Molecular epidemiology of Cryptosporidium in humans and cattle in The Netherlands

Molecular identification and genetic diversity analysis of Cryptosporidium spp. infecting dogs from central and northern Jordan: Detection of zoonotic genotype IId

Cryptosporidium spp. are common causes of gastrointestinal disease in both humans and animals. This was a cross-sectional study conducted to determine the infection rate and genetic characteristics of Cryptosporidium infecting dogs in Jordan. A total of 249 faecal samples were collected from stray, pet, and breeding dogs from kennels (independent of their clinical condition) across three governorates in Jordan (Amman and Zarqa in Central Jordan and Irbid in Northern Jordan). Faecal samples were screened for Cryptosporidium using polymerase chain reaction (PCR) targeting the 18S rRNA gene, revealing an overall infection rate of 18.9% (47 out of 249). Cryptosporidiosis was significantly associated with indoor dogs, dogs cohabiting with other animals, and consuming raw food. Among the successfully sequenced samples, 25 (58.1%) were Cryptosporidium canis, 15 (34.9%) were Cryptosporidium parvum, and three (7.0%) were Cryptosporidium baileyi. Multiple diversity tests were employed, indicating low genetic differentiation between the studied populations of C. parvum and C. canis. Stability was observed for C. parvum, with minimal expansion observed for C. canis. Notably, each species exhibited a single dominant haplotype, consistent with the AMOVA results, where most of the variability occurred within populations. Further genotyping of C. parvum and C. canis was conducted by sequencing the gp60 gene. C. parvum isolates worldwide displayed solely the zoonotic IId genotypes, namely, IIdA20G1, IIdA22G1, IIdA18G1, and IIdA19G1. In contrast, the C. canis isolates exhibited the animal subtypes XXe and XXd. Consequently, dogs may serve as a source of infection with C. parvum and pose a public health risk in Jordan.

First microscopic and molecular identification of Cryptosporidium spp. in fat sand rats (Psammomys obesus) in Egypt and their potential zoonotic implications

Introduction

Rodents, thriving in human-altered environments, pose significant public health risks due to their role as reservoirs for numerous zoonotic parasites. Among these, Cryptosporidium spp. are recognized globally as leading causes of waterborne and foodborne diarrheal illnesses in humans. The specific role of fat sand rats (Psammomys obesus) in the transmission of Cryptosporidium spp. in Egypt and the genotypic characteristics of the circulating species in these animals remain poorly understood.

Methods

In this study, a total of 150 individual fat sand rat stool samples were collected from the saline marsh periurban areas of Abu-Rawash, Giza, Egypt. The samples were initially screened for the presence of Cryptosporidium spp. using light and scanning electron microscopy to characterize the parasite's oocysts. Furthermore, molecular identification and characterization of the parasite were carried out on selected microscopy-positive samples (n = 30) using conventional polymerase chain reaction (PCR) targeting the Cryptosporidium oocyst wall protein (COWP) gene. A subset of these positive samples by PCR was subjected to sequencing, with the resulting sequences deposited in GenBank™ and analyzed through phylogenetic methods.

Results

Conventional microscopy revealed that 46.7% (70/150; 95% CI: 38.7-54.6) of the analyzed stool samples contained structures consistent with Cryptosporidium oocysts. Moreover, the molecular analysis confirmed Cryptosporidium species in DNA from all 30 stool samples previously identified as heavily infected through microscopy. Notably, the phylogenetic analysis identified Cryptosporidium parvum (C. parvum) in the sequenced samples, likely originating from the rats' native habitats. These identified species have been deposited in GenBank™ under the accession numbers OM817461 (C. parvum FSA-1), OM817462 (C. parvum FSA-2), and OM817463 (C. parvum FSA-3) and revealed closed genetic identity with those species reported from human and other animal species in the same geographic location.

Conclusion

Overall, this study represents the first morphological and genetic identification of C. parvum isolated from fecal samples of fat sand rats trapped from periurban areas in Egypt. These findings provide valuable insights into the potential zoonotic implications of rodents in disease transmission at the national level, offering crucial information for public health awareness campaigns and informing local authorities.

Cryptosporidium species and subtypes in Norway: predominance of C. parvum and emergence of C. mortiferum

PCR-based diagnostics has revealed the previously largely unknown Cryptosporidium transmission and infections in high-income countries. This study aimed to determine domestic and imported subtypes of Cryptosporidium species in Norway, evaluate their demographic distribution, and identify potential small outbreaks. Cryptosporidium-positive human faecal samples were obtained from six medical microbiology laboratories between February 2022 and January 2024, together with 22 Cryptosporidium-positive animal samples. Species and subtypes were identified by sequencing PCR products from gp60 and SSU rRNA genes. Most cryptosporidiosis cases occurred during late summer/early autumn, primarily in children and young adults. Of 550 human samples, 359 were successfully characterized molecularly (65%), revealing infection with 10 different Cryptosporidium species. C. parvum occurred in 245 (68%) human isolates with IIa and IId being major allele families, with distinct regional distribution patterns of common subtypes. A kindergarten outbreak with 5 cases was due to C. parvum IIaA14G1R1. C. mortiferum was identified in 33 (9.2%) human cases of which 24 were known to be of domestic origin, making it the second most common species in human autochthonous cases in Norway. All C. mortiferum isolates were of the same genotype; XIVaA20G2T1, including 13 cases from a suspected small outbreak in Trøndelag. C. hominis occurred in 68 typed cases (19%), but mostly in infections acquired abroad, with allele families Ib and If occurring most often. In conclusion, this study of recent Cryptosporidium spp. and subtypes in Norway, highlights the predominance of C. parvum and the emergence of C. mortiferum among autochthonous cases.

Cryptosporidium Infections in Neonatal Calves on a Dairy Farm

This study was conducted with the aim of the molecular identification of the protozoan parasite Cryptosporidium spp. in calves in the early stage of their development on a dairy farm in Eastern Slovakia. Twenty-five Holstein and Holstein cross calves were included in the study and monitored from their birth to the fifth week of life (1-5 weeks). Fresh fecal samples were collected from the same group of calves each week, except during the fourth week, and with the exception of Sample 8. All samples were analyzed using the Ziehl-Neelsen staining method and coproantigen was tested using the ELISA test as the screening method. Using the ELISA method, the highest incidence of cryptosporidiosis was observed in the second week of life of the calves, while the antigen was detected in 21 (91.6%) calves. Using the Ziehl-Neelsen staining method, the highest incidence was also observed in the second week, with an incidence rate of 62.5%. Positive isolates confirmed by the ELISA test were molecularly characterized. The species and subtypes of Cryptosporidium in the positive isolates were identified using PCR and the sequence analysis of the small subunit of the ribosomal 18S RNA (ssu rRNA) and the 60 kDa glycoprotein (gp60) genes of the parasite. The sequence analysis of 29 isolates at the 18S rRNA loci confirmed the presence of two species-Cryptosporidium parvum and Cryptosporidium ryanae. Out of 29 isolates, 25 were assigned to the species C. parvum, with the gp60 locus identified as genotype IIaA17G1R1. Among the individual animal groups, calves are the most common reservoirs of the C. parvum zoonotic species. This disease has significant public health implications as contact with livestock and their feces and working with barn manure are major sources of infection, not only for other animals but also for humans.

