Phylogenies based on combined mitochondrial and nuclear sequences conflict with morphologically defined genera in the eimeriid coccidia (Apicomplexa)

A new genus and species of isosporoid coccidium from captive green tree frogs, Ranoidea caerulea (Anura: Hylidae)

A new genus and a new species of isosporoid coccidium (Apicomplexa: Conoidasida: Eimeriorina) are described and illustrated from green tree frogs (Ranoidea caerulea) (Anura: Hylidae) imported from Papua New Guinea and Indonesia. The described species has disporocystic and tetrasporozoic oocysts without a Stieda body. Nine species originally belonging to the genus Isospora Schneider, 1881 in the family Eimeriidae Minchin, 1903 described from Anura are recognized as members of the new genus and new combinations of the species names are proposed. The phylogenetic analyses of partial gene fragments of 18S rRNA and mitochondrial cytochrome c oxidase subunit 1 genes from isosporoid oocysts from green tree frogs suggested that isosporoid oocysts without Stieda bodies from anurans should be placed in the Sarcocystidae and no longer belong in the Eimeriidae.

Morphological identification and phylogenetic analysis of Eimeria coypi and Eimeria fluviatilis (Apicomplexa: Eimeriidae) isolated from nutrias (Myocastor coypus [Rodentia]) in Japan

The nutria (Myocastor coypus) is a semiaquatic rodent that originally inhabited South America. However, the animals have spread to different continents as alien species, and their numbers are quickly increasing, especially in North America, Europe, and Eastern Asia including Japan. Although nutrias have been suggested to serve as reservoirs for pathogens, including parasites, there have been few reports on this subject. In the present study, we surveyed the gastrointestinal parasites in nutrias living in Japan to better understand their prevalence in nutrias. We collected 72 samples of intestinal contents or feces from nutrias in Osaka and Okayama Prefectures. We found that 49 (68.1 %) samples were positive for Eimeria parasites, and two types of oocysts were identified: ellipsoidal (Type A) and subspherical (Type B) oocysts. In addition, Strongyloides myopotami was detected in 44 samples, and Capillaria spp. and Fasciola spp. were detected in one and three samples, respectively. Based on the morphologies of the detected Eimeria oocysts, Types A and B were identified to be E. coypi and E. fluviatilis, respectively. Phylogenetic analyses after PCR and sequencing targeting the cytochrome c oxidase subunit I gene placed the sequences of E. fluviatilis (Type B) as a cluster between the sequences of Eimeria derived from rodents. The sequences of the three subgenotypes of E. coypi (Type A) were included in the cluster containing the sequences of Eimeria spp. from rodents of multiple species, which is referred to as the Apionodes supercluster, and is separate from other clades. It has been suggested that Eimeria spp. from rodents in this cluster can quickly adapt to infect different hosts. Although further analyses are needed to construct more detailed phylogenetic trees, our results revealed the genetical positions of Eimeria spp. in nutrias. In addition, our results may be helpful when considering host specificity as well as host switching by the pathogen.

A systematic review of the genus Tyzzeria Allen, 1936 (Chromista: Apicomplexa), including the molecular phylogenetic position of Tyzzeria parvula (Kotlán, 1933) Klimeš, 1963

Tyzzeria Allen, 1936 is a coccidian genus traditionally associated with Anseriformes, although there are descriptions of Tyzzeria spp. from junglefowls, snakes, skinks and mice. In this sense, the current study performs a taxonomic review of Tyzzeria spp., evaluating those that should be valid, invalid or that require further studies for validation. Along with this review, oocysts morphologically identified as Tyzzeria parvula (Kotlán, 1933) Klimeš, 1963 were recovered from fecal samples of swan geese Anser cygnoid (Linnaeus, 1758) in the mountainous region of the State of Rio de Janeiro, which were molecularly identified through the sequencing of a locus of the small subunit ribosomal RNA (18S) gene, providing the first deposit of the genus Tyzzeria in GenBank. Finally, this sequence of T. parvula prompted a broad phylogenetic analysis covering species of the main chromist taxa, which evidenced homoplasies associated with taxonomic characters of gametogony, basic oocyst configuration and excystation structures; in addition to positioning T. parvula in a monophyletic group within the order Eimeriida together with Schellackia spp., Eimeria spp. and Caryospora-like spp. from reptiles and amphibians.

