Genetic Diversity and Population Structure of Cryptosporidium

Molecular Epidemiology of Human Cryptosporidiosis in Low- and Middle-Income Countries

Cryptosporidiosis is one of the most important causes of moderate to severe diarrhea and diarrhea-related mortality in children under 2 years of age in low- and middle-income countries. In recent decades, genotyping and subtyping tools have been used in epidemiological studies of human cryptosporidiosis. Results of these studies suggest that higher genetic diversity of Cryptosporidium spp. is present in humans in these countries at both species and subtype levels and that anthroponotic transmission plays a major role in human cryptosporidiosis. Cryptosporidium hominis is the most common Cryptosporidium species in humans in almost all the low- and middle-income countries examined, with five subtype families (namely, Ia, Ib, Id, Ie, and If) being commonly found in most regions. In addition, most Cryptosporidium parvum infections in these areas are caused by the anthroponotic IIc subtype family rather than the zoonotic IIa subtype family. There is geographic segregation in Cryptosporidium hominis subtypes, as revealed by multilocus subtyping. Concurrent and sequential infections with different Cryptosporidium species and subtypes are common, as immunity against reinfection and cross protection against different Cryptosporidium species are partial. Differences in clinical presentations have been observed among Cryptosporidium species and C. hominis subtypes. These observations suggest that WASH (water, sanitation, and hygiene)-based interventions should be implemented to prevent and control human cryptosporidiosis in low- and middle-income countries.

Molecular Diversity of Giardia duodenalis, Cryptosporidium spp., and Blastocystis sp. in Symptomatic and Asymptomatic Schoolchildren in Zambézia Province (Mozambique)

Infections by the protist enteroparasites Giardia duodenalis, Cryptosporidium spp., and, to a much lesser extent, Blastocystis sp. are common causes of childhood diarrhoea in low-income countries. This molecular epidemiological study assesses the frequency and molecular diversity of these pathogens in faecal samples from asymptomatic schoolchildren (n = 807) and symptomatic children seeking medical attention (n = 286) in Zambézia province, Mozambique. Detection and molecular characterisation of pathogens was conducted by polymerase chain reaction (PCR)-based methods coupled with Sanger sequencing. Giardia duodenalis was the most prevalent enteric parasite found [41.7%, 95% confidence interval (CI): 38.8‒44.7%], followed by Blastocystis sp. (14.1%, 95% CI: 12.1‒16.3%), and Cryptosporidium spp. (1.6%, 95% CI: 0.9‒2.5%). Sequence analyses revealed the presence of assemblages A (7.0%, 3/43) and B (88.4%, 38/43) within G. duodenalis-positive children. Four Cryptosporidium species were detected, including C. hominis (30.8%; 4/13), C. parvum (30.8%, 4/13), C. felis (30.8%, 4/13), and C. viatorum (7.6%, 1/13). Four Blastocystis subtypes were also identified including ST1 (22.7%; 35/154), ST2 (22.7%; 35/154), ST3 (45.5%; 70/154), and ST4 (9.1%; 14/154). Most of the genotyped samples were from asymptomatic children. This is the first report of C. viatorum and Blastocystis ST4 in Mozambique. Molecular data indicate that anthropic and zoonotic transmission (the latter at an unknown rate) are important spread pathways of diarrhoea-causing pathogens in Mozambique.

Prevalence and multilocus genotyping of Cryptosporidium spp. in cattle in Jiangxi Province, southeastern China

Cryptosporidium is a genus of single-celled protozoa, infecting a wide range of animals and humans. Although Cryptosporidium infections of cattle have been reported in some provinces in China, there is no available information on the prevalence and predominant species of Cryptosporidium in cattle in Jiangxi province. To investigate the prevalence of Cryptosporidium in cattle in Jiangxi province of China, 556 fecal samples were collected from eight farms in four cities and the SSU rRNA locus of Cryptosporidium was amplified from the DNA of each fecal sample by PCR. The overall prevalence of Cryptosporidium was 12.8% (71/556) in cattle in Jiangxi province, with 24.3% (54/222) in Nanchang city, 7.8% (13/166) in Gao'an city, 3.7% (4/108) in Xinyu city, and 0.0% (0/60) in Ji'an city. The differences of the prevalence rates by region, breed, and age groups were statistically significant. All positive PCR products of Cryptosporidium were successfully sequenced and identified as three Cryptosporidium species, namely Cryptosporidium bovis (1/556, 0.18%), Cryptosporidium ryanae (7/556, 1.3%), and Cryptosporidium andersoni (63/556, 11.3%). Furthermore, 36 C. andersoni isolates were successfully classified into three MLST (multilocus sequence typing) subtypes based on four genetic loci (MS1, MS2, MS3, and MS16). The predominant MLST subtype was A4, A4, A4, A1 (n = 30). These findings not only revealed the prevalence and predominant species of Cryptosporidium in cattle in Jiangxi province, but also provided a baseline for studying the genetic structure of C. andersoni, offering a novel resource for better understanding of the epidemiology of Cryptosporidium infection in cattle in Jiangxi province, southeastern China.

Development of a Subtyping Tool for Zoonotic Pathogen Cryptosporidium canis

Cryptosporidium canis is an important cause of cryptosporidiosis in canines and humans. Studies of the transmission characteristics of C. canis are currently hampered by the lack of suitable subtyping tools. In this study, we conducted a genomic survey of the pathogen and developed a subtyping tool targeting the partial 60-kDa glycoprotein gene (gp60). Seventy-six isolates previously identified as C. canis were analyzed using the new subtyping tool. Amplicons of the expected size were obtained from 49 isolates, and phylogenetic analysis identified 10 subtypes clustered into five distinct groups (XXa to XXe). The largest group, XXa, contained 43 isolates from four subtypes that differed slightly from each other at the nucleotide level, while groups XXb to XXe contain one to three isolates each. The similar distributions of subtypes in humans and canines suggest that zoonotic transmission might play an important role in the epidemiology of C. canis In addition, suspected zoonotic transmission of C. canis between dogs and humans in a household was confirmed using the subtyping tool. The subtyping tool and data generated in this study might improve our understanding of the transmission of this zoonotic pathogen.

Molecular characterization of Cryptosporidium isolates from humans in Ontario, Canada

BACKGROUND

Cryptosporidiosis is a gastrointestinal disease with global distribution. It has been a reportable disease in Canada since 2000; however, routine molecular surveillance is not conducted. Therefore, sources of contamination are unknown. The aim of this project was to identify species and subtypes of Cryptosporidium in clinical cases from Ontario, the largest province in Canada, representing one third of the Canadian population, in order to understand transmission patterns.

METHODS

A total of 169 frozen, banked, unpreserved stool specimens that were microscopy positive for Cryptosporidium over the period 2008-2017 were characterized using molecular tools. A subset of the 169 specimens were replicate samples from individual cases. DNA was extracted directly from the stool and nested PCR followed by Sanger sequencing was conducted targeting the small subunit ribosomal RNA (SSU) and glycoprotein 60 (gp60) genes.

RESULTS

Molecular typing data and limited demographic data were obtained for 129 cases of cryptosporidiosis. Of these cases, 91 (70.5 %) were due to Cryptosporidium parvum and 24 (18.6%) were due to Cryptosporidium hominis. Mixed infections of C. parvum and C. hominis occurred in four (3.1%) cases. Five other species observed were Cryptosporidium ubiquitum (n = 5), Cryptosporidium felis (n = 2), Cryptosporidium meleagridis (n = 1), Cryptosporidium cuniculus (n = 1) and Cryptosporidium muris (n = 1). Subtyping the gp60 gene revealed 5 allelic families and 17 subtypes of C. hominis and 3 allelic families and 17 subtypes of C. parvum. The most frequent subtype of C. hominis was IbA10G2 (22.3%) and of C. parvum was IIaA15G2R1 (62.4%).

CONCLUSIONS

The majority of isolates in this study were C. parvum, supporting the notion that zoonotic transmission is the main route of cryptosporidiosis transmission in Ontario. Nonetheless, the observation of C. hominis in about a quarter of cases suggests that anthroponotic transmission is also an important contributor to cryptosporidiosis pathogenesis in Ontario.

