What is Cryptosporidium? Reappraising its biology and phylogenetic affinities

Protozoan parasites of birds from the Tremembé formation (Oligocene of the Taubaté Basin), São Paulo, Brazil

OBJECTIVE

To analyze the presence of protozoan parasites in bird coprolites from the Tremembé Formation (Oligocene of the Taubaté Basin).

MATERIALS

Twenty avian coprolites embedded in pyrobituminous shale matrices.

METHODS

Samples were rehydrated and subjected to spontaneous sedimentation.

RESULTS

Paleoparasitological analyses revealed oocysts compatible with the Eimeriidae family (Apicomplexa) and one single Archamoebae (Amoebozoa) cyst.

CONCLUSIONS

The present work increases the amount of information about the spread of infections throughout the Cenozoic Era and reveals that the Brazilian paleoavifauna played an important role in the Apicomplexa and Amoebozoa life cycles.

SIGNIFICANCE

This is the first record of protozoans in avian coprolites from the Oligocene of Brazil. These findings can help in the interpretation of phylogenies of coccidian parasites of modern birds, as certain taxonomic characters observed in the Oligocene Protozoa characterize monophyletic groups in current molecular phylogenetic analyses.

LIMITATIONS

None of the oocysts were sporulated; therefore, it is not possible to identify the morphotypes to genus or species.

SUGGESTIONS FOR FURTHER RESEARCH

Our results create new perspectives related to biogeographic studies of the parasitic groups described and may improve the understanding of the temporal amplitude of parasitic evolutionary relationships between Protozoans and birds.

A NEW EIMERIA SPECIES (APICOMPLEXA: EIMERIIDAE) PARASITIZING COMMERCIAL CHUKAR PARTRIDGES (ALECTORIS CHUKAR) IN SOUTHERN ONTARIO

A commercial producer hatching and rearing chukar partridges (Alectoris chukar) in Ontario, Canada had flocks experiencing coccidiosis. Microscopic analysis of Eimeria species isolated from a field sample indicated the presence of 2 distinct oocyst morphotypes; the most abundant species was determined to be Eimeria chapmani, based on oocyst morphology and sequence-based genotyping, and the less abundant, second Eimeria sp. was an undescribed parasite. Oocysts of the unknown Eimeria sp. were large and oval-shaped; dimensions averaged 27.9 μm by 17.0 μm (shape index = 1.65 μm). Oocysts contained at least 1 polar granule and 4 almond-shaped sporocysts with average dimensions measuring 12.5 μm by 6.9 μm (shape index = 1.83). Each sporocyst featured a Stieda body, sub-Stieda body, and sporocyst residuum; a sporocyst contained 2 sporozoites that each possessed a small anterior refractile body and a larger posterior refractile body. Virtually all oocysts sporulated after 24 hr when suspended in potassium dichromate at room temperature (22 C) on a rotary platform. Experimental infections with various doses of oocysts demonstrated elevated parasite shedding from birds gavaged with higher challenge doses; fecundity generally decreased in heavier infections. The approximate prepatent period of the parasite was 4-5 days (unsporulated oocysts observed histologically at 90 hr postinfection and in feces by day 5) and patency lasted until day 12 postinfection. To characterize the endogenous development of the Eimeria sp., tissues were collected at 8 regions along the intestinal tract (including the ceca and rectum) every 6 hr throughout the estimated prepatent period. Parasites were observed to infect the descending and ascending duodenum, midjejunum, proximal and distal ileum, and the ceca. The endogenous stages identified included intracellular sporozoites, 3 generations of merogony, and gametogonic stages. Sequences of the mitochondrial genome (GenBank MW934555) and nuclear 18S ribosomal DNA (GenBank MW934259) were obtained using polymerase chain reaction amplification for Sanger sequencing, and these were unique from all published sequences on GenBank. Molecular data, in conjunction with the unique biology of the Eimeria sp. isolated from the chukar partridge flock, support that this coccidium is new to science.

Origin and arrangement of actin filaments for gliding motility in apicomplexan parasites revealed by cryo-electron tomography

The phylum Apicomplexa comprises important eukaryotic parasites that invade host tissues and cells using a unique mechanism of gliding motility. Gliding is powered by actomyosin motors that translocate host-attached surface adhesins along the parasite cell body. Actin filaments (F-actin) generated by Formin1 play a central role in this critical parasitic activity. However, their subcellular origin, path and ultrastructural arrangement are poorly understood. Here we used cryo-electron tomography to image motile Cryptosporidium parvum sporozoites and reveal the cellular architecture of F-actin at nanometer-scale resolution. We demonstrate that F-actin nucleates at the apically positioned preconoidal rings and is channeled into the pellicular space between the parasite plasma membrane and the inner membrane complex in a conoid extrusion-dependent manner. Within the pellicular space, filaments on the inner membrane complex surface appear to guide the apico-basal flux of F-actin. F-actin concordantly accumulates at the basal end of the parasite. Finally, analyzing a Formin1-depleted Toxoplasma gondii mutant pinpoints the upper preconoidal ring as the conserved nucleation hub for F-actin in Cryptosporidium and Toxoplasma. Together, we provide an ultrastructural model for the life cycle of F-actin for apicomplexan gliding motility.

Regulatory Functions of Hypoxia in Host-Parasite Interactions: A Focus on Enteric, Tissue, and Blood Protozoa

Body tissues are subjected to various oxygenic gradients and fluctuations and hence can become transiently hypoxic. Hypoxia-inducible factor (HIF) is the master transcriptional regulator of the cellular hypoxic response and is capable of modulating cellular metabolism, immune responses, epithelial barrier integrity, and local microbiota. Recent reports have characterized the hypoxic response to various infections. However, little is known about the role of HIF activation in the context of protozoan parasitic infections. Growing evidence suggests that tissue and blood protozoa can activate HIF and subsequent HIF target genes in the host, helping or hindering their pathogenicity. In the gut, enteric protozoa are adapted to steep longitudinal and radial oxygen gradients to complete their life cycle, yet the role of HIF during these protozoan infections remains unclear. This review focuses on the hypoxic response to protozoa and its role in the pathophysiology of parasitic infections. We also discuss how hypoxia modulates host immune responses in the context of protozoan infections.

