

Taxonomy and molecular epidemiology of Cryptosporidium and Giardia - a 50 year perspective (1971-2021)

The protozoan parasites Cryptosporidium and Giardia are significant causes of diarrhoea worldwide and are responsible for numerous waterborne and foodborne outbreaks of diseases. Over the last 50 years, the development of improved detection and typing tools has facilitated the expanding range of named species. Currently at least 44 Cryptosporidium spp. and >120 genotypes, and nine Giardia spp., are recognised. Many of these Cryptosporidium genotypes will likely be described as species in the future. The phylogenetic placement of Cryptosporidium at the genus level is still unclear and further research is required to better understand its evolutionary origins. Zoonotic transmission has long been known to play an important role in the epidemiology of cryptosporidiosis and giardiasis, and the development and application of next generation sequencing tools is providing evidence for this. Comparative whole genome sequencing is also providing key information on the genetic mechanisms for host specificity and human infectivity, and will enable One Health management of these zoonotic parasites in the future.

CRYPTOSPORIDIUM SPP. IN PET DWARF WINTER WHITE RUSSIAN HAMSTERS (PHODOPUS SUNGORIS SUNGORIS) IN CHINA

Cryptosporidium spp. have been identified in a wide range of hosts, such as humans and domestic and wild animals, while less information about the prevalence of Cryptosporidium spp. in pet hamsters is documented. A total of 351 dwarf winter white Russian hamsters' fecal specimens were collected from 6 pet markets from the cities of Luzhou and Ziyang in Sichuan province in the southwestern part of China. The prevalence of Cryptosporidium spp. determined with nested-PCR amplification of the partial small-subunit (SSU) rRNA gene was 39.32% (138/351). The highest prevalence of Cryptosporidium spp. was in pet market 5 (79.49%, 62/78), followed by pet market 6 (38.64%, 17/44). The lowest prevalence of Cryptosporidium spp. was observed in pet market 3 (14.89%, 7/47). Statistically significant differences in the prevalence of Cryptosporidium spp. were observed among different pet markets (χ2 = 76.386, df = 5, P < 0.05), and a further post hoc test revealed that only pet market 5 was significantly different from other pet markets. Molecular analysis showed that 4 different Cryptosporidium species or genotypes were identified: Cryptosporidium parvum (n = 127), Cryptosporidium chipmunk genotype III (n = 6), Cryptosporidium andersoni (n = 4), and Cryptosporidium wrairi (n = 1). The identification of Cryptosporidium spp. was further tested with the 60-kDa glycoprotein (GP60) gene, and the positive rate was 29.7% (41/138). This is the first molecular report on Cryptosporidium spp. infection in dwarf winter white Russian hamsters in China. With C. parvum and C. andersoni being identified in both humans and pet hamsters, these findings suggest that pet hamsters may be potential reservoirs of zoonotic Cryptosporidium species and subtypes.

Sparse Evidence for Giardia intestinalis, Cryptosporidium spp. and Microsporidia Infections in Humans, Domesticated Animals and Wild Nonhuman Primates Sharing a Farm-Forest Mosaic Landscape in Western Uganda

Zoonotic pathogen transmission is considered a leading threat to the survival of non-human primates and public health in shared landscapes. Giardia spp., Cryptosporidium spp. and Microsporidia are unicellular parasites spread by the fecal-oral route by environmentally resistant stages and can infect humans, livestock, and wildlife including non-human primates. Using immunoassay diagnostic kits and amplification/sequencing of the region of the triosephosphate isomerase, small ribosomal subunit rRNA and the internal transcribed spacer genes, we investigated Giardia, Cryptosporidium, and microsporidia infections, respectively, among humans, domesticated animals (livestock, poultry, and dogs), and wild nonhuman primates (eastern chimpanzees and black and white colobus monkeys) in Bulindi, Uganda, an area of remarkably high human-animal contact and spatial overlap. We analyzed 137 fecal samples and revealed the presence of G. intestinalis assemblage B in two human isolates, G. intestinalis assemblage E in one cow isolate, and Encephalitozoon cuniculi genotype II in two humans and one goat isolate. None of the chimpanzee and colobus monkey samples were positive for any of the screened parasites. Regular distribution of antiparasitic treatment in both humans and domestic animals in Bulindi could have reduced the occurrence of the screened parasites and decreased potential circulation of these pathogens among host species.

Subtyping Cryptosporidium xiaoi, a Common Pathogen in Sheep and Goats

Cryptosporidiosis is a significant cause of diarrhea in sheep and goats. Among the over 40 established species of Cryptosporidium, Cryptosporidium xiaoi is one of the dominant species infecting ovine and caprine animals. The lack of subtyping tools makes it impossible to examine the transmission of this pathogen. In the present study, we identified and characterized the 60-kDa glycoprotein (gp60) gene by sequencing the genome of C. xiaoi. The GP60 protein of C. xiaoi had a signal peptide, a furin cleavage site of RSRR, a glycosylphosphatidylinositol anchor, and over 100 O-glycosylation sites. Based on the gp60 sequence, a subtyping tool was developed and used in characterizing C. xiaoi in 355 positive samples from sheep and goats in China. A high sequence heterogeneity was observed in the gp60 gene, with 94 sequence types in 12 subtype families, namely XXIIIa to XXIIIl. Co-infections with multiple subtypes were common in these animals, suggesting that genetic recombination might be responsible for the high diversity within C. xiaoi. This was supported by the mosaic sequence patterns among the subtype families. In addition, a potential host adaptation was identified within this species, reflected by the exclusive occurrence of XXIIIa, XXIIIc, XXIIIg, and XXIIIj in goats. This subtyping tool should be useful in studies of the genetic diversity and transmission dynamics of C. xiaoi.