The Age-Related Cryptosporidium Species Distribution in Asymptomatic Cattle from North-Western SPAIN

Simple Summary

An age-related distribution of Cryptosporidium species has been reported in cattle, with the pathogenic and zoonotic C. parvum being predominant in suckling calves, C. bovis and C. ryanae being predominant in post-weaned calves and C. andersoni being predominant in adults. However, variants to this pattern have recently been reported. Unravelling the age-related species distribution pattern in cattle from a particular region will allow determining those age classes posing a higher risk to public and animal health. Thus, fecal samples from asymptomatic cattle were collected in north-western Spain. Cryptosporidium detection and species identification was performed by molecular methods. Cryptosporidium prevalence was 16.7%; it significantly decreased with age. Cryptosporidium andersoni, C. bovis, C. occultus, C. parvum, C. ryanae and C. xiaoi were identified. Cryptosporidium parvum was predominant in calves younger than 1 month and C. bovis was predominant in the rest of the age groups. The presence of C. parvum in all age groups implies animal and public health concerns. The predominance of C. bovis in cattle older than 1 month supports the idea that the age-related pattern of Cryptosporidium species described in cattle is not fully consistent, and thus further studies are needed to identify those factors determining the species distribution.

Abstract

An age-related distribution of Cryptosporidium species has been reported in cattle, with C. parvum being predominant in suckling calves, C. bovis and C. ryanae being predominant in post-weaned calves and C. andersoni being predominant in adults. However, variants to this pattern have recently been reported. Thus, fecal samples (n = 594) from asymptomatic cattle were collected in north-western Spain. Animals were classified as <1 month (G1), 1–2 months (G2), 2–12 months (G3), 12–24 months (G4) and >2 years (G5). Cryptosporidium detection and species identification were performed by SSU rRNA PCR. Individual Cryptosporidium prevalence was 16.7%; it significantly decreased with age. Cryptosporidium parvum was predominant in G1 and C. bovis was predominant in the rest of the age classes; C. bovis and C. ryanae were especially prevalent in G2 and G3. Cryptosporidium occultus was not found in suckling calves. Finally, C. andersoni and C. xiaoi were occasionally detected in G5. The presence of C. parvum in all age classes implies significant animal and public health concerns. The predominance of C. bovis in cattle older than 1 month supports the idea that the age-related pattern of Cryptosporidium species described in cattle is not fully consistent, and thus further studies are still needed to identify those factors determining the species distribution.

Subtype Characterization and Zoonotic Potential of Cryptosporidium felis in Cats in Guangdong and Shanghai, China

Cryptosporidiumfelis is an important cause of feline and human cryptosporidiosis. However, the transmission of this pathogen between humans and cats remains controversial, partially due to a lack of genetic characterization of isolates from cats. The present study was conducted to examine the genetic diversity of C. felis in cats in China and to assess their potential zoonotic transmission. A newly developed subtyping tool based on a sequence analysis of the 60-kDa glycoprotein (gp60) gene was employed to identify the subtypes of 30 cat-derived C. felis isolates from Guangdong and Shanghai. Altogether, 20 C. felis isolates were successfully subtyped. The results of the sequence alignment showed a high genetic diversity, with 13 novel subtypes and 2 known subtypes of the XIXa subtype family being identified. The known subtypes were previously detected in humans, while some of the subtypes formed well-supported subclusters with human-derived subtypes from other countries in a phylogenetic analysis of the gp60 sequences. The results of this study confirmed the high genetic diversity of the XIXa subtype family of C. felis. The common occurrence of this subtype family in both humans and cats suggests that there could be cross-species transmission of C. felis.

Occurrence of Cryptosporidium and Giardia in wild birds from Qinghai Lake on the Qinghai-Tibetan Plateau, China

Cryptosporidium and Giardia are important intestinal zoonotic pathogens that can infect various hosts and cause diarrhoeal diseases. There are few reports of the epidemiological prevalence and molecular characterization of Cryptosporidium and Giardia in wild birds around Qinghai Lake and in the surrounding areas on the Qinghai-Tibetan Plateau, Northwest China. Therefore, the aim of this study was to determine the Cryptosporidium spp. and Giardia duodenalis genotypes and their epidemiological prevalence in wild birds by PCR amplification. To our knowledge, this is the first report of a variety of Cryptosporidium spp. and G. duodenalis infections in wild birds from that area, with overall prevalence rates of 8.98% (61/679) and 3.39% (23/679), respectively. Furthermore, PCR sequencing confirmed the presence of Cryptosporidium baileyi (n = 3), Cryptosporidium parvum (n = 58), and G. duodenalis assemblage B (n = 19) and E (n = 4) in wild birds from the areas around Qinghai Lake. The results of the present study demonstrated the wide distribution of Cryptosporidium and Giardia among wild birds, which has potential public health significance. Moreover, the study findings also provided useful molecular epidemiological data for monitoring and investigating the two parasitic protozoa in wild animals and surrounding environments.

Cryptosporidiosis outbreak caused by Cryptosporidium parvum subtype IIdA20G1 in neonatal calves

Cryptosporidium parvum is a major zoonotic pathogen responsible for outbreaks of severe diarrhoea in humans and calves. Almost all investigations of cryptosporidiosis outbreaks caused by C. parvum have focused on its IIa subtype family in industrialized nations. From December 2018 to April 2019, approximately 200 neonatal calves on a large cattle farm in Hebei Province, China, were diagnosed with watery diarrhoea and over 40 died. To investigate the cause of the outbreak, faecal samples were taken during and after the outbreak from neonatal calves of ≤4 weeks of age (n = 40 and n = 56) and older calves of 4-24 weeks of age (n = 79 and n = 38). A total of 18 faecal samples collected from ill calves at the peak of the outbreak were analysed for four common enteric pathogens using an enzymatic immunoassay (EIA). In addition, 75 samples from neonatal calves were tested for rotavirus by EIA. All samples were analysed for Cryptosporidium spp. using PCR and sequencing techniques. Of the initial 18 samples from sick calves, ten were positive for C. parvum, five for rotavirus, and one for coronavirus. The overall prevalence of rotavirus in neonatal calves was 20.0% (15/75), with no significant differences during and after the outbreak. In contrast, Cryptosporidium parvum infections were significantly higher during the outbreak (60.0%, 24/40) than after the outbreak (30.4%, 17/56; p = .004). Cryptosporidium parvum infection was associated with the presence of watery diarrhoea in neonatal calves (OR = 11.19), while no association was observed between C. bovis infection and diarrhoea. All C. parvum isolates were identified as subtype IIdA20G1. This is one of the few reports of outbreaks of severe diarrhoea caused by C. parvum IId subtypes in calves. More attention should be directed towards the dissemination of C. parvum in China.

Comparative genomics revealed adaptive admixture in Cryptosporidium hominis in Africa

Cryptosporidiosis is a major cause of diarrhoeal illness among African children, and is associated with childhood mortality, malnutrition, cognitive development and growth retardation. Cryptosporidium hominis is the dominant pathogen in Africa, and genotyping at the glycoprotein 60 (gp60) gene has revealed a complex distribution of different subtypes across this continent. However, a comprehensive exploration of the metapopulation structure and evolution based on whole-genome data has yet to be performed. Here, we sequenced and analysed the genomes of 26 C. hominis isolates, representing different gp60 subtypes, collected at rural sites in Gabon, Ghana, Madagascar and Tanzania. Phylogenetic and cluster analyses based on single-nucleotide polymorphisms showed that isolates predominantly clustered by their country of origin, irrespective of their gp60 subtype. We found a significant isolation-by-distance signature that shows the importance of local transmission, but we also detected evidence of hybridization between isolates of different geographical regions. We identified 37 outlier genes with exceptionally high nucleotide diversity, and this group is significantly enriched for genes encoding extracellular proteins and signal peptides. Furthermore, these genes are found more often than expected in recombinant regions, and they show a distinct signature of positive or balancing selection. We conclude that: (1) the metapopulation structure of C. hominis can only be accurately captured by whole-genome analyses; (2) local anthroponotic transmission underpins the spread of this pathogen in Africa; (3) hybridization occurs between distinct geographical lineages; and (4) genetic introgression provides novel substrate for positive or balancing selection in genes involved in host-parasite coevolution.

High Prevalence of Cryptosporidium meleagridis in Domestic Pigeons (Columba livia domestica) Raises a Prospect of Zoonotic Transmission in Babylon Province, Iraq

Cryptosporidium is one of the most common protozoan’s parasites with remarkable infectivity of a wide range of animals, including mammals and birds. Domestic pigeons (Columba livia domestica) act as a potential reservoir for several species of Cryptosporidium because they live in close proximity to humans. This study was conducted to assess the genetic diversity of Cryptosporidium in domestic pigeons in Iraq. A total of one hundred samples obtained from feces of domestic pigeons in Babylon province were included. After being exposed to microbial examination, all fecal samples were subsequently screened by nested polymerase chain reaction (PCR) for the possible recognition of Cryptosporidium species. Microscopy tests detected only 14/100 (14%) of infection with Cryptosporidium, while molecular tests detected 21/100 (21%) of the same targeted parasite. Sequencing experiments showed a high prevalence of C. meleagridis with 13/21 (61.90%), followed by C. baileyi with 7/21 (33.33%), while only one infection was detected with C. hominis (1/21) (4.76%). No co-infection with mixed Cryptosporidium spp. was observed, and sex factor was not found to affect the infection rate. In conclusion, this study informed a high prevalence of C. meleagridis in domestic pigeons than both C. baileyi and C. hominis, respectively, signifying a higher zoonotic potential of C. meleagridis between domestic pigeons and their handlers. This finding may raise more questions with regard to the increasing infectivity of C. meleagridis in human. This is the first important screening study in Iraq that uses molecular methods for the detection of Cryptosporidium in domesticated pigeons.