Apical Secretory Glycoprotein Complex Contributes to Cell Attachment and Entry by Cryptosporidium parvum

Cryptosporidium parvum is an enteric pathogen that invades epithelial cells in the intestine, where it resides at the apical surface in a unique epicellular location. Compared with those of related apicomplexan parasites, the processes of host cell attachment and invasion by C. parvum are poorly understood. The streamlined C. parvum genome contains numerous mucin-like glycoproteins, several of which have previously been shown to mediate cell attachment, although the majority are unstudied. Here, we identified the antigens recognized by monoclonal antibody (MAb) 1A5, which stains the apical end of sporozoites and mature merozoites. Immunoprecipitation with MAb 1A5 followed by mass spectrometry identified a heterodimer comprised of paralogous proteins which are related to additional orthologs in the genome of C. parvum and related species. Paralogous glycoproteins recognized by MAb 1A5 heterodimerize as a complex displayed on the parasite surface, and they also interact with lectins that suggest that they contain mucin-like, O-linked oligosaccharides. Although the gene encoding one of the paralogs was readily disrupted by CRISPR/Cas9 gene editing, its partner, which contains a mucin-like domain related to GP900, was refractory to deletion. Combined with the ability of MAb 1A5 to partially neutralize host cell attachment by sporozoites, these findings define a new family of secretory glycoproteins that participate in cell invasion by Cryptosporidium spp. IMPORTANCE Although Cryptosporidium is extremely efficient at penetrating mucus and invading epithelial cells in the intestine, the mechanism of cell attachment is poorly understood. To expand our understanding of this process, we characterized the antigens recognized by a monoclonal antibody that stains the apical end of invasive stages called sporozoites and merozoites. Our studies identify a family of glycoproteins that form heterodimers on the parasite cell surface to facilitate host cell attachment and entry. By further defining the role of mucin-like glycoproteins in host cell attachment, our studies may lead to strategies to disrupt cell adhesion and thereby decrease infection.

Targeting the alternative oxidase (AOX) for human health and food security, a pharmaceutical and agrochemical target or a rescue mechanism?

Some of the most threatening human diseases are due to a blockage of the mitochondrial electron transport chain (ETC). In a variety of plants, fungi, and prokaryotes, there is a naturally evolved mechanism for such threats to viability, namely a bypassing of the blocked portion of the ETC by alternative enzymes of the respiratory chain. One such enzyme is the alternative oxidase (AOX). When AOX is expressed, it enables its host to survive life-threatening conditions or, as in parasites, to evade host defenses. In vertebrates, this mechanism has been lost during evolution. However, we and others have shown that transfer of AOX into the genome of the fruit fly and mouse results in a catalytically engaged AOX. This implies that not only is the AOX a promising target for combating human or agricultural pathogens but also a novel approach to elucidate disease mechanisms or, in several cases, potentially a therapeutic cure for human diseases. In this review, we highlight the varying functions of AOX in their natural hosts and upon xenotopic expression, and discuss the resulting need to develop species-specific AOX inhibitors.

An update on Cryptosporidium biology and therapeutic avenues

Cryptosporidium species has been identified as an important pediatric diarrheal pathogen in resource-limited countries, particularly in very young children (0–24 months). However, the only available drug (nitazoxanide) has limited efficacy and can only be prescribed in a medical setting to children older than one year. Many drug development projects have started to investigate new therapeutic avenues. Cryptosporidium’s unique biology is challenging for the traditional drug discovery pipeline and requires novel drug screening approaches. Notably, in recent years, new methods of oocyst generation, in vitro processing, and continuous three-dimensional cultivation capacities have been developed. This has enabled more physiologically pertinent research assays for inhibitor discovery. In a short time, many great strides have been made in the development of anti-Cryptosporidium drugs. These are expected to eventually turn into clinical candidates for cryptosporidiosis treatment in the future. This review describes the latest development in Cryptosporidium biology, genomics, transcriptomics of the parasite, assay development, and new drug discovery.

A multi-epitope vaccine candidate developed from unique immunogenic epitopes against Cryptosporidium hominis by utilizing an immunoinformatics-driven approach

An immunoinformatics-based strategy is being investigated to identify prospective multi-subunit vaccine candidates against Cryptosporidium hominis (C. hominis). We used a systematic technique based on protein structure to create a competent multi-subunit vaccine candidate against C. hominis, with the likelihood of antigenicity, allergenicity, and transmembrane helices as the screening criteria. Using the suitable linkers, the best-screened epitopes such as B-cell epitopes (BCL), Helper T-lymphocytes (HTL), and cytotoxic T-lymphocytes (CTL) were linked together to intensify and develop the presentation and processing of the antigenic molecules. The greatest 3 D model of the component protein was created with the help of modeling software called Raptorax. The validation of the modeled protein was accomplished via the use of PROCHECK. Furthermore, using the ClusPro web server, the projected modeled structure was docked with known receptor TLR-4 to determine their interactions. A molecular dynamics (MD) simulation was used to investigate the stability of the multi-subunit vaccine bound with TLR-4 based on the docking score. Aside from that, the codon optimization and in silico expression demonstrate the possibility of high expression and simple purification of the vaccine product resulting from codon optimization. The overall findings indicated that the multi-subunit vaccine might be a viable vaccination candidate against C. hominis.Communicated by Ramaswamy H. Sarma.

Comparative proteomics reveals Cryptosporidium parvum manipulation of the host cell molecular expression and immune response

Cryptosporidium is a life-threating protozoan parasite belonging to the phylum Apicomplexa, which mainly causes gastroenteritis in a variety of vertebrate hosts. Currently, there is a re-emergence of Cryptosporidium infection; however, no fully effective drug or vaccine is available to treat Cryptosporidiosis. In the present study, to better understand the detailed interaction between the host and Cryptosporidium parvum, a large-scale label-free proteomics study was conducted to characterize the changes to the proteome induced by C. parvum infection. Among 4406 proteins identified, 121 proteins were identified as differentially abundant (> 1.5-fold cutoff, P < 0.05) in C. parvum infected HCT-8 cells compared with uninfected cells. Among them, 67 proteins were upregulated, and 54 proteins were downregulated at 36 h post infection. Analysis of the differentially abundant proteins revealed an interferon-centered immune response of the host cells against C. parvum infection and extensive inhibition of metabolism-related enzymes in the host cells caused by infection. Several proteins were further verified using quantitative real-time reverse transcription polymerase chain reaction and western blotting. This systematic analysis of the proteomics of C. parvum-infected HCT-8 cells identified a wide range of functional proteins that participate in host anti-parasite immunity or act as potential targets during infection, providing new insights into the molecular mechanism of C. parvum infection.