Advances in molecular epidemiology of cryptosporidiosis in dogs and cats

The use of molecular tools has led to the identification of several zoonotic Cryptosporidium spp. in dogs and cats. Among them, Cryptosporidium canis and Cryptosporidium felis are dominant species causing canine and feline cryptosporidiosis, respectively. Some Cryptosporidium parvum infections have also been identified in both groups of animals. The identification of C. canis, C. felis and C. parvum in both pets and owners suggests the possible occurrence of zoonotic transmission of Cryptosporidium spp. between humans and pets. However, few cases of such concurrent infections have been reported. Thus, the cross-species transmission of Cryptosporidium spp. between dogs or cats and humans has long been a controversial issue. Recently developed subtyping tools for C. canis and C. felis should be very useful in identification of zoonotic transmission of both Cryptosporidium spp. Data generated using these tools have confirmed the occurrence of zoonotic transmission of these two Cryptosporidium spp. between owners and their pets, but have also shown the potential presence of host-adapted subtypes. Extensive usage of these subtyping tools in epidemiological studies of human cryptosporidiosis is needed for improved understanding of the importance of zoonotic transmission of Cryptosporidium spp. from pets.

Cryptosporidium ratti n. sp. (Apicomplexa: Cryptosporidiidae) and genetic diversity of Cryptosporidium spp. in brown rats (Rattus norvegicus) in the Czech Republic

The diversity and biology of Cryptosporidium that is specific for rats (Rattus spp.) are not well studied. We examined the occurrence and genetic diversity of Cryptosporidium spp. in wild brown rats (Rattus norvegicus) by microscopy and polymerase chain reaction (PCR)/sequencing targeting the small subunit rDNA (SSU), actin and HSP70 genes. Out of 343 faecal samples tested, none were positive by microscopy and 55 were positive by PCR. Sequence analysis of SSU gene revealed the presence of Cryptosporidium muris (n = 4), C. andersoni (n = 3), C. ryanae (n = 1), C. occultus (n = 3), Cryptosporidium rat genotype I (n = 23), Cryptosporidium rat genotype IV (n = 16) and novel Cryptosporidium rat genotype V (n = 5). Spherical oocysts of Cryptosporidium rat genotype I obtained from naturally-infected rats, measuring 4.4-5.4 μm × 4.3-5.1 μm, were infectious to the laboratory rats, but not to the BALB/c mice (Mus musculus) nor Mongolian gerbils (Meriones unguiculatus). The prepatent period was 3 days post infection and the patent period was longer than 30 days. Naturally- and experimentally-infected rats showed no clinical signs of disease. Percentage of nucleotide similarities at the SSU, actin, HSP70 loci between C. ratti n. sp. and the rat derived C. occultus and Cryptosporidium rat genotype II, III, IV, and V ranged from 91.0 to 98.1%. These genetic variations were similar or greater than that observed between closely related species, i.e. C. parvum and C. erinacei (93.2-99.5%). Our morphological, genetic and biological data support the establishment of Cryptosporidium rat genotype I as a new species, Cryptosporidium ratti n. sp.

Subtyping Cryptosporidium ryanae: A Common Pathogen in Bovine Animals

Cryptosporidium ryanae is one of the most common species for cryptosporidiosis in cattle. However, little is known of the genetic characteristics of C. ryanae due to the lack of subtyping tools. In the present study, the 60-kDa glycoprotein (gp60) gene of C. ryanae was identified in whole genome sequence data and analyzed for sequence characteristics using bioinformatics tools. The protein it encodes had some of the typical characteristics of GP60 proteins, with a signal peptide, a furin cleavage site, and a glycosylphosphatidylinositol anchor at the C terminus of the protein, and numerous O-glycosylation sites. The gene sequence was used in the development of a subtyping tool, which was used in characterizing C. ryanae from 110 specimens from dairy cattle, 2 from beef cattle, 6 from yaks, and 4 from water buffaloes in China. Altogether, 17 subtypes from 8 subtype families were recognized, namely XXIa to XXIh. Possible host adaption was identified within this species, reflected by the unique occurrence of XXIa, XXIc, and XXIh in dairy cattle, yaks, and water buffaloes, respectively. Some geographical differences were detected in the distribution of subtype families in dairy cattle; specimens from southern China showed higher genetic diversity than from northern China, and the XXIa subtype family was only seen in dairy cattle in southern and eastern China. The gp60-based subtyping tool should be useful in molecular epidemiological studies of the transmission of C. ryanae.

A retrospective epidemiological analysis of human Cryptosporidium infection in China during the past three decades (1987-2018)

Background

Cryptosporidiosis is an emerging infectious disease of public health significance worldwide. The burden of disease caused by Cryptosporidium varies between and within countries/areas. To have a comprehensive understanding of epidemiological status and characteristics of human Cryptosporidium infection in China since the first report in 1987, a retrospective epidemiological analysis was conducted by presenting differences in the prevalence of Cryptosporidium by province, year, population, living environment and season and possible transmission routes and risk factors as well as genetic characteristics of Cryptosporidium in humans.

Methodology/Principal findings

A systematic search was conducted to obtain epidemiological papers of human Cryptosporidium infection/cryptosporidiosis from PubMed and Chinese databases. Finally, 164 papers were included in our analysis. At least 200,054 people from 27 provinces were involved in investigational studies of Cryptosporidium, with an average prevalence of 2.97%. The prevalence changed slightly over time. Variable prevalences were observed: 0.65–11.15% by province, 1.89–47.79% by population, 1.77–12.87% and 0–3.70% in rural and urban areas, respectively. The prevalence peak occurred in summer or autumn. Indirect person-to-person transmission was documented in one outbreak of cryptosporidiosis in a pediatric hospital. 263 Cryptosporidium isolates were obtained, and seven Cryptosporidium species were identified: C. hominis (48.3%), C. andersoni (22.43%), C. parvum (16.7%), C. meleagridis (8.36%), C. felis (3.04%), C. canis (0.76%) and C. suis (0.38%).