Comparative genomic analysis of the principal Cryptosporidium species that infect humans

Cryptosporidium parasites are ubiquitous and can infect a broad range of vertebrates and are considered the most frequent protozoa associated with waterborne parasitic outbreaks. The intestine is the target of three of the species most frequently found in humans: C. hominis, C. parvum, and. C. meleagridis. Despite the recent advance in genome sequencing projects for this apicomplexan, a broad genomic comparison including the three species most prevalent in humans have not been published so far. In this work, we downloaded raw NGS data, assembled it under normalized conditions, and compared 23 publicly available genomes of C. hominis, C. parvum, and C. meleagridis. Although few genomes showed highly fragmented assemblies, most of them had less than 500 scaffolds and mean coverage that ranged between 35X and 511X. Synonymous single nucleotide variants were the most common in C. hominis and C. meleagridis, while in C. parvum, they accounted for around 50% of the SNV observed. Furthermore, deleterious nucleotide substitutions common to all three species were more common in genes associated with DNA repair, recombination, and chromosome-associated proteins. Indel events were observed in the 23 studied isolates that spanned up to 500 bases. The highest number of deletions was observed in C. meleagridis, followed by C. hominis, with more than 60 species-specific deletions found in some isolates of these two species. Although several genes with indel events have been partially annotated, most of them remain to encode uncharacterized proteins.

Identification of Uncommon Cryptosporidium viatorum (a Novel Subtype XVcA2G1c) and Cryptosporidium andersoni as Well as Common Giardia duodenalis Assemblages A and B in Humans in Myanmar

Cryptosporidium and Giardia are two important zoonotic intestinal protozoa responsible for diarrheal diseases in humans and animals worldwide. Feces from infected hosts, water and food contaminated by Cryptosporidium oocysts and Giardia cysts as well as predictors such as poverty have been involved in their transmission. Myanmar is one of the world’s most impoverished countries. To date, there are few epidemiological studies of Cryptosporidium and Giardia in humans. To understand the prevalence and genetic characterization of Cryptosporidium spp. and Giardia duodenalis in humans in Myanmar, a molecular epidemiological investigation of the two protozoa was conducted in four villages of Shan State. 172 fecal specimens were collected from Wa people (one each) and identified for the presence of Cryptosporidium spp. and G. duodenalis by sequence analysis of their respective small subunit ribosomal RNA genes. 1.74% of investigated people were infected with Cryptosporidium spp.—C. andersoni (n = 2) and C. viatorum (n = 1) while 11.05% infected with G. duodenalis—assemblages A (n = 6) and B (n = 13). By sequence analysis of 60-kDa glycoprotein gene, the C. viatorum isolate belonged to a novel subtype XVcA2G1c. DNA preparations positive for G. duodenalis were further subtyped. Five of them were amplified and sequenced successfully: different assemblage B sequences (n = 2) at the triosephosphate isomerase (tpi) locus; sub-assemblage AII sequence (n = 1) and identical assemblage B sequences (n = 2) at the β-giardin (bg) locus. This is the first molecular epidemiological study of Cryptosporidium spp. and G. duodenalis in humans in Myanmar at both genotype and subtype levels. Due to unclear transmission patterns and dynamics of Cryptosporidium spp. and G. duodenalis, future research effort should focus on molecular epidemiological investigations of the two parasites in humans and animals living in close contact in the investigated areas, even in whole Myanmar. These data will aid in making efficient control strategies to intervene with and prevent occurrence of both diseases.

Neonatal Mouse Gut Metabolites Influence Cryptosporidium parvum Infection in Intestinal Epithelial Cells

Cryptosporidium sp. occupies a unique intracellular niche that exposes the parasite to both host cell contents and the intestinal lumen, including metabolites from the diet and produced by the microbiota. Both dietary and microbial products change over the course of early development and could contribute to the changes seen in susceptibility to cryptosporidiosis in humans and mice.

The protozoan parasite Cryptosporidium sp. is a leading cause of diarrheal disease in those with compromised or underdeveloped immune systems, particularly infants and toddlers in resource-poor localities. As an enteric pathogen, Cryptosporidium sp. invades the apical surface of intestinal epithelial cells, where it resides in close proximity to metabolites in the intestinal lumen. However, the effect of gut metabolites on susceptibility to Cryptosporidium infection remains largely unstudied. Here, we first identified which gut metabolites are prevalent in neonatal mice when they are most susceptible to Cryptosporidium parvum infection and then tested the isolated effects of these metabolites on C. parvum invasion and growth in intestinal epithelial cells. Our findings demonstrate that medium or long-chain saturated fatty acids inhibit C. parvum growth, perhaps by negatively affecting the streamlined metabolism in C. parvum, which is unable to synthesize fatty acids. Conversely, long-chain unsaturated fatty acids enhanced C. parvum invasion, possibly by modulating membrane fluidity. Hence, gut metabolites, either from diet or produced by the microbiota, influence C. parvum growth in vitro and may also contribute to the early susceptibility to cryptosporidiosis seen in young animals.

Cryptosporidium Species and C. parvum Subtypes in Farmed Bamboo Rats

Bamboo rats (Rhizomys sinensis) are widely farmed in Guangdong, China, but the distribution and public health potential of Cryptosporidium spp. in them are unclear. In this study, 724 fecal specimens were collected from bamboo rats in Guangdong Province and analyzed for Cryptosporidium spp. using PCR and sequence analyses of the small subunit rRNA gene. The overall detection rate of Cryptosporidium spp. was 12.2% (88/724). By age, the detection rate in animals under 2 months (23.2% or 13/56) was significantly higher than in animals over 2 months (11.2% or 75/668; χ² = 6.95, df = 1, p = 0.0084). By reproduction status, the detection rate of Cryptosporidium spp. in nursing animals (23.1% or 27/117) was significantly higher than in other reproduction statuses (6.8% or 4/59; χ² = 7.18, df = 1, p = 0.0074). Five Cryptosporidium species and genotypes were detected, including Cryptosporidium bamboo rat genotype I (n = 49), C. parvum (n = 31), Cryptosporidium bamboo rat genotype III (n = 5), C. occultus (n = 2), and C. muris (n = 1). The average numbers of oocysts per gram of feces for these Cryptosporidium spp. were 14,074, 494,636, 9239, 394, and 323, respectively. The genetic uniqueness of bamboo rat genotypes I and III was confirmed by sequence analyses of the 70 kDa heat shock protein and actin genes. Subtyping C. parvum by sequence analysis of the 60 kDa glycoprotein gene identified the presence of IIoA15G1 (n = 20) and IIpA6 (n = 2) subtypes. The results of this study indicated that Cryptosporidium spp. are common in bamboo rats in Guangdong, and some of the Cryptosporidium spp. in these animals are known human pathogens.

Subtype distribution of zoonotic pathogen Cryptosporidium felis in humans and animals in several countries

Cryptosporidium felis is the major etiologic agent of cryptosporidiosis in felines and has been reported in numerous human cryptosporidiosis cases. Sequence analysis of the 60-kDa glycoprotein (gp60) gene has been developed for subtyping C. felis recently. In this study, 66 C. felis isolates from the United States, Jamaica, Peru, Portugal, Slovakia, Nigeria, Ethiopia, Kenya, China, India and Australia were subtyped using the newly established tool. Forty-four specimens yielded gp60 sequences, generating 23 subtypes clustered in 4 subtype families (XIXa, XIXc, XIXd and XIXe) with high bootstrap support in a phylogenetic analysis of sequence data. Among them, XIXa showed high genetic diversity at the nucleotide level, with the formation of 18 subtypes from both cats and humans with different geographic distribution. In contrast, all 11 XIXd isolates derived from humans from various countries had identical sequences. Results of this study improve our understanding of the genetic diversity, host specificity and transmission dynamics of C. felis.