Isospora pichororei n. sp. (Chromista: Apicomplexa: Eimeriidae) from rufous-capped spinetails Synallaxis ruficapilla Vieillot, 1819 (Passeriformes: Furnariidae: Synallaxiinae) in South America

Spinetails are a suboscine passerines of the genus Synallaxis Vieillot, 1818 which have great interest for ornithology, given the wide diversity of 37 species that are distributed throughout the Neotropical region. Despite this wide diversity and distribution, Synallaxis spp. have never been recorded as hosts of coccidian parasites. In this context, the current study describes a new species of Isospora Schneider, 1881 from rufous-capped spinetails Synallaxis ruficapilla Vieillot, 1819 captured in the Itatiaia National Park, which is a federal conservation unit in Southeastern Brazil. The oocysts of Isospora pichororei Genovez-Oliveira & Berto n. sp. are subspheroidal to ovoidal, measuring on average 25 by 21 μm. Micropyle is present, but discrete. Oocyst residuum absent, but one or two polar granules are present. Sporocysts are ellipsoidal with slightly pointed posterior end, measuring on average 17 by 10 μm. Stieda and sub-Stieda bodies are present. Sporocyst residuum is clustered among the vermiform sporozoites, which have striations, refractile bodies and nucleus. This morphology was different from the other Isospora spp. recorded in the host family Furnariidae. Molecular identification was targeted by the amplification and sequencing of a locus of the mitochondrial cytochrome c oxidase subunit 1 (cox1) gene. This sequence had the highest similarity of 99.5% with a sequence deposited for Isospora oliveirai Ortúzar-Ferreira & Berto, 2020, which is a coccidian species that parasitizes suboscine tityrids Schiffornis virescens (Lafresnaye, 1838), also in the Itatiaia National Park. Phylogenetic analysis grouped some species in subclades, including I. pichororei with I. oliveirai; however, it was inconclusive in an expectation of parasite-host coevolution. Finally, I. pichororei is established as new to science, being the first description from Synallaxinae and the third description from Furnariidae. Furthermore, this is the first Isospora sp. from the host family Furnariidae to have a molecular supplementation by sequencing a locus of the cox1 gene of the mitochondrial genome.

Organellar genome dynamics of exogenous stages of Eimeria tenella

BACKGROUND

Coccidia are a group of intracellular protozoal parasites within the phylum Apicomplexa. Eimeria tenella, one of the species that cause intestinal coccidiosis in poultry, can cause significant mortality and morbidity. Diploid oocysts of Eimeria species are shed in the feces of an infected host and must sporulate to achieve infectivity. This process results in eight haploid infectious units, called sporozoites, held within a single oocyst. Each Eimeria spp. parasite possesses a single apicoplast and a single mitochondrion, both of which carry multiple copies of their respective organellar genomes. Reports of copy numbers of organellar genomes have varied widely.

METHODS

We report the application of quantitative polymerase chain reaction (qPCR), supported by next-generation sequencing, for the quantification of the extranuclear genomes relative to the nuclear genome over the course of sporulation and following its completion.

RESULTS

At 64 elapsed hours, 93.0% of oocysts were fully sporulated; no increase in percent sporulation was observed after this time. Apicoplast relative genome copy number showed several significant shifts up to 72 elapsed hours, after which no significant shifts were observed. Oocysts were shed with approximately 60% the amount of apicoplast DNA present at 72 h, after which point no significant shifts in apicoplast genome relative abundance occurred. Mitogenome relative copy number showed only two significant shifts, from 16 to 24 elapsed hours and from 24 to 32 elapsed hours. Oocysts were shed with approximately 28% the amount of mitochondrial DNA that was present at the time sporulation was deemed morphologically complete, at 64 elapsed hours.