Conclusions/Significances

This systematic review reflects current epidemiological status and characteristics of Cryptosporidium in humans in China. These data will be helpful to develop efficient control strategies to intervene with and prevent occurrence of human Cryptosporidium infection/cryptosporidiosis in China as well as have a reference effect to other countries. Further studies should focus on addressing a high frequency of C. andersoni in humans and a new challenge with respect to cryptosporidiosis with an increasing population of elderly people and patients with immunosuppressive diseases.

Cryptosporidium is a major cause of diarrheal disease in humans globally. Due to the lack of effective drug treatment and vaccine prevention against cryptosporidiosis, it is particularly important to develop efficient control strategies to intervene with and prevent Cryptosporidium infection in humans. The present review presented and analyzed epidemiological status and characteristics of Cryptosporidium infection in humans in China since the first report in 1987. To date, epidemiological investigations of Cryptosporidium infecion have been carried out in different populations in 27 provinces, autonomous regions, and municipalities. Average prevalence of Cryptosporidium was 2.97% (5,933/200,054). Like other infectious disease, due to poor sanitation conditions in rural areas, people living in rural areas had a significantly higher prevalence of Cryptosporidium (1.77–12.87%) than those living in urban areas (0–3.70%). Seven Cryptosporidium species were identified, including C. hominis, C. andersoni, C. parvum, C. meleagridis, C. felis, C. canis and C. suis. This retrospective epidemiological analysis indicates wide geographical distribution of human Cryptosporidium infection/cryptosporidiosis in China.

Cryptosporidium hominis infections in non-human animal species: revisiting the concept of host specificity

Parasites in the genus Cryptosporidium, phylum Apicomplexa, are found worldwide in the intestinal tract of many vertebrate species and in the environment. Driven by sensitive PCR methods, and the availability of abundant sequence data and reference genomes, the taxonomic complexity of the genus has steadily increased; 38 species have been named to date. Due to its public health importance, Cryptosporidium hominis has long attracted the interest of the research community. This species was initially described as infectious to humans only. This perception has persisted in spite of an increasing number of observations of natural and experimental infections of animals with this species. Here we summarize and discuss this literature published since 2000 and conclude that the host range of C. hominis is broader than originally described. The evolving definition of the C. hominis host range raises interesting questions about host specificity and the evolution of Cryptosporidium parasites.

Cryptosporidium parvum and Cryptosporidium hominis subtypes in crab-eating macaques

BACKGROUND

Non-human primates are often infected with human-pathogenic Cryptosporidium hominis subtypes, but rarely with Cryptosporidium parvum. In this study, 1452 fecal specimens were collected from farmed crab-eating macaques (Macaca fascicularis) in Hainan, China during the period April 2016 to January 2018. These specimens were analyzed for Cryptosporidium species and subtypes by using PCR and sequence analysis of the 18S rRNA and 60 kDa glycoprotein (gp60) genes, respectively.

RESULTS

Altogether, Cryptosporidium was detected using 18S rRNA-based PCR in 132 (9.1%) sampled animals, with significantly higher prevalence in females (12.5% or 75/599 versus 6.1% or 43/706), younger animals (10.7% or 118/1102 in monkeys 1-3-years-old versus 4.0% or 14/350 in those over 3-years-old) and animals with diarrhea (12.6% or 46/365 versus 7.9% or 86/1087). Four Cryptosporidium species were identified, namely C. hominis, C. parvum, Cryptosporidium muris and Cryptosporidium ubiquitum in 86, 30, 15 and 1 animal, respectively. The identified C. parvum, C. hominis and C. ubiquitum were further subtyped by using gp60 PCR. Among them, C. parvum belonged to subtypes in two known subtype families, namely IIoA14G1 (in 18 animals) and IIdA19G1 (in 2 animals). In contrast, C. hominis mostly belonged to two new subtype families Im and In, which are genetically related to Ia and Id, respectively. The C. hominis subtypes identified included ImA18 (in 38 animals), InA14 (in six animals), InA26 (in six animals), InA17 (in one animal) and IiA17 (in three animals). The C. ubiquitum isolates belonged to subtype family XIId. By subtype, ImA18 and IIoA14G1 were detected in animals with diarrhea whereas the remaining ones were mostly found in asymptomatic animals. Compared with C. parvum and C. muris, higher oocyst shedding intensity was observed in animals infected with C. hominis, especially those infected with the Im subtype family.

CONCLUSIONS

Data from the study suggest that crab-eating macaques are infected with diverse C. parvum and C. hominis subtypes. The C. parvum IIo subtype family previously seen in rodents in China has apparently expanded its host range.

First detection of Cryptosporidium spp. in red-bellied tree squirrels (Callosciurus erythraeus) in China

Cryptosporidium spp. are opportunistic pathogens that cause diarrhea in a variety of animal hosts. Although they have been reported in many animals, no information has been published on the occurrence of Cryptosporidium spp. in red-bellied tree squirrels (Callosciurus erythraeus). A total of 287 fecal specimens were collected from Sichuan province in China; the prevalence of Cryptosporidium spp., measured by nested-PCR amplification of the partial small-subunit (SSU) rRNA gene, was 1.4% (4/287). Three different Cryptosporidium species or genotypes were identified: Cryptosporidium parvum (n = 1), Cryptosporidium wrairi (n = 1), and Cryptosporidium rat genotype II (n = 2). The present study is the first report of Cryptosporidium infection in red-bellied tree squirrels in China. Although there is a relatively low occurrence of Cryptosporidium, the presence of C. parvum and C. wrairi, which were previously reported in humans, indicates that red-bellied tree squirrels may be a source of zoonotic cryptosporidiosis in China.

Molecular prevalence and subtyping of Cryptosporidium hominis among captive long-tailed macaques (Macaca fascicularis) and rhesus macaques (Macaca mulatta) from Hainan Island, southern China

BACKGROUND

Cryptosporidium is an important zoonotic parasite that is commonly found in non-human primates (NHPs). Consequently, there is the potential for transmission of this pathogen from NHPs to humans. However, molecular characterization of the isolates of Cryptosporidium from NHPs remains relatively poor. The aim of the present work was to (i) determine the prevalence; and (ii) perform a genetic characterization of the Cryptosporidium isolated from captive Macaca fascicularis and M. mulatta on Hainan Island in southern China.