Cryptosporidium parvum, Cryptosporidium ryanae, and Cryptosporidium bovis in samples from calves in Austria

Fecal samples of 177 calves of up to 180 days of age with diarrhea from 70 farms in Austria were examined to obtain information on the occurrence of Cryptosporidium species. Initially, all samples were examined by phase-contrast microscopy. Cryptosporidium-positive samples (55.4%; n = 98) were screened by gp60 PCR, resulting in 68.4% (n = 67) C. parvum-positive samples. The remaining 31 gp60-PCR-negative and the phase-contrast microscopy negative samples (n = 79) were screened by PCR targeting a 700 bp fragment of the 18S rRNA gene. Sequencing of the PCR products revealed the presence of C. parvum (n = 69), C. ryanae (n = 11), and C. bovis (n = 7). The latter two species have never been described in Austria. C. parvum-positive samples were genotyped at the gp60 gene locus, featuring four subtypes (IIaA15G2R1, IIaA21G2R1, IIaA19G2R1, IIaA14G1R1). The most frequently detected subtype IIaA15G2R1 (n = 52) was present in calves from 30 different farms. IIaA14G1R1 (n = 5) occurred on a single farm, subtype IIaA21G2R1 (n = 4) on two farms, and subtype IIaA19G2R1 (n = 4) on three farms. The results confirm the widespread occurrence of zoonotic C. parvum in diarrheic calves.

Development of novel methodology for the molecular differentiation of Cryptosporidium parvum gp60 subtypes via high resolution melting analysis

Cryptosporidium species subtypes are generally identified via DNA sequencing of the gp60 gene tandem repeat motif region. Due to the immunogenic nature of its glycoprotein products, gp60 is subject to host selective pressures, genetic recombination and evolutionary processes that drive extensive polymorphism at this locus. The elucidation of the polymorphic nature of this gene has led to the current mainstay in Cryptosporidium subtyping nomenclature.

This study aimed to develop a real-time polymerase chain reaction based method utilising a post-PCR application, high resolution melting (HRM) analysis, in conjunction with the abovementioned gp60 nomenclature system, in order to differentiate between Cryptosporidium parvum gp60 subtypes. Subtype differentiation is based on the difference between the melting temperatures of individual subtypes conferred by variations in the polymorphic region of gp60.

• Nested gp60 primers were designed to amplify a target region of <200 base pairs for effective HRM analysis

• This method presents a rapid, sensitive, cost effective alternative to conventional sequencing.

• This method is highly flexible and may be applied to other loci in order to facilitate multi-locus analysis and improve the discriminative abilities of the method.

Parasitic diseases of equids in Iran (1931-2020): a literature review

Parasitic infections can cause many respiratory, digestive and other diseases and contribute to some performance conditions in equids. However, knowledge on the biodiversity of parasites of equids in Iran is still limited. The present review covers all the information about parasitic diseases of horses, donkeys, mules and wild asses in Iran published as articles in Iranian and international journals, dissertations and congress papers from 1931 to July 2020. Parasites so far described in Iranian equids include species of 9 genera of the Protozoa (Trypanosoma, Giardia, Eimeria, Klossiella, Cryptosporidium, Toxoplasma, Neospora, Theileria and Babesia), 50 helminth species from the digestive system (i.e., 2 trematodes, 3 cestodes and 37 nematodes) and from other organs (i.e., Schistosoma turkestanica, Echinococcus granulosus, Dictyocaulus arnfieldi, Parafilaria multipapillosa, Setaria equina and 3 Onchocerca spp.). Furthermore, 16 species of hard ticks, 3 mite species causing mange, 2 lice species, and larvae of 4 Gastrophilus species and Hippobosca equina have been reported from equids in Iran. Archeoparasitological findings in coprolites of equids include Fasciola hepatica, Oxyuris equi, Anoplocephala spp. and intestinal strongyles. Parasitic diseases are important issues in terms of animal welfare, economics and public health; however, parasites and parasitic diseases of equines have not received adequate attention compared with ruminants and camels in Iran. The present review highlights the knowledge gaps related to equines about the presence, species, genotypes and subtypes of Neospora hughesi, Sarcocystis spp., Trichinella spp., Cryptosporidium spp., Giardia duodenalis, Blastocystis and microsporidia. Identification of ticks vectoring pathogenic parasites, bacteria and viruses has received little attention, too. The efficacy of common horse wormers also needs to be evaluated systematically.

Genetic Diversity of Cryptosporidium in Bactrian Camels (Camelus bactrianus) in Xinjiang, Northwestern China

Cryptosporidium species are ubiquitous enteric protozoan pathogens of vertebrates distributed worldwide. The purpose of this study was to gain insight into the zoonotic potential and genetic diversity of Cryptosporidium spp. in Bactrian camels in Xinjiang, northwestern China. A total of 476 fecal samples were collected from 16 collection sites in Xinjiang and screened for Cryptosporidium by PCR. The prevalence of Cryptosporidium was 7.6% (36/476). Six Cryptosporidium species, C. andersoni (n = 24), C. parvum (n = 6), C. occultus (n = 2), C. ubiquitum (n = 2), C. hominis (n = 1), and C. bovis (n = 1), were identified based on sequence analysis of the small subunit (SSU) rRNA gene. Sequence analysis of the gp60 gene identified six C. parvum isolates as subtypes, such as If-like-A15G2 (n = 5) and IIdA15G1 (n = 1), two C. ubiquitum isolates, such as subtype XIIa (n = 2), and one C. hominis isolate, such as Ixias IkA19G1 (n = 1). This is the first report of C. parvum, C. hominis, C. ubiquitum, and C. occultus in Bactrian camels in China. These results indicated that the Bactrian camel may be an important reservoir for zoonotic Cryptosporidium spp. and these infections may be a public health threat in this region.

Cryptosporidium infections in sheep farms from Italy

Cryptosporidiosis is recognized as being a significant cause of gastrointestinal illness due to its wide range of vertebrate hosts, including humans. Infection with Cryptosporidium spp. is especially common in young domestic ruminants (calves, lambs and goat kids) and has been associated with economic losses worldwide. In contrast to cattle, to date, detailed studies on Cryptosporidium infections in sheep from Europe are still limited; thus, their importance as reservoirs of Cryptosporidium species with implications on animal and public health still needs to be clarified. This study evaluates the prevalence and zoonotic potential of Cryptosporidium spp. in sheep farms in Italy. A total of 915 individual faecal samples divided into three different animal categories were collected from 61 sheep farms. Each sample was examined by microscopy of faecal smears stained by modified Ziehl-Neelsen and by biomolecular techniques. Cryptosporidium oocysts were detected in 10.1% of the animals examined and in 34.4% of the farms. The prevalence of Cryptosporidium spp. was significantly higher (χ² = 51.854; P < 0.001) in diarrhoeic samples than in pasty or normal faeces. Genotype analyses showed the presence of two Cryptosporidium species: C. parvum and C. ubiquitum. Subtyping analysis of C. parvum isolates revealed the presence of subtypes IIa15G2R1 and IIdA20G1 and of subtype XIIa for C. ubiquitum. These findings have public health implications since both Cryptosporidium species identified are considered zoonotic, and C. parvum is the second-most common Cryptosporidium species infecting humans. Our data reveal that lambs, especially those excreting diarrhoeic faeces, may be important reservoirs of Cryptosporidium. We also highlight the need to establish adequate control and monitoring programmes for the control of this infection in sheep farms primarily through coprological monitoring.

Asymptomatic Cryptosporidium infections in ewes and lambs are a source of environmental contamination with zoonotic genotypes of Cryptosporidium parvum

Protozoan parasites of the Cryptosporidium genus cause severe cryptosporidiosis in newborn lambs. However, asymptomatic infections also occur frequently in lambs and ewes. In sheep, the most commonly detected Cryptosporidium species are C. ubiquitum, C. xiaoi and C. parvum. Due to a lack of relevant information about such infections in France, we investigated the situation on five dairy sheep farms in the Pyrénées-Atlantiques Department in south-western France in December 2017. Individual fecal samples were collected from 79 female lambs (5–17 days old) and their mothers (72 ewes). Oocysts were screened using Heine staining before and after Bailenger concentrations. Cryptosporidium species identification and genotyping were performed using real-time PCR and gp60 gene sequencing. No cases of clinical cryptosporidiosis were observed in the 79 lambs. Microscopically, Cryptosporidium spp. oocysts were observed in only one lamb on one farm (prevalence 1.3%) and one ewe on another farm (prevalence 1.4%). By contrast, Cryptosporidium spp. DNA was detected in 17 ewes (prevalence ranging from 10.5% to 50% depending on the farm) and in 36 lambs (prevalence ranging from 0% to 77.8% depending on the farm). Only zoonotic Cryptosporidium parvum IId and IIa genotypes were identified when genotyping was possible. Cryptosporidium ubiquitum and C. xiaoi were detected on one and three farms, respectively. We conclude that healthy young lambs and their mothers during the peripartum period could be a source of environmental contamination with oocysts.

Development of an immunocompetent mouse model susceptible to Cryptosporidium tyzzeri infection

AIMS

Immunocompromised mice are extensively used in the screening of vaccines and drugs for Cryptosporidium, but this study model does not reflect the real status of infection in immunocompetent animals. This study aimed to provide an optimized animal model for future studies of Cryptosporidium vaccine.

