Molecular characterization of crane Coccidia, Eimeria gruis and E. reichenowi, found in feces of migratory cranes

Metabarcoding of protozoa and helminth in black-necked cranes: a high prevalence of parasites and free-living amoebae

Parasites and free-living amoebae (FLA) are common pathogens that pose threats to wildlife and humans. The black-necked crane (Grus nigricollis) is a near-threatened species and there is a shortage of research on its parasite diversity. Our study aimed to use noninvasive methods to detect intestinal parasites and pathogenic FLA in G. nigricollis using high-throughput sequencing (HTS) based on the 18S rDNA V9 region. A total of 38 fresh fecal samples were collected in Dashanbao, China, during the overwintering period (early-, middle I-, middle II-, and late-winter). Based on the 18S data, eight genera of parasites were identified, including three protozoan parasites: Eimeria sp. (92.1%) was the dominant parasite, followed by Tetratrichomonas sp. (36.8%) and Theileria sp. (2.6%). Five genera of helminths were found: Echinostoma sp. (100%), Posthodiplostomum sp. (50.0%), Euryhelmis sp. (26.3%), Eucoleus sp. (50.0%), and Halomonhystera sp. (2.6%). Additionally, eight genera of FLA were detected, including the known pathogens Acanthamoeba spp. (n = 13) and Allovahlkampfia spp. (n = 3). Specific PCRs were used to further identify the species of some parasites and FLA. Furthermore, the 18S data indicated significant changes in the relative abundance and genus diversity of the protozoan parasites and FLA among the four periods. These results underscore the importance of long-term monitoring of pathogens in black-necked cranes to protect this near-endangered species.

Examining the molecular epidemiology of Giardia and Eimeria species in Japan: a comprehensive review

Globally, animals and humans suffer from diarrheal illnesses due to protozoan parasites such as Giardia and Eimeria species. The molecular epidemiology of these parasites in Japan is summarized in this review. In humans, researchers found only one main species of Giardia, which is most referred to as G. lamblia, but it's also known by different names like G. duodenalis or G. intestinalis. However, within this species, six assemblages (A, B, C, D, E, and F) were found in animals, and assemblage B was frequently recorded in human and monkey populations, whereas assemblages A and E were predominant in calves. Assemblage A was found in sika deer and assemblages A, C, D, and F were predominant in dogs, cats, and ferret. Eimeria bovis, E. zuernii, and other species found in animals made up the group of species known as Eimeria spp., with E. bovis and E. zuernii being the most common in cattle. Our review highlighted a notable lack of data investigations regarding these two pathogens in water and environmental sources. Giardia cysts were found in the few studies that have been done on water sources, suggesting that water may play a significant role in the transmission of Giardia species. Our review suggests that further research is necessary to fully comprehend the molecular diversity and dynamics of transmission of Giardia spp. and Eimeria spp. in humans, animals, and environmental sources in Japan.

Comparative molecular analyses of Eimeria Schneider (Apicomplexa: Eimeriidae) species from rock ptarmigan in Iceland, Svalbard-Norway, and Japan

The rock ptarmigan (Lagopus muta) has a Holarctic breeding distribution and is found in arctic and sub-arctic regions. Isolated populations and glacial relicts occur in alpine areas south of the main range, like the Pyrenees in Europe, the Pamir mountains in Central Asia, and the Japanese Alps. In recent decades considerable effort has been made to clarify parasite infections in the rock ptarmigan. Seven Eimeria spp. have been reported parasitizing rock ptarmigan. Two of those species, E. uekii and E. raichoi parasitizing rock ptarmigan (L. m. japonica) in Japan, have been identified genetically. Here we compare partial sequences of nuclear (18S rRNA) and mitochondrial (COI) genes and we detail the morphology of sporulated oocysts of E. uekii and E. raichoi from Japan, E. muta and E. rjupa, from the rock ptarmigan (L. m. islandorum) in Iceland, and two undescribed eimerian morphotypes, Eimeria sp. A, and Eimeria sp. B, from rock ptarmigan (L. m. hyperborea) in Norway (Svalbard in the Norwegian Archipelago). Two morphotypes, ellipsoidal and spheroidal, are recognized for each of the three host subspecies. Our phylogenetic analysis suggests that the ellipsoidal oocyst types, E. uekii, E. muta, and Eimeria sp. A (Svalbard-Norway) are identical and infects rock ptarmigan in Japan, Iceland, and Svalbard-Norway, respectively. Eimeria uekii was first described in Japan in 1981 so that E. muta, described in Iceland in 2007, and Eimeria sp. A in Svalbard-Norway are junior synonyms of E. uekii. Also, phylogenetic analysis shows that the spheroidal oocyst types, E. rjupa and Eimeria sp. B (Svalbard-Norway), are identical, indicating that rock ptarmigan in Iceland and Svalbard-Norway are infected by the same Eimeria species and differ from E. raichoi in Japan.