Cryptosporidium parvum is an emerging zoonotic pathogen transmitted via the fecal–oral route, and is considered a leading cause of moderate-to-severe diarrheal disease in young children in resource limited areas. After infection, C. parvum parasitizes intestinal epithelial cells and evokes an inflammatory immune response, leading to severe damage of the intestinal mucosa. The infection can be lethal to immunosuppressed individuals. However, no fully effective drug or vaccine is available for cryptosporidiosis, and the pathogenesis and immune mechanisms during C. parvum infection are obscure. Thus, an in-depth understanding of host-parasite interaction is needed. Hence, we established a C. parvum-infected HCT-8 cell model and performed comparative quantitative proteomic analyses to profile global host-parasite interactions and determine the molecular mechanisms that are activated during infection, aiming to offer new insights into the treatment of Cryptosporidium.

Hide-and-Seek: A Game Played between Parasitic Protists and Their Hosts

After invading the host organism, a battle occurs between the parasitic protists and the host's immune system, the result of which determines not only whether and how well the host survives and recovers, but also the fate of the parasite itself. The exact weaponry of this battle depends, among others, on the parasite localisation. While some parasitic protists do not invade the host cell at all (extracellular parasites), others have developed successful intracellular lifestyles (intracellular parasites) or attack only the surface of the host cell (epicellular parasites). Epicellular and intracellular protist parasites have developed various mechanisms to hijack host cell functions to escape cellular defences and immune responses, and, finally, to gain access to host nutrients. They use various evasion tactics to secure the tight contact with the host cell and the direct nutrient supply. This review focuses on the adaptations and evasion strategies of parasitic protists on the example of two very successful parasites of medical significance, Cryptosporidium and Leishmania, while discussing different localisation (epicellular vs. intracellular) with respect to the host cell.

Nutrient Acquisition and Attachment Strategies in Basal Lineages: A Tough Nut to Crack in the Evolutionary Puzzle of Apicomplexa

Apicomplexa are unicellular eukaryotes that parasitise a wide spectrum of invertebrates and vertebrates, including humans. In their hosts, they occupy a variety of niches, from extracellular cavities (intestine, coelom) to epicellular and intracellular locations, depending on the species and/or developmental stages. During their evolution, Apicomplexa thus developed an exceptionally wide range of unique features to reach these diversified parasitic niches and to survive there, at least long enough to ensure their own transmission or that of their progeny. This review summarises the current state of knowledge on the attachment/invasive and nutrient uptake strategies displayed by apicomplexan parasites, focusing on trophozoite stages of their so far poorly studied basal representatives, which mostly parasitise invertebrate hosts. We describe their most important morphofunctional features, and where applicable, discuss existing major similarities and/or differences in the corresponding mechanisms, incomparably better described at the molecular level in the more advanced Apicomplexa species, of medical and veterinary significance, which mainly occupy intracellular niches in vertebrate hosts.

Cryptosporidium: Host-Parasite Interactions and Pathogenesis

Purpose of Review

Cryptosporidium spp. (C. hominis and C. parvum) are a major cause of diarrhea-associated morbidity and mortality in young children globally. While C. hominis only infects humans, C. parvum is a zoonotic parasite that can be transmitted from infected animals to humans. There are no treatment or control measures to fully treat cryptosporidiosis or prevent the infection in humans and animals. Our knowledge on the molecular mechanisms of Cryptosporidium-host interactions and the underlying factors that govern infectivity and disease pathogenesis is very limited.

Recent Findings

Recent development of genetics and new animal models of infection, along with progress in cell culture platforms to complete the parasite lifecycle in vitro, is greatly advancing the Cryptosporidium field.

Summary

In this review, we will discuss our current knowledge of host-parasite interactions and how genetic manipulation of Cryptosporidium and promising infection models are opening the doors towards an improved understanding of parasite biology and disease pathogenesis.

Metabolic Signatures of Cryptosporidium parvum-Infected HCT-8 Cells and Impact of Selected Metabolic Inhibitors on C. parvum Infection under Physioxia and Hyperoxia

Cryptosporidium parvum is an apicomplexan zoonotic parasite recognized as the second leading-cause of diarrhoea-induced mortality in children. In contrast to other apicomplexans, C. parvum has minimalistic metabolic capacities which are almost exclusively based on glycolysis. Consequently, C. parvum is highly dependent on its host cell metabolism. In vivo (within the intestine) infected epithelial host cells are typically exposed to low oxygen pressure (1-11% O₂, termed physioxia). Here, we comparatively analyzed the metabolic signatures of C. parvum-infected HCT-8 cells cultured under both, hyperoxia (21% O₂), representing the standard oxygen condition used in most experimental settings, and physioxia (5% O₂), to be closer to the in vivo situation. The most pronounced effect of C. parvum infection on host cell metabolism was, on one side, an increase in glucose and glutamine uptake, and on the other side, an increase in lactate release. When cultured in a glutamine-deficient medium, C. parvum infection led to a massive increase in glucose consumption and lactate production. Together, these results point to the important role of both glycolysis and glutaminolysis during C. parvum intracellular replication. Referring to obtained metabolic signatures, we targeted glycolysis as well as glutaminolysis in C. parvum-infected host cells by using the inhibitors lonidamine [inhibitor of hexokinase, mitochondrial carrier protein (MCP) and monocarboxylate transporters (MCT) 1, 2, 4], galloflavin (lactate dehydrogenase inhibitor), syrosingopine (MCT1- and MCT4 inhibitor) and compound 968 (glutaminase inhibitor) under hyperoxic and physioxic conditions. In line with metabolic signatures, all inhibitors significantly reduced parasite replication under both oxygen conditions, thereby proving both energy-related metabolic pathways, glycolysis and glutaminolysis, but also lactate export mechanisms via MCTs as pivotal for C. parvum under in vivo physioxic conditions of mammals.