Molecular Detection and Distribution of Giardia duodenalis and Cryptosporidium spp. Infections in Wild and Domestic Animals in Portugal

Enteric protozoan parasites Giardia duodenalis, Cryptosporidium spp., and, to a lesser extent, the ciliate Balantioides coli are responsible for severe human and animal intestinal disorders globally. However, limited information is available on the occurrence and epidemiology of these parasites in domestic, but especially wild species in Portugal. To fill this gap of knowledge, we have investigated G. duodenalis, Cryptosporidium spp., and B. coli occurrence, distribution, genetic diversity, and zoonotic potential by analyzing 756 fecal samples from several wild carnivores (n = 288), wild ungulates (n = 242), and domestic species (n = 226) collected across different areas of mainland Portugal. Overall, infection rates were 16.1% (122/756; 95% CI: 13.59-18.96) for G. duodenalis and 2.7% (20/756; CI: 1.62-4.06) for Cryptosporidium spp., while no ungulate sample analyzed yielded positive results for B. coli. Giardia duodenalis was found across a wide range of hosts and sampling areas, being most prevalent in the Iberian lynx (26.7%), the Iberian wolf (24.0%), and the domestic dog (23.9%). Cryptosporidium spp. was only identified in wild boar (8.4%), red fox (3.4%), Iberian lynx (3.3%), red deer (3.1%), and Iberian wolf (2.5%). Sequence analysis of G. duodenalis determined zoonotic assemblage A (subassemblage AI) in one roe deer sample, canine-specific assemblages C and D in Iberian wolf, red fox, and domestic dog, and ungulate-specific assemblage E in wild boar, sheep, cattle, and horse. Six Cryptosporidium species were identified: C. scrofarum in wild boar, C. canis in the Iberian wolf and red fox, C. ubiquitum in red deer and wild boar, C. felis in the Iberian lynx, and both C. ryanae and C. occultus in red deer. Giardia duodenalis and Cryptosporidium spp. coinfections were observed in 0.7% (5/756) of the samples. This is the first, most comprehensive, and largest molecular-based epidemiology study of its kind carried out in Portugal, covering a wide range of wild and domestic hosts and sampling areas. The detection of zoonotic Cryptosporidium spp. and G. duodenalis subassemblage AI demonstrates the role of wild and domestic host species in the transmission of these agents while representing a potential source of environmental contamination for other animals and humans.

Follow-up investigation into Cryptosporidium prevalence and transmission in Western European dairy farms

Cryptosporidium parvum is an enteric parasite and a major contributor to acute enteritis in calves worldwide, causing an important economic burden for farmers. This parasite poses a major public health threat through transmission between livestock and humans. Our previous pilot study in Western Europe revealed a high prevalence of Cryptosporidium in calves of dairy farms. In the sequel study herein, 936 faecal samples were collected from the same 51 dairy farms across Belgium, France, and the Netherlands. Following DNA extraction, Cryptosporidium screening was carried out using nested-PCR amplification targeting the SSU rRNA gene. All positive samples were sequenced, and phylogenetic analyses were used to identify the Cryptosporidium spp. present. The 60 kDa glycoprotein (gp60) gene was also sequenced to determine the C. parvum subtypes present. Prevalence of Cryptosporidium ranged from 23.3% to 25%, across the three countries surveyed. The parasite was found in most of the farms sampled, with 90.2% testing positive. Cryptosporidium parvum, C. bovis, C. ryanae and C. andersoni were all identified, with the former being the most predominant, representing 71.4% of all infections. Cryptosporidium parvum was associated with pre-weaned calves, while other species were associated with older animals. Subtyping of gp60 gene revealed nine subtypes, eight of which have previously been reported to cause clinical disease in humans. Similarly to the first study, vertical transmission was not a major contributor to Cryptosporidium spread. Our study highlights the need for further investigation into cryptosporidiosis transmission, and future studies will require a One Health approach to reduce the impact of this disease.

Population genetics of Cryptosporidium parvum subtypes in cattle in Poland: the geographical change of strain prevalence and circulation over time

Background

Cryptosporidium parvum (C. parvum) is a cosmopolitan parasite that infects various livestock animals including cattle. Microsatellite typing tools for identification of C. parvum subtypes are currently employed to better understand the species-specific epidemiology of cattle cryptosporidiosis. The aim of this study was to analyse the population genetics of C. parvum strains infecting cattle and recognise geographical distribution and time-span correlations in subtype prevalence in Poland. In total, 1601 faecal samples were collected from 2014 to 2018 from healthy cattle from dairy, meat and mixed breeds at the age of 1 week to 4 months. The 267 farms visited were randomly selected and represented all Polish provinces. PCR–RFLP based identification of C. parvum at the 18 small subunit ribosomal RNA (SSU rRNA) locus was performed, followed by strain subtyping by GP60-PCR. 

Results

The overall prevalence of C. parvum in Polish cattle was estimated at 6.2% (100/1601). Animals below the age of 1 month were the major host for this parasite. Excluding one breed, that of dairy-meat mixed, there were no significant differences observed between breed and presence of C. parvum infections (95% TPI_{All breeds}: 1.67–73.53%; POPR = 0.05—0.95). Infected animals were detected in 15 out of 16 Polish provinces, with significant regional prevalence diffrences (Kruskal–Wallis rank sum test, Kruskal–Wallis χ² = 13.46, p < 0.001). When the population genetics of C. parvum strains were analysed, 11 parasite subtypes from the IIa and IId genetic families were identified. Compared to other parasite strains, IIaA17G1R1 and IIaA17G2R1 appeared at statistically significantly higher frequency (F-test, F = 3.39; p = 0.0003). The prevalence of C. parvum subtypes in cattle was breed-related (Chi-squared test, χ² = 143.6; p < 0.001).

Conclusions

The analysis of the population genetics of C. parvum subtypes showed that strains from the IIa subtype family predominated in the tested cattle population. However, relations in changes of subtype prevalence and circulation over time were observed. They were associated with the disappearance of some strains and emergence of new variants from the same genetic family in different geographical locations.

C. parvum subtypes from the IIa allele family predominated in the tested cattle. The prevalence of C. parvum subtypes in cattle was breed-related. Dynamicity in the population C. parvum strains circulating in cattle was shown.

Cryptosporidium and Giardia infections in humans in Tigray, Northern Ethiopia: an unexpectedly low occurrence of anthropozoonotic transmission

Enteric protozoans Cryptosporidium spp. and Giardia duodenalis are among the leading causes of diarrhoea in children. These parasites have particular impact in low- and middle-income countries. In these countries, people often live in close contact with their animals, highlighting the potential role of zoonotic routes of transmission in disease spread. The occurrence and species/genotypes of Cryptosporidium and Giardia duodenalis infecting humans in Tigray, Ethiopia were investigated, along with the risk associated with infection. Stool samples from 249 asymptomatic people (4-80 years of age) in four rural districts in Tigray and 58 from symptomatic young children (1-33 months) attending health centres in Mekelle, Tigray's main city, were analysed for Cryptosporidium oocysts and Giardia cysts. Participants in the rural areas completed questionnaires regarding potential risk factors, with emphasis on livestock contact and sources of water. The occurrence of Cryptosporidium infection was 6% and 5% in people in the rural districts and young children from Mekelle, respectively; equivalent figures for Giardia infection were 29% and 14%. Molecular characterization of Cryptosporidium isolates revealed C. ubiquitum, subtype XIIa in a sample from rural districts, and C. hominis subtype IdA17 (1 sample) and IbA9G3 (2 samples) in infants from Mekelle with diarrhoea. For Giardia, Assemblage B predominated (22/25; 88%), but we also identified three samples with Assemblage A (AII). Our major finding was that, despite the close contact between people and livestock in our rural study sites, transmission of Cryptosporidium and Giardia between humans and their animals seems to be surprisingly uncommon. Our results are discussed in relation to other relevant studies, and also draws attention to the possibility that introduction of zoonotic species and/or subtypes, such as C. parvum, could have serious consequences for both human and animal health. As our study was conducted in Tigray, further investigation in different settings in Ethiopia could provide relevant information on transmission and zoonotic potential, and the potential for spread of zoonotic transmission. In addition, given the importance of these two parasites in causing diarrhoea in children, this information is vital for developing effective appropriate interventions against transmission that can be applied not only in Tigray or Ethiopia, but throughout Africa and beyond.