CONCLUSIONS

The characterization of the dynamics of genome abundance in exogenous stages sheds new light on the basic biology of Eimeria spp. and supports the use of extranuclear targets for molecular modes of parasite quantification and identification with improved sensitivity and accuracy.

Isospora similisi recovered from a new host, Saltator aurantiirostris, with supplementary molecular data and notes on its taxonomy and distribution in the Neotropical region

This article reports on a golden-billed saltator Saltator aurantiirostris Vieillot, 1817, kept in captivity outside its natural distribution area, in the proximities of the Itatiaia National Park, as a new host for Isospora similisi Coelho, Berto, Neves, Oliveira, Flausino & Lopes, 2013. Additionally, a supplementary molecular identification is provided through the sequencing of three non-overlapping loci of mitochondrial DNA and one locus of the 18S small subunit ribosomal RNA (18S) gene. All the taxonomic features of the I. similisi oocysts shed by S. aurantiirostris were equivalent to those originally described from Saltator similis d'Orbigny & Lafresnaye, 1837. The new sequenced loci were identical, or showed 99.9% similarity, to the samples of I. similisi from S. similis and S. aurantiirostris, confirming the same species from both hosts. Lastly, I. similisi is estimated as a junior synonym of Isospora formarum McQuistion & Capparella, 1992, due to the morphological similarities and wide distribution of its hosts in the Neotropical region. Therefore, this study encourages future taxonomic inquiries into I. similisi collected from other Saltator spp. in order to establish this synonymization of I. formarum with I. similisi, and hence, its wide distribution and dispersion in the Neotropical region, including across the Andes mountains.

Molecular phylogenetic analysis and seasonal dynamics of Eimeria species infecting broilers of Kashmir, India

Globally, the poultry industry is seriously threatened by coccidiosis caused by various species of Eimeria. This protozoan parasite inhabits the epithelial lining of the gastrointestinal tract of poultry globally and can cause serious clinical disease. The present study was carried out on poultry farms located in various regions of Kashmir, India, to investigate the prevalence and phylogenetic relationships of Eimeria species affecting broiler chickens. Over a period of one year, fecal samples were collected from 60 poultry farms in Kashmir and morphological and molecular techniques were employed for Eimeria species identification. Results revealed a high prevalence of coccidiosis, with 58.3% (35/60) of farms positive for Eimeria. The most prevalent species were E. tenella (31/35, 88.6%) followed by E. acervulina (25/35, 71.4%), E. maxima (19/35, 54.3%), E. mitis (18/35, 51.4%), and E. necatrix (9/35, 25.7%). Seasonal variation in prevalence was also observed, with the highest rates in autumn (86.7%) and summer (66.7%). Additionally, younger birds (3-4 weeks) exhibited higher infection rates (85.7%) compared to older birds (57.9%) (5-6 weeks). Mixed infection was found in 94.2% (33/35) of positive farms. Phylogenetic analysis using ITS1 sequences confirmed species clustering and revealed evolutionary relationships among Eimeria species. E. tenella and E. necatrix formed a distinct clade, while E. acervulina formed another. The study underscores the importance of molecular techniques in accurate species identification and provides valuable insights into the epidemiology of coccidiosis in poultry in Kashmir. Effective control strategies, including vaccination and improved management practices, are necessary to mitigate the economic losses associated with this widespread poultry disease.

Genetic diversity and occurrence of Eimeria species causing cattle coccidiosis in Kashmir, India

