Predominant virulent IbA10G2 subtype of Cryptosporidium hominis in human isolates in Barcelona: a five-year study

Detection and Molecular Diversity of Cryptosporidium spp. and Giardia duodenalis in the Endangered Iberian Lynx (Lynx pardinus), Spain

Cryptosporidium spp. and Giardia duodenalis are the main non-viral causes of diarrhoea in humans and domestic animals globally. Comparatively, much less information is currently available in free-ranging carnivore species in general and in the endangered Iberian lynx (Lynx pardinus) in particular. Cryptosporidium spp. and G. duodenalis were investigated with molecular (PCR and Sanger sequencing) methods in individual faecal DNA samples of free-ranging and captive Iberian lynxes from the main population nuclei in Spain. Overall, Cryptosporidium spp. and G. duodenalis were detected in 2.4% (6/251) and 27.9% (70/251) of the animals examined, respectively. Positive animals to at least one of them were detected in each of the analysed population nuclei. The analysis of partial ssu rRNA gene sequences revealed the presence of rodent-adapted C. alticolis (n = 1) and C. occultus (n = 1), leporid-adapted C. cuniculus (n = 2), and zoonotic C. parvum (n = 2) within Cryptosporidium, and zoonotic assemblages A (n = 5) and B (n = 3) within G. duodenalis. Subgenotyping analyses allowed for the identification of genotype VaA19 in C. cuniculus (gp60 locus) and sub-assemblages AI and BIII/BIV in G. duodenalis (gdh, bg, and tpi loci). This study represents the first molecular description of Cryptosporidium spp. and G. duodenalis in the Iberian lynx in Spain. The presence of rodent/leporid-adapted Cryptosporidium species in the surveyed animals suggests spurious infections associated to the Iberian lynx's diet. The Iberian lynx seems a suitable host for zoonotic genetic variants of Cryptosporidium (C. parvum) and G. duodenalis (assemblages A and B), although the potential risk of human transmission is regarded as limited due to light parasite burdens and suspected low excretion of infective (oo)cysts to the environment by infected animals. More research should be conducted to ascertain the true impact of these protozoan parasites in the health status of the endangered Iberian lynx.

Molecular characterization of Cryptosporidium spp. obtained from fecal samples of immunosuppressed patients from Brazil

Background:

Cryptosporidium spp. are pathogenic protozoans that play an important role in developing diseases in the elderly, children, and immunosuppressed individuals.

Methods:

The objective of this study was to detect and genetically characterize Cryptosporidium spp. in kidney transplanted patients (n = 97 samples; group 1) and immunosuppressed individuals from an outpatient clinic suspected of having Cryptosporidium infection (n = 53 samples; group 2). All fecal samples were analyzed by parasitological stool examination, immunochromatographic test, and real-time polymerase chain reaction (real-time PCR). Cryptosporidium-positive samples were tested using nested PCR for the gp60 gene, followed by sequencing for subtype determination.

Results:

Parasitological examination was negative in all Group 1, and positive in four Group 2 samples. Real-time PCR revealed Cryptosporidium in 13 samples: four in Group 1 (three C. hominis and one C. parvum) and nine in Group 2 (seven C. hominis, one C. parvum, and one mixed C. hominis/C. parvum). The immunochromatographic test was reactive in 11 samples (four in Group 1 and seven in Group 2). All 11 C. hominis isolates were identified as subtype IbA10G2 and one C. parvum as subtype IIbA15G2R1. All C. hominis belonged to subtype IbA10G2, which is recognized as the most prevalent and pathogenic subtype.

Conclusions:

This study showed, for the first time, that the presence of Cryptosporidium subtypes is considered more virulent in Brazilian transplanted kidney patients.