Evaluation of the host specificity of Eimeria uekii and Eimeria raichoi for Japanese rock ptarmigans by oocyst transfer to taxonomically related birds

Eimeria spp. are protozoan parasites that are commonly found in a broad range of vertebrate hosts. These parasites generally exhibit strict host specificity, but some Eimeria spp. can infect groups of closely related species such as species within a genus or family. Compared with Eimeria spp. that infect livestock, limited information is available about such infections in wild animals including data on host specificity, virulence, and prevalence. The Japanese rock ptarmigan, Lagopus muta japonica, is an endangered bird belonging to the family Phasianidae, order Galliformes, and inhabits only alpine areas of Japan. In conservation efforts for these birds, two Eimeria spp., E. uekii and E. raichoi, were frequently detected. Here, we examined cross-transmission of the parasites to other bird species to characterize their infectivity as well as the development of experimental bird models to contribute to conservation programs by the oocyst transfer. Consequently, among the examined eight bird species (chickens, Japanese pheasants, turkeys, chukar partridges, quails, helmeted guineafowls and ducks), only turkeys (family Phasianidae, order Galliformes) could be infected with E. raichoi. However, the number of oocysts per feces was relatively low, and few parasites in the intestinal mucosa could be found by histopathological analyses. These results might indicate that E. uekii and E. raichoi are highly adapted to Japanese rock ptarmigans that inhabit the alpine zone although further studies are anticipated.

Occurrence, Histopathological Findings, and Molecular Identification of Pathogenic Eimeria Infections in Rabbits (Mammalia: Lagomorpha) in Japan

PURPOSE

Eimeria spp. are commonly found among rabbits (Mammalia: Lagomorpha) worldwide. Among the 11 Eimeria species, several are highly virulent, including E. intestinalis and E. flavescens, which cause intestinal coccidiosis, and E. stiedae, which causes hepatic coccidiosis. Unlike other countries, the occurrence of Eimeria infections in rabbits in Japan remains unknown, except for one reported case of natural infection.

METHODS

We surveyed Eimeria infections in clinically affected rabbits over the past approximately 10 years at Livestock Hygiene Centers in 42 prefectures. A total of 16 tissue samples (14 liver, 1 ileum, and 1 cecum) were collected from 15 rabbits in 6 prefectures.

RESULTS

Characteristic histopathologic findings were observed, especially around the bile ducts, depending on the developmental stages of the parasites. Eimeria stiedae and E. flavescens were successfully identified by PCR and sequencing analyses in 5 liver samples and 1 cecum sample, respectively.

CONCLUSION

Our results could enhance understanding of infection with Eimeria spp. in rabbits in Japan and contribute to pathological or molecular diagnoses.

Botanicals: A promising approach for controlling cecal coccidiosis in poultry

Avian species have long struggled with the problem of coccidiosis, a disease that affects various parts of the intestine, including the anterior gut, midgut, and hindgut. Among different types of coccidiosis, cecal coccidiosis is particularly dangerous to avian species. Chickens and turkeys are commercial flocks; thus, their parasites have remained critical due to their economic importance. High rates of mortality and morbidity are observed in both chickens and turkeys due to cecal coccidiosis. Coccidiostats and coccidiocidal chemicals have traditionally been added to feed and water to control coccidiosis. However, after the EU banned their use because of issues of resistance and public health, alternative methods are being explored. Vaccines are also being used, but their efficacy and cost-effectiveness remain as challenges. Researchers are attempting to find alternatives, and among the alternatives, botanicals are a promising choice. Botanicals contain multiple active compounds such as phenolics, saponins, terpenes, sulfur compounds, etc., which can kill sporozoites and oocysts and stop the replication of Eimeria. These botanicals are primarily used as anticoccidials due to their antioxidant and immunomodulatory activities. Because of the medicinal properties of botanicals, some commercial products have also been developed. However, further research is needed to confirm their pharmacological effects, mechanisms of action, and methods of concentrated preparation. In this review, an attempt has been made to summarize the plants that have the potential to act as anticoccidials and to explain the mode of action of different compounds found within them.