METHODS

A total of 223 fresh fecal samples were collected from captive M. fascicularis (n = 193) and M. mulatta (n = 30). The fecal specimens were examined for the presence of Cryptosporidium spp. by polymerase chain reaction (PCR) and sequencing of the partial small subunit (SSU) rRNA gene. The Cryptosporidium-positive specimens were subtyped by analyzing the 60-kDa glycoprotein (gp60) gene sequence.

RESULTS

Cryptosporidium spp. were detected in 5.7% (11/193) of M. fascicularis. All of the 11 Cryptosporidium isolates were identified as C. hominis. Subtyping of nine of these isolates identified four unique gp60 subtypes of C. hominis. These included IaA20R3a (n = 1), IoA17a (n = 1), IoA17b (n = 1), and IiA17 (n = 6). Notably, subtypes IaA20R3a, IoA17a, and IoA17b were novel subtypes which have not been reported previously.

CONCLUSIONS

To our knowledge, this is the first reported detection of Cryptosporidium in captive M. fascicularis from Hainan Island. The molecular characteristics and subtypes of the isolates here provide novel insights into the genotypic variation in C. hominis.

Genomics and molecular epidemiology of Cryptosporidium species

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

Molecular characterization and epidemiological investigation of Cryptosporidium hominis IkA18G1 and C. hominis monkey genotype IiA17, two unusual subtypes diagnosed in Swedish patients

Cryptosporidium hominis is considered a strictly human-adapted species, and it is only occasionally diagnosed in animals. However, two variants, C. hominis monkey genotype and C. hominis Ik, were originally described in non-human hosts, monkeys and horses, respectively. During a Swedish national Cryptosporidium study, where all samples were analyzed at the small subunit rRNA and the 60 kDa (gp60) glycoprotein loci, we identified two patients infected with C. hominis monkey genotype (subtype IiA17) and two infected with C. hominis subtype IkA18G1. The isolates were further analyzed at the actin and the 70 kDa heat shock protein loci, and these analyses showed that these two subtype families are closely related to each other and to human-adapted C. hominis as well as to Cryptosporidium cuniculus. The two patients with C. hominis monkey genotype infection (a father and son) had visited a monkey farm in Thailand prior to infection, while the two cases with C. hominis Ik were unrelated, both probably infected in Sweden. This is the first time that a monkey genotype infection in humans has been related to contact with monkeys and where the gp60 subtype was identified. It is also the first time that human infection caused by C. hominis subtype Ik is described. Even though we were not able to detect any parasites in the animal samples, zoonotic transmission cannot be ruled out in any of these cases because both subtype families are regarded as animal adapted.

Molecular detection and genetic characterizations of Cryptosporidium spp. in farmed foxes, minks, and raccoon dogs in northeastern China

Cryptosporidium spp. are common intestinal protozoa causing diarrhea in humans and a variety of animal species. With the recent development of fur industry, a large number of fur animals are farmed worldwide, especially in China. The existence of identical Cryptosporidium species/genotypes in humans and fur animals suggests zoonotic potential. In order to assess the presence of zoonotic Cryptosporidium species and/or genotypes in farmed fur animals, 367 fecal specimens were collected from 213 foxes, 114 minks and 40 raccoon dogs farmed in Heilongjiang, Jilin, and Liaoning provinces, northeastern China, during the period from June 2014 to October 2016. By PCR and sequencing of the partial small subunit (SSU) rRNA gene of Cryptosporidium, 20 of 367 (5.4%) animal samples were found to be infected, corresponding to 12 of 213 fox samples (5.6%) and 8 of 114 mink samples (7.0%) screened. Three Cryptosporidium species/genotypes were identified: C. canis (n = 17), C. meleagridis (n = 1) and Cryptosporidium mink genotype (n = 2). Two host-adapted C. canis types (C. canis dog genotype and C. canis fox genotype) were found. By PCR and sequencing of the partial 60 kDa glycoprotein (gp60) encoding gene, one mink genotype isolate was successfully subtyped as XcA5G1R1. The three Cryptosporidium species/genotypes identified in this study have been previously reported in humans suggesting that fur animals infected with Cryptosporidium spp. may pose a risk of zoonotic transmission of cryptosporidiosis, especially for the people working in fur animal farming and processing industry.

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.

First description of Cryptosporidium ubiquitum XIIa subtype family in farmed fur animals

This study investigated the prevalence of Cryptosporidium in farmed fur animals in the Czech Republic and Poland. A total of 480 faecal samples were collected from fur animals, including 300 American mink (Mustela vison), 60 silver foxes (Vulpes vulpes), 50 long-tailed chinchillas (Chinchilla lanigera), and 70 nutrias (Myocastor coypus), at 14 farms. Samples were examined for the presence of Cryptosporidium using microscopy (following aniline-carbol-methyl violet staining) and sequence analysis of PCR amplified products. Three mink and two chinchillas from two different farms tested positive for Cryptosporidium ubiquitum DNA. The presence of C. ubiquitum DNA was not associated with diarrhoea. Subtyping of C. ubiquitum isolates by sequence analysis of the 60-kDa glycoprotein gene showed that isolates belonged to the XIIa subtype family, which was previously restricted to humans and ruminants. This suggests that C. ubiquitum subtype XIIa has a broader host range than previously reported.