Global population genomics of two subspecies of Cryptosporidium hominis during 500 years of evolution

Cryptosporidiosis is a major global health problem and a primary cause of diarrhea, particularly in young children in low- and middle-income countries (LMICs). The zoonotic Cryptosporidium parvum and anthroponotic Cryptosporidium hominis cause most human infections. Here, we present a comprehensive whole-genome study of C. hominis, comprising 114 isolates from 16 countries within five continents. We detect two lineages with distinct biology and demography, which diverged circa 500 years ago. We consider these lineages two subspecies and propose the names C. hominis hominis and C. hominis aquapotentis (gp60 subtype IbA10G2). In our study, C. h. hominis is almost exclusively represented by isolates from LMICs in Africa and Asia and appears to have undergone recent population contraction. In contrast, C. h. aquapotentis was found in high-income countries, mainly in Europe, North America, and Oceania, and appears to be expanding. Notably, C. h. aquapotentis is associated with high rates of direct human-to-human transmission, which may explain its success in countries with well-developed environmental sanitation infrastructure. Intriguingly, we detected genomic regions of introgression following secondary contact between the subspecies. This resulted in high diversity and divergence in genomic islands of putative virulence genes, including muc5 (CHUDEA2_430) and a hypothetical protein (CHUDEA6_5270). This diversity is maintained by balancing selection, suggesting a co-evolutionary arms race with the host. Finally, we find that recent gene flow from C. h. aquapotentis to C. h. hominis, likely associated with increased human migration, maybe driving the evolution of more virulent C. hominis variants.

Cryptosporidiosis is predominantly an urban, anthroponotic infectious disease among Zambian children

BACKGROUND

Cryptosporidium species are leading causes of diarrhoea in children and immunocompromised individuals. This study aimed to characterise Cryptosporidium species from children in rural and urban settings of Zambia.

METHODS

Stool samples collected from 490 children aged <5 y with diarrhoea were assessed for Cryptosporidium oocysts microscopically. A structured questionnaire was used to collect demographic and socioeconomic characteristics. Positive samples were subjected to PCR and gp60 sequence analysis.

RESULTS

The overall prevalence was 10% (50/490, 95% CI 7.8 to 13.2) with a peak in March, the late rainy season. Children who came from households where boiling water was not practised (OR=2.5, 95% CI 1.29 to 5.17; p=0.007) or who had experienced recurrent episodes of diarrhoea (OR=9.31, 95% CI 3.02 to 28.73; p=0.001) were more likely to have Cryptosporidium infection. Genotyping of 16 positive samples (14 from urban and 2 from rural sources) revealed Cryptosporidium hominis (14/16) and Cryptosporidium parvum (2/16). The Cryptosporidium hominis subtypes identified were Ia, Ib and Ie with subtype families IeAIIG3 (1), IbA9G3R2 (2), IaA31R3 (3), IbA9G3 (5), IaA27R3 (1), IaA30R3 (1) and Ia (1). Subtypes IbA9G3 and Ia were identified in children from a rural area. Cryptosporidium parvum subtypes were IIcA5G3R2 (1) and IIcA5G3a (1).

CONCLUSIONS

All isolates successfully genotyped were C. hominis or anthroponotic C. parvum, suggesting that anthroponotic transmission dominates in Lusaka and the surrounding countryside.

Draft Genome Assemblies of Two Cryptosporidium hominis Isolates from New Zealand

Cryptosporidium hominis is a protozoan parasite that causes gastrointestinal disease in humans worldwide. Here, we report on draft whole-genome sequences of two clinical isolates of C. hominis that were purified from patients with cryptosporidiosis in New Zealand.

Absence of Cryptosporidium hominis and dominance of zoonotic Cryptosporidium species in patients after Covid-19 restrictions in Auckland, New Zealand

Coronavirus disease-2019 (Covid-19) nonpharmaceutical interventions have proven effective control measures for a range of respiratory illnesses throughout the world. These measures, which include isolation, stringent border controls, physical distancing and improved hygiene also have effects on other human pathogens, including parasitic enteric diseases such as cryptosporidiosis. Cryptosporidium infections in humans are almost entirely caused by two species: C. hominis, which is primarily transmitted from human to human, and Cryptosporidium parvum, which is mainly zoonotic. By monitoring Cryptosporidium species and subtype families in human cases of cryptosporidiosis before and after the introduction of Covid-19 control measures in New Zealand, we found C. hominis was completely absent after the first months of 2020 and has remained so until the beginning of 2021. Nevertheless, C. parvum has followed its typical transmission pattern and continues to be widely reported. We conclude that ~7 weeks of isolation during level 3 and 4 lockdown period interrupted the human to human transmission of C. hominis leaving only the primarily zoonotic transmission pathway used by C. parvum. Secondary anthroponotic transmission of C. parvum remains possible among close contacts of zoonotic cases. Ongoing 14-day quarantine measures for new arrivals to New Zealand have likely suppressed new incursions of C. hominis from overseas. Our findings suggest that C. hominis may be controlled or even eradicated through nonpharmaceutical interventions.