Next-generation sequencing amplicon analysis of the genetic diversity of Eimeria populations in livestock and wildlife samples from Australia

Eimeria is an important coccidian enteric parasite that infects a wide range of hosts and can cause substantial economic losses in the poultry and livestock industries. It is common for multiple Eimeria species to infect individual hosts, and this can make species identification difficult due to morphological similarities between species and mixed chromatograms when using Sanger sequencing. Relatively few studies have applied next-generation amplicon sequencing (NGS) to determining the genetic diversity of Eimeria species in different hosts. The present study screened 408 faecal samples from a range of hosts including livestock and wildlife using a previously developed quantitative polymerase chain reaction (qPCR) at the 18S locus and conducted amplicon NGS on the positives using a ~ 455-bp fragment of the 18S locus. A total of 41 positives (10.1%) were identified by qPCR from various hosts and NGS was successful for 38 of these positives. Fifteen Eimeria species and three genotypes were detected by NGS: E. ferrisi, E. kanyana, E. potoroi, E. quokka, E. setonicis, E. trichosuri, E. reichenowi, E. angustus, E. ahsata, E. auburnensis, E. bovis, E. brasiliensis, E. christenseni, E. crandallis, E. ovinoidalis, Eimeria sp. (JF419345), Eimeria sp. (JF419349) and Eimeria sp. (JF419351). Mixed infections were detected in 55.3% (21/38) of positive samples. The most striking finding was the identification of the same species in different hosts. This could be due to contamination and/or mechanical transmission or may provide support for previous studies suggesting that Eimeria species can infect not just closely related hosts but different genera and further research is required. This is also the first study to audit Eimeria populations in livestock (sheep and cattle) by NGS and could be applied in the future to determine the extent of pathogenic species and outcomes of Eimeria control strategies.

Molecular identification of Eimeria species in liver and feces of naturally infected rabbits in Japan

Among the 11 species of Eimeria in rabbits, some of which are known to be pathogenic and cause enteritis, E. stiedae induces severe liver lesions resulting in elevated mortality. Unlike in other countries, the incidence and prevalence of the parasites in rabbits have not been reported in Japan. In the present study, we histopathologically analyzed hepatic coccidiosis in a rabbit and attempted several primers to genetically identify the parasites and investigated the prevalence of Eimeria species at the same farm. In the liver of the affected rabbit, we observed fibrosis and edema around multiple bile ducts and epithelial cell hyperplasia of the bile ducts. Large numbers of developing parasites of Eimeria spp., mainly oocysts, were present in the bile ducts. PCR and sequencing analyses with the published primers for Cyclospora and Eimeria spp. were used to successfully identify the parasites in the liver as E. stiedae. The oocysts of Eimeria spp. were detected in 13 out of 20 fecal samples collected from other rabbits at the farm, and five Eimeria spp. (E. perforans, E. flavescens, E. exigua, E. magna, and E. vejdovskyi) were genetically confirmed. Our results provide the first indication that Eimeria spp., including highly pathogenic species, are present in Japan and the primer set used herein can be a useful tool for the identification of rabbit Eimeria spp.

Morphological and molecular identification of Eimeria tetartooimia oocysts from a Japanese green pheasant (Galliformes; Phasianidae; Phasianus versicolor) at a zoo in Japan

We detected Eimeria oocysts from Japanese green pheasants (Phasianus versicolor) at a zoo in Osaka, Japan. The oocyst isolates were subspherical or ovoidal shaped and measured 17.2 (range 14.7-20.0) μm in length and 14.8 (13.3-16.7) μm in width with a length/width (L/W) ratio of 1.2 (1.0-1.4) and each had one polar granule. The oocysts lacked a residuum and micropyle. Sporocysts measured 9.8 (6.7-13.3) μm in length and 5.9 (4.7-7.3) μm in width, with a L/W ratio of 1.2 (1.1-1.4). Compared to previously published values, this strain shows morphological similarities with an isolate of E. teetartooimia from ring-necked pheasants from other countries. Phylogenetic analysis of the 18S rRNA and mitochondrial cytochrome c oxidase subunit I genes places the isolate in a clade related to chicken Eimeria spp., such as E. acervulina or E. brunetti. Although further analysis is needed, this information can be helpful for the diagnosis and determination of virulence of Eimeria spp. in pheasants.

Molecular characterization of enteric coccidia from domestic ferrets (Mustela putorius furo)

Combined morphometric and molecular characterization of coccidia that infect domestic ferrets (Mustela putorius furo) was completed to improve the diagnostic specificity of 'coccidiosis' in this host. Coccidia-positive fecal samples (n = 11) and formalin-fixed paraffin-embedded intestinal tissues (n = 3) from domestic ferrets were collected from diagnostic laboratories in Canada and Europe. An average of 3.5 and 13 domestic ferret fecal samples per year were coccidia-positive when tested by Canadian and European diagnostic laboratories, respectively, during the period 2008-2015. Oocyst morphometrics and sequence genotyping at two loci (nuclear 18S rDNA [nu 18S] and mitochondrial cytochrome c oxidase subunit I [mt COI]) were conducted on all samples. The first nu 18S and mt COI sequences for Cystoisospora laidlawi, and the first mt COI sequence for Eimeria furonis were generated during this study. Phylogenetic analysis of the mitochondrial COI sequences demonstrated that E. furonis was most closely related to E. ictidea isolated from a black-footed ferret (Mustela nigripes) and that C. laidlawi was closely related to C. canis and C. felis. The identifications provided by diagnostic laboratories of the specific parasite species present in a sample showed poor agreement with their identifications based on genotyping obtained in this study. Molecular techniques appear to be essential for determining the specific coccidial species responsible for individual and group outbreaks of coccidiosis and for further understanding of eimeriid host-parasite relationships.