Molecular characterization of Cryptosporidium and Giardia from the Tasmanian devil (Sarcophilus harrisii)

The Tasmanian devil (Sarcophilus harrisii) is a carnivorous marsupial found only in the wild in Tasmania, Australia. Tasmanian devils are classified as endangered and are currently threatened by devil facial tumour disease, a lethal transmissible cancer that has decimated the wild population in Tasmania. To prevent extinction of Tasmanian devils, conservation management was implemented in 2003 under the Save the Tasmanian Devil Program. This study aimed to assess if conservation management was altering the interactions between Tasmanian devils and their parasites. Molecular tools were used to investigate the prevalence and diversity of two protozoan parasites, Cryptosporidium and Giardia, in Tasmanian devils. A comparison of parasite prevalence between wild and captive Tasmanian devils showed that both Cryptosporidium and Giardia were significantly more prevalent in wild devils (p < 0.05); Cryptosporidium was identified in 37.9% of wild devils but only 10.7% of captive devils, while Giardia was identified in 24.1% of wild devils but only 0.82% of captive devils. Molecular analysis identified the presence of novel genotypes of both Cryptosporidium and Giardia. The novel Cryptosporidium genotype was 98.1% similar at the 18S rDNA to Cryptosporidium varanii (syn. C. saurophilum) with additional samples identified as C. fayeri, C. muris, and C. galli. Two novel Giardia genotypes, TD genotype 1 and TD genotype 2, were similar to G. duodenalis from dogs (94.4%) and a Giardia assemblage A isolate from humans (86.9%). Giardia duodenalis BIV, a zoonotic genotype of Giardia, was also identified in a single captive Tasmanian devil. These findings suggest that conservation management may be altering host-parasite interactions in the Tasmanian devil, and the presence of G. duodenalis BIV in a captive devil points to possible human-devil parasite transmission.

First report of Cryptosporidium canis in foxes (Vulpes vulpes) and raccoon dogs (Nyctereutes procyonoides) and identification of several novel subtype families for Cryptosporidium mink genotype in minks (Mustela vison) in China

Despite the rapid and extensive advances in molecular epidemiology of Cryptosporidium in humans and a variety of animals, the prevalence and genetic traits of the parasite in wildlife bred in captivity and the role of the neglected hosts in zoonotic transmission of human cryptosporidiosis are rarely understood. This study investigated the prevalence, species/genotype, and subtype of Cryptosporidium in farmed fur animals in China and assessed the possibility of zoonotic transmission. Three of 191 (1.6%) foxes (Vulpes vulpes), 17 of 162 (10.5%) raccoon dogs (Nyctereutes procyonoides), and 48 of 162 (29.6%) minks (Mustela vison) were positive for Cryptosporidium by nested PCRs targeting the small subunit rRNA gene. Sequence analysis indicated the presence of only Cryptosporidium canis in foxes and raccoon dogs. There is no significant difference in prevalence between young and adult foxes (or raccoon dogs). Three Cryptosporidium species or genotype including C. canis, Cryptosporidium meleagridis, and mink genotype were determined in minks aged five to six months. Subtyping based on nucleotide and amino acid sequence polymorphisms of the 60kDa glycoprotein facilitated identification of three novel subtype families named as Xb to Xd for Cryptosporidium mink genotype. The presence of zoonotic C. canis, C. meleagridis, and Cryptosporidium mink genotype in captive-bred fur animals is of public health concerns. The findings expanded the host ranges of C. canis and C. meleagridis and confirmed genetic diversity at the subtype level in Cryptosporidium mink genotype. This is the first study reporting Cryptosporidium infections in foxes and raccoon dogs in China.

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.

Emergence of Cryptosporidium hominis Monkey Genotype II and Novel Subtype Family Ik in the Squirrel Monkey (Saimiri sciureus) in China

A single Cryptosporidium isolate from a squirrel monkey with no clinical symptoms was obtained from a zoo in Ya'an city, China, and was genotyped by PCR amplification and DNA sequencing of the small-subunit ribosomal RNA (SSU rRNA), 70-kDa heat shock protein (HSP70), Cryptosporidium oocyst wall protein, and actin genes. This multilocus genetic characterization determined that the isolate was Cryptosporidium hominis, but carried 2, 10, and 6 nucleotide differences in the SSU rRNA, HSP70, and actin loci, respectively, which is comparable to the variations at these loci between C. hominis and the previously reported monkey genotype (2, 3, and 3 nucleotide differences). Phylogenetic studies, based on neighbor-joining and maximum likelihood methods, showed that the isolate identified in the current study had a distinctly discordant taxonomic status, distinct from known C. hominis and also from the monkey genotype, with respect to the three loci. Restriction fragment length polymorphisms of the SSU rRNA gene obtained from this study were similar to those of known C. hominis but clearly differentiated from the monkey genotype. Further subtyping was performed by sequence analysis of the gene encoding the 60-kDa glycoprotein (gp60). Maximum homology of only 88.3% to C. hominis subtype IdA10G4 was observed for the current isolate, and phylogenetic analysis demonstrated that this particular isolate belonged to a novel C. hominis subtype family, IkA7G4. This study is the first to report C. hominis infection in the squirrel monkey and, based on the observed genetic characteristics, confirms a new C. hominis genotype, monkey genotype II. Thus, these results provide novel insights into genotypic variation in C. hominis.

North American tree squirrels and ground squirrels with overlapping ranges host different Cryptosporidium species and genotypes

Wildlife-associated Cryptosporidium are an emerging cause of cryptosporidiosis in humans. The present study was undertaken to determine the extent to which North American tree squirrels and ground squirrels host zoonotic Cryptosporidium species and genotypes. Fragments of the Cryptosporidium 18S rRNA and actin genes were amplified and sequenced from fecal samples obtained from three tree squirrel and three ground squirrel species. In tree squirrels, Cryptosporidium was identified in 40.5% (17/42) of American red squirrels (Tamiasciurus hudsonicus), 40.4% (55/136) of eastern gray squirrels (Sciurus carolinensis), and 28.6% (2/7) of fox squirrels (Sciurus niger). Human-pathogenic Cryptosporidium ubiquitum and Cryptosporidium skunk genotype were the most prevalent species/genotypes in tree squirrels. Because tree squirrels live in close proximity to humans and are frequently infected with potentially zoonotic Cryptosporidium species/genotypes, they may be a significant reservoir of infection in humans. In ground squirrels, Cryptosporidium was detected in 70.2% (33/47) of 13-lined ground squirrels (Ictidomys tridecemlineatus), 35.1% (27/77) of black-tailed prairie dogs (Cynomys ludovicianus), and the only golden-mantled ground squirrel (Callospermophilus lateralis) that was sampled. Cryptosporidium rubeyi and ground squirrel genotypes I, II, and III were identified in isolates from these ground squirrel species. In contrast to the Cryptosporidium infecting tree squirrels, these species/genotypes appear to be specific for ground squirrels and are not associated with human disease.