Age and episode-associated occurrence of Cryptosporidium species and subtypes in a birth-cohort of dairy calves

The role of species-specific immunity in infection patterns of Cryptosporidium spp. in humans and farm animals is not well understood. In the present study, the dynamics of Cryptosporidium infections in a natural cryptosporidiosis model was examined using genotyping, subtyping and whole genome sequencing tools. In a cross-sectional survey of Cryptosporidium spp. in 934 dairy cattle on one farm, marked age-associated differences in the distribution of Cryptosporidium species and C. bovis subtypes were observed. In a closely followed longitudinal birth cohort study of 81 calves over a 9-month period, shedding of C. parvum oocysts started at 4 days, peaked at 2 weeks, and ended mostly by 4 weeks. In contrast, the shedding of C. bovis oocysts started at 2 weeks, peaked initially at 6 weeks, and had a second wave during 15^th to 23^rd weeks. For C. ryanae, calves had mostly only one episode of infection, with accumulative infection increasing much slower than C. parvum and C. bovis. Overall, the accumulative infection rates and mean duration of oocyst shedding for calves in the cohort were 97.4% (76/78) and 2.3 weeks, 100.0% (80/80) and 3.9 weeks, and 78.7% (63/80) and 3.2 weeks for C. parvum, C. bovis, and C. ryanae, respectively. The oocyst shedding intensity was much lower in C. bovis and C. ryanae infections compared with C. parvum infection, and in the second episode of C. bovis infection compared with the first episode. The two episodes of C. bovis infections were caused by different genome types that differed mostly in nine genes. Cryptosporidium parvum infection was associated with the occurrence of watery diarrhea. Data from the natural history study of cryptosporidiosis indicate that despite the existence of acquired immunity against homologous pathogens, neonatal animals experience waves of Cryptosporidium infections by different species and genome types. This article is protected by copyright. All rights reserved.

Cross-Border Investigations on the Prevalence and Transmission Dynamics of Cryptosporidium Species in Dairy Cattle Farms in Western Mainland Europe

Cryptosporidium is an apicomplexan parasitic protist, which infects a wide range of hosts, causing cryptosporidiosis disease. In farms, the incidence of this disease is high in animals such as cows, leading to extensive economic loss in the livestock industry. Infected cows may also act as a major reservoir of Cryptosporidium spp., in particular C. parvum, the most common cause of cryptosporidiosis in these animals. This poses a risk to the trading of livestock, to other farms via breeding centres, and to human health. This study is a part of a global project aimed at strategies to tackle cryptosporidiosis. To reach this target, it was essential to determine whether prevalence was dependent on the studied countries or if the issue was borderless. Indeed, C. parvum occurrence was assessed across dairy farms in certain regions of Belgium, France, and the Netherlands. At the same time, the animal-to-animal transmission of the circulating C. parvum subtypes was studied. To accomplish this, we analysed 1084 faecal samples, corresponding to 57 dairy farms from all three countries. To this end, 18S rRNA and gp60 genes fragments were amplified, followed by DNA sequencing, which was subsequently used for detection and subtyping C. parvum. Bioinformatic and phylogenetic methods were integrated to analyse and characterise the obtained DNA sequences. Our results show 25.7%, 24.9% and 20.8% prevalence of Cryptosporidium spp. in Belgium, France, and the Netherlands respectively. Overall, 93% of the farms were Cryptosporidium positive. The gp60 subtyping demonstrated a significant number of the C. parvum positives belonged to the IIa allelic family, which has been also identified in humans. Therefore, this study highlights how prevalent C. parvum is in dairy farms and further suggests cattle as a possible carrier of zoonotic C. parvum subtypes, which could pose a threat to human health.

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.

The prevalence and genetic characterisation of Cryptosporidium isolates from cattle in Kiruhura district, South Western Uganda

Cryptosporidium is an emerging opportunistic zoonotic pathogen that causes diarrheal illness in a wide range of hosts including livestock and humans. This study set out to establish the prevalence of Cryptosporidium as well as the circulating genotypes in order to elucidate the potential role of cattle in the spread of human cryptosporidiosis. Rectal coprological samples from 363 cattle in 11 households in Kiruhura district, Southwestern Uganda were collected and screened for the presence of Cryptosporidium oocysts using the phenol auramine staining method followed by fluorescent microscopy. DNA was extracted from the microscopy positive samples and the COWP gene amplified using PCR. PCR products were sequenced and subjected to phylogenetic analysis. Additionally a multiplex realtime PCR was used to identify the Cryptosporidium spp. Multivariable mixed effect logistic regression models were used to identify potential risk factors for Cryptosporidium infection. The overall prevalence of Cryptosporidium was 7.7% (95% CI 5.1-10.9), and herd level prevalence was 33.3% (95% CI 18.5-52.2). We found a statistically significant difference (OR = 30.78, 95% CI 4.31-219.95, p = 0.001) between infection in bulls as compared to cows. There was no significant difference in the prevalence among the different cattle breeds sampled. All the sequenced COWP gene DNA amplicons were confirmed to be C. hominis, with 93%-100% identity to sequences in the GenBank. The amplification of the small subunit rRNA by multiplex realtime PCR further established that the isolates in this study are C. hominis. This study represents the first time naturally occurring C. hominis has been detected from cattle in Uganda.

Comparison of three diagnostic methods in the diagnosis of cryptosporidiosis and gp60 subtyping of Cryptosporidium parvum in diarrheic calves in Central Anatolia Region of Turkey

The aim of this study was to compare three diagnostic methods for the diagnosis of cryptosporidiosis and to detect subtypes ofCryptosporidium parvum by sequences analyses of gp60 gene in diarrheic calves in several herds in Konya province located in Central Anatolia Region of Turkey. Fecal samples were collected from a total of 194 pre-weaned calves (n=158, ≤15 days old, and n=36, 15 to 40 days old), with diarrhoea. For comparative diagnosis, all samples were examined by modified Ziehl-Neelsen staining of fecal smears for the presence of oocyst, nested PCR-RFLP of SSU rRNA and TaqMan qPCR for the detection of Cryptosporidium DNA. A total of 92 (47.4%) and 104 (53.6%) out of the examined samples were found positive by microscopic examination and molecular tools, respectively. The diagnostic sensitivity and specificity of microscopic identification were determined as 88.5% and 100.0%, respectively compared to molecular assays. Cryptosporidium parvum was the only detected species in all positive samples by species-specific qPCR and nested PCR-RFLP assays. Species identifications were further confirmed by sequence analyses of the SSU rRNA PCR products. There was no statistically significant difference in C. parvum prevalence between early pre-weaned calves and calves older than 15 days. The sequence analyses of the gp60 gene of C. parvum isolates revealed a one subtype IIaA13G2R1 belonging to zoonotic family IIa in diarrheic calves

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.

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.

Epidemiology of Cryptosporidiosis in France from 2017 to 2019

Cryptosporidiosis is currently recognized worldwide as a leading cause of moderate to severe diarrhea. In Europe, large water- and foodborne outbreaks have been reported, highlighting the widespread distribution of the parasite and its important health impact. Surveillance networks have been progressively set up and the aim of this study was to present recent epidemiological data obtained in France from 2017 to 2019 by the National Reference Center-Expert Laboratory of cryptosporidiosis (Centre National de Référence-Laboratoire Expert cryptosporidioses CNR-LE). Data were obtained from online reports of volunteer network participants and stools were sent to the CNR-LE for species identification and GP60 genotyping. During this period, data from 750 online reports were available. Cryptosporidiosis occurred predominantly in young children (<5 years old) and in young adults, especially during late summer. Most patients were immunocompetent (60%), and deaths were reported only in immunocompromised patients. Cryptosporidium parvum was largely predominant (72% of cases) over C. hominis (24%) and some other uncommon species. C. parvum GP60 subtypes IIa and IId were the most represented, which suggests frequent zoonotic transmission. For C. hominis, subtypes IbA10G2 and IaA22R2 were predominant.

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.