Exploring Eimeria Genomes to Understand Population Biology: Recent Progress and Future Opportunities

Eimeria, protozoan parasites from the phylum Apicomplexa, can cause the enteric disease coccidiosis in all farmed animals. Coccidiosis is commonly considered to be most significant in poultry; due in part to the vast number of chickens produced in the World each year, their short generation time, and the narrow profit margins associated with their production. Control of Eimeria has long been dominated by routine chemoprophylaxis, but has been supplemented or replaced by live parasite vaccination in a minority of production sectors. However, public and legislative demands for reduced drug use in food production is now driving dramatic change, replacing reliance on relatively indiscriminate anticoccidial drugs with vaccines that are Eimeria species-, and in some examples, strain-specific. Unfortunately, the consequences of deleterious selection on Eimeria population structure and genome evolution incurred by exposure to anticoccidial drugs or vaccines are unclear. Genome sequence assemblies were published in 2014 for all seven Eimeria species that infect chickens, stimulating the first population genetics studies for these economically important parasites. Here, we review current knowledge of eimerian genomes and highlight challenges posed by the discovery of new, genetically cryptic Eimeria operational taxonomic units (OTUs) circulating in chicken populations. As sequencing technologies evolve understanding of eimerian genomes will improve, with notable utility for studies of Eimeria biology, diversity and opportunities for control.

Molecular identification of Eimeria hestermani and Eimeria prionotemni from a red-necked wallaby (Macropodidae; Macropus rufogriseus) in Japan

To date, more than 50 Eimeria spp. have been isolated from marsupials of the family Macropodidae. Although 18 species of Eimeria have been previously detected from multiple animal species belonging to the genus Macropus of the family, limited genetic analyses of the parasites are available, and their pathogenicity remains unclear. Here, we report the isolation of Eimeria spp. from a zoo specimen of red-necked wallaby (Macropodidae; Macropus rufogriseus). Specifically, two distinct types of Eimeria oocysts were recovered, one from the feces before treatment with an anthelmintic and the second from the intestinal contents after death of the animal. The oocysts obtained from the two sources were morphologically identified as E. hestermani and E. prionotemni, respectively. We successfully determined partial gene sequences from the two isolates, including segments of the 18S rRNA genes, and for the first time have used phylogenetic analyses of these sequences to assign the species to distinct clades. In combination with further genetic data, these results are expected to help elucidate the pathogenicity and host ranges of Eimeria spp. within the respective family and genus.

Eimeria melogale n. sp. (Apicomplexa: Eimeriidae) in the Javan ferret-badger (Melogale orientalis)

The Javan ferret-badger Melogale orientalis (Carnivora: Mustelidae: Helictidinae) is a small carnivore endemic to Indonesia. In the family Mustelidae, 10 Eimeria, 12 Cystoisopora, one Isospora, and one Hammondia species are known, but no eimeriid coccidia has been yet described in the subfamily Helictinidae (ferret badgers). Coproscopic examination of Javan ferret-badgers imported into the Czech Republic revealed the presence of coccidian oocysts. Sporulated oocysts differ from other Eimeria known in the family Mustelidae by their small size (12.4-16.1 × 10.4-13.4 μm) and ovoidal shape. Morphological data and phylogenetic analyses of 18S rRNA and COI genes indicated a new species of Eimeria found in faecal samples of Javan ferret badgers. The species is described as E. melogale n. sp.

Molecular identification of two Eimeria species, E. uekii and E. raichoi as type B, in wild Japanese rock ptarmigans, Lagopus muta japonica

Thus far, two types of Eimeria parasites (E. uekii and type B) have been morphologically identified in wild Japanese rock ptarmigans, Lagopus muta japonica. Although high prevalences were reported for these parasites, genetic analyses have not been conducted. We first clarified the phylogenetic positions of two eimerian isolates using genetic analyses of 18S rRNA and mitochondrial cytochrome c oxidase subunit I gene regions. Consequently, of 61 samples examined, 21 and 11 samples were positive for E. uekii and type B, respectively. Additionally, the infection rate increased in the summer. Molecular analyses revealed both Eimeria isolates formed their own clusters; E. uekii was included in clades of chicken Eimeria and type B was include in clades of turkey Eimeria. Based on our findings in this study and previous data, we herein propose type B as E. raichoi. These genetic data will be helpful to conduct detailed classification and understand the impact of these parasites for conservation of endangered Japanese rock ptarmigans.