A novel genotyping method for Cryptosporidium hominis

Cryptosporidiosis remains the leading protozoan induced cause of diarrhoea-associated mortality worldwide. Cryptosporidium hominis, the anthroponotically transmitted species within the Cryptosporidium genus, contributes significantly to the global burden of infection, accounting for the majority of clinical cases in many countries. This study applied high resolution melting analysis, a post-real-time PCR application, to the differentiation of six globally prevalent C. hominisgp60-subtypes. This novel method targeted three microsatellite, tandem repeat containing genetic markers, gp60, the genetic marker upon which current Cryptosporidium subtype nomenclature is based, MSB, and MSE, by which to differentiate between C. hominis isolates. This multi-locus approach successfully differentiated between all six C. hominisgp60-subtypes studied, some of which, such as IbA10G2, are known to exhibit global ubiquity. Thus, this method has the potential to be universally employed as a sensitive, cost effective and highly reproducible means to rapidly differentiate between C. hominisgp60-subtypes. Such a method would be of particular utility in epidemiological studies and outbreak scenarios, providing cost effective, clinically accessible alternative to DNA sequencing. The success of this preliminary study also supports further analysis of an expanded C. hominisgp60-subtype range and the potential expansion of the multi-locus panel in order to improve the discriminatory power of this approach.

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.

Dairy Calves in Uruguay Are Reservoirs of Zoonotic Subtypes of Cryptosporidium parvum and Pose a Potential Risk of Surface Water Contamination

Cryptosporidium parvum, a major cause of diarrhea in calves, is of concern given its zoonotic potential. Numerous outbreaks of human cryptosporidiosis caused by C. parvum genetic subtypes are reported yearly worldwide, with livestock or water being frequently identified sources of infection. Although cryptosporidiosis has been reported from human patients in Uruguay, particularly children, epidemiologic information is scant and the role of cattle as reservoirs of zoonotic subtypes of C. parvum has not been explored. In this study, we aimed to (a)-identify C. parvum subtypes infecting dairy calves in Uruguay (including potentially zoonotic subtypes), (b)-assess their association with calf diarrhea, (c)-evaluate their spatial clustering, and (d)-assess the distance of infected calves to surface watercourses draining the farmlands and determine whether these watercourses flow into public water treatment plants. Feces of 255 calves that had tested positive for Cryptosporidium spp. by antigen ELISA were selected. Samples had been collected from 29 dairy farms in seven Uruguayan departments where dairy farming is concentrated and represented 170 diarrheic and 85 non-diarrheic calves. Selected samples were processed by nested PCRs targeting the 18S rRNA and gp60 genes followed by sequencing to identify C. parvum subtypes. Of seven C. parvum subtypes detected in 166 calves, five (identified in 143 calves on 28/29 farms) had been identified in humans elsewhere and have zoonotic potential. Subtype IIaA15G2R1 was the most frequent (53.6%; 89/166), followed by IIaA20G1R1 (24.1%; 40/166), IIaA22G1R1 (11.4%; 19/166), IIaA23G1R1 (3.6%; 6/166), IIaA17G2R1 (3%; 5/166), IIaA21G1R1 (2.4%; 4/166), and IIaA16G1R1 (1.8%; 3/166). There were no significant differences in the proportions of diarrheic and non-diarrheic calves infected with any of the C. parvum subtypes. Two spatial clusters were detected, one of which overlapped with Uruguay's capital city and its main water treatment plant (Aguas Corrientes), harvesting surface water to supply ~1,700,000 people. Infected calves on all farms were within 20–900 m of a natural surface watercourse draining the farmland, 10 of which flowed into six water treatment plants located 9–108 km downstream. Four watercourses flowed downstream into Aguas Corrientes. Calves are reservoirs of zoonotic C. parvum subtypes in Uruguay and pose a public health risk.