Why the -omic future of Apicomplexa should include gregarines

Gregarines, a polyphyletic group of apicomplexan parasites infecting mostly non-vertebrates hosts, remains poorly known at taxonomic, phylogenetic and genomic levels. However, it represents an essential group for understanding evolutionary history and adaptive capacities of apicomplexan parasites to the remarkable diversity of their hosts. Because they have a mostly extracellular lifestyle, gregarines have developed other cellular developmental forms and host-parasite interactions, compared with their much better studied apicomplexan cousins, intracellular parasites of vertebrates (Hemosporidia, Coccidia, Cryptosporidia). This review highlights the promises offered by the molecular exploration of gregarines, that have been until now left on the side of the road of the comparative -omic exploration of apicomplexan parasites. Elucidating molecular bases for both their ultrastructural, functional and behavioural similarities and differences, compared with those of the typical apicomplexan models, is expected to provide entirely novel clues on the adaptive capacities developed by Apicomplexa over evolution. A challenge remains to identify which gregarines should be explored in priority, as recent metadata from open and host-associated environments have confirmed how underestimated is our current view on true gregarine biodiversity. It is now time to turn to gregarines to widen the currently highly skewed view we have of adaptive mechanisms developed by Apicomplexa.

Does apicortin, a characteristic protein of apicomplexan parasites and placozoa, occur in Eumetazoa?

Apicortin is a characteristic protein of apicomplexan parasites which has recently been identified in their free-living cousins, chromerids as well. The placozoan Trichoplax adhaerens is the only animal possessing this protein and apicortin is one of its most abundant proteins. The recently published transcriptome of the cnidarian Porites astreoides contains an apicortin-like sequence. Other cnidarians do not have it, thus it is its first occurrence not only in this phylum but also in Eumetazoa. However, its translated amino acid sequence is more similar to apicomplexan apicortins than to that of T. adhaerens, the GC ratio is much higher than either the genome-wide GC ratio of P. astreoides or that of the placozoan apicortin gene, and phylogenetic analyses suggest that this apicortin has an apicomplexan origin. Although these data might be indicative for a horizontal gene transfer event, we should be cautious to state it; it is more probable that it is a contamination from a gregarine, a marine Apicomplexa. Thus T. adhaerens remains the only animal where the presence of apicortin is proved.

Genomic and Proteomic Evidence for the Presence of a Peroxisome in the Apicomplexan Parasite Toxoplasma gondii and Other Coccidia

Apicomplexans are successful parasites responsible for severe human diseases including malaria, toxoplasmosis, and cryptosporidiosis. For many years, it has been discussed whether these parasites are in possession of peroxisomes, highly variable eukaryotic organelles usually involved in fatty acid degradation and cellular detoxification. Conflicting experimental data has been published. With the age of genomics, ever more high quality apicomplexan genomes have become available, that now allow a new assessment of the dispute. Here, we provide bioinformatic evidence for the presence of peroxisomes in Toxoplasma gondii and other coccidians. For these organisms, we have identified a complete set of peroxins, probably responsible for peroxisome biogenesis, division, and protein import. Moreover, via a global screening for peroxisomal targeting signals, we were able to show that a complete set of fatty acid β-oxidation enzymes is equipped with either PTS1 or PTS2 sequences, most likely mediating transport of these factors to putative peroxisomes in all investigated Coccidia. Our results further imply a life cycle stage-specific presence of peroxisomes in T. gondii and suggest several independent losses of peroxisomes during the evolution of apicomplexan parasites.

Response of cell lines to actual and simulated inoculation with Cryptosporidium proliferans

The need for an effective treatment against cryptosporidiosis has triggered studies in the search for a working in vitro model. The peculiar niche of cryptosporidia at the brush border of host epithelial cells has been the subject of extensive debates. Despite extensive research on the invasion process, it remains enigmatic whether cryptosporidian host-parasite interactions result from an active invasion process or through encapsulation. We used HCT-8 and HT-29 cell lines for in vitro cultivation of the gastric parasite Cryptosporidium proliferans strain TS03. Using electron and confocal laser scanning microscopy, observations were carried out 24, 48 and 72 h after inoculation with a mixture of C. proliferans oocysts and sporozoites. Free sporozoites and putative merozoites were observed apparently searching for an appropriate infection site. Advanced stages, corresponding to trophozoites and meronts/gamonts enveloped by parasitophorous sac, and emptied sacs were detected. As our observations showed that even unexcysted oocysts became enveloped by cultured cell projections, using polystyrene microspheres, we evaluated the response of cell lines to simulated inoculation with cryptosporidian oocysts to verify innate and parasite-induced behaviour. We found that cultured cell encapsulation of oocysts is induced by parasite antigens, independent of any active invasion/motility.

The truth about in vitro culture of Cryptosporidium species

Cryptosporidium research has focused on the development of infection control, and effective therapy that has thus far been hampered by the inability to culture Cryptosporidium in vitro. Other limitations include inadequate animal models, cumbersome screening procedures for chemotherapeutic approaches and a lack of tools for genetic manipulation. These limitations can, however, be eased by the improvement and focused development of in vitro cultivation. The ability to culture relevant Cryptosporidium isolates in vitro and to propagate the life cycle stages that are responsible for causing disease in an infected host is still a critical link. This ability will facilitate other relevant approaches, e.g., the ability to knockout genes and the application of broader screening for drug discoveries and vaccine developments, in combination with new discoveries on the parasite's basic biology, genetic manipulation and new life cycle stages. Success in this effort represents an essential step towards significant progress in the control of cryptosporidiosis.

Genomics of apicomplexan parasites

The increasing prevalence of infections involving intracellular apicomplexan parasites such as Plasmodium, Toxoplasma, and Cryptosporidium (the causative agents of malaria, toxoplasmosis, and cryptosporidiosis, respectively) represent a significant global healthcare burden. Despite their significance, few treatments are available; a situation that is likely to deteriorate with the emergence of new resistant strains of parasites. To lay the foundation for programs of drug discovery and vaccine development, genome sequences for many of these organisms have been generated, together with large-scale expression and proteomic datasets. Comparative analyses of these datasets are beginning to identify the molecular innovations supporting both conserved processes mediating fundamental roles in parasite survival and persistence, as well as lineage-specific adaptations associated with divergent life-cycle strategies. The challenge is how best to exploit these data to derive insights into parasite virulence and identify those genes representing the most amenable targets. In this review, we outline genomic datasets currently available for apicomplexans and discuss biological insights that have emerged as a consequence of their analysis. Of particular interest are systems-based resources, focusing on areas of metabolism and host invasion that are opening up opportunities for discovering new therapeutic targets.