METHODS AND RESULTS

Three mouse strains (ICR, BALB/c and KM) with or without immunosuppression were compared after challenge with Cryptosporidium tyzzeri (C tyzzeri). The results indicated that ICR mice shed a greater number of faecal oocysts (20 346 ± 203 oocysts/g) compared with BALB/c (2077 ± 142 oocysts/g) and KM mice (3207 ± 431 oocysts/g) after experimental infection with C tyzzeri (P < .001). However, ICR mouse model is uniquely effective for C tyzzeri, not for other Cryptosporidium spp. such as C parvum. ICR mice were then used to determine the immunoreactions and immunoprotection of P23-DNA vaccine (pVAX1-P23) to C tyzzeri experimental infection. The results showed that a significant increase in anti-P23 antibody levels was induced by the pVAX1-P23 vaccine. Compared to pVAX1, TB and blank control mice, pVAX1-P23 immunized mice produced specific spleen cell proliferation as well as enhanced IL-5, IL-12p70 and IFN-γ production in sera. After challenge with 5 × 10⁶ C tyzzeri oocysts, the oocyst shedding of the pVAX1-P23 immunized group was reduced by 69.94% comparing to the infection control.

CONCLUSION

These results provide an optimized animal model for the study of prophylactic vaccines and this model might be applied to other candidates against Cryptosporidium, not only for pVAX1-P23.

Cryptosporidiosis and Giardiasis in Buffaloes (Bubalus bubalis)

Cryptosporidium spp. and Giardia duodenalis infect the gastrointestinal tracts of animals and humans. Both parasite groups are distributed worldwide and cause significant economic losses in animal productivity. Infected hosts presenting with and without clinical manifestations can eliminate infective forms of these protozoa, which are particularly important to One Health. Compared to the published research on cattle, relatively few studies have examined the epidemiology of cryptosporidiosis and giardiasis in buffaloes. This short review describes the global occurrence of Cryptosporidium spp. and G. duodenalis in buffaloes, including the molecular techniques employed for the identification of species/assemblages and genotypes of these protozoa. Genetic analyses of isolates of G. duodenalis and Cryptosporidium spp. from various sources (environmental, animal, and human) have been performed to investigate their epidemiology. In buffaloes, the species Cryptosporidium parvum, Cryptosporidium ryanae, Cryptosporidium bovis, and Cryptosporidium suis-like have been characterized, as well as assemblages A and E of G. duodenalis. We demonstrate that buffaloes can be infected by species of Cryptosporidium spp. and G. duodenalis assemblages with zoonotic potential. Epidemiological studies that utilize molecular biology techniques represent an important resource for efforts to control and prevent the spread of these protozoans.

Molecular characterization of Cryptosporidium spp. from patients with diarrhoea in Lusaka, Zambia

Cryptosporidium is a major etiological agent of diarrhoeal diseases among children and immune-compromised individuals in sub-Saharan African countries. We conducted a study to determine the prevalence and genetic characteristics of Cryptosporidium spp. in stool samples from patients with diarrhoea who presented at the University Teaching Hospital in Lusaka, Zambia. Cryptosporidium species and subtypes from 71 microscopically confirmed cryptosporidiosis stool samples collected between 2017 and 2019 were determined by polymerase chain reaction followed by partial sequencing of the small subunit rRNA and 60-kDa glycoprotein (gp60) gene. Additionally, data for the period between 2014 and 2019 were reviewed and analysed for cryptosporidiosis seasonal and age distribution. Cryptosporidium was more prevalent in the rainy season. The highest number of cases was reported among the 1–4 year age group. By sequence analysis of the 71 positive isolates, Cryptosporidium hominis (n = 42; 59.2%), C. parvum (n = 27; 38%), C. felis (n = 1; 1.4%), and C. meleagridis (n = 1; 1.4%) were identified. Four C. hominis subtype families (Ia, Ib, Id, and Ie) and three C. parvum subtype families (IIc, IIe, and IIs) were identified. The most frequent subtypes were IeA11G3T3 (n = 20; 28.2%), IIcA5G3 (n = 12; 16.9%), IIeA12G1 (n = 11; 15.5%) and IaA30R3 (n = 10; 14.1%). The observed species/subtypes of C. hominis and C. parvum indicated that the infection was mainly transmitted through the anthroponotic route. The identification of C. felis and C. meleagridis suggests that an atypical zoonotic transmission cycle also exists.

Cryptosporidium Infections in Africa-How Important Is Zoonotic Transmission? A Review of the Evidence

Cryptosporidium, a protozoan parasite in the phylum Apicomplexa, is the etiological agent of cryptosporidiosis, an intestinal infection characterized by profuse watery diarrhea. Over 30 species of Cryptosporidium are recognized, some host specific whereas others infect a broader host range. Cryptosporidium hominis and Cryptosporidium parvum are the species most commonly associated with human infection; C. hominis is largely associated only with human infections, but C. parvum is also associated with infection in animals, especially young ruminants. In some regions, cryptosporidiosis is a serious veterinary problem, particularly for calves, and lambs. Many outbreaks of human cryptosporidiosis have been associated with zoonotic transmission following contact with infected animals. In Africa, where cryptosporidiosis is a major contributor to pediatric morbidity and mortality, evidence suggests transmission is principally anthroponotic. Given the frequent close contact between humans and animals in Africa, the apparent predominance of human-to-human transmission is both interesting and puzzling. In this article, after a brief "text book" introduction to the parasite, we consider in separate sections the different aspects of relevance to Cryptosporidium transmission in African countries, describing different aspects of the various species and subtypes in human and animal infections, considering livestock management practices in different African countries, and looking for any characteristic "hot spots" where zoonotic transmission has apparently occurred. Studies where transmission networks have been investigated are particularly relevant. Finally, in a separate section, we try to gather these different strands of evidence together in order to assess the reasons behind the apparent predominance of anthroponotic transmission in Africa. Reviewing the available evidence provides an opportunity to re-think transmission pathways, not only in Africa but also elsewhere, and also to pose questions. Does the predominance of human-to-human transmission in Africa reflect a relative absence of zoonotic C. parvum in African livestock? Are Africans less susceptible to zoonotic Cryptosporidium infection, perhaps resulting from early immunostimulation by C. hominis or due to inherent genetic traits? Is the African environment-in all its variety-simply more detrimental to oocyst survival? Will the so-called hypertransmissible subtypes, currently relatively rare in Africa, be introduced from Europe or elsewhere, and, if so, will they fade out or establish and spread? Our intention with this manuscript is not only to summarize and consolidate diverse data, thereby providing an overview of data gaps, but also to provide food for thought regarding transmission of a parasite that continues to have a considerable impact on both human and animal health.

Molecular characterization of Cryptosporidium spp. in minks (Neovison vison), blue foxes (Vulpes lagopus), and raccoon dogs (Nyctereutes procyonoides) in farms from Xinjiang, Northwest China

The objective of this study was to determine the infection rate and genetic diversity of Cryptosporidium spp. in minks, foxes, and raccoon dogs, farmed in the Xinjiang Uygur Autonomous Region, Northwest China. Fresh fecal specimens were collected from individual cages of farmed minks (n = 214), blue foxes (n = 35), and raccoon dogs (n = 39) and examined using nested PCR based on the Cryptosporidium spp. small subunit rRNA gene. Cryptosporidium spp. was detected in 35 cages (12.2%, 35/288), with a higher infection rate detected in raccoon dogs (20.5%) compared with minks (12.1%) and blue foxes (2.9%). Sequence analysis showed that Cryptosporidium canis was the only species identified in blue foxes and raccoon dogs, while in the 26 Cryptosporidium-positive mink specimens, Cryptosporidium mink genotype (n = 17), C. canis (n = 7), and Cryptosporidium parvum (n = 2) were identified. Further analysis based on the 60-kDa glycoprotein (gp60) gene determined that both C. parvum isolates belonged to the subtype IIdA15G1, while eight of the 17 Cryptosporidium mink genotype isolates were a novel subtype that we have named XeA5G1. To the best of our knowledge, this is the first report of C. parvum subtype IIdA15G1 infection in minks. Since all the Cryptosporidium species/genotypes identified in minks, foxes, and raccoon dogs from Xinjiang have been previously found in humans, our results suggest that these fur animals may play a role in the transmission of zoonotic Cryptosporidium.