Molecular Diversity of Giardia duodenalis, Cryptosporidium spp. and Blastocystis sp. in Asymptomatic School Children in Leganés, Madrid (Spain)

Enteric parasites including Giardia duodenalis, Cryptosporidium spp., and to a lesser extent, Blastocystis sp. and Enterocytozoon bieneusi, are major worldwide contributors to diarrhoeal disease. Assessing their molecular frequency and diversity is important to ascertain the sources of infection, transmission dynamics, and zoonotic potential. Little molecular information is available on the genotypes of these pathogens circulating in apparently healthy children. Here, we show that asymptomatic carriage of G. duodenalis (17.4%, 95% CI: 15.5‒19.4%), Blastocystis sp. (13.0%, 95% CI: 11.4‒14.8%), and Cryptosporidium spp. (0.9%, 95% CI: 0.5‒1.5%) is common in children (1‒16 years; n = 1512) from Madrid, Spain. Our genotyping data indicate that; (i) the observed frequency and diversity of parasite genetic variants are very similar to those previously identified in Spanish clinical samples, so that the genotype alone does not predict the clinical outcome of the infection, (ii) anthroponotic transmission accounts for a large proportion of the detected cases, highlighting that good personal hygiene practices are important to minimizing the risk of infection, (iii) Blastocystis ST4 may represent a subtype of the parasite with higher pathogenic potential, and (iv) Enterocytozoon bieneusi does not represent a public health concern in healthy children.

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.

Occurrence and molecular characterization of Giardia duodenalis cysts and Cryptosporidium oocysts in raw water samples from the Rímac River, Peru

Giardia and Cryptosporidium are potentially pathogenic protozoa which are ubiquitous in ambient surface water. The present study included 60 samples of surface water from three sampling sites from the Rímac River, Lima and Callao, Peru, to detect the occurrence of Giardia spp. and Cryptosporidium spp. and to perform molecular characterization of specimens found. Water samples were concentrated using the membrane filtration technique, and following elution, cysts and oocysts were visualized by direct immunofluorescence assay (IFA). For molecular characterization, tpi and bg gene fragments and 18S rRNA were amplified by nested PCR for Giardia and Cryptosporidium, respectively, followed by sequencing and phylogenetic analysis. Giardia cysts were found in 93.3% of the analyzed samples, whereas Cryptosporidium oocysts were detected in 15%. The positivity of the Giardia cysts was 86.6% (n = 26) in 2014, while Cryptosporidium oocysts were not detected. In 2015, both protozoa were found in raw water samples, with all 30 samples collected positive for Giardia cysts (100.0%) and 9 positive for Cryptosporidium oocysts (30.0%). Oocysts were detected in 20.0% of water samples from sites 1 (mean 5.25 oocysts/L) and 2 (mean 52.3 oocysts/L), while at site 3, oocysts were detected in 50.0% of raw water samples (mean 193.6 oocysts/L). The presence of Giardia duodenalis assemblage A was confirmed in several samples by the phylogenetic positioning of the bg and tpi genes, and the sub-assemblage AII was predominant (8/9). Sequencing for Cryptosporidium resulted in profiles compatible with Cryptosporidium hominis, Cryptosporidium meleagridis, and Cryptosporidium baileyi. This is the first time that the presence of G. duodenalis assemblage A/sub-assemblage AII and Cryptosporidium species has been reported in surface water samples in Peru. These Cryptosporidium species and the Giardia duodenalis assemblage are associated with human disease which highlights the potential risk to public health and the need to increase environmental monitoring measures to protect this water body.