Ocorrência de Cryptosporidium spp. em animais exóticos de companhia no Brasil

RESUMOA infecção por algumas espécies ou genótipos de Cryptosporidiumrepresenta um risco em potencial para a saúde pública, principalmente por causa de morbidade e mortalidade em crianças de zero a cinco anos de idade e em pacientes imunodeprimidos. Embora existam alguns relatos de infecção por Cryptosporidiumem animais de companhia, sua participação na epidemiologia da criptosporidiose humana é incerta, e a literatura sobre esse tema ainda é bastante escassa. O objetivo deste estudo foi determinar a ocorrência e realizar a classificação molecular deCryptosporidiumspp. em amostras fecais de animais exóticos criados como animais de estimação no Brasil. Um total de 386 amostras de seis espécies de animais foi colhido e armazenado em solução de dicromato de potássio 5% a 4°C. Os oocistos foram purificados por centrífugo-sedimentação em água/éter, seguindo-se a extração de DNA genômico e a realização da nestedPCR para amplificação de fragmento parcial do gene da subunidade 18S do rRNA. Positividade para Cryptosporidiumspp. foi observada em 11,40% (44/386) das amostras. O sequenciamento de fragmentos amplificados permitiu a identificação de Cryptosporidium tyzzeri em camundongos,Cryptosporidium murisem camundongos, hamster e chinchila, Cryptosporidium parvumem chinchila, Cryptosporidiumgenótipo hamsterem hamstere Cryptosporidiumsp. em porquinho-da-índia. Os resultados deste estudo mostram que há uma variedade de espécies de Cryptosporidiumpresentes em animais exóticos de companhia no Brasil. Os dados sugerem que esses animais podem participar da epidemiologia da criptosporidiose humana, particularmente por seu estreito convívio.

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.

Occurrence of novel and rare subtype families of Cryptosporidium in bamboo rats (Rhizomys sinensis) in China

This report is the first to describe Cryptosporidium infection in bamboo rats (Rhizomys sinensis). Ninety-two fresh fecal specimens were collected from a pet market in Ya'an City, China. One Cryptosporidium isolate from an asymptomatic host and two isolates from separate hosts with diarrhea were obtained by using Sheather's sucrose flotation technique and modified acid-fast staining. The Cryptosporidium spp. were genotyped by nested PCR and nucleotide sequencing of the small subunit rRNA (SSU rRNA), 70-kDa heat shock protein (HSP70), oocyst wall protein (COWP), and actin genes: isolates were identified as Cryptosporidium parvum with minor nucleotide differences at all four loci. Further subtyping was performed by PCR amplification and DNA sequence analysis of the 60-kDa glycoprotein (gp60) gene: two subtype families were detected, including a novel C. parvum subtype IIpA9 and a rare subtype IIoA13G1 (only reported in diarrheal patients of Sweden). Our results suggest that the bamboo rat is a reservoir host of C. parvum. Significantly, we discovered that the rare C. parvum subtype family IIo is also a zoonotic subtype and confirmed C. parvum subtype IIpA9 as a novel subtype family.

Subtyping Cryptosporidium ubiquitum,a zoonotic pathogen emerging in humans

Cryptosporidium ubiquitum is an emerging zoonotic pathogen. In the past, it was not possible to identify an association between cases of human and animal infection. We conducted a genomic survey of the species, developed a subtyping tool targeting the 60-kDa glycoprotein (gp60) gene, and identified 6 subtype families (XIIa–XIIf) of C. ubiquitum. Host adaptation was apparent at the gp60 locus; subtype XIIa was found in ruminants worldwide, subtype families XIIb–XIId were found in rodents in the United States, and XIIe and XIIf were found in rodents in the Slovak Republic. Humans in the United States were infected with isolates of subtypes XIIb–XIId, whereas those in other areas were infected primarily with subtype XIIa isolates. In addition, subtype families XIIb and XIId were detected in drinking source water in the United States. Contact with C. ubiquitum–infected sheep and drinking water contaminated by infected wildlife could be sources of human infections.

Multilocus typing of Cryptosporidium spp. and Giardia duodenalis from non-human primates in China

Non-human primates (NHPs) are commonly infected with Cryptosporidium spp. and Giardia duodenalis. However, molecular characterisation of these pathogens from NHPs remains scarce. In this study, 2,660 specimens from 26 NHP species in China were examined and characterised by PCR amplification of 18S rRNA, 70kDa heat shock protein (hsp70) and 60kDa glycoprotein (gp60) gene loci for Cryptosporidium; and 1,386 of the specimens by ssrRNA, triosephosphate isomerase (tpi) and glutamate dehydrogenase (gdh) gene loci for Giardia. Cryptosporidium was detected in 0.7% (19/2660) specimens of four NHP species including rhesus macaques (0.7%), cynomolgus monkeys (1.0%), slow lorises (10.0%) and Francois' leaf monkeys (6.7%), belonging to Cryptosporidium hominis (14/19) and Cryptosporidium muris (5/19). Two C. hominis gp60 subtypes, IbA12G3 and IiA17 were observed. Based on the tpi locus, G. duodenalis was identified in 2.2% (30/1,386) of specimens including 2.1% in rhesus macaques, 33.3% in Japanese macaques, 16.7% in Assam macaques, 0.7% in white-headed langurs, 1.6% in cynomolgus monkeys and 16.7% in olive baboons. Sequence analysis of the three targets indicated that all of the Giardia-positive specimens belonged to the zoonotic assemblage B. Highest sequence polymorphism was observed at the tpi locus, including 11 subtypes: three known and eight new ones. Phylogenetic analysis of the subtypes showed that most of them were close to the so-called subtype BIV. Intragenotypic variations at the gdh locus revealed six types of sequences (three known and three new), all of which belonged to so-called subtype BIV. Three specimens had co-infection with C. hominis (IbA12G3) and G. duodenalis (BIV). The presence of zoonotic genotypes and subtypes of Cryptosporidium spp. and G. duodenalis in NHPs suggests that these animals can potentially contribute to the transmission of human cryptosporidiosis and giardiasis.