Cryptosporidium and Cryptosporidiosis: The Perspective from the Gulf Countries

The present review discusses the burden of cryptosporidiosis in the Gulf Cooperation Council (GCC), which is underreported and underestimated. It emphasizes that the Cryptosporidium parasite is infecting inhabitants and expatriates in the Gulf countries. Children under 5 years are a vulnerable group that is particularly affected by this parasitic disease and can act as carriers, who contribute to the epidemiology of the disease most probably via recreational swimming pools. Various risk factors for cryptosporidiosis in the GCC countries are present, including expatriates, predisposing populations to the infection. Water contamination, imported food, animal contact, and air transmission are also discussed in detail, to address their significant role as a source of infection and, thus, their impact on disease epidemiology in the Gulf countries' populations.

Genetic Diversity and Population Structure of Cannabis Based on the Genome-Wide Development of Simple Sequence Repeat Markers

Cannabis has been used as a source of nutrition, medicine, and fiber. However, lack of genomic simple sequence repeat (SSR) markers had limited the genetic research on Cannabis species. In the present study, 92,409 motifs were identified, and 63,707 complementary SSR primer pairs were developed. The most abundant SSR motifs had six repeat units (36.60%). The most abundant type of motif was dinucleotides (70.90%), followed by trinucleotides, tetranucleotides, and pentanucleotides. We randomly selected 80 pairs of genomic SSR markers, of which 69 (86.25%) were amplified successfully; 59 (73.75%) of these were polymorphic. Genetic diversity and population structure were estimated using the 59 (72 loci) validated polymorphic SSRs and three phenotypic markers. Three hundred ten alleles were identified, and the major allele frequency ranged from 0.26 to 0.85 (average: 0.56), Nei’s genetic diversity ranged from 0.28 to 0.82 (average: 0.56), and the expected heterozygosity ranged from 0.28 to 0.81 (average: 0.56). The polymorphism information content ranged from 0.25 to 0.79 (average: 0.50), the observed number of alleles ranged from 2 to 8 (average: 4.13), and the effective number of alleles ranged from 0.28 to 0.81 (average: 0.5). The Cannabis population did not show mutation-drift equilibrium following analysis via the infinite allele model. A cluster analysis was performed using the unweighted pair group method using arithmetic means based on genetic distances. Population structure analysis was used to divide the germplasms into two subgroups. These results provide guidance for the molecular breeding and further investigation of Cannabis.

Prevalence of Cryptosporidium in pigs in China: A systematic review and meta-analysis

Cryptosporidium is an important zoonotic parasite that can infect a variety of hosts, including pigs and humans, through water and food. Many studies on Cryptosporidium infection in pigs have been reported worldwide. However, the meta-analysis of Cryptosporidium infection in pigs in China has not been published. This study retrieved articles related to Cryptosporidium in pigs in China by using four databases: Chinese National Knowledge Infrastructure (CNKI), PubMed, VIP Chinese journal database and Wanfang Data. We retrieved 40 studies related to Cryptosporidium infection in China, and those articles were harvested from the inception to 1 January 2020. We estimated that the overall prevalence of pigs with Cryptosporidium in the selected period was 12.2% (4,349/30,404). In the sampling year subgroup, the prevalence rate after 2010 was the lowest at 8.7% (2,087/18,100). In Northern China, the Cryptosporidium prevalence was 47.9% (34/71). By contrast, the prevalence of Cryptosporidium in Southwestern China was only 6.9% (778/6,445). The infection rate of Cryptosporidium in diarrhoea pigs of 15.6% (74/384) was higher than that in non-diarrhoea pigs at 10.8% (378/2,840). Among the four age groups, the prevalence of weaning pigs of 16.2% (530/3,243) was the highest, and the difference was significant (p < .05). The prevalence of Cryptosporidium in extensive farming was 25.7% (660/3,121), which was significantly higher than in intensive farming 8.7% (566/6,336), and the prevalence of infection was related to the farming modes (p < .05). We also analysed the impact of different geographic factor subgroups (longitude, latitude, precipitation, temperature, humidity, climate and altitude) on the prevalence of pigs. The results showed that cryptosporidiosis was widespread in pigs in China. We suggest that appropriate control schemes should be developed according to the differences in breeding patterns and geographic conditions in different regions, and effective management measures should be developed to reduce the spread between pigs.

Phenotypic screening techniques for Cryptosporidium drug discovery

Introduction: Two landmark epidemiological studies identified Cryptosporidium spp. as a significant cause of diarrheal disease in pediatric populations in resource-limited countries. Notably, nitazoxanide is the only approved drug for treatment of cryptosporidiosis but shows limited efficacy. As a result, many drug discovery efforts have commenced to find improved treatments. The unique biology of Cryptosporidium presents challenges for traditional drug discovery methods, which has inspired new assay platforms to study parasite biology and drug screening. Areas covered: The authors review historical advancements in phenotypic-based assays and techniques for Cryptosporidium drug discovery, as well as recent advances that will define future drug discovery. The reliance on phenotypic-based screens and repositioning of phenotypic hits from other pathogens has quickly created a robust pipeline of potential cryptosporidiosis therapeutics. The latest advances involve new in vitro culture methods for oocyst generation, continuous culturing capabilities, and more physiologically relevant assays for testing compounds. Expert opinion: Previous phenotypic screening techniques have laid the groundwork for recent cryptosporidiosis drug discovery efforts. The resulting improved methodologies characterize compound activity, identify, and validate drug targets, and prioritize new compounds for drug development. The most recent improvements in phenotypic assays are poised to help advance compounds into clinical development.

Diversity of Cryptosporidium spp. in wild rodents from the Canary Islands, Spain

BACKGROUND

Cryptosporidium spp. are worldwide protozoan parasites which include species that can lead to cryptosporidiosis in humans. Different animal species can serve as reservoirs and sources of dissemination of the disease, such as rodent species due their potential in transmitting zoonotic pathogens to humans and other animals. In the Canary Islands (Spain), Cryptosporidium parvum and Cryptosporidium hominis have been identified in patients with diarrhea. However, the occurrence of Cryptosporidium spp. in possible reservoirs in this archipelago remains unclear. Considering the zoonotic potential of these protozoans, the aim of the present study was to determine the presence of Cryptosporidium spp. in peridomestic wild rodents and the possible role of these mammals as a source of transmission of these protozoans in Canary Islands.

METHODS

A total of 179 rodents belonging to Rattus rattus and Mus musculus domesticus from four Canary Islands, La Palma, El Hierro, Tenerife and Lanzarote, were analyzed. Feces were screened for Cryptosporidium spp. by nested PCR of the 18S ribosomal RNA fragment and the sequences used for phylogenetic analyses.

RESULTS

Cryptosporidium spp. were found widely distributed with an overall prevalence of 12.30% in rodents (13.86% for R. rattus and 10.25% for M. m. domesticus). The overall prevalence by island was 19.60% for Tenerife, 7.14% for La Palma, 5.71% for El Hierro and 0% for Lanzarote. Cryptosporidium tyzzeri, Cryptosporidium meleagridis, Cryptosporidium muris and Cryptosporidium sp. rat genotype I and II/III were successfully identified, in addition to two unidentified Cryptosporidium genotypes.

CONCLUSIONS

This study contributes to the knowledge of the biodiversity and distribution of Cryptosporidium spp. in wild rodents from the Canary Islands, highlighting the presence of three zoonotic species, C. tyzzeri, C. meleagridis and C. muris, being the first detection of these three species in wild rodents in the Canary Islands and the first report of C. meleagridis in R. rattus. Given the results obtained in our study, future studies in non-sampled areas are required to better understand the epidemiology of these protozoans in wild rodents in the archipelago.

Prevalence and molecular characterization of Cryptosporidium spp. in pigs in Xinjiang, China

Cryptosporidium spp. are distributed ubiquitously worldwide, and pigs are considered as one of the main reservoir hosts. Eight hundred one porcine fecal specimens were collected from seven intensive pig farms in Xinjiang Uygur Autonomous Region, China. Cryptosporidium spp. were screened via PCR amplification of the small ribosomal subunit RNA gene, and 143 specimens (17.9%, 143/801) from all seven farms tested positive for Cryptosporidium spp. Cryptosporidium prevalence in the pigs differed significantly among farms (p < 0.01). The highest Cryptosporidium spp. prevalence in post-weaned pigs was 39.5% (111/281), followed by fattening pigs (23.2%, 30/129), pre-weaned pigs (1.2%, 2/169), and sows (0/222). Significant differences were observed between age groups (p < 0.01). C. suis was the predominantly identified species (62.9%, 90/143), followed by C. scrofarum (35.7%, 51/143), and C. parvum (1.4%, 2/143). Two C. parvum specimens were subtyped by analyzing the 60-kDa glycoprotein (gp60) gene sequences and were identified as IIdA14G1 and IIdA15G1. To our knowledge, this is the first report of C. parvum infection in pigs in China. The identification of three Cryptosporidium species, including zoonotic C. parvum in pigs in Xinjiang raises concern for the health of both swine animals and personnel in the pig industry.