Occurrence and genetic diversity of Cryptosporidium and Giardia in urban wastewater treatment plants in north-eastern Spain

This study was designed to investigate the presence and removal efficiency of Cryptosporidium and Giardia in wastewater treatment plants at the 20 most populated towns in Aragón (north-eastern Spain). Samples of influent and effluent wastewater and dewatered sewage sludge were collected seasonally from 23 plants and processed according to USEPA Method 1623. All samples from raw and treated wastewater tested positive for Giardia, at an average concentration of 3247±2039cysts/l and 50±28cysts/l, respectively. Cryptosporidium was identified in most samples from both raw (85/92) and treated (78/92) wastewaters in a concentration significantly lower than Giardia, at both influent (96±105oocysts/l) and effluent samples (31±70oocysts/l) (P<0.001). The (oo)cyst counts peaked in summer in most plants. The removal efficiency was higher for Giardia (1.06-log to 2.34-log) than Cryptosporidium (0.35-log to 1.8-log). Overall, high removal efficiency values were found for Giardia after secondary treatment based on activated sludge, while tertiary treatment (microfiltration, chlorination and/or ultraviolet irradiation) was needed to achieve the greatest removal or inactivation of Cryptosporidium. Most samples of treated sludge were positive for Giardia (92/92) and Cryptosporidium (45/92), at an average concentration of 20-593cysts/g and 2-44oocyst/g, respectively. The molecular characterization of Cryptosporidium oocysts and Giardia cysts were attempted at the SSU rRNA/GP60 and bg/tpi loci, respectively. G. duodenalis sub-assemblage AII was identified in all plants, with a large proportion of samples (15/47) harboring mixed assemblages (AII+B). Nine Cryptosporidium species and six subtypes were identified, with C. parvum IIaA15G2R1 being the most prevalent. The presence of significant numbers of (oo)cysts in samples of final effluents and treated sludge reveals the limited efficacy of conventional treatments in removing (oo)cysts and highlights the potential environmental impact and public health risks associated with disposal and reclamation of wastewater.

Improving the genotyping resolution of Cryptosporidium hominis subtype IbA10G2 using one step PCR-based amplicon sequencing

Cryptosporidium hominis gp60 subtype IbA10G2 is a common cause of cryptosporidiosis. This subtype is responsible for many waterborne outbreaks as well as sporadic cases and is considered virulent and highly important in the epidemiology of cryptosporidiosis. Due to low heterogeneity within the genome of C. hominis it has been difficult to identify epidemiological markers with higher resolution than gp60. However, new markers are required in order to improve outbreak investigations and studies of the transmission dynamics of this clinically important subtype. Based on the whole genome sequences of 17 C. hominis isolates, we have identified several differential loci and developed a new sequence based typing panel with higher resolution than gp60. An amplicon sequencing method was also developed which is based on a one-step PCR which can be sequenced using a Next Generation Sequencing (NGS) platform. Such a system provides a rapid and high-throughput workflow. A panel of nine loci with 10 single nucleotide variants (SNV) was selected and evaluated using clinical IbA10G2 isolates from sporadic, cluster and outbreak associated cases. The specimens were separated into 10 different genetic profiles named sequence types (STs). All isolates within an outbreak or cluster belonged to the same ST, including several samples from the two large waterborne outbreaks which occurred in Sweden between 2010 and 2011 indicating that these outbreaks might be linked. The results demonstrate the methods suitability for improved genotyping of C. hominis IbA10G2.

Molecular diversity and frequency of the diarrheagenic enteric protozoan Giardia duodenalis and Cryptosporidium spp. in a hospital setting in Northern Spain

Background

Human giardiosis and cryptosporidiosis are caused by the enteric protozoan parasites Giardia duodenalis and Cryptosporidium spp. Both pathogens are major contributors to the global burden of diarrhoeal disease, affecting primarily children and immunodebilitated individuals in resource-poor settings. Giardiosis and cryptosporidiosis also represent an important, often underestimate, public health threat in developed countries. In Spain only limited information is currently available on the epidemiology of these infections. Molecular data on the diversity, frequency, geographical distribution, and seasonality of G. duodenalis assemblages/sub-assemblages and Cryptosporidium species/sub-genotypes are particularly scarce.