This study focuses on the occurrence, identification, and molecular characterization of Eimeria species causing coccidiosis in cattle in the Kashmir Valley, India. Coccidiosis, caused by apicomplexan parasites of the genus Eimeria, poses a significant threat to global cattle farming. Conventional techniques for identification, which rely on the morphology of sporulated oocysts, have drawbacks, leading to the adoption of molecular techniques to accurately delimit species. A total of 190 cattle were sampled in nine farms and parasitological examination revealed an occurrence of 45.7% for Eimeria spp. Molecular analysis using PCR and sequencing identified three predominant species: E. zuernii, E. alabamensis, and E. bovis. The study highlights the widespread occurrence of these species globally, as supported by previous research conducted in Bangladesh, Austria, Egypt, and Brazil. The phylogenetic analysis based on internal transcribed spacer (ITS-1) gene sequences revealed distinct clusters for E. zuernii and E. bovis, while E. alabamensis formed a separate clade. The genetic diversity and phylogenetic connections provide insights into the evolutionary relationships among these Eimeria species. This study contributes valuable information for understanding the epidemiology and genetic diversity of cattle coccidiosis in the Kashmir Valley, emphasizing the importance of molecular characterization for accurate species identification.

Phylogenetic analysis of Eimeria tenella isolates from chicken of sub-tropical mountains of Meghalaya, India

BACKGROUND

Coccidiosis is the most common and pathogenic intestinal disease caused by different species of Eimeria is chicken. In this study, we describe the prevalence, molecular diagnosis and evolutionary insight of Eimeria tenella in chicken of Meghalaya's sub-tropical mountainous area.

METHODS AND RESULTS

Faecal samples (337 no.) and dead chicks (298 no.) were collected every month from January to July' 2023 from poultry farms (4nos.) in and around Umiam, Ri-Bhoi, Meghalaya. The chicks were categorized into different age groups viz. < 3, 3-6 and > 6 weeks. Samples were examined by flotation techniques and post-mortem. The oocysts were sporulated in 2.5% potassium dichromate solution. Eimeria tenella's 18 S rRNA gene genomic DNA was extracted, amplified, and sequenced. Fecal sample and postmortem examinations revealed 24.04% and 33.22% infections of Eimeria sp., respectively. Oocyst per gram (OPG) was recorded highest and lowest in July (26,500) and February (9800), respectively. Amplification of the 18 S rRNA small subunit gene (SSU) by Polymerase Chain Reaction (PCR) revealed a 1790 bp band size. The amplicon was sequenced and deposited in the NCBI database. BLAST analyses of the SSU rRNA gene of E. tenella, Umiam, Meghalaya isolate (OR458392.1) revealed sequence similarities of more than 99% with SSU rRNA gene sequences available in the NCBI database. Pair wise alignment exhibited nucleotide homology ranging from 71.59 to 100.0% with the maximum sequence homology (100.0%) shared with the E. tenella isolate from Turkey (HQ680474.1) and the lowest homology of 95.6% with UK (HG994972.1). Umiam isolate were found to have 97.08% and 100.0% nucleotide similarities with E. tenella from both the UK (AF026388.1) and the USA (U40264.1), respectively. However, nucleotide similarities of 98.24%, 85.33%, 84.75% and 81.35% were observed with E. tenella strain Bangalore (JX312808.1), E. tenella isolate Kerala-1 (JX093898.1), E. tenella isolate Kerala-3 (JX093900.1) and E. tenella isolate Kerala-2 (JX093899.1), respectively. Phylogenetic analysis of SSU rRNA sequences of E. tenella Umiam, Meghalaya isolate with cognate sequences throughout the world revealed these sequences are distinct but at the same time share a close phylogenetic relationship with Indian isolates from Bangalore and Andhra Pradesh. In addition, the distant phylogenetic relationship was observed with cognate gene sequences of United States of America, Canada, China.

CONCLUSION

Phylogenetic analysis of SSU rRNA sequences of E. tenella Umiam, Meghalaya isolate with cognate sequences throughout the world revealed these sequences are distinct but at the same time share a close phylogenetic relationship with Indian isolates from Bangalore and Andhra Pradesh. Distant phylogenetic relationship was observed with cognate gene sequences of United States of America, Canada, China.

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.