The red fox (Vulpes vulpes) as a potential natural reservoir of human cryptosporidiosis by Cryptosporidium hominis in Northwest Spain

Giardia duodenalis and Cryptosporidium spp. are ubiquitous intestinal protozoa that parasitize domestic and wild animals, as well as human beings. Due to their zoonotic potential, the objective of the present study was to determine the presence of these pathogens in the fox population (Vulpes vulpes) located in Northwest Spain. A total of 197 faecal samples from legally hunted foxes were collected in the autonomous region of Galicia. The presence of G. duodenalis and Cryptosporidium spp. was investigated by PCR-based methods amplifying the small subunit ribosomal RNA (ssu rRNA) gene of the parasites. Attempts to genotype obtained positive samples were subsequently conducted at the glutamate dehydrogenase (gdh) and β-giardin (bg) genes of G. duodenalis, and the 60 kDa glycoprotein (gp60) gene of Cryptosporidium. Giardia duodenalis and Cryptosporidium spp. were identified in 19 (9.6%) and 12 (6.1%) of the investigated samples, respectively. However, five Cryptosporidium species were detected at the ssu rRNA locus: C. hominis (33.4%, 4/12), C. canis (25.0%, 3/12), C. parvum (16.7%, 2/12), C. ubiquitum (8.3%, 1/12) and C. suis (8.3%, 1/12). An additional Cryptosporidium-positive sample was identified at the genus level only. Typing and subtyping of Giardia- and Cryptosporidium-positive samples were unsuccessful. The detection of C. hominis in wild foxes indicates the probable overlapping of sylvatic and domestic cycles of this parasite in rural settings. Besides, this finding raises the question of whether red foxes may act as natural reservoirs of C. hominis. The detection of C. parvum and C. suis is suggestive of active transmission events between farm and wild animals, opening up the possibility of transmission to human beings.

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

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

Genetic Diversity of Cryptosporidium parvum in Neonatal Dairy Calves in Xinjiang, China

Cryptosporidium parvum has been identified as a major cause of diarrhea and diarrhea-associated deaths in young children and neonatal calves. Infections can remain asymptomatic but may lead to malnutrition and persistent growth retardation. To assess the relationship between C. parvum genetic diversity and pathogenicity in neonatal dairy calves and determine the cause of diarrhea among these calves, 232 fecal samples from neonatal dairy calves on 12 farms in Xinjiang, China, were characterized for Cryptosporidium presence based on the small subunit rRNA gene. The Cryptosporidium prevalence was 38.4% (89/232), and three species were detected with restriction fragment length polymorphism analysis, including C. parvum (the significantly dominant species), C. ryanae, and C. bovis. Cryptosporidium prevalence was significantly higher in neonatal dairy calves with diarrhea (52.6%, 51/97) than in calves without diarrhea (28.1%, 38/135). All C. parvum-positive samples were analyzed based on the 60 KDa glycoprotein gene, and IIdA15G1, IIdA20G1, IIdA14G1, and IIdA19G1 were successfully subtyped. These data indicate that C. parvum may be a major contributor to diarrheal disease in neonatal dairy calves, and C. parvum subtypes from neonatal dairy calves in Xinjiang exhibited high genetic diversity.

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

Background

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

Methods

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

Results

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

Conclusions

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

Comparative genetic diversity of Cryptosporidium species causing human infections

Parasites sometimes expand their host range and cause new disease aetiologies. Genetic changes can then occur due to host-specific adaptive alterations, particularly when parasites cross between evolutionarily distant hosts. Characterizing genetic variation in Cryptosporidium from humans and other animals may have important implications for understanding disease dynamics and transmission. We analyse sequences from four loci (gp60, HSP-70, COWP and actin) representing multiple Cryptosporidium species reported in humans. We predicted low genetic diversity in species that present unusual human infections due to founder events and bottlenecks. High genetic diversity was observed in isolates from humans of Cryptosporidium meleagridis, Cryptosporidium cuniculus, Cryptosporidium hominis and Cryptosporidium parvum. A deviation of expected values of neutrality using Tajima's D was observed in C. cuniculus and C. meleagridis. The high genetic diversity in C. meleagridis and C. cuniculus did not match our expectations but deviations from neutrality indicate a recent decrease in genetic variability through a population bottleneck after an expansion event. Cryptosporidium hominis was also found with a significant Tajima's D positive value likely caused by recent population expansion of unusual genotypes in humans. These insights indicate that changes in genetic diversity can help us to understand host-parasite adaptation and evolution.

Prevalence and Characterization of Cryptosporidium Species and Genotypes in Four Farmed Deer Species in the Northeast of China

Cryptosporidiosis is a major public health problem in humans and animals. Information on the prevalence and molecular diversity of Cryptosporidium in farmed deer in northeastern China is limited. In this study, the prevalence of these parasites was investigated in four farmed deer species, including 125 reindeer, 109 red deer, 86 sika deer, and 18 Siberian roe deer by nested PCR amplification of the partial small subunit of ribosomal RNA (SSU rRNA) gene. C. ubiquitum isolates were subtyped using nested PCR and sequence analysis of the 60-kDa glycoprotein (gp60) gene. The overall prevalence of Cryptosporidium was 7.1%, with 15.1% for sika deer, 4.0% for reindeer, 4.6% for red deer, and 5.6% for roe deer. C. ubiquitum (n = 4), C. xiaoi (n = 2), and Cryptosporidium deer genotype (n = 18) were identified. All four C. ubiquitum isolates belonged to the XIIa subtype (n = 4). This study confirms that Cryptosporidium deer genotype is widely occurring in deer in the investigated areas. Presence of zoonotic C. ubiquitum XIIa subtype indicates that farmed deer represent potential source of zoonotic cryptosporidia and might pose a threat to human health.

Molecular characterization and zoonotic potential of Enterocytozoon bieneusi, Giardia duodenalis and Cryptosporidium sp. in farmed masked palm civets (Paguma larvata) in southern China

BACKGROUND

Masked palm civets are known to play an important role in the transmission of some zoonotic pathogens. However, the distribution and zoonotic potential of Enterocytozoon bieneusi, Giardia duodenalis and Cryptosporidium spp. in these animals remain unclear.

METHODS

A total of 889 fecal specimens were collected in this study from farmed masked palm civets in Hainan, Guangdong, Jiangxi and Chongqing, southern China, and analyzed for these pathogens by nested PCR and DNA sequencing.

RESULTS

Altogether, 474 (53.3%), 34 (3.8%) and 1 (0.1%) specimens were positive for E. bieneusi, G. duodenalis and Cryptosporidium sp., respectively. Sequence analysis revealed the presence of 11 novel E. bieneusi genotypes named as PL1-PL11 and two known genotypes Peru8 and J, with PL1 and PL2 accounting for 90% of E. bieneusi infections. Phylogenetically, PL4, PL5, PL9, PL10 and PL11 were clustered into Group 1, while PL1, PL2, PL3, PL6, PL7 and PL8 were clustered into Group 2. Assemblage B (n = 33) and concurrence of B and D (n = 1) were identified among G. duodenalis-positive animals. Further multilocus genotyping of assemblage B has revealed that all 13 multilocus genotypes in civets formed a cluster related to those from humans. The Cryptosporidium isolate from one civet was identified to be genetically related to the Cryptosporidium bamboo rat genotype II.

CONCLUSIONS

To the best of our knowledge, this first report of enteric protists in farmed masked palm civets suggests that these animals might be potential reservoirs of zoonotic E. bieneusi and G. duodenalis genotypes.

Molecular identification of Cryptosporidium spp. in pet snakes in Beijing, China

Few reports of Cryptosporidium spp. in snakes in China have been published. To determine the infection rate and document the presence of Cryptosporidium in pet snakes using molecular methods, 273 fecal samples were collected from eight species of pet snakes from 13 pet households in Beijing, China, and were examined by PCR amplification of the small subunit ribosomal RNA gene. Cryptosporidium was detected from 17 of 273 (6.2%) samples, and nine out of 13 households tested positive for Cryptosporidium with a range of 3.3 to 33.3% among households showing significant difference (p < 0.01). The infection rate of Cryptosporidium for females and males was 6.5% (13/201) and 5.6% (4/72), respectively, showing no significant difference (p > 0.05). Six out of eight pet snake species tested positive for Cryptosporidium with a range of 4.2 to 9.1% among species, showing no significant difference (p > 0.05). Two Cryptosporidium species were identified: Cryptosporidium serpentis in 10 samples and Cryptosporidium varanii in seven samples. No zoonotic Cryptosporidium species occur in our study populations.