Methods

A longitudinal molecular epidemiological survey was conducted between July 2015 to September 2016 in patients referred to or attended at the Hospital San Pedro (La Rioja, Northern Spain) that tested positive for G. duodenalis (N = 106) or Cryptosporidium spp. (N = 103) by direct microscopy and/or a rapid lateral flow immunochromatographic assay. G. duodenalis infections were subsequently confirmed by real-time PCR and positive isolates assessed by multi-locus sequence genotyping of the glutamate dehydrogenase and β-giardin genes of the parasite. Cryptosporidium species and sub-genotypes were investigated at the 60 kDa glycoprotein or the small subunit ribosomal RNA genes of the parasite. Sociodemographic and clinical parameters of infected patients were also gathered and analysed.

Principal findings

Out of 90 G. duodenalis-positive isolates by real-time PCR a total of 16 isolates were successfully typed. AII (44%, 7/16) was the most prevalent sub-assemblage found, followed by BIV (31%, 5/16) and BIII (19%, 3/16). A discordant genotype result AII/AIII was identified in an additional (6%, 1/16) isolate. No mixed infections A+B were detected. Similarly, a total of 81 Cryptosporidium spp. isolates were successfully typed, revealing the presence of C. hominis (81%, 66/81) and C. parvum (19%, 15/81). Obtained GP60 sequences were assigned to sub-type families Ib (73%, 59/81) within C. hominis, and IIa (7%, 6/81) and IId (2%, 2/81) within C. parvum. A marked inter-annual variation in Cryptosporidium cases was observed.

Conclusions

Human giardiasis and cryptosporidiosis are commonly identified in patients seeking medical care in Northern Spain and represent a more important health concern than initially thought. Assemblage A within G. duodenalis and sub-genotype IbA10G2 within C. hominis were the genetic variants of these parasite species more frequently found circulating in the population under study. Molecular data presented here seem to suggest that G. duodenalis and Cryptosporidium infections arise through anthroponotic rather than zoonotic transmission in this Spanish region.

Genomic Variation in IbA10G2 and Other Patient-Derived Cryptosporidium hominis Subtypes

In order to improve genotyping and epidemiological analysis of Cryptosporidium spp., genomic data need to be generated directly from a broad range of clinical specimens. Utilizing a robust method that we developed for the purification and generation of amplified target DNA, we present its application for the successful isolation and whole-genome sequencing of 14 different Cryptosporidium hominis patient specimens. Six isolates of subtype IbA10G2 were analyzed together with a single representative each of 8 other subtypes: IaA20R3, IaA23R3, IbA9G3, IbA13G3, IdA14, IeA11G3T3, IfA12G1, and IkA18G1. Parasite burden was measured over a range of more than 2 orders of magnitude for all samples, while the genomes were sequenced to mean depths of between 17× and 490× coverage. Sequence homology-based functional annotation identified several genes of interest, including the gene encoding Cryptosporidium oocyst wall protein 9 (COWP9), which presented a predicted loss-of-function mutation in all the sequence subtypes, except for that seen with IbA10G2, which has a sequence identical to the Cryptosporidium parvum reference Iowa II sequence. Furthermore, phylogenetic analysis showed that all the IbA10G2 genomes form a monophyletic clade in the C. hominis tree as expected and yet display some heterogeneity within the IbA10G2 subtype. The current report validates the aforementioned method for isolating and sequencing Cryptosporidium directly from clinical stool samples. In addition, the analysis demonstrates the potential in mining data generated from sequencing multiple whole genomes of Cryptosporidium from human fecal samples, while alluding to the potential for a higher degree of genotyping within Cryptosporidium epidemiology.

Zoonotic Cryptosporidium Species in Animals Inhabiting Sydney Water Catchments

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

Genetic diversity of Cryptosporidium identified in clinical samples from cities in Brazil and Argentina