It's official - Cryptosporidium is a gregarine: What are the implications for the water industry?

Parasites of the genus Cryptosporidium are a major cause of diarrhoea and ill-health in humans and animals and are frequent causes of waterborne outbreaks. Until recently, it was thought that Cryptosporidium was an obligate intracellular parasite that only replicated within a suitable host, and that faecally shed oocysts could survive in the environment but could not multiply. In light of extensive biological and molecular data, including the ability of Cryptosporidium to complete its life cycle in the absence of a host and the production of novel extracellular stages, Cryptosporidium has been formally transferred from the Coccidia, to a new subclass, Cryptogregaria, with gregarine parasites. In this review, we discuss the close relationship between Cryptosporidium and gregarines and discuss the implications for the water industry.

A method for identification of highly conserved elements and evolutionary analysis of superphylum Alveolata

Background

Perfectly or highly conserved DNA elements were found in vertebrates, invertebrates, and plants by various methods. However, little is known about such elements in protists. The evolutionary distance between apicomplexans can be very high, in particular, due to the positive selection pressure on them. This complicates the identification of highly conserved elements in alveolates, which is overcome by the proposed algorithm.

Results

A novel algorithm is developed to identify highly conserved DNA elements. It is based on the identification of dense subgraphs in a specially built multipartite graph (whose parts correspond to genomes). Specifically, the algorithm does not rely on genome alignments, nor pre-identified perfectly conserved elements; instead, it performs a fast search for pairs of words (in different genomes) of maximum length with the difference below the specified edit distance. Such pair defines an edge whose weight equals the maximum (or total) length of words assigned to its ends. The graph composed of these edges is then compacted by merging some of its edges and vertices. The dense subgraphs are identified by a cellular automaton-like algorithm; each subgraph defines a cluster composed of similar inextensible words from different genomes. Almost all clusters are considered as predicted highly conserved elements. The algorithm is applied to the nuclear genomes of the superphylum Alveolata, and the corresponding phylogenetic tree is built and discussed.

Conclusion

We proposed an algorithm for the identification of highly conserved elements. The multitude of identified elements was used to infer the phylogeny of Alveolata.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-016-1257-5) contains supplementary material, which is available to authorized users.

Identification of invasion proteins of Cryptosporidium parvum

Host cell interactions and invasion by Cryptosporidium is a complex process mediated by zoites ligand-host cell receptors. Knowledge of proteins involved in this process will enable entry level inhibitors to be tried as therapeutic agents. In the present study, invasion proteins of Cryptosporidium parvum were studied in vitro. Cryptosporidium sporozoites membrane proteins were isolated and Cy5 dye labelled. They were then allowed to interact with the intact host cells. The interacting proteins were identified using 2-dimensional gel electrophoresis followed by mass spectrometry analysis. Sixty-one proteins were identified including twenty-seven previously reported invasion proteins. The newly identified proteins such as serine/threonine protein kinase, PI4 kinase, Hsp105 and coiled coil may have their roles in the parasitic invasion process. Thus, a new approach was used in the study to identify the probable proteins involved in invasion and/or host-parasite interactions. The advantage of this method is that it takes only a months' time instead of decades to identify these proteins involved in invasion process.

Origin of a major infectious disease in vertebrates: The timing of Cryptosporidium evolution and its hosts

Protozoan parasites of the genus Cryptosporidium infect all vertebrate groups and display some host specificity in their infections. It is therefore possible to assume that Cryptosporidium parasites evolved intimately aside with vertebrate lineages. Here we propose a scenario of Cryptosporidium–Vertebrata coevolution testing the hypothesis that the origin of Cryptosporidium parasites follows that of the origin of modern vertebrates. We use calibrated molecular clocks and cophylogeny analyses to provide and compare age estimates and patterns of association between these clades. Our study provides strong support for the evolution of parasitism of Cryptosporidium with the rise of the vertebrates about 600 million years ago (Mya). Interestingly, periods of increased diversification in Cryptosporidium coincides with diversification of crown mammalian and avian orders after the Cretaceous-Palaeogene (K-Pg) boundary, suggesting that adaptive radiation to new mammalian and avian hosts triggered the diversification of this parasite lineage. Despite evidence for ongoing host shifts we also found significant correlation between protozoan parasites and vertebrate hosts trees in the cophylogenetic analysis. These results help us to understand the underlying macroevolutionary mechanisms driving evolution in Cryptosporidium and may have important implications for the ecology, dynamics and epidemiology of cryptosporidiosis disease in humans and other animals.

Parasites

Parasites are an important cause of human disease worldwide. The clinical severity and outcome of parasitic disease is often dependent on the immune status of the host. Specific parasitic diseases discussed in this chapter are amebiasis, giardiasis, cryptosporidiosis, cyclosporiasis, cystoisosporiasis, microsporidosis, granulomatous amebic encephalitis, toxoplasmosis, leishmaniasis, Chagas disease, malaria, babesiosis, strongyloidiasis, and scabies.

Wider than Thought Phylogenetic Occurrence of Apicortin, A Characteristic Protein of Apicomplexan Parasites

Apicomplexan parasites cause serious illnesses, including malaria, in humans and domestic animals. The presence of apicortins is predominantly characteristic of this phylum. All the apicomplexan species sequenced contain an apicortin which unites two conserved domains: DCX and partial p25alpha. This paper identifies novel apicortin orthologs in silico and corrects in several cases the erroneous sequences of hypothetical apicortin proteins of Cryptosporidium, Eimeria, and Theileria genera published in databases. Plasmodium apicortins, except from Plasmodium gallinaceum, differ significantly from the other apicomplexan apicortins. The feature of this ortholog suggests that only orthologs of Plasmodiums hosted by mammals altered significantly. The free-living Chromerida, Chromera velia, and Vitrella brassicaformis, contain three paralogs. Their apicomplexan-type and nonapicomplexan-type apicortins might be "outparalogs." The fungal ortholog, Rozella allomycis, found at protein level, and the algal Nitella mirabilis, found as Transcriptome Shotgun Assembly (TSA), are similar to the known Opisthokont (Trichoplax adhaerens, Spizellomyces punctatus) and Viridiplantae (Nicotiana tabacum) ones, since they do not contain the long, unstructured N-terminal part present in apicomplexan apicortins. A few eumetazoan animals possess apicortin-like (partial) sequences at TSA level, which may be either contaminations or the result of horizontal gene transfer; in some cases the contamination has been proved.