Molecular detection of genotypes and subtypes of Cryptosporidium infection in diarrheic calves, lambs, and goat kids from Turkey

The studies on Cryptosporidium infections of animals in Turkey mostly rely on microscopic observation. Few data are available regarding the prevalence of Cryptosporidium genotypes and subtypes infection. The aim of this study is to analyse the detection of Cryptosporidium genotypes and subtypes from young ruminants. A total of 415 diarrheic fecal specimens from young ruminants were examined for the Cryptosporidium detection by use of nested PCR of the small subunit ribosomal RNA (SSU rRNA) gene and the highly polymorphic 60 kDa glycoprotein (gp60) gene followed by sequence analyses. The results of this study revealed that 25.6% (106 of 415) of the specimens were positive for Cryptosporidium spp. infection. We identified 27.4% (91/333), 19.4% (13/67), and 13.4% (2/15) of positivity in calves, lambs and goat kids, respectively. Genotyping of the SSU rRNA indicated that almost all positive specimens were of C. parvum, except for one calf which was of C. bovis. Sequence analysis of the gp60 gene revealed the most common zoonotic subtypes (IIa and IId) of C. parvum. We detected 11 subtypes (IIaA11G2R1, IIaA11G3R1, IIaA12G3R1, IIaA13G2R1, IIaA13G4R1, IIaA14G1R1, IIaA14G3R1, IIaA15G2R1, IIdA16G1, IIdA18G1, IIdA22G1); three of them (IIaA12G3R1, IIaA11G3R1 and IIaA13G4R1) was novel subtypes found in calves and lambs. Additionally, three subtypes (IIaA11G2R1, IIaA14G3R1, and IIdA16G1) were detected in young ruminants for the first time in Turkey. These results indicate the high infection of Cryptosporidium in Turkey and propose that young ruminants are likely a major reservoir of C. parvum and a potential source of zoonotic transmission.

Prevalence and genotyping of bovine Cryptosporidium species in the Mediterranean and Central Anatolia Region of Turkey

The prevalence of Cryptosporidium species in calves and heifers with relation to diarrhea from several herds was investigated in this study. Fecal samples were collected from 135 and 120 pre-weaned calves and 79 and 130 heifers raised in the Central Anatolia (CAR) and Mediterranean Regions (MR) of Turkey, respectively. A total of 86 post-weaned calves in CAR were also included in the study. For diagnostic comparison, all samples were examined by microscopic examination, SSU rRNA nested PCR and TaqMan real-time PCR for the presence of oocyst and Cryptosporidium DNA. In total, 102 (34.0 %) and 93 (37.2 %) of the examined samples from CAR and MR were found positive for Cryptosporidium DNA with both nested PCR and real-time PCR analyses, respectively with an overall prevalence of 35.5 %. The diagnostic sensitivity and specificity of microscopic examination were determined as 68.7 % and 100.0 % compared to molecular tools, respectively. RFLP and sequence analyses of the SSU rRNA from the PCR products revealed that 138 (70.8 %) out of 195 positive isolates were C. parvum further confirming the species-specific real-time PCR results. Among the remaining 57 (29.2 %) positive isolates, 30 (15.4 %) and 27 (13.8 %) were characterized as C. ryanae and C. bovis, respectively. C. parvum was the dominant species in pre-weaned calves especially with diarrhea while C. bovis and C. ryanae were mostly found in post-weaned calves and heifers. The sequence analyses of the gp60 gene of C. parvum isolates revealed two subtypes (IIaA13G2R1, IIaA14G1R1) belonging to zoonotic family IIa, with IIaA13G2R1 being the most common in diarrheic calves.

Prevalence and molecular characterization of Cryptosporidium species in poultry in Bangladesh

Cryptosporidium is an opportunistic parasite that has been reported in >30 avian hosts worldwide, however, there is no information regarding Cryptosporidium spp. in poultry in Bangladesh. Accordingly, we investigated the prevalence of Cryptosporidium spp. in poultry at open live bird markets in Bangladesh. A total of 197 samples were randomly collected from poultry at open live bird markets in Bangladesh and screened for the detection of Cryptosporidium. Initial microscopic examination revealed Cryptosporidium spp. was observed in 19.8% (39/197) of the poultry specimens. Subsequent nested PCR targeting the 18S rRNA gene revealed that 15.7% (31/197) of the samples were Cryptosporidium positive. Of these 31 samples, 17 were Cryptosporidium baileyi (8.7%), 12 were Cryptosporidium meleagridis (6.0%), and 2 were Cryptosporidium parvum (1.0%). Nucleotide sequence analysis of the GP60 gene of the C. meleagridis revealed that two subtypes (IIIbA21G1R1 and IIIbA23G1R1), which were found in broiler, native and sonali chickens and a pigeon, matched those previously reported in humans and poultry. We identified two novel subtypes (IIIbA21G2R1 and IIIbA20G2R1) in sonali chickens, a broiler chicken and a layer chicken. We also amplified the GP60 gene of C. parvum and found two subtypes (IIaA11G2R1 and IIaA13G2R1) in a sonali and a broiler chicken that were previously reported in calf. These findings suggest that poultry can be a source of cryptosporidial infections for humans and animals in Bangladesh. This is the first molecular investigation of Cryptosporidium genotypes and subtypes in poultry at open live bird markets in Bangladesh.

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Cryptosporidium genotypes and subtypes in poultry in Bangladesh have been investigated firstly.

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Cryptosporidium baileyi, C. meleagridis and C. parvum are identified while C. baileyi is predominant species in poultry.

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Two novel subtypes (IIIbA21G2R1 and IIIbA20G2R1) of the C. meleagridis in chickens are detected.

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Cryptosporidium parasites are common among the live bird markets in Bangladesh.

Direct Sequencing of Cryptosporidium in Stool Samples for Public Health

The protozoan parasite Cryptosporidium is an important cause of diarrheal disease (cryptosporidiosis) in humans and animals, with significant morbidity and mortality especially in severely immunocompromised people and in young children in low-resource settings. Due to the sexual life cycle of the parasite, transmission is complex. There are no restrictions on sexual recombination between sub-populations, meaning that large-scale genetic recombination may occur within a host, potentially confounding epidemiological analysis. To clarify the relationships between infections in different hosts, it is first necessary to correctly identify species and genotypes, but these differentiations are not made by standard diagnostic tests and more sophisticated molecular methods have been developed. For instance, multilocus genotyping has been utilized to differentiate isolates within the major human pathogens, Cryptosporidium parvum and Cryptosporidium hominis. This has allowed mixed populations with multiple alleles to be identified: recombination events are considered to be the driving force of increased variation and the emergence of new subtypes. As yet, whole genome sequencing (WGS) is having limited impact on public health investigations, due in part to insufficient numbers of oocysts and purity of DNA derived from clinical samples. Moreover, because public health agencies have not prioritized parasites, validation has not been performed on user-friendly data analysis pipelines suitable for public health practitioners. Nonetheless, since the first whole genome assembly in 2004 there are now numerous genomes of human and animal-derived cryptosporidia publically available, spanning nine species. It has also been demonstrated that WGS from very low numbers of oocysts is possible, through the use of amplification procedures. These data and approaches are providing new insights into host-adapted infectivity, the presence and frequency of multiple sub-populations of Cryptosporidium spp. within single clinical samples, and transmission of infection. Analyses show that although whole genome sequences do indeed contain many alleles, they are invariably dominated by a single highly abundant allele. These insights are helping to better understand population structures within hosts, which will be important to develop novel prevention strategies in the fight against cryptosporidiosis.

First identification of Cryptosporidium parvum zoonotic subtype IIaA15G2R1 in diarrheal lambs in France

To date, no information is available about the presence of Cryptosporidium spp. in French sheep, nor their potential role as zoonotic reservoirs. A total of 23 fecal samples were collected from diarrheic lambs (<11 days old) from seven randomly selected farms. Cryptosporidium-oocysts were detected microscopically with Direct Immunofluorescence Assays (DFA) in 23/23 (100%) of fecal samples. PCR-RFLP of the 18S rRNA gene was used to determine species in all samples, and only Cryptosporidium parvum was identified. Isolates were subtyped by sequencing the 60 kDa glycoprotein (gp60) gene. Two zoonotic subtypes within the IIa subtype family were identified, including IIaA15G2R1 (22/23) and IIaA16G3R1 (1/23). This study reports for the first time the identification and genotyping of zoonotic C. parvum subtypes from lambs in France. Sheep could thus play an important role as potential reservoirs for this zoonotic protist.