Cryptosporidiumspecies in humans and animals: current understanding and research needs

Cryptosporidiumis increasingly recognized as one of the major causes of moderate to severe diarrhoea in developing countries. With treatment options limited, control relies on knowledge of the biology and transmission of the members of the genus responsible for disease. Currently, 26 species are recognized as valid on the basis of morphological, biological and molecular data. Of the nearly 20Cryptosporidiumspecies and genotypes that have been reported in humans,Cryptosporidium hominisandCryptosporidium parvumare responsible for the majority of infections. Livestock, particularly cattle, are one of the most important reservoirs of zoonotic infections. Domesticated and wild animals can each be infected with severalCryptosporidiumspecies or genotypes that have only a narrow host range and therefore have no major public health significance. Recent advances in next-generation sequencing techniques will significantly improve our understanding of the taxonomy and transmission ofCryptosporidiumspecies, and the investigation of outbreaks and monitoring of emerging and virulent subtypes. Important research gaps remain including a lack of subtyping tools for manyCryptosporidiumspecies of public and veterinary health importance, and poor understanding of the genetic determinants of host specificity ofCryptosporidiumspecies and impact of climate change on the transmission ofCryptosporidium.

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

Cryptosporidium meleagridis is a common cause of cryptosporidiosis in avian hosts and the third most common species involved in human cryptosporidiosis. Sequencing of the highly polymorphic 60-kDa glycoprotein (gp60) gene is a frequently used tool for investigation of the genetic diversity and transmission dynamics of Cryptosporidium. However, few studies have included gp60 sequencing of C. meleagridis. One explanation may be that the gp60 primers currently in use are based on Cryptosporidium hominis and Cryptosporidium parvum sequence data, potentially limiting successful amplification of the C. meleagridis gp60 gene. We therefore aimed to design primers for better gp60 subtyping of C. meleagridis. Initially, ∼1,440 bp of the gp60 locus of seven C. meleagridis isolates were amplified using primers flanking the open reading frame. The obtained sequence data (∼1,250 bp) were used to design primers for a nested PCR targeting C. meleagridis. Twenty isolates (16 from human and 4 from poultry) previously identified as C. meleagridis by analysis of small subunit (SSU) rRNA genes were investigated. Amplicons of the expected size (∼900 bp) were obtained from all 20 isolates. The subsequent sequence analysis identified 3 subtype families and 10 different subtypes. The most common subtype family, IIIb, was identified in 12 isolates, represented by 6 subtypes, 4 new and 2 previously reported. Subtype family IIIe was found in 3 isolates represented by 3 novel, distinct subtypes. Finally, IIIgA31G3R1 was found in 1 human isolate and 4 poultry isolates, all originating from a previously reported C. meleagridis outbreak at a Swedish organic farm.

Multilocus patterns of genetic variation across Cryptosporidium species suggest balancing selection at the gp60 locus

Cryptosporidium is an apicomplexan protozoan that lives in most vertebrates, including humans. Its gp60 gene is functionally involved in its attachment to host cells, and its high level of genetic variation has made it the reference marker for sample typing in epidemiological studies. To understand the origin of such high diversity and to determine the extent to which this classification applies to the rest of the genome, we analysed the patterns of variation at gp60 and nine other nuclear loci in isolates of three Cryptosporidium species. Most loci showed low genetic polymorphism (πS <1%) and similar levels of between-species divergence. Contrastingly, gp60 exhibited very different characteristics: (i) it was nearly ten times more variable than the other loci; (ii) it displayed a significant excess of polymorphisms relative to between-species differences in a maximum-likelihood Hudson-Kreitman-Aguadé test; (iii) gp60 subtypes turned out to be much older than the species they were found in; and (iv) showed a significant excess of polymorphic variants shared across species from random expectations. These observations suggest that this locus evolves under balancing selection and specifically under negative frequency-dependent selection (FDS). Interestingly, genetic variation at the other loci clusters very well within the groups of isolates defined by gp60 subtypes, which may provide new tools to understand the genome-wide patterns of genetic variation of the parasite in the wild. These results suggest that gp60 plays an active and essential role in the life cycle of the parasite and that genetic variation at this locus might be essential for the parasite's long-term success.

Coevolution of Cryptosporidium tyzzeri and the house mouse (Mus musculus)

Two house mouse subspecies occur in Europe, eastern and northern Mus musculus musculus (Mmm) and western and southern Mus musculus domesticus (Mmd). A secondary hybrid zone occurs where their ranges meet, running from Scandinavia to the Black Sea. In this paper, we tested a hypothesis that the apicomplexan protozoan species Cryptosporidium tyzzeri has coevolved with the house mouse. More specifically, we assessed to what extent the evolution of this parasite mirrors divergence of the two subspecies. In order to test this hypothesis, we analysed sequence variation at five genes (ssrRNA, Cryptosporidium oocyst wall protein (COWP), thrombospondin-related adhesive protein of Cryptosporidium 1 (TRAP-C1), actin and gp60) in C. tyzzeri isolates from Mmd and Mmm sampled along a transect across the hybrid zone from the Czech Republic to Germany. Mmd samples were supplemented with mice from New Zealand. We found two distinct isolates of C. tyzzeri, each occurring exclusively in one of the mouse subspecies (C. tyzzeri-Mmm and C. tyzzeri-Mmd). In addition to genetic differentiation, oocysts of the C. tyzzeri-Mmd subtype (mean: 4.24×3.69μm) were significantly smaller than oocysts of C. tyzzeri-Mmm (mean: 4.49×3.90 μm). Mmm and Mmd were susceptible to experimental infection with both C. tyzzeri subtypes; however, the subtypes were not infective for the rodent species Meriones unguiculatus, Mastomys coucha, Apodemus flavicollis or Cavia porcellus. Overall, our results support the hypothesis that C. tyzzeri is coevolving with Mmm and Mmd.