In vitro excystation of Cryptosporidium muris oocysts and viability of released sporozoites in different incubation media

This study aimed to evaluate and document the excystation process of Cryptosporidium muris oocysts in various incubation media, and to monitor the behaviour of excysting and freshly excysted sporozoites. A test of oocyst viability, using fluorescent double staining with fluorescein diacetate and propidium iodide, was performed prior to each experimental assay. Light microscope observations confirmed that relatively often only three sporozoites were released; the fourth one either left the oocyst later together with a residual body or remained trapped within the oocyst wall. These results suggest that successful oocyst excystation is not limited by the viability of all four sporozoites. Darkening of oocysts to opaque and their specific movement (the so-called "oocyst dancing") preceded the final excystation and liberation of sporozoites, while the dormant oocysts appeared refractive. The process of excystation in C. muris is not gradual as generally described in cryptosporidia but very rapid in an eruptive manner. Experiments were performed using oocysts stored at 4 °C for various time periods, as well as oocysts freshly shed from host rodents (Mastomys coucha) of different ages. The most suitable medium supporting high excystation rate (76 %) and prolonged motility of sporozoites was RPMI 1640, enriched with 5 % bovine serum albumin (BSA). Our results emphasize that to reliably evaluate the success of in vitro excystation of cryptosporidia, not only the number of released sporozoites in a set time period should be taken into consideration but also their subsequent activity (motility), as it is expected to be essential for the invasion of host cells.

Inhibition of Calcium-Dependent Protein Kinase 1 (CDPK1) In Vitro by Pyrazolopyrimidine Derivatives Does Not Correlate with Sensitivity of Cryptosporidium parvum Growth in Cell Culture

Cryptosporidiosis is a serious diarrheal disease in immunocompromised patients and malnourished children, and treatment is complicated by a lack of adequate drugs. Recent studies suggest that the natural occurrence of a small gatekeeper residue in serine threonine calcium-dependent protein kinase 1 (CDPK1) of Cryptosporidium parvum might be exploited to target this enzyme and block parasite growth. Here were explored the potency with which a series of pyrazolopyrimidine analogs, which are selective for small gatekeeper kinases, inhibit C. parvum CDPK1 and block C. parvum growth in tissue culture in vitro. Although these compounds potently inhibited kinase activity in vitro, most had no effect on parasite growth. Moreover, among those that were active against parasite growth, there was a very poor correlation with their 50% inhibitory concentrations against the enzyme. Active compounds also had no effect on cell invasion, unlike the situation in Toxoplasma gondii, where these compounds block CDPK1, prevent microneme secretion, and disrupt cell invasion. These findings suggest that CPDK1 is not essential for C. parvum host cell invasion or growth and therefore that it is not the optimal target for therapeutic intervention. Nonetheless, several inhibitors with low micromolar 50% effective concentrations were identified, and these may affect other essential targets in C. parvum that are worthy of further exploration.

Glycoproteins and Gal-GalNAc cause Cryptosporidium to switch from an invasive sporozoite to a replicative trophozoite

The apicomplexan parasite Cryptosporidium causes cryptosporidiosis, a diarrheal disease that can become chronic and life threatening in immunocompromised and malnourished people. There is no effective drug treatment for those most at risk of severe cryptosporidiosis. The disease pathology is due to a repeated cycle of host cell invasion and parasite replication that amplifies parasite numbers and destroys the intestinal epithelium. This study aimed to better understand the Cryptosporidium replication cycle by identifying molecules that trigger the switch from invasive sporozoite to replicative trophozoite. Our approach was to treat sporozoites of Cryptosporidium parvum and Cryptosporidium hominis, the species causing most human cryptosporidiosis, with various media under axenic conditions and examine the parasites for rounding and nuclear division as markers of trophozoite development and replication, respectively. FBS had a concentration-dependent effect on trophozoite development in both species. Trophozoite development in C. parvum, but not C. hominis, was enhanced when RPMI supplemented with 10% FBS (RPMI-FBS) was conditioned by HCT-8 cells for 3h. The effect of non-conditioned and HCT-8 conditioned RPMI-FBS on trophozoite development was abrogated by proteinase K and sodium metaperiodate pretreatment, indicating a glycoprotein trigger. Cryptosporidium parvum and C. hominis trophozoite development also was triggered by Gal-GalNAc in a concentration-dependent manner. Cryptosporidium parvum replication was greatest following treatments with Gal-GalNAc, followed by conditioned RPMI-FBS and non-conditioned RPMI-FBS (P<0.05). Cryptosporidium hominis replication was significantly less than that in C. parvum for all treatments (P<0.05), and was greatest at the highest tested concentration of Gal-GalNAc (1mM).

Cryptosporidium infections in birds - a review

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

Protococcidian Eleutheroschizon duboscqi, an Unusual Apicomplexan Interconnecting Gregarines and Cryptosporidia

This study focused on the attachment strategy, cell structure and the host-parasite interactions of the protococcidian Eleutheroschizon duboscqi, parasitising the polychaete Scoloplos armiger. The attached trophozoites and gamonts of E. duboscqi were detected at different development stages. The parasite develops epicellularly, covered by a host cell-derived, two-membrane parasitophorous sac forming a caudal tipped appendage. Staining with Evans blue suggests that this tail is protein-rich, supported by the presence of a fibrous substance in this area. Despite the ultrastructural evidence for long filaments in the tail, it stained only weakly for F-actin, while spectrin seemed to accumulate in this area. The attachment apparatus consists of lobes arranged in one (trophozoites) or two (gamonts) circles, crowned by a ring of filamentous fascicles. During trophozoite maturation, the internal space between the parasitophorous sac and parasite turns translucent, the parasite trilaminar pellicle seems to reorganise and is covered by a dense fibrous glycocalyx. The parasite surface is organised in broad folds with grooves in between. Micropores are situated at the bottom of the grooves. A layer of filaments organised in bands, underlying the folds and ending above the attachment fascicles, was detected just beneath the pellicle. Confocal microscopy, along with the application of cytoskeletal drugs (jasplakinolide, cytochalasin D, oryzalin) confirmed the presence of actin and tubulin polymerised forms in both the parasitophorous sac and the parasite, while myosin labelling was restricted to the sac. Despite positive tubulin labelling, no microtubules were detected in mature stages. The attachment strategy of E. duboscqi shares features with that of cryptosporidia and gregarines, i.e. the parasite itself conspicuously resembles an epicellularly located gregarine, while the parasitophorous sac develops in a similar manner to that in cryptosporidia. This study provides a re-evaluation of epicellular development in other apicomplexans and directly compares their niche with that of E. duboscqi.