Application of different DNA extraction procedures, library preparation protocols and sequencing platforms: impact on sequencing results

In this study three DNA extraction procedures, two library preparation protocols and two sequencing platforms were applied to analyse six bacterial cultures and their corresponding DNA obtained as part of a proficiency test. The impact of each variable on sequencing results was assessed using the following parameters: reads quality, assembly and alignment statistics; number of single nucleotide polymorphisms (SNPs), detected applying assembly- and alignment-based strategies; antimicrobial resistance genes (ARGs), identified on de novo assemblies of all sequenced genomes. The investigated nucleic acid extraction procedures, library preparation kits and sequencing platforms do not significantly affect de novo assembly statistics and number of SNPs and ARGs. The only exception was observed for two duplicates, which were associated to one PCR-based library preparation kit. Results from this comparative study can support researchers in the choice toward the available pre-sequencing and sequencing options, and might suggest further comparisons to be performed.

Molecular characterization of Cryptosporidium isolates from diarrheal dairy calves in France

Cryptosporidium is an obligate intracellular protist parasite infecting a wide range of vertebrate hosts and causes significant intestinal disease in both animals and humans, as some species are zoonotic. Cattle and especially calves have been identified as one of the most common reservoirs of this protist. However, little is known about the genetics of Cryptosporidium in calves in some regions of France. The aim of this study was to detect and isolate Cryptosporidium spp. in faecal samples from naturally infected pre-weaned calves (≤45 days-old) in France. A total of 35 diarrhoeic pre-weaned calf faecal samples were collected from 26 dairy cattle farms in six departments (French administrative provinces). Cryptosporidium presence was established by microscopically screening samples for oocystes with an immunofluorescent (DFA) staining method. DFA-positive samples were then analysed by PCR-RFLP and 18S rRNA gene sequencing to determine species. Cryptosporidium parvum-positive samples were subtyped via nested PCR analysis of a partial fragment of the 60 kDa glycoprotein (gp60) gene product. Data were then integrated into phylogenetic tree analysis. DFA revealed the presence of Cryptosporidium oocysts in 31 out of 35 (88%) samples. Combined with 18S rRNA gene analysis results, C. parvum was detected in 30 samples. Subtyping analysis in 27/30 samples (90%) of the C. parvum isolates revealed two zoonotic subtype families, IIa (24/27) and IId (3/27). Four subtypes were recognised within the subtype family IIa, including the hypertransmissible IIaA15G2R1 subtype that is the most frequently reported worldwide (21/27), IIaA17G3R1 (1/27), IIaA17G1R1 (1/27), and IIaA19G1R1 (1/27). Two subtypes were recognised within the IId subtype family including IIdA22G1 (2/27) and IIdA27G1 (1/27). These findings illustrate the high occurrence of Cryptosporidium in calves in dairy herds and increase the diversity of molecularly characterised C. parvum isolates with the first description of IIaA17G3R1, IIaA19G1R1, and IId subtypes in France. The presence of zoonotic C. parvum subtype families (IIa, IId) in this study suggests that pre-weaned calves are likely to be a significant reservoir of zoonotic C. parvum, and highlights the importance of animal to human cryptosporidiosis transmission risk. Further molecular studies in calves and small ruminants from other French regions are required to better understand the epidemiology of cryptosporidiosis in France.

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Faecal samples from pre-weaned diarrheal calves were analysed

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Cryptosporidium spp. was detected in 30 samples out of 35.

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C. parvum was the only species identified

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Two zoonotic subtype families were identified: IIa and IId

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The hyper-transmissible IIaA15G2R1 was the dominant C. parvum subtype

New insights into the detection and molecular characterization of Cryptosporidium with emphasis in Brazilian studies: a review

Cryptosporidium spp. is a pathogenic protozoan present in the gastrointestinal tract of several hosts. This protozoan was originally classified as within the Coccidia Class and has recently been reclassified to gregarine based on studies that observed the evolutionary phases from the process of excision and sequencing of the 18S rRNA gene. Molecular biology techniques have become diagnostic tools and have also been used to understand the epidemiology of Cryptosporidium spp., since several species of this genus are very similar morphologically and morphometrically. Molecular techniques have been used in the identification of parasites, at the species and subtypes levels and to study disease transmission. The laboratory diagnosis of human cryptosporidiosis can be made by parasite detection methods, such as optical microscopy, antigens or genetic material detection, as well as serum antibodies raised to Cryptosporidium spp. Molecular methods were developed and allowed, not only an extensive revision of the taxonomy, but also an improvement in the laboratory diagnosis. In Brazil, there are few reports of Cryptosporidium spp. outbreaks in humans and all of them took place in nurseries. A few epidemiological studies developed in Brazil have used molecular methods for the detection of Cryptosporidium spp., as well as genotyping studies of their species and subtypes. The use of real-time PCR, together with microscopy and immunochromatography techniques, would result in a more precise diagnosis of cryptosporidiosis. The analysis of genotypes, subtypes and clonality of Cryptosporidium could be useful to understand and define the prognosis and severity of infections.

Prevalence of Cryptosporidium parvum in dairy calves and GP60 subtyping of diarrheic calves in central Argentina

Cryptosporidiosis of calves is caused by the enteroprotozoan Cryptosporidium spp. The disease results in intense diarrhea of calves associated with substantial economic losses in dairy farming worldwide. The aim of this study was to determine calf, herd, and within-herd Cryptosporidium prevalence and identify Cryptosporidium species and subtypes in calves with diarrhea in intensive dairy herds in central Argentina. A total of 1073 fecal samples were collected from 54 randomly selected dairy herds. Cryptosporidium-oocysts were isolated and concentrated from fecal samples using formol-ether and detected by light microscopy with the modified Ziehl-Neelsen technique. Overall prevalence of oocyst-excreting calves was found to be 25.5% (274/1073) (95% C.I. 22.9; 28.1%). Of the herds studied, 89% (48/54) included at least one infected calf, whereas within-herd prevalence ranged from the absence of infection to 57% (20/35). A highly significant association was found between the presence of diarrhea and C. parvum infection (χ² = 55.89, p < 0.001). For species determination, genomic DNA isolated from oocyst-positive fecal samples was subjected to PCR-RFLP of the 18S rRNA gene resulting exclusively in Cryptosporidium parvum identification. C. parvum isolates of calves displaying diarrhea and high rate of excretion of oocysts were subtyped by PCR amplification and direct sequencing of the 60 kDa glycoprotein (GP60) gene. Altogether five GP60 subtypes, designated IIaA18G1R1, IIaA20G1R1, IIaA21G1R1, IIaA22G1R1, and IIaA24G1R1 were identified. Interestingly, IIaA18G1R1 and IIaA20G1R1 were predominant in calves with diarrhea and high infection intensity. Notably, IIaA24G1R1 represents a novel, previously unrecognized C. parvum subtype. The subtype IIaA18G1R1, frequently found in this study, is strongly implicated in zoonotic transmission. These results suggest that calves might be an important source for human cryptosporidiosis in Argentina.

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.

NMR metabolomics reveals effects of Cryptosporidium infections on host cell metabolome

Background

Cryptosporidium is an important gut microbe whose contributions towards infant and immunocompromise patient mortality rates are steadily increasing. Over the last decade, we have seen the development of various tools and methods for studying Cryptosporidium infection and its interactions with their hosts. One area that is sorely overlooked is the effect infection has on host metabolic processes.

Results

Using a ¹H nuclear magnetic resonance approach to metabolomics, we have explored the nature of the mouse gut metabolome as well as providing the first insight into the metabolome of an infected cell line. Statistical analysis and predictive modelling demonstrated new understandings of the effects of a Cryptosporidium infection, while verifying the presence of known metabolic changes. Of note is the potential contribution of host derived taurine to the diarrhoeal aspects of the disease previously attributed to a solely parasite-based alteration of the gut environment, in addition to other metabolites involved with host cell catabolism.