Reevaluation of Hemoparasites in the Black Spiny-Tailed Iguana (Ctenosaura similis) with the First Pathological and Molecular Characterizations of Lankesterella desseri n. sp. and Redescription of Hepatozoon gamezi

Hemoprotozoa are microorganisms that parasitize the blood and possess intricate life cycles. Despite the complexity of their nature, little is known about the biology of hemoprotozoa in reptilian hosts. In this study, we conducted disease surveillance on blood samples collected from six black spiny-tailed iguanas (Ctenosaura similis) exhibiting clinical signs. We found two different types of hemoparasites in the blood films and further confirmed they belong to the genera Lakesterella and Hepatozoon through molecular methods. In the tissue section from a dead iguana infected only with Lakesterella sp., parasites were also found in melanomacrophages of the liver and kidney. Since Lakesterella sp. infection has not been reported in C. similis, we propose this hemococcidian as a new species, Lankesterella desseri n. sp. The Hepatozoon parasites discovered in this study were classified as Hepatozoon gamezi based on their morphological characteristics, particularly the notable deformation of all infected erythrocytes, and this classification was further corroborated through molecular biological and phylogenetic analyses. This is the first hemoprotozoa investigation in C. similis with pathological and molecular characterization of these pathogens. We suggest that more studies are needed to understand the epidemiology, transmission, and impact of these parasites on their hosts and ecosystems.

Eimeria zuernii (Eimeriidae: Coccidia): mitochondrial genome and genetic diversity in the Chinese yak

BACKGROUND

Coccidiosis caused by Eimeria zuernii (Eimeriidae: Coccidia) represents a significant economic threat to the bovine industry. Understanding the evolutionary and genetic biology of E. zuernii can assist in new interaction developments for the prevention and control of this protozoosis.

METHODS

We defined the evolutionary and genetic characteristics of E. zuernii by sequencing the complete mitogenome and analyzing the genetic diversity and population structure of 51 isolates collected from eight yak breeding parks in China.

RESULTS

The 6176-bp mitogenome of E. zuernii was linear and encoded typical mitochondrial contents of apicomplexan parasites, including three protein-coding genes [PCGs; cytochrome c oxidase subunits I and III (cox1 and cox3), and cytochrome b (cytb)], seven fragmented small subunit (SSU) and 12 fragmented large subunit (LSU) rRNAs. Genome-wide comparative and evolutionary analyses showed cytb and cox3 to be the most and least conserved Eimeria PCGs, respectively, and placed E. zuernii more closely related to Eimeria mephitidis than other Eimeria species. Furthermore, cox1-based genetic structure defined 24 haplotypes of E. zuernii with high haplotype diversities and low nucleotide diversities across eight geographic populations, supporting a low genetic structure and rapid evolutionary rate as well as a previous expansion event among E. zuernii populations.

CONCLUSIONS

To our knowledge, this is the first study presenting the phylogeny, genetic diversity, and population structure of the yak E. zuernii, and such information, together with its mitogenomic data, should contribute to a better understanding of the genetic and evolutionary biological studies of apicomplexan parasites in bovines.

In vitro cultivation methods for coccidian parasite research

The subclass Coccidia comprises a large group of protozoan parasites, including important pathogens of humans and animals such as Toxoplasma gondii, Neospora caninum, Eimeria spp., and Cystoisospora spp. Their life cycle includes a switch from asexual to sexual stages and is often restricted to a single host species. Current research on coccidian parasites focuses on cell biology and the underlying mechanisms of protein expression and trafficking in different life stages, host cell invasion and host-parasite interactions. Furthermore, novel anticoccidial drug targets are evaluated. Given the variety of research questions and the requirement to reduce and replace animal experimentation, in vitro cultivation of Coccidia needs to be further developed and refined to meet these requirements. For these purposes, established culture systems are constantly improved. In addition, new in vitro culture systems lately gained considerable importance in research on Coccidia. Well established and optimized in vitro cultures of monolayer cells can support the viability and development of parasite stages and even allow completion of the life cycle in vitro, as shown for Cystoisospora suis and Eimeria tenella. Furthermore, new three-dimensional cell culture models are used for propagation of Cryptosporidium spp. (close relatives of the coccidians), and the infection of three-dimensional organoids with T. gondii also gained popularity as the interaction between the parasite and host tissue can be studied in more detail. The latest advances in three-dimensional culture systems are organ-on-a-chip models, that to date have only been tested for T. gondii but promise to accelerate research in other coccidians. Lastly, the completion of the life cycle of C. suis and Cryptosporidium parvum was reported to continue in a host cell-free environment following the first occurrence of asexual stages. Such axenic cultures are becoming increasingly available and open new avenues for research on parasite life cycle stages and novel intervention strategies.