Common occurrence of zoonotic pathogen Cryptosporidium meleagridis in broiler chickens and turkeys in Algeria

Only a small number of birds have been identified by molecular techniques as having Cryptosporidium meleagridis, the third most important species for human cryptosporidiosis. In this study, using PCR-RFLP analysis of the small subunit (SSU) rRNA gene, we examined the ileum of 90 dead chickens from 23 farms and 57 dead turkeys from 16 farms in Algeria for Cryptosporidium spp. C. meleagridis-positive specimens were subtyped by sequence analysis of the 60 kDa glycoprotein gene. Cryptosporidium infection rates were 34% and 44% in chickens and turkeys, respectively, with all positive turkeys (25) and most positive chickens (26/31) having C. meleagridis. All C. meleagridis specimens belonged to a new subtype family. The frequent occurrence of C. meleagridis in chickens and turkeys illustrates the potential for zoonotic transmission of cryptosporidiosis in Algeria.

Molecular and phylogenetic approaches for assessing sources of Cryptosporidium contamination in water

The high sequence diversity and heterogeneity observed within species or genotypes of Cryptosporidium requires phylogenetic approaches for the identification of novel sequences obtained from the environment. A long-term study on Cryptosporidium in the agriculturally-intensive South Nation River watershed in Ontario, Canada was undertaken, in which 60 sequence types were detected. Of these sequence types 33 were considered novel with no identical matches in GenBank. Detailed phylogenetic analysis identified that most sequences belonged to 17 previously described species: Cryptosporidium andersoni, Cryptosporidium baileyi, Cryptosporidium hominis, Cryptosporidium parvum, Cryptosporidium ubiquitum, Cryptosporidium meleagridis, muskrat I, muskrat II, deer mouse II, fox, vole, skunk, shrew, W12, W18, W19 and W25 genotypes. In addition, two new genotypes were identified, W27 and W28. C. andersoni and the muskrat II genotype were most frequently detected in the water samples. Species associated with livestock made up 39% of the total molecular detections, while wildlife associated species and genotypes accounted for 55% of the Cryptosporidium identified. The human pathogenic species C. hominis and C. parvum had an overall prevalence of 1.6% in the environment, indicating a small risk to humans from the Cryptosporidium present in the watershed. Phylogenetic analysis and knowledge of host-parasite relationships are fundamental in using Cryptosporidium as a source-tracking or human health risk assessment tool.

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.

Cryptosporidiosis-an overview

Apicomplexan protozoan parasites of the genus Cryptosporidium infect the gastrointestinal tract and lungs of a wide variety of animals, including humans. The majority of human infections are due to either Cryptosporidium hominis (C. hominis) and/or Cryptosporidium parvum (C. parvum). The parasite has a complex life cycle that includes both asexual and sexual stages. While there are invasive free living stages, proliferation and differentiation take place within a unique parasitrophorous vacuole under the host cell brush border but outside the host cell cytoplasm. Infection is spread by environmentally resistant spores that primarily contaminate drinking water and occasionally food sources, which may cause significant outbreaks of diarrhea that generally lasts less than 2 w in immunocompetent individuals. In immunodeficient or immunosuppressed individuals, diarrhea may be copious and can result in significant morbidity and mortality, particularly in AIDS patients. Although diagnosis is relatively simple, effective drug treatment, particulary for infections in immunodeficient patients, has not been uniformly successful. This overview summarizes the species known to infect humans, aspects of the parasite life cycle, sources of infection, the pathophysiology of cryptosporidiosis, the immune response to infection, diagnosis, treatment and some aspects of cryptosporidiosis in China.

Cryptosporidium tyzzeri n. sp. (Apicomplexa: Cryptosporidiidae) in domestic mice (Mus musculus)

The Cryptosporidium in the small intestine of domestic mice (Mus musculus) was initially described as Cryptosporidium parvum. Recent genetic and biologic characterization of Cryptosporidium isolates indicate that domestic mice are infected with several morphologically indistinguishable intestinal Cryptosporidium parasites with different host specificities, including C. parvum sensu stricto, mouse genotype I, and mouse genotype II. In this study, the morphological, biological, and genetic characteristics of the Cryptosporidium mouse genotype I are described. As a full re-description of C. parvum was made in 1985 for isolates from calves and humans and the name C. parvum has been widely used for the parasite that is infectious to both ruminants and humans, the mouse genotype I is named as Cryptosporidium tyzzeri. Oocysts of the new species (4.64±0.05 μm ×4.19±0.06 μm, with a mean shape index of 1.11±0.02; n=69) are slightly smaller than those of the re-described C. parvum. The prepatent period was six and seven days, and the patent period was 24-28 and 28-29 days in neonatal and adult mice, respectively. Oocysts were not infectious to lambs and calves. Light, transmission electron and scanning electron microscopy studies of the new species showed the presence of developmental stages in the microvillar brush border of the jejunum and ileum of experimentally infected mice, with the infection most intensive in the ileum. It had nucleotide sequences significantly different from C. parvum at the small subunit rRNA, 70 kDa heat shock protein, oocyst wall protein, actin, and the 60 kDa glycoprotein genes. Based on the morphological, genetic, and biological data and in compliance of established Cryptosporidium species naming criteria, this geographically widespread parasite is named as a new species in honor of Ernest Edward Tyzzer, who pioneered Cryptosporidium research.