Conclusion

This approach will spearhead our understanding of the Cryptosporidium-host metabolic exchange and provide novel targets for tackling this deadly parasite.

Distribution of Cryptosporidium parvum gp60 subtypes in calf herds of Saxony, Germany

Cryptosporidiosis is a common protozoan parasitic infection that causes diarrhoea in neonatal calves. The high shedding of environmentally resistant oocysts facilitates outbreaks of cryptosporidiosis in humans. In total, 58 farms (512 calves) in Germany (Saxony and Brandenburg) were visited three times each. Faecal samples of pre-weaned calves were microscopically examined for oocysts of Cryptosporidium spp. using Heine staining and were scored with regard to their consistency. Overall, 88.9% of calves tested microscopically positive for Cryptosporidium spp. in at least one sample, and the excretion of oocysts was significantly (P < 0.01) associated with a higher faecal score (diarrhoea). After DNA extraction from pooled farm isolates, 47 samples were successfully subtyped by sequence analysis of the 60 kDa glycoprotein gene (gp60). All isolates belonged to subtype family IIa. IIaA15G2R1 was the most common subtype (present on 66% of the farms), followed by IIaA16G3R1 (13%). Subtypes IIaA14G1R1, IIaA14G2R1, IIaA1612R1, IIaA16G2R1, IIaA17G1R1, IIaA17G2R1, IIaA17G4R1 and IIaA19G2R1 were found sporadically. This is the first description of gp60 subtype IIaA17G4R1 in cattle in Germany.

Diversity of Cryptosporidium spp. in Apodemus spp. in Europe

The genetic diversity of Cryptosporidium spp. in Apodemus spp. (striped field mouse, yellow-necked mouse and wood mouse) from 16 European countries was examined by PCR/sequencing of isolates from 437 animals. Overall, 13.7% (60/437) of animals were positive for Cryptosporidium by PCR. Phylogenetic analysis of small-subunit rRNA, Cryptosporidium oocyst wall protein and actin gene sequences showed the presence of Cryptosporidium ditrichi (22/60), Cryptosporidium apodemi (13/60), Cryptosporidium apodemus genotype I (8/60), Cryptosporidium apodemus genotype II (9/60), Cryptosporidium parvum (2/60), Cryptosporidium microti (2/60), Cryptosporidium muris (2/60) and Cryptosporidium tyzzeri (2/60). At the gp60 locus, novel gp60 families XVIIa and XVIIIa were identified in Cryptosporidium apodemus genotype I and II, respectively, subtype IIaA16G1R1b was identified in C. parvum, and subtypes IXaA8 and IXcA6 in C. tyzzeri. Only animals infected with C. ditrichi, C. apodemi, and Cryptosporidium apodemus genotypes shed oocysts that were detectable by microscopy, with the infection intensity ranging from 2000 to 52,000 oocysts per gram of faeces. None of the faecal samples was diarrheic in the time of the sampling.

Prevalence and genotypic identification of Cryptosporidium spp., Giardia duodenalis and Enterocytozoon bieneusi in pre-weaned dairy calves in Guangdong, China

Background

Cryptosporidium spp., Giardia duodenalis and Enterocytozoon bieneusi are common enteric pathogens in humans and animals. Data on the transmission of these pathogens are scarce from Guangdong, China, which has a subtropical monsoon climate and is the epicenter for many emerging infectious diseases. This study was conducted to better understand the prevalence and identity of the three pathogens in pre-weaned dairy calves in Guangdong.

Methods

The occurrence and genetic identity of three pathogens were analyzed by polymerase chain reaction. PCR-positive products were sequenced to determine the species and genotypes. A Chi-square test was used to compare the prevalence of pathogens among sampling dates, age groups, or clinical signs.

Results

The detection rates of Cryptosporidium spp., G. duodenalis and E. bieneusi were 24.0% (93/388), 74.2% (288/388) and 15.7% (61/388), respectively. Three Cryptosporidium species were detected, including C. bovis (n = 73), C. parvum (n = 12) and C. ryanae (n = 7); one animal had concurrence of C. bovis and C. parvum. C. parvum was the dominant species during the first two weeks of life, whereas C. bovis and C. ryanae were mostly seen at 3–9 weeks of age. Sequence analysis identified the C. parvum as subtype IIdA19G1. Assemblage E (n = 282), assemblage A (n = 1), and concurrence of A and E (n = 5) were identified among G. duodenalis-positive animals using multilocus genotyping (MLG). Altogether, 15, 10 and 17 subtypes of assemblage E were observed at the bg, gdh and tpi loci, respectively, forming 49 assemblage E MLGs. The highest detection rate of G. duodenalis was found in winter. Sequence analysis identified genotypes J (n = 57), D (n = 3) and one concurrence of J and D among E. bieneusi-positive animals. The detection rate of E. bieneusi was significantly higher in spring (38.0%; 41/108) than in summer (7.2%; 8/111) and winter (7.1%; 12/169).

Conclusions

These results indicate a common occurrence of C. parvum subtype IIdA19G1, G. duodenalis assemblage E, and E. bieneusi genotype J in pre-weaned dairy calves in Guangdong. More studies are needed to understand the unique genetic characteristics and zoonotic potential of the three enteric pathogens in the province.

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

Background

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

Methods

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

Results

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

Conclusions

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

Electronic supplementary material

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

Molecular epidemiology of Cryptosporidium spp. in calves in Estonia: high prevalence of Cryptosporidium parvum shedding and 10 subtypes identified

We investigated the molecular epidemiology of Cryptosporidium spp. in Estonia by testing fecal samples from 486 calves aged &lt;2 months, raised on 53 cattle farms, for the presence of Cryptosporidium DNA. The parasites were identified and characterized by sequencing of the 18S rRNA gene and of the 60 kDa glycoprotein (gp60) gene. Moreover, using a questionnaire, we surveyed factors that could be relevant for animal-to-human and human-to-animal transmission of Cryptosporidium spp. on the farms. Cryptosporidium spp. were shed by 23% of the investigated calves and at least one shedding calf was found on 66% of the farms. Cryptosporidium parvum was the most common species shed, while C. bovis and C. ryanae were also detected. More than half of the calves aged 8-14 days shed C. parvum. Nine previously described C. parvum subtypes (IIaA14G1R1, IIaA16G1R1, IIaA17G1R1, IIaA18G1R1, IIaA19G1R1, IIaA20G1R1, IIaA21G1R1, IIaA22G1R1 and IIaA16G2R1) and an apparently novel subtype IIlA21R2 were found. Calves from farms that reported spreading manure on fields during spring had 10 times higher odds to shed Cryptosporidium spp. in their feces than calves from farms that did not. Calves aged 8-14 days had higher odds to shed IIa18G1R1 as well as IIaA16G1R1 than younger calves.

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.

First report of Cryptosporidium parvum in a dromedary camel calf from Western Australia

Cryptosporidium is an important enteric parasite that can contribute large numbers of infectious oocysts to drinking water catchments. As a result of its resistance to disinfectants including chlorine, it has been responsible for numerous waterborne outbreaks of gastroenteritis. Wildlife and livestock play an important role in the transmission of Cryptosporidium in the environment. Studies conducted outside Australia have indicated that camels may also play a role in the transmission of zoonotic species of Cryptosporidium. Despite Australia being home to the world's largest camel herd, nothing is known about the prevalence and species of Cryptosporidium infecting camels in this country. In the present study, C. parvum was identified by PCR amplification and sequencing of a formalin-fixed intestinal tissue specimen from a one-week old dromedary camel (Camelus dromedarius). Subtyping analysis at the glycoprotein 60 (gp60) locus identified C. parvum subtype IIaA17G2R1, which is a common zoonotic subtype reported in humans and animals worldwide. Histopathological findings also confirmed the presence of large numbers of variably-sized (1-3 µm in diameter) circular basophilic protozoa - consistent with Cryptosporidium spp.- adherent to the mucosal surface and occasionally free within the lumen. Further analysis of the prevalence and species of Cryptosporidium in camel populations across Australia are essential to better understand their potential for contamination of drinking water catchments.