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Molecular analyses revealed Eimeria isolates from Japanese rock ptarmigans formed own clades.

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The species was phylogenetically closely related to virulent chicken Eimeria spp.

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Based on morphological data and sequences, Eimeria type B was proposed as a new species E. raichoi.

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These parasites could be the key factor for conservation of the endangered birds.

Prevalence and genetic characterization of eimeriid coccidia from feces of black-necked cranes, Grus nigricollis

Disseminated visceral coccidiosis (DVC) is a widely distributed intestinal and extraintestinal disease of cranes caused by eimeriid coccidia and has lethal pathogenicity to several crane species. Here, feces of 164 black-necked cranes collected in Dashanbao Black-necked Crane National Nature Reserve, China, were examined to determine the prevalence of coccidial oocysts. Of the 164 fecal samples, 76 (46.3%) were positive for oocysts of Eimeria, including E. gruis in 59 (35.9%), E. reichenowi in 52 (31.7%), and E. bosquei in 47 (28.7%) by microscopic observation. Sixty-eight (89.5%) of these positive samples included two or more morphologically identifiable species of Eimeria. The nearly full length 18S rRNA gene (18S rRNA; about 1.8 kb) and partial mitochondrial cytochrome c oxidase I gene (COX1; about 1.3 kb) from oocysts of each morphologically distinct species of Eimeria were amplified, sequenced, and analyzed. BLAST searches using these new 18S rRNA sequences for E. gruis, E. reichenowi, or E. bosquei showed the most similar sequences were those of E. gruis (98.7-99.7% identity), E. reichenowi (97.9-100% identity), or E. gruis (98.6-99.6% identity) isolated from different species of Grus. BLAST searches using the new COX1 sequences for the three species of Eimeria showed that no nucleotide sequences of Eimeria and Isospora coccidia in GenBank have more than 83.0% identity with these species. Identities among the new COX1 sequences were 91.8% for E. gruis and E. reichenowi, 94.5% for E. gruis and E. bosquei, and 91.3% for E. reichenowi and E. bosquei. Phylogenetic analysis based on 18S rRNA or COX1 sequences indicated that Eimeria spp. in black-necked cranes were clustered together with other previously identified Eimeria species from different cranes.

Molecular epidemiology and point mutations in ITS1 and 18S rDNA genes of Eimeria ninakohlyakimovae and E. christenseni isolated from Indian goats

Epidemiology and molecular characterization of Eimeria was carried in goats reared under semi-arid region of west Uttar Pradesh, India. A total of 1285 faecal samples from different goat breeds (Jamunapari, Jakhrana and Barbari) were examined for presence of Eimerian oocysts over a period of eight months along with faecal oocysts count. All raw data of faecal oocyst counts (FOC) were transformed by log_e (OPG+ 100) before analysis. All fixed effects like breed, age, months of sample collections along with their interaction were considered in analysis. The overall prevalence of Eimeria infection in goats was 73.85%. Breed wise prevalence in Barbari, Jamunapari and Jakhrana breed was 68.62, 79.70 and 72% respectively. Prevalence observed in 2-6M, 6-12M and >12M was as 70.83, 79.88 and 71.74% respectively. Gender wise prevalence as observed in male and female goats was 71.95 and 74.43% respectively. In oocyst per gram (OPG) data analysis the fixed effects like breed, age, months of sample collection and age versus gender interaction had significant effect on log transformed faecal oocysts counts (LFOC). The overall least square means of OPG was 4.673±0.007 (1403OPG). Of the three goat breeds, Jamunapari had highest OPG (2886OPG) compared to Jakhrana (875OPG) and Barbari (523OPG). Mean OPG in 2-6month age goats was significantly higher than the corresponding values in 6-12 and >12months, significant variation was found among monthly OPG means and wet months showed higher faecal oocysts discharge. Nine Eimeria species were identified infecting goats and E. arloingi and E. ninakohlyakimovae were most frequent and predominant species. Molecular characterization for coccidial infection was conducted using two genes i.e. 18S rDNA and ITS-1 genes which amplified 637bp and <500bp (E. ninakohlyakimovae) and >500bp (E. christenseni and E. alijevi) respectively. The ITS1 gene was analysed by sequencing, E. christenseni was found showing nucleotide similarity with E. bovis and E. ellipsoidalis whereas 3' end of the sequence were highly conserved. The ITS1 gene of E. ninakohlyakimovae was found more homologous to E. bovis, E. ellipsoidalis and E. zuernii but for 33rd nucleotide thymidine residue deletion and 5th position G→A mutation. The 18S rDNA sequences of E. ninakohlyakimovae and E. christenseni were studied for evolutionary divergence analysis and maximum divergence was noticed between E. ninakohlyakimovae and E. christenseni (0.0605). The phylogenetic tree showed E. ninakohlyakimovae was placed in same clade with other Eimeria spp. compared, but E. christenseni being placed in a different clade as an out-group.