The identification and characterisation of Cryptosporidiumgenotypes and subtypes are fundamental to the study of cryptosporidiosis epidemiology, aiding in prevention and control strategies. The objective was to determine the genetic diversity ofCryptosporidium in samples obtained from hospitals of Rio de Janeiro, Brazil, and Buenos Aires, Argentina. Samples were analysed by microscopy and TaqMan polymerase chain reaction (PCR) assays forCryptosporidium detection, genotyped by nested-PCR-restriction fragment length polymorphism (RFLP) analysis of the 18S rRNA gene and subtyped by DNA sequencing of the gp60 gene. Among the 89 samples from Rio de Janeiro, Cryptosporidium spp were detected in 26 by microscopy/TaqMan PCR. In samples from Buenos Aires,Cryptosporidium was diagnosed in 15 patients of the 132 studied. The TaqMan PCR and the nested-PCR-RFLP detected Cryptosporidium parvum, Cryptosporidium hominis, and co-infections of both species. In Brazilian samples, the subtypes IbA10G2 and IIcA5G3 were observed. The subtypes found in Argentinean samples were IbA10G2, IaA10G1R4, IaA11G1R4, and IeA11G3T3, and mixed subtypes of Ia and IIa families were detected in the co-infections. C. hominis was the species more frequently detected, and subtype family Ib was reported in both countries. Subtype diversity was higher in Buenos Aires than in Rio de Janeiro and two new subtypes were described for the first time.

Human cryptosporidiosis in Europe

Cryptosporidium has emerged as a significant cause of diarrhoeal disease worldwide, with severe health consequences for very young, malnourished children living in endemic areas and for individuals with highly impaired T-cell functions. In Europe, as elsewhere, the burden of disease has been difficult to measure as a result of the lack of appropriate, standardized surveillance and monitoring systems. The recent occurrence of large water- and foodborne outbreaks in several EU countries, as well as the results of many surveys of human and animal cryptosporidiosis, indicate that this parasite is widespread. Specific subtypes of the zoonotic Cryptosporidium parvum and the anthroponotic C. hominis are responsible for the majority of human cases in Europe. No treatment is currently available to clear the infection, but recent progress in genetic engineering of the parasite, coupled with advances in genomics, have opened important avenues for future research. Here we explore the possible reasons for underascertainment of cryptosporidiosis and the importance of accurate diagnosis in clinical management, the epidemiology of human cryptosporidiosis and key messages from recent outbreaks to highlight important interventions and emerging public health issues.

Molecular genotyping and sub-genotyping of Cryptosporidium spp. isolates from symptomatic individuals attending two major public hospitals in Madrid, Spain

Infections by members of the protozoan genus Cryptosporidium are among the most common causes of human gastrointestinal illness worldwide. In Spain cryptosporidiosis is not a compulsory notifiable disease, so the actual burden of the infection in both clinical and general populations remains largely unknown. We present here data on the diversity and frequency of the Cryptosporidium species and sub-genotypes identified in symptomatic individuals seeking medical care in two major hospitals in Madrid, Spain, between December 2013 and January 2015. Initial detection of the parasite was conducted on a total of 122 stool samples collected from 120 patients by microscopy with modified Ziehl-Neelsen and/or immunochromatographic tests. We used immunofluorescence, PCR-based methods and sequence analyses of the 60-kDa (GP60) glycoprotein and the small subunit ribosomal RNA (SSU rRNA) genes for confirmatory purposes and to characterize Cryptosporidium isolates. A total of 110 patients were confirmed with cryptosporidiosis. Overall, 101 isolates were successfully sub-genotyped at the GP60 locus, and an additional seven at the SSU rRNA locus. The analyses of all amplicons defined 10 distinct sequence types representing the GP60 family sub-genotypes IbA10G2 (78.7%), IeA11G3T3 (3.7%) of C. hominis, and the GP60 family sub-types IIaA15G2R1 (5.6%), IIaA18G6R1 (0.9%), IIcA5G3a (0.9%), IIdA18G1 (0.9%), IIdA19G1 (0.9%), IIdA21G1 (0.9%), and IIdA22G1 (0.9%) of C. parvum. A single isolate was assigned to C. felis (0.9%), two C. parvum isolates (1.9%) could not be characterized at the sub-genotype level and an additional four isolates (3.7%) were not typable. These results strongly suggest that transmission of cryptosporidiosis is mostly anthroponotic in origin in the clinical sample under study. We expect that our molecular epidemiological data will make a significant contribution to unravel the actual epidemiological situation of cryptosporidiosis in Spain, providing health care and policy makers with solid baseline information to unavoidably improve the national surveillance system and allocate additional resources to research, diagnosis, and treatment of cryptosporidiosis.