Prevalence and zoonotic potential of intestinal protozoans in bovines in Northern India

Bovines, and especially cattle, have a dual position of appreciation in India, being both important in the food industry as providers of dairy products, and, culturally, being considered as holy creatures that must not be harmed, killed or eaten. This status means that cattle have a paradoxical existence in India; as they are worshipped and protected, they are able to roam freely among humans, but they are also often left to fend for themselves. The water buffalo represents a significant contributor to the Indian agricultural economy as well as general social development, and are in this way somehow replacing the indigenous cattle. The vast numbers of roaming cattle without clear owners are difficult to look after in terms of veterinary healthcare and appropriate interventions when necessary, and have no regular supply of food. This article describes an investigation of the occurrence of Cryptosporidium spp. and Giardia duodenalis in bovines either roaming the streets or being kept in animal holdings in and around Chandigarh, a city in Northern India, and addresses the zoonotic potential of these protozoan parasites shed from bovines living in close contact with humans. 294 animals of all ages were sampled, and the majority of the positive samples were found from calves. The overall prevalence of Giardia was 8.2% and Cryptosporidium was 2.4%. Non-zoonotic assemblages were predominantly found in the case of the Giardia - positive samples, and in the case of Cryptosporidium, as well as non-zoonotic genotypes, zoonotic subgroups previously described from infected human infections in this area, were identified, indicating that there may be sharing of intestinal parasites in these settings, where cattle live in close contact with humans.

Cryptosporidium-associated diarrhoea in neonatal calves in Algeria

Neonatal calf diarrhoea triggered by the enteric protozoan parasite Cryptosporidium is a leading cause of morbidity and mortality in calves aged 1-month-old or younger globally. Infected cattle in general and calves in particular have also been demonstrated as major contributors of zoonotic C. parvum oocysts in the environment and have been linked to a number of waterborne outbreaks of human cryptosporidiosis. Little is known on the occurrence, geographical distribution, and molecular diversity of Cryptosporidium infections affecting bovine populations in Algeria. In this study faecal specimens were randomly collected from 460 cattle aged between two days and 18 months on 10 farms located in the provinces of Aïn Defla, Blida, Sétif, and Tizi Ouzou between the autumn of 2015 and the spring of 2016. Faecal samples were microscopically examined using the modified Ziehl-Neelsen acid-fast technique as screening method. Microscopy-positive samples were confirmed by a commercial coproantigen enzyme-linked immunosorbent assay (Bio-X Diagnostics). The identification of Cryptosporidium species and sub-genotypes in confirmed samples was conducted by PCR and sequence analyses of the small subunit ribosomal RNA (ssu rRNA) and the 60 kDa glycoprotein (gp60) genes of the parasite. Overall, 52.2% (240/460) of the investigated cattle tested positive to Cryptosporidium by microscopy. The infection was widespread in all 10 farms surveyed, but was significantly more prevalent in those from Blida in the central part of the country. Bovine cryptosporidiosis affected cattle of all age groups but with different outcomes. Pre-weaned (up to one month old) calves typically presented with diarrhoea, whereas older animals mostly harboured sub-clinical infections. The commercial ELISA used only detected 15.8% (38/240) of the samples that previously tested positive by microscopy, demonstrating a poor performance in field epidemiological surveys. Sequence analysis of the 29 isolates generated at the ssu rRNA loci confirmed the presence of four Cryptosporidium species including C. parvum (72.4%), C. bovis (13.8%), C. andersoni, (3.4%), and C. ryanae (3.4%). Two additional isolates (7.0%) could only be identified at the genus level. Eight out of the 21 isolates assigned to C. parvum were identified as sub-genotype IIaA16G2R1 at the gp60 locus. C. parvum was almost exclusively found infecting pre-weaned calves, whereas C. ryanae and C. andersoni were only detected in asymptomatic animals. Bovine cryptosporidiosis is highly endemic in the surveyed area and represents a veterinary public health concern that should be adequately tackled by Algerian veterinary health authorities and policy makers.

Cryptosporidium spp. infection in Iranian children and immunosuppressive patients: A systematic review and meta-analysis

BACKGROUND

Cryptosporidiosis is an important cause of diarrhea in children and immunosuppressive patients. The current study was intended to evaluate the prevalence rate of Cryptosporidium infection and clarify the epidemiological characteristics of the infection in both children and immunosuppressive patients in Iran.

METHODS

Five English electronic databases including PubMed, Google Scholar, Science Direct, Scopus and Cochrane, and two Persian language databases Magiran and Scientific Information Database were searched. Additionally, reports from the Iranian congresses of parasitology and graduate student thesis dissertations were assessed manually.

RESULTS

Out of 1856 studies from the literature search, our search resulted in a total of 27 articles published from 1991 to 2016. These include 14 reports on cryptosporidiosis in children and 13 papers regarding immunosuppressive patients. 8520 children and 2015 immunosuppressed cases were evaluated. Oocysts of Cryptosporidium were found in 3.8% and 8% children cases and immunosuppressed patients, respectively. There was a relatively high variation in the prevalence estimates among different studies, and the Q statistics was high among articles regarding children (p<0.0001) and also between records regarding immunosuppressed patients (p<0.0001). Findings showed that the prevalence rates of Cryptosporidium infection are significantly higher in children under 5 years (P=0.00).

CONCLUSIONS

In summary, the present study provides a comprehensive view of the epidemiology of Cryptosporidium in children and immunosuppressive patients in Iran. Furthermore, a multidisciplinary and multicenter study to evaluate the real prevalence of Cryptosporidium infection and to determine its risk factors using an adequate sample size and standardized methods is highly recommended.

Widespread Occurrence of Zoonotic Cryptosporidium Species and Subtypes in Dairy Cattle from Northeast China: Public Health Concerns

Bovine cryptosporidiosis constitutes a threat to the livestock industry and public health worldwide. In the present study we investigated dairy cattle of all ages in northeast China for the prevalence and genetic traits of Cryptosporidium. Nested polymerase chain reaction of the small subunit rRNA gene was used to identify Cryptosporidium species or genotype. The parasite was detected in 130 of 537 (24.2%) animals sampled from the cities of Harbin (35.2%, 69/196) and Qiqihar (32.1%, 61/190). Cryptosporidium parvum (87/130) was identified as the dominant species by sequence analysis followed by Cryptosporidium bovis (28/130), Cryptosporidium ryanae (5/130), Cryptosporidium andersoni (2/130), Cryptosporidium suis-like genotype (2/130), and mixed C. ryanae/ C. bovis (1/130). Subtyping of C. parvum isolates was based on the DNA polymorphisms of the 60-kDa glycoprotein gene. Subtyping of the C. parvum isolates recognized subtypes IIdA15G1 (24/87) in Harbin and IIdA20G1 (48/87) in Qiqihar. A diversity of Cryptosporidium species/genotype and subtypes was identified in cattle from northeast China. Widespread occurrence of human-pathogenic Cryptosporidium species and subtypes is of public health significance. This is the first study reporting C. parvum subtype IIdA20G1 in China. The findings improve the epidemiological knowledge of bovine cryptosporidiosis in China, highlighting the importance of ongoing Cryptosporidium surveillance.