Detection of human intestinal protozoan parasites in vegetables and fruits: a review

Diarrheal diseases caused by intestinal protozoan parasites are a major food-borne public health problem across the world. Vegetables and fruits provide important nutrients and minerals, but are also common sources of some food-borne human pathogenic microorganisms. The contamination of raw vegetables and fruits with human pathogenic parasites are now a global public health threat, despite the health benefits of these foods in non-pharmacological prophylaxes against diseases. A large number of reports have documented the contamination of vegetables or fruits with human pathogenic microorganisms. In this paper, we reviewed the contamination and detection methods of human pathogenic intestinal protozoans that are frequently recovered from raw vegetables and fruits. The protozoan parasites include Cryptosporidium spp., Giardia duodenalis, Cyclospora cayetanensis, Entamoeba spp., Toxoplasma gondii, Balantioides coli, Blastocystis sp., Cystoisospora belli and Enterocytozoon bieneusi. The risk factors involved in the contamination of vegetables and fruits with parasites are also assessed.

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.

Prevalence and Molecular Genotyping of Cryptosporidium Spp. in Diarrheic Patients from Bandar Abbas City, Southern Iran

Background: Cryptosporidium species are recognized as one of the most important gastrointestinal pathogens of humans and livestock. Objectives: This study aimed to determine the prevalence and sub-genotypes of Cryptosporidium spp. among diarrheic patients in Bandar Abbas City, Iran. Methods: Diarrheic fecal samples were collected from 170 patients in three hospitals of Bandar Abbas, Iran, from October 2018 to May 2019. Initial parasitological identification of Cryptosporidium spp. was performed by modified Ziehl-Neelsen (ZN) staining. For molecular analysis, the positive specimens and the suspected ones of Cryptosporidium spp. were evaluated by sequence analysis of the 60-kDa glycoprotein gene (gp60). The collected data were analyzed using SPSS software and the relationship between the variables and the presence of Cryptosporidium spp. assessed by the chi-square test. To assess the degree of agreement between PCR and ZN staining, Cohen’s kappa-index was applied. Results: Of the 170 diarrheic patients, 98 (57.6%) were male, and 72 (42.4%) were female. Prevalence of Cryptosporidium spp. by parasitological examination was 1.8% (3/170). However, using PCR, Cryptosporidium spp. was detected in 12% (6/50) of the positive microscopically samples (3 samples) and 47 suspected specimens. Sequence analysis of the gp60 gene showed that all of the positive isolates were Cryptosporidium parvum in which all subtypes belonged to allele family IId. Two distinct nucleotide sequences obtained from this study were deposited in GenBank under the accession numbers MN820453 and MN820454. Conclusions: The predominance of C. parvum (subtype family IId) in this study emphasizes the importance of zoonotic Cryptosporidium transmission in Bandar Abbas, Southern Iran.

Molecular Characterization of Cryptosporidium spp. in Brandt's Vole in China

Cryptosporidium spp. are important intestinal parasites that infect humans and various animals, including wildlife. Currently, few epidemiological data in wild rodents, especially in voles, are available. In the present study, a total of 678 Brandt's vole feces samples were collected from Maodeng Livestock Farm and East Ujimqin, Inner Mongolia. The overall prevalence of Cryptosporidium spp. was 18.7%. Significant differences were not found between genders but between locations and weight groups. Moreover, three known species/genotypes, C. suis, Cryptosporidium environmental sequence and muskrat genotype II, and a novel Cryptosporidium species/genotypes of Brandt's vole was identified. To the best of our knowledge, this is the first report of Cryptosporidium spp. infection in Brandt's vole worldwide. These findings imply Brandt's voles might be a potential source of human cryptosporidiosis.

Common occurrence of Cryptosporidium hominis in children attending day-care centers in Medellin, Colombia

Cryptosporidium spp. are apicomplexan protozoa associated with chronic diarrhea in AIDS and other immunocompromised patients, and one of the commonest causes of childhood diarrhea and malnutrition, particularly in low-income settings. In Colombia, there are few molecular epidemiological studies on Cryptosporidium spp.; thereby, the transmission dynamics of this parasite in the country is poorly known. This study evaluated the diversity of Cryptosporidium at species, subtype family, and subtype level in children attending various day-care centers in Medellin, Colombia. Two hundred and ninety stool samples from children < 5 years of age were collected from April to November of 2015. All samples were processed by PCR and sequence analysis of the ssu RNA gene and the gp60 gene. An infection rate of 2.4% was observed, with only two Cryptosporidium species identified: C. hominis (6/7) and C. meleagridis (1/7). Cryptosporidium hominis isolates belonged to the subtypes IbA10G2, IaA13R6 and IaA13R7; IIIbA26G1R1 C. meleagridis subtype was also detected. There is a C. hominis predominance in the children evaluated, suggesting an important role of the anthroponotic transmission cycle in the day-care centers analyzed. Further investigation is required to determine infection sources and susceptible hosts in order to define appropriate management of cryptosporidiosis.

First report of Cryptosporidium spp. infection and risk factors in black-boned goats and black-boned sheep in China

Cryptosporidium is an opportunistic protozoan parasite that can inhabit in the gastrointestinal tract of various hosts. Cryptosporidium infection in black-boned goats and black-boned sheep may pose a threat to the survival and productivity, causing considerable economic losses to the livestock industry. However, it is yet to know whether black-boned goats and black-boned sheep in China are infected with Cryptosporidium. Thus, the objective of the present study was to investigate the prevalence and associated risk factors of Cryptosporidium infection in black-boned goats and black-boned sheep in Yunnan province, China. A total of 590 fecal samples were obtained from black-boned goats and black-boned sheep from five counties in Yunnan province, and the prevalence and species distribution of Cryptosporidium were determined by amplification of the 18S rDNA fragment using the nested PCR. The overall Cryptosporidium prevalence was 13.2% (78/590), with 18.0% (55/305) in black-boned goats and 8.1% (23/285) in black-boned sheep. The age and sampling site were identified as main factors that result in significant differences in Cryptosporidium prevalence. Three species, namely C. muris, C. xiaoi, and C. ubiquitum, were identified in black-boned goats and black-boned sheep in the present study, with C. muris (46/78) as the predominant species. This is the first report of Cryptosporidium infection in black-boned goats and black-boned sheep in China, and the findings will facilitate better understanding, prevention, and control of Cryptosporidium infection in black-boned goats and black-boned sheep in China.

Prevalence and genotypic identification of Cryptosporidium in free-ranging and farm-raised donkeys (Equus asinus asinus) in Xinjiang, China

The prevalence and zoonotic potential of Cryptosporidium in donkeys is poorly understood. Here, 680 fecal specimens were collected from 178 free-ranging and 502 farmed donkeys in Xinjiang, China. Cryptosporidium was identified using PCR amplification of the small subunit of ribosomal DNA. Cryptosporidium-positive isolates were subtyped using PCR analysis of the 60 kDa glycoprotein gene (gp60). The overall prevalence of Cryptosporidium was 2.4% (16/680), with 3.2% (16/502) in farmed donkeys and 0% (0/178) in free-ranging donkeys. Cryptosporidium hominis (n = 13), C. parvum (n = 1) and Cryptosporidium horse genotype (n = 2) were identified. The C. hominis isolates belonged to two subtypes, IkA16 (n = 9) and IkA16G1 (n = 4). The subtype of C. parvum was IIdA15G1, whereas the two Cryptosporidium horse genotype isolates were of subtype VIaA15G4. The predominance of C. hominis in donkeys suggests that these animals are infected through human contact.

Molecular identification of Cryptosporidium spp. in alpacas (Vicugna pacos) in China

Cryptosporidium is a ubiquitous protozoan in human and animals. To investigate the genetic diversity of Cryptosporidium spp. in alpaca (Vicugna pacos) in China, 484 fecal samples from alpacas were collected at nine sites, and Cryptosporidium spp. were screened with PCR amplification of the small subunit ribosome RNA (SSU rRNA) locus. Cryptosporidium spp. infected 2.9% (14/484) of the alpacas. Of the nine collection sites, two were positive for Cryptosporidium, Wensu (3.0%, 3/100) and Qinghe (31.4%, 11/35). Three Cryptosporidium species were identified: C. parvum (n = 2), C. ubiquitum (n = 1), and C. occultus (n = 11). Cryptosporidium parvum and C. ubiquitum were further subtyped with the 60-kDa glycoprotein locus (gp60). The two C. parvum isolates were subtype IIdA15G1, but the one C. ubiquitum isolate was not subtyped successfully. A phylogenetic analysis indicated that the Cryptosporidium isolates clustered with previously identified species. To our knowledge, this is the first report of Cryptosporidium infections in alpacas in China and provides baseline data for the study of Cryptosporidium in alpacas in China.

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First report of Cryptosporidium spp. infections (with 2.9%) in alpacas in China.

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Three zoonotic Cryptosporidium species were identified in alpacas.

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It provides the molecular characteristic data for the study of Cryptosporidium in alpacas.