Extracellular excystation and development of Cryptosporidium: tracing the fate of oocysts within Pseudomonas aquatic biofilm systems

Background

Aquatic biofilms often serve as environmental reservoirs for microorganisms and provide them with a nutrient-rich growth environment under harsh conditions. With regard to Cryptosporidium, biofilms can serve as environmental reservoirs for oocysts, but may also support the growth of additional Cryptosporidium stages.

Results

Here we used confocal laser scanning microscopy, scanning electron microscopy (SEM), and flow cytometry to identify and describe various Cryptosporidium developmental stages present within aquatic biofilm systems, and to directly compare these to stages produced in cell culture. We also show that Cryptosporidium has the ability to form a parasitophorous vacuole independently, in a host-free biofilm environment, potentially allowing them to complete an extracellular life cycle. Correlative data from confocal and SEM imaging of the same cells confirmed that the observed developmental stages (including trophozoites, meronts, and merozoites) were Cryptosporidium. These microscopy observations were further supported by flow cytometric analyses, where excysted oocyst populations were detected in 1, 3 and 6 day-old Cryptosporidium-exposed biofilms, but not in biofilm-free controls.

Conclusions

These observations not only highlight the risk that aquatic biofilms pose in regards to Cryptosporidium outbreaks from water distribution systems, but further indicate that even simple biofilms are able to stimulate oocyst excystation and support the extracellular multiplication and development of Cryptosporidium within aquatic environments.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-014-0281-8) contains supplementary material, which is available to authorized users.

CDPKs of Cryptosporidium parvum--stage-specific expression in vitro

Cryptosporidium parvum is a zoonotic agent that bears a high risk for the health of particularly immunocompromised humans and animals. As currently available drugs and therapies against cryptosporidiosis do not turn out satisfactory, more intensive research on the control of this parasite is necessary. The genus Cryptosporidium is unique within the phylum Apicomplexa as its localisation is intracellular but extracytoplasmatic. Infection of host cells is initially a parasite-driven process, but the signalling events and their downstream actions within Cryptosporidium are poorly understood. Calcium-dependent protein kinases (CDPKs) are probably involved in the regulation of invasion and egress. Previously described in plants, algae and other Apicomplexa, CDPKs are not found in vertebrates. They are thus promising targets for pharmaceutical intervention. While CDPK1 is well characterised in Toxoplasma gondii (TgCDPK1) and Plasmodium falciparum (PfCDPK1), only little information exists about the expression and function of CDPK in C. parvum. Here, we describe results of the in silico analysis of seven CpCDPKs. Five CpCDPKs contain potential sites for N-myristoylation and N-palmitoylation. In a nested 3' rapid amplification of cDNA ends (RACE)-PCR, expression of six CpCDPKs resulted in distinct bands in infected cell cultures and extracts of freshly excysted sporozoites. The length of the 3' untranslated region (3' UTR) is described as well. Our results indicate CDPK expression to be stage specific on the mRNA level.

Transcriptomic analysis reveals evidence for a cryptic plastid in the colpodellid Voromonas pontica, a close relative of chromerids and apicomplexan parasites

Colpodellids are free-living, predatory flagellates, but their close relationship to photosynthetic chromerids and plastid-bearing apicomplexan parasites suggests they were ancestrally photosynthetic. Colpodellids may therefore retain a cryptic plastid, or they may have lost their plastids entirely, like the apicomplexan Cryptosporidium. To find out, we generated transcriptomic data from Voromonas pontica ATCC 50640 and searched for homologs of genes encoding proteins known to function in the apicoplast, the non-photosynthetic plastid of apicomplexans. We found candidate genes from multiple plastid-associated pathways including iron-sulfur cluster assembly, isoprenoid biosynthesis, and tetrapyrrole biosynthesis, along with a plastid-type phosphate transporter gene. Four of these sequences include the 5' end of the coding region and are predicted to encode a signal peptide and a transit peptide-like region. This is highly suggestive of targeting to a cryptic plastid. We also performed a taxon-rich phylogenetic analysis of small subunit ribosomal RNA sequences from colpodellids and their relatives, which suggests that photosynthesis was lost more than once in colpodellids, and independently in V. pontica and apicomplexans. Colpodellids therefore represent a valuable source of comparative data for understanding the process of plastid reduction in humanity's most deadly parasite.

Cryptosporidiuminfections: molecular advances

Cryptosporidiumhost cell interaction remains fairly obscure compared with other apicomplexans such asPlasmodiumorToxoplasma. The reason for this is probably the inability of this parasite to complete its life cyclein vitroand the lack of a system to genetically modifyCryptosporidium. However, there is a substantial set of data about the molecules involved in attachment and invasion and about the host cell pathways involved in actin arrangement that are altered by the parasite. Here we summarize the recent advances in research on host cell infection regarding the excystation process, attachment and invasion, survival in the cell, egress and the available data on omics.

Studies on coccidian oocysts (Apicomplexa: Eucoccidiorida)

The oocysts of the coccidia are robust structures, frequently isolated from the feces or urine of their hosts, which provide resistance to mechanical damage and allow the parasites to survive and remain infective for prolonged periods. The diagnosis of coccidiosis, species description and systematics, are all dependent upon characterization of the oocyst. Therefore, this review aimed to the provide a critical overview of the methodologies, advantages and limitations of the currently available morphological, morphometrical and molecular biology based approaches that may be utilized for characterization of these important structures. It has become apparent that no single methodology is sufficient to fully characterize these structures and the majority of researchers favor the use of combinational or polyphasic approaches.