Coccidian Parasites and Conservation Implications for the Endangered Whooping Crane (Grus americana)

While the population of endangered whooping cranes (Grus americana) has grown from 15 individuals in 1941 to an estimated 304 birds today, the population growth is not sufficient to support a down-listing of the species to threatened status. The degree to which disease may be limiting the population growth of whooping cranes is unknown. One disease of potential concern is caused by two crane-associated Eimeria species: Eimeria gruis and E. reichenowi. Unlike most species of Eimeria, which are localized to the intestinal tract, these crane-associated species may multiply systemically and cause a potentially fatal disease. Using a non-invasive sampling approach, we assessed the prevalence and phenology of Eimeria oocysts in whooping crane fecal samples collected across two winter seasons (November 2012–April 2014) at the Aransas National Wildlife Refuge along the Texas Gulf coast. We also compared the ability of microscopy and PCR to detect Eimeria in fecal samples. Across both years, 26.5% (n = 328) of fecal samples were positive for Eimeria based on microscopy. Although the sensitivity of PCR for detecting Eimeria infections seemed to be less than that of microscopy in the first year of the study (8.9% vs. 29.3%, respectively), an improved DNA extraction protocol resulted in increased sensitivity of PCR relative to microscopy in the second year of the study (27.6% and 20.8%, respectively). The proportion of positive samples did not vary significantly between years or among sampling sites. The proportion of Eimeria positive fecal samples varied with date of collection, but there was no consistent pattern of parasite shedding between the two years. We demonstrate that non-invasive fecal collections combined with PCR and DNA sequencing techniques provides a useful tool for monitoring Eimeria infection in cranes. Understanding the epidemiology of coccidiosis is important for management efforts to increase population growth of the endangered whooping crane.

First amplification of Eimeria hessei DNA from the lesser horseshoe bat (Rhinolophus hipposideros) and its phylogenetic relationships with Eimeria species from other bats and rodents

Although coccidian parasites of the genus Eimeria are among the best-documented parasites in bats, few Eimeria species found in bats have been characterised using molecular tools, and none of the characterised species are found in European countries. Phylogenetic relationships of Eimeria species that parasitise bats and rodents can be related to the morphology of oocysts, independently from host range, suggesting that these species are derived from common ancestors. In the present study, we isolated a partial sequence of the Eimeria hessei 18S rRNA gene from the lesser horseshoe bat (Rhinolophus hipposideros), a European bat species. Droppings from lesser horseshoe bats were collected from 11 maternity roosts located in France that were positive for the presence of the parasite. Through morphological characterisation, the oocysts detected in the lesser horseshoe bat droppings were confirmed to be E. hessei. The unique E. hessei sequence obtained through molecular analysis belonged to a clade that includes both rodent and bat Eimeria species. However, the E. hessei oocysts isolated from the bat droppings did not show morphological similarities to rodent Eimeria species.

Host-parasite incongruences in rodent Eimeria suggest significant role of adaptation rather than cophylogeny in maintenance of host specificity

The degree of host specificity, its phylogenetic conservativeness and origin are virtually unknown in Eimeria. This situation is largely due to the inadequate sample of eimerian molecular data available for reliable phylogenetic analyses. In this study, we extend the data set by adding 71 new sequences of coccidia infecting 16 small-mammal genera, mostly rodents. According to the respective feasibility of PCR gene amplification, the new samples are represented by one or more of the following genes: nuclear 18S rRNA, plastid ORF 470, and mitochondrial COI. Phylogenetic analyses of these sequences confirm the previous hypothesis that Eimeria, in its current morphology-based delimitation, is not a monophyletic group. Several samples of coccidia corresponding morphologically to other genera are scattered among the Eimeria lineages. More importantly, the distribution of eimerians from different hosts indicates that the clustering of eimerian species is influenced by their host specificity, but does not arise from a cophylogenetic/cospeciation process; while several clusters are specific to a particular host group, inner topologies within these clusters do not reflect host phylogeny. This observation suggests that the host specificity of Eimeria is caused by adaptive rather than cophylogenetic processes.