Identification of Eimeria tenella sporozoite immunodominant mimotopes by random phage-display peptide libraries-a proof of concept study

INTRODUCTION

Coccidiosis, caused by parasites of numerous Eimeria species, has long been recognized as an economically significant disease in the chicken industry worldwide. The rise of anti-coccidian resistance has driven a search for other parasite management techniques. Recombinant antigen vaccination presents a highly feasible alternative. Properly identifying antigens that might trigger a potent immune response is one of the major obstacles to creating a viable genetically modified vaccine.

METHODS

This study evaluated a reverse immunology approach for the identification of B-cell epitopes. Antisera from rabbits and hens inoculated with whole-sporozoites of E. tenella were used to identify Western blot antigens. The rabbit IgG fraction from the anti-sporozoite serum exhibited the highest reactogenicity; consequently, it was purified and utilized to screen two random Phage-display peptide libraries (12 mer and c7c mer). After three panning rounds, 20 clones from each library were randomly selected, their nucleotide sequences acquired, and their reactivity to anti-sporozoite E. tenella serum assessed. The selected peptide clones inferred amino acid sequences matched numerous E. tenella proteins.

RESULTS AND CONCLUSIONS

The extracellular domain of the epidermal growth factor-like (EGF-like) repeats, and the thrombospondin type-I (TSP-1) repeats of E. tenella micronemal protein 4 (EtMIC4) matched with the c7c mer selected clones CNTGSPYEC (2/20) and CMSTGLSSC (1/20) respectively. The clone CSISSLTHC that matched with a conserved hypothetical protein of E. tenella was widely selected (3/20). Selected clones from the 12-mer phage display library AGHTTQFNSKTT (7/20), GPNSAFWAGSER (2/20) and HFAYWWNGVRGP (8/20) showed similarities with a cullin homolog, elongation factor-2 and beta-dynein chain a putative E. tenella protein, respectively. Four immunodominant clones were previously selected and used to immunize rabbits. By ELISA and Western blot, all rabbit anti-clone serums detected E. tenella native antigens.

DISCUSSION

Thus, selected phagotopes contained recombinant E. tenella antigen peptides. Using antibodies against E. tenella sporozoites, this study demonstrated the feasibility of screening Phage-display random peptide libraries for true immunotopes. In addition, this study looked at an approach for finding novel candidates that could be used as an E. tenella recombinant epitope-based vaccine.

Hastening Progress in Cyclospora Requires Studying Eimeria Surrogates

Cyclospora cayetanensis is an enigmatic human parasite that sickens thousands of people worldwide. The scarcity of research material and lack of any animal model or cell culture system slows research, denying the produce industry, epidemiologists, and regulatory agencies of tools that might aid diagnosis, risk assessment, and risk abatement. Fortunately, related species offer a strong foundation when used as surrogates to study parasites of this type. Species of Eimeria lend themselves especially well as surrogates for C. cayetanensis. Those Eimeria that infect poultry can be produced in abundance, share many biological features with Cyclospora, pose no risk to the health of researchers, and can be studied in their natural hosts. Here, we overview the actual and potential uses of such surrogates to advance understanding of C. cayetanensis biology, diagnostics, control, and genomics, focusing on opportunities to improve prevention, surveillance, risk assessment, and risk reduction. Studying Eimeria surrogates accelerates progress, closing important research gaps and refining promising tools for producers and food safety regulators to monitor and ameliorate the food safety risks imposed by this emerging, enigmatic parasite.