Life cycle ofCryptosporidium murisin two rodents with different responses to parasitization

This study focuses on mapping the life cycle ofCryptosporidium murisin two laboratory rodents; BALB/c mice and the southern multimammate ratMastomys coucha, differing in their prepatent and patent periods. Both rodents were simultaneously experimentally inoculated with viable oocysts ofC. muris(strain TS03). Animals were dissected and screened for the presence of the parasite using a combined morphological approach and nested PCR (SSU rRNA) at different times after inoculation. The occurrence of first developmental stages ofC. murisin stomach was detected at 2·5 days post-infection (dpi). The presence of Type II merogony, appearing 36 h later than Type I merogony, was confirmed in both rodents. Oocysts exhibiting different size and thickness of their wall were observed from 5 dpi onwards in stomachs of both host models. The early phase of parasitization in BALB/c mice progressed rapidly, with a prepatent period of 7·5–10 days; whereas inM. coucha, the developmental stages ofC. muriswere first observed 12 h later in comparison with BALB/c mice and prepatent period was longer (18–21 days). Similarly, the patent periods of BALB/c mice andM. couchadiffered considerably, i.e. 10–15 daysvschronic infection throughout the life of the host, respectively.

Combined amplicon pyrosequencing assays reveal presence of the apicomplexan "type-N" (cf. Gemmocystis cylindrus) and Chromera velia on the Great Barrier Reef, Australia

Background

The coral is predominantly composed of the metabolically dependent coral host and the photosynthetic dinoflagellate Symbiodinium sp. The system as a whole interacts with symbiotic eukaryotes, bacteria and viruses. Gemmocystiscylindrus (cf. “type-N” symbiont) belonging to the obligatory parasitic phylum Apicomplexa (Alveolata) is ubiquitous in the Caribbean coral, but its presence in the Great Barrier Reef coral has yet to be documented. Approaches allowing identification of the healthy community from the pathogenic or saprobic organisms are needed for sustainable coral reef monitoring.

Methods & Principal Findings

We investigated the diversity of eukaryotes associated with a common reef-building corals from the southern Great Barrier Reef. We used three tag encoded 454 amplicon pyrosequencing assays targeting eukaryote small-subunit rRNA gene to demonstrate the presence of the apicomplexan type-N and a photosynthetic sister species to Apicomplexa - Chromeravelia. Amplicon pyrosequencing revealed presence of the small-subunit rRNA genes of known eukaryotic pathogens (Cryptosporidium and Cryptococcus). We therefore conducted bacterial tag encoded amplicon pyrosequencing assay for small-subunit rRNA gene to support effluent exposure of the coral. Bacteria of faecal origin (Enterobacteriales) formed 41% of total sequences in contrast to 0-2% of the coral-associated bacterial communities with and without C. velia, respectively.

Significance

This is the first time apicomplexan type-N has been detected in the Great Barrier Reef. Eukaryote tag encoded amplicon pyrosequencing assays demonstrate presence of apicomplexan type-N and C. Velia in total coral DNA. The data highlight the need for combined approaches for eukaryotic diversity studies coupled with bacterial community assessment to achieve a more realistic goals of defining the holobiont community and assessing coral disease. With increasing evidence of Apicomplexa in coral reef environments, it is important not only to understand the evolution of these organisms but also identify their potential as pathogens.

The enigma of eugregarine epicytic folds: where gliding motility originates?

Background

In the past decades, many studies focused on the cell motility of apicomplexan invasive stages as they represent a potential target for chemotherapeutic intervention. Gregarines (Conoidasida, Gregarinasina) are a heterogeneous group that parasitize invertebrates and urochordates, and are thought to be an early branching lineage of Apicomplexa. As characteristic of apicomplexan zoites, gregarines are covered by a complicated pellicle, consisting of the plasma membrane and the closely apposed inner membrane complex, which is associated with a number of cytoskeletal elements. The cell cortex of eugregarines, the epicyte, is more complicated than that of other apicomplexans, as it forms various superficial structures.

Results

The epicyte of the eugregarines, Gregarina cuneata, G. polymorpha and G. steini, analysed in the present study is organised in longitudinal folds covering the entire cell. In mature trophozoites and gamonts, each epicytic fold exhibits similar ectoplasmic structures and is built up from the plasma membrane, inner membrane complex, 12-nm filaments, rippled dense structures and basal lamina. In addition, rib-like myonemes and an ectoplasmic network are frequently observed. Under experimental conditions, eugregarines showed varied speeds and paths of simple linear gliding. In all three species, actin and myosin were associated with the pellicle, and this actomyosin complex appeared to be restricted to the lateral parts of the epicytic folds. Treatment of living gamonts with jasplakinolide and cytochalasin D confirmed that actin actively participates in gregarine gliding. Contributions to gliding of specific subcellular components are discussed.

Conclusions

Cell motility in gregarines and other apicomplexans share features in common, i.e. a three-layered pellicle, an actomyosin complex, and the polymerisation of actin during gliding. Although the general architecture and supramolecular organisation of the pellicle is not correlated with gliding rates of eugregarines, an increase in cytoplasmic mucus concentration is correlated. Furthermore, our data suggest that gregarines utilize several mechanisms of cell motility and that this is influenced by environmental conditions.

A novel clade of unique eukaryotic ribonucleotide reductase R2 subunits is exclusive to apicomplexan parasites

Apicomplexa are protist parasites of tremendous medical and economic importance, causing millions of deaths and billions of dollars in losses each year. Apicomplexan-related diseases may be controlled via inhibition of essential enzymes. Ribonucleotide reductase (RNR) provides the only de novo means of synthesizing deoxyribonucleotides, essential precursors for DNA replication and repair. RNR has long been the target of antibacterial and antiviral therapeutics. However, targeting this ubiquitous protein in eukaryotic pathogens may be problematic unless these proteins differ significantly from that of their respective host. The typical eukaryotic RNR enzymes belong to class Ia, and the holoenzyme consists minimally of two R1 and two R2 subunits (α₂β₂). We generated a comparative, annotated, structure-based, multiple-sequence alignment of R2 subunits, identified a clade of R2 subunits unique to Apicomplexa, and determined its phylogenetic position. Our analyses revealed that the apicomplexan-specific sequences share characteristics with both class I R2 and R2lox proteins. The putative radical-harboring residue, essential for the reduction reaction by class Ia R2-containing holoenzymes, was not conserved within this group. Phylogenetic analyses suggest that class Ia subunits are not monophyletic and consistently placed the apicomplexan-specific clade sister to the remaining class Ia eukaryote R2 subunits. Our research suggests that the novel apicomplexan R2 subunit may be a promising candidate for chemotherapeutic-induced inhibition as it differs greatly from known eukaryotic host RNRs and may be specifically targeted.