Genetic characterization and phylogenetic analysis of Eimeria arloingi in Iranian native kids

Among the 16 species of Eimeria from goats, Eimeria arloingi and Eimeria ninakohlyakimovae are regarded as the most pathogenic species in the world and cause clinical caprine coccidiosis. E. arloingi is known to be an important cause of coccidiosis in Iranian kids. Molecular analyses of two portions of nuclear ribosomal DNA (internal transcribed spacer1 (ITS1) and 18S rDNA) were used for the genetic characterization of the E. arloingi. Comparison of the sequencing data of E. arloingi obtained in the present study (ITS1: KC507793 and 18S rDNA: KC507792) with other Eimeria species in the GenBank database revealed a particularly close relationship between E. arloingi and Eimeria spp. from the cattle and sheep. The phylogram based on the ITS1 sequences shows that the E. arloingi, Eimeria bovis, and Eimeria zuernii formed a distinct group separate from the other remaining Eimeria spp. in cattle and poultry. In pairwise alignment, 18S rDNA sequence derived from E. arloingi showed 99% similarity to Eimeria ahsata with differences observed at only three nucleotides. This study showed that the ITS1 and 18S rDNA gene are useful genetic markers for the specific identification and differentiation of Eimeria spp. in ruminants.

Third lineage of rodent eimerians: morphology, phylogeny and re-description of Eimeria myoxi (Apicomplexa: Eimeriidae) from Eliomys quercinus (Rodentia: Gliridae)

Coccidian oocysts from feces of 46 individuals of the garden dormouse, Eliomys quercinus (Rodentia: Gliridae), were morphologically and molecularly characterized. Both morphological and sequence data (18S rDNA and ORF 470) showed low variability, indicating that all samples represent a single species. By comparison with published morphological descriptions of coccidia from glirid rodents, we determined that the samples represent Eimeria myoxi. Molecular data suggest that this species does not fall within the 2 known rodent-specific groups but branches as a third independent lineage. However, its exact position in respect to other eimerian clusters could not be established due to the lack of phylogenetic information at this taxonomic level for the 18S rRNA and ORF 470 genes. Based on these results, we provide a re-description of Eimeria myoxi, which contains morphological and molecular characteristics sufficient for its further unequivocal identification.

Disseminated visceral coccidiosis in Eurasian cranes (Grus grus) in the UK

Clinical disease and mortalities due to disseminated visceral coccidiosis were identified for the first time in a group of captive juvenile Eurasian cranes (Grus grus) in the UK during 2008. Presumptive diagnosis was made from the finding of granulomatous nodules in the liver, spleen and other organs at gross postmortem examination, and confirmed histologically by the presence of intracellular coccidial stages within lesions. The species of coccidian was determined to be Eimeria reichenowi on the basis of faecal oocyst morphology and sequencing of 18S rDNA by PCR. A further outbreak of clinical disease occurred in the same enclosure in 2009, affecting a new group of juvenile Eurasian cranes and demoiselle cranes (Anthropoides virgo) and indicating the persistence of infective oocysts in the environment. Clinical sampling of birds during both years demonstrated positive results from examination of both faecal samples and peripheral blood smears.

Eimeria trichosuri: phylogenetic position of a marsupial coccidium, based on 18S rDNA sequences

Phylogenetic analysis of the genus Eimeria suggests that parasite and host have coevolved over broad evolutionary timescales. Here we extend this analysis by determining the 18S rDNA gene sequence of the marsupial coccidium, Eimeria trichosuri, and assessing its phylogenetic position relative to Eimeria from birds, reptiles and placental mammals. This analysis placed E. trichosuri clones in a clade that diverged before the major clade comprising species from placental mammals. The position of E.trichosuri is consistent with host phylogeny where marsupials represent an ancient evolutionary line that predates the placental mammal line.

Genetical survey of novel type of Cryptosporidium andersoni in cattle in Japan

Previously, we reported that an isolate of novel type of Cryptosporidium andersoni detected in cattle in Japan contained Type A (identical to C. andersoni reported previously) and Type B (having a thymine nucleotide insertion unlike the Type A) genotypes in the 18S rRNA gene. Here, we conducted an extensive investigation of Cryptosporidium infections in adult cattle in Japan from 2004 to 2007. Consequently, Cryptosporidium sp. were detected in 12 of the 205 cattle examined (5.9%), and partial sequences of the Cryptosporidium oocyst wall protein (COWP) gene in all isolates were identical to those of the previously reported data for C. andersoni whereas two signals were observed in the sequence of the partial 18S rRNA gene in all the isolates. In transmission studies using five of the isolates, they all infected SCID mice. Modified multiplex PCR using DNA of a single oocyst isolated from the infected SCID mice revealed that the partial sequences in the 18S rRNA gene of 40-80% of 10 isolates were identical to the Type A genotype of C. andersoni and those of other samples were identical to the Type B genotype. These results suggested that the C. andersoni novel type is widespread in cattle throughout Japan, and have multiple copies (Types A and B) in the 18S rRNA gene.