Rodents as a reservoir of infection caused by multiple zoonotic species/genotypes of C. parvum, C. hominis, C. suis, C. scrofarum, and the first evidence of C. muskrat genotypes I and II of rodents in Europe

Cryptosporidium spp. is an important causative agent of intestinal parasitoses-induced diarrhoea in humans and animals worldwide. Rodents (small mammals), the main reservoir of infections, are globally expanded and overpopulated, which increases the risk of transfer of human and zoonotic pathogens from the genus Cryptosporidium. In this study, Cryptosporidium was detected in wild immunocompetent asymptomatic small mammals. Altogether 262 fecal samples were collected from five areas in Eastern Slovakia from four different rodent species (Myodes glareolus, Apodemus agrarius, Apodemus flavicollis, Rattus norvegicus), eight samples originated from two insectivore species (Sorex araneus, Crocidura suaveolens), and two sample from a carnivore Mustela nivalis. The samples were examined using a method modified in our laboratory, based on the use of specific primers on a small subunit rRNA (18S rRNA) gene for species identification, and amplification of GP60 gene coding 60-kDa glycoprotein for genotype determination. The following species were identified: Cryptosporidium parvum (n=15), genotypes IIaA18G3R1 (n=11; KU311673), IIaA10G1R1 (n=1; KU311670), IIcA5G3a (n=1; KU311669), IIiA10 (n=2; KU311672); Cryptosporidium suis (n=4; KU311671); Cryptosporidium scrofarum (n=28); Cryptosporidium environment sp. (n=12; KU311677); Cryptosporidium muskrat genotype I (n=3; KU311675); Cryptosporidium muskrat genotype II (n=3; KU311676). From one of the rodent, the species Cryptosporidium hominis genotype IbA10G2 (KU311668) was identified for the first time. The results of this study indicate low host specificity of the detected Cryptosporidium species and imply the importance of free-living small mammals in urban and suburban habitats as a potential source of human cryptosporidiosis.

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

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

Longitudinal monitoring of Cryptosporidium species in pre-weaned dairy calves on five farms in Shanghai, China

In pre-weaned dairy calves, the zoonotic and pathogenic species Cryptosporidium parvum is the dominant Cryptosporidium species in most industrialized nations. In several studies in China, however, C. bovis has been the dominant one. To further examine the distribution of Cryptosporidium species in pre-weaned dairy calves in China, 818 fecal specimens were collected from five farms in Shanghai, with repeated samplings (up to five times) on each farm. PCR-restriction fragment length polymorphism (RFLP) analysis of the small subunit rRNA gene was used to detect and genotype Cryptosporidium spp. Cryptosporidium parvum was subtyped by sequence analysis of the 60kDa glycoprotein gene. Cryptosporidium occurrence on farms varied between 25.0% (Farm 2) and 55.0% (Farm 4), with a mean infection rate of 37.0%. Three Cryptosporidium species were detected, including C. bovis (193/303 or 63.7%), C. parvum (72/303 or 23.8%) and C. ryanae (32/303 or 10.6%). Concurrent infection of C. bovis and C. ryanae was detected in six (1.9%) animals. During the first two samplings, C. bovis was the dominant species on four farms and C. parvum was detected on only one farm (Farm 1). One of the study farms (Farm 3) started to have C. parvum at the third sampling. C. parvum was associated with the occurrence of moderate or watery diarrhea, while C. bovis was not. All C. parvum were subtype IIdA19G1, which is dominant in China but rare elsewhere. Genotyping and subtyping results indicated that the introduction of C. parvum to Farm 3 was caused by brief housing of several bull calves from another farm. Data from the study suggest that C. parvum is still uncommon in pre-weaned dairy calves in China and measures should be developed to prevent its spread in the country.

Diversity of Cryptosporidium species occurring in sheep and goat breeds reared in Poland

The aim of this study was molecular identification of Cryptosporidium species and assessment of their prevalence in different breeds of sheep and goat reared in Poland. In addition, the relationship between animal age, breed type, and the frequency of Cryptosporidium infections was determined. Fecal samples from 234 lambs and 105 goat kids aged up to 9 weeks, representing 24 breeds and their cross-breeds were collected from 71 small ruminant farms across Poland. The identification of Cryptosporidium species was performed at the 18 SSU ribosomal RNA (rRNA) and COWP loci followed by subtyping of C. parvum and C. hominis strains at GP60 gene locus. The presence of Cryptosporidium DNA at the 18 SSU rRNA locus was detected in 45/234 (19.2%) lamb feces samples and in 39/105 (37.1%) taken from goats. The following Cryptosporidium species: C. xiaoi, C. bovis, C. ubiquitum, C. parvum, and C. hominis were detected in small ruminants. Infections caused by C. xiaoi were predominant without favoring any tested animal species. Subsequent GP60 subtyping revealed the presence of C. parvum IIaA17G1R1 subtype in sheep and IIdA23G1 subtype in goats. IIdA23G1 subtype was detected in a goat host for the first time. There were no significant differences found in frequency of infections between the age groups (<3 and 3-9 weeks) of lambs (P = 0.14, α > 0.05) or goat kids (P = 0.06, α > 0.05). In addition, there was no correlation observed between the frequency in occurrence of particular parasite species and breed type in relation to native sheep breeds (F = 0.11; P = 0.990 > 0.05). In the case of goats, more breed-related differences in parasite occurrence were found. The results of this study improve our knowledge on the breed-related occurrence of Cryptosporidium infections in the population of small ruminants reared in Poland.

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

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

Global Microbial Identifier

Human and animal populations are increasingly confronted with emerging and re-emerging infections and often such infections are exchanged between these populations, e.g. through food. A more effective and uniform approach to the prevention of these microbial threats is essential. The technological advances in the next generation sequencing field and decreasing costs of these tests provide novel opportunities in understanding the dynamics of infection—even in real time—through the analysis of microbial genome diversity. The projected significant increase in whole (microbial) genome sequencing (WGS) will likely also enable a much better understanding of the pathogenesis of the infection and the molecular basis of the host response to infection. But the full potential of these advances will only transpire if the data in this area become transferable and thereby comparable, preferably in open-source systems. There is therefore an obvious need to develop a global system of whole microbial genome databases to aggregate, share, mine and use microbiological genomic data, to address global public health and clinical challenges, and most importantly to identify and diagnose infectious diseases. The global microbial identifier (GMI) initiative, aims to build a database of whole microbial genome sequencing data linked to relevant metadata, which can be used to identify microorganisms, their communities and the diseases they cause. It would be a platform for storing whole genome sequencing (WGS) data of microorganisms, for the identification of relevant genes and for the comparison of genomes to detect outbreaks and emerging pathogens. To harness the full potential of WGS, a shared global database of genomes linked to relevant metadata and the necessary software tools needs to be generated, hence the global microbial identifier (GMI) initiative. This tool will ideally be used in amongst others in the diagnosis of infectious diseases in humans and animals, in the identification of microorganisms in food and environment, and to track and trace microbial agents in all arenas globally. This will require standardization and extensive investments in computational analytical tools. In addition, the wider introduction of WGS in clinical diagnostics can accelerate developments in health care in many poor countries. This overview describes the growing network of stakeholders behind GMI, the contours of the database, and the IT structures needed to serve the GMI user community. It discusses what essentially can be done by a global GMI tool and how the GMI organization could help achieve these goals.

Human cryptosporidiosis in Iran: a systematic review and meta-analysis

Cryptosporidiosis caused by Cryptosporidium spp. is an important parasitic disease that can be life-threatening for children and immunocompromised patients. This systematic review and meta-analysis was designed to determine the prevalence rate of Cryptosporidium infection and related risk factors among the Iranian general population. We searched electronic databases including Google Scholar, PubMed, Science Direct, Scopus and Proquest for articles in English and SID, Magiran, IranMedex, and IranDoc for articles in Persian. Out of 4816 studies identified in the electronic search, 94 articles were eligible for inclusion in the systematic review and meta-analysis. The prevalence rate of cryptosporidiosis by using the random effect model among children, healthy people, and gastroenteritis and immunocompromised patients in Iran was estimated as 3.65, 2.94, 1.29, and 4.54%, respectively. Findings of a phylogenetic analysis inferred by gp60 and 18S ribosomal RNA markers indicated that most of the infection rate belonged to C. parvum (particularly subtype IIaA15G2R1) and C. hominis among understudied groups. The present study is the first systematic review and meta-analysis providing a comprehensive view of the prevalence of human cryptosporidiosis and its related risk factors in Iran. It seems that the awareness of Cryptosporidium prevalence, risk factors, and disease complications may be required for developing effective strategies to prevent infection.