Phylogenetic relationships among Eimeria spp. (Apicomplexa, Eimeriidae) infecting rabbits: evolutionary significance of biological and morphological features

Monophyly of all 11 valid Eimeria species from rabbits (Oryctolagus cuniculus Linnaeus, 1758) was revealed based on nuclear 18S rDNA sequence data. This finding implies that these species, which vary considerably in terms of their morphology and biology, diversified on a single host or several closely related species. Phylogenetic analysis divided rabbit Eimeria species into 2 sister lineages, corresponding to the presence/absence of the oocyst residuum. Other morphological or biological traits (oocyst shape and size, presence/absence of oocyst inner structures, pathogenicity, infection site, pre-patent and patent periods, sporulation time, and number of asexual generations) do not explicitly correlate with the phylogeny of rabbit coccidia.

Detection of a mixed infection of a novel Cryptosporidium andersoni and its subgenotype in Japanese cattle

Cryptosporidium oocysts were detected in the feces of cattle in Saga, Japan. Isolates were morphologically large. We attempted to identify the species or genotypes of the isolates by analyzing the partial sequences of the 18S rRNA and Cryptosporidium oocyst wall protein (COWP) genes, and measuring the infectivity in mice. The isolates showed 100% homology with Cryptosporidium andersoni in the COWP gene sequence and it could be transmitted to mice, but in the 18S rRNA gene, there was an additional signal in the ABI sequence chromatogram. To examine the additional signal, we analyzed both the 18S rRNA and the COWP gene sequences of a single oocyst passaged from mice using a modified multiplex PCR that was able to amplify both genes. As a result, it was revealed that two distinct genotypes (Types A and B) of a novel C. andersoni type existed in the 18S rRNA gene, whereas the COWP gene sequences of both oocysts were identical to C. andersoni. Although the sequence of the 18S rRNA gene of Type A was identical to that of C. andersoni, that of Type B had a thymine insertion and was not identical to any sequence registered with GenBank. Here we report that this is a new type of C. andersoni.

Genetical identification of coccidia in red-crowned crane, Grus japonensis

We genetically analyzed eimerian oocysts isolated from the red-crowned crane (Grus japonensis) in Hokkaido, a northern island of Japan. Two types of oocysts of which shapes were similar to Eimeria gruis and E. reichenowi were found. Nearly the total length of the 18S ribosomal RNA gene (about 1.7 kbp in length) was amplified from single oocyst of each type and was sequenced. The respective sequences showed high similarity to those of published partial sequences (349 bp) of E. gruis type oocyst and E. reichenowi type oocyst isolated from the hooded crane (G. monacha) and the white-naped crane (G. vipio) in Izumi, in the southern island of Japan. Phylogenetic analysis indicated that E. gruis type and E. reichenowi type are different species, and suggested that these crane coccidia have evolved independently from the intestinal parasitizing Eimeria species.

DESCRIPTION AND PHYLOGENY OF A NEW SPECIES OF EIMERIA FROM DOUBLE-CRESTED CORMORANTS (PHALACROCORAX AURITUS) NEAR FORT GAINES, GEORGIA

The renal parasite Eimeria auritusi has caused several mortality events in double-crested cormorants (DCC; Phalacrocorax auritus) in the Midwest and southeastern United States. This parasite has only been detected during large-scale outbreaks, and its presence and prevalence in healthy populations of cormorants is unknown. In this study, 80 DCC were collected from the Chattahoochee River near Fort Gaines, Georgia, and examined for kidney and intestinal coccidia. Eighteen (22.5%) and 56 (70%) of the DCC were positive for E. auritusi and a new species of intestinal Eimeria, respectively. Oocysts of the new intestinal Eimeria species had a thin colorless wall, were ovoid with rare bumps on the outer surface, and measured 17.1 microm +/- 1.5 x 14.7 microm +/- 1.0 (16-18.5 x 13-17), with an average length:width ratio of 1.17 microm (1.03-1.29). A prominent micropyle (4-4.5 microm) was present, and a large oval-to-round polar body (2.5 microm) was located beneath the micropyle. Sporocysts were ovoid and measured 9.6 microm +/- 0.6 x 5.9 microm +/- 0.5 (8.5-10.5 x 5-6.5), with an average length:width ratio of 1.63 (1.3-1.82) with small stieda body present. Amplification and sequencing of a fragment of the 18S rRNA gene indicated that the 2 DCC Eimeria species and 2 Eimeria species from cranes were in a separate group from other Eimeriidae. These data indicate that E. auritusi and this new species of intestinal Eimeria are prevalent in this apparently healthy DCC population. The cause of renal coccidiosis outbreaks in other populations of cormorants is unknown but could be due to crowding or stress during the winter months or some other associated pathogen or immunosuppressor that might predispose individuals to clinical disease.