A new Eimeria coccidian species (Apicomplexa: Eimeriidae) from Père David's deer (Elaphurus davidianus Milne-Edwards, 1866) in Dafeng Milu National Nature Reserve in Jiangsu Province, eastern China

Background

Eimeria coccidiosis is a significant intestinal parasitic disease, which can lead to weight loss, disease and even death of many animals. At present, there is no information about the prevalence of Eimeria among the world’s endangered species of Père David’s deer (Elaphurus davidianus). Therefore, the purpose of this study is to identify an unknown Eimeria genus in the Père David’s deer in Dafeng Milu National Nature Reserve, China.

Results

A new Eimeria species is described from Père David’s deer. Sporulated oocysts (n = 54) are pyriform, with a rough, yellowish brown, 2-layered oocyst wall (2.5 μm thick). A numerous small granules are dispersed randomly on the wall. Oocysts measured 41.2 (39.2–42.8) μm × 29.5 (27.9–30.5) μm, oocyst length/width (L/W) ratio, 1.4. Oocyst residuum, a polar granule and a polar cap are absent. The micropyle (3.5 μm wide) is present. Sporocysts are spindle shaped, 18.2 (16.5–20.0) μm × 10.5 (9.8–11.9) μm, sporocyst L/W ratio, 1.7 (1.5–1.9). A thin convex Stieda body is present and the sporocyst residuum is composed of numerous small granules less than 2.0 μm in diameter dispersed randomly. Each sporocyst contained 2 comma-shaped sporozoites in head-to-tail arrangement. A nucleus is located immediately anterior to the posterior, strong refractive and subspherical refractile body (~ 8 μm). Molecular analysis was conducted at the 18S, ITS-1 and COI loci.

Conclusion

Based on the morphological and molecular data, this isolate is a new species of coccidian parasite, which is named Eimeria davidianusi after its host, the Père David’s deer (Elaphurus davidianus).

Supplementary Information

The online version contains supplementary material available at 10.1186/s12917-022-03308-2.

The First Isospora Species (Apicomplexa: Eimeriidae) Described from the Northern Yellow-Shafted Flicker (Colaptes auratus luteus) in Ontario, Canada

PURPOSE

Members of the genus Isospora commonly infect a wide variety of wild birds. By combining morphometric and genetic data, we are able to differentiate and describe a new apicomplexan parasite, Isospora picoflavae n. sp., from the Northern Yellow-shafted Flicker (Colaptes auratus luteus) in Ontario, Canada.

METHODS

Unsporulated oocysts were observed in intestinal contents obtained during necropsy; these oocysts completed exogenous sporulation within 7 days at room temperature. Complete nuclear 18S rDNA and complete mitochondrial genome sequences were obtained from this previously undescribed Isospora sp. to compare with related coccidia.

RESULTS

Sporulated oocysts were subspherical in shape measuring an average of 22.7 × 21.7 μm (n = 53; mean shape index 1.05) containing a near-spherical polar granule. Sporocysts were ovoidal to ellipsoidal in shape, measuring an average size of 17.0 × 10.5 μm (n = 9; mean shape index 1.62). Sporocyst residuum was concentrated in an irregular, spherical mass in the middle of each sporocyst. The isolated oocysts differed morphologically from other Isospora species reported to infect members of the family Picidae. Based on phylogenetic analyses using either combined nuclear 18S rDNA and mitochondrial cytochrome c oxidase I (COI) sequences or complete mitochondrial genome sequences, this Isospora sp. n. isolated from the Northern Flicker grouped within a clade containing Isospora species described from various passeriform hosts.

CONCLUSION

Based on combined morphological and molecular data, the oocysts found in the gastrointestinal contents of Colaptes auratus luteus represent a new species of Isospora named herein as Isospora picoflavae n. sp.

Phylogenetic analysis of Eimeria tenella isolated from the litter of different chicken farms in Mymensingh, Bangladesh

Background

Eimeria tenella is the most pathogenic intracellular protozoan parasite of seven Eimeria species causing chicken coccidiosis around the world. This species is particularly responsible for caecal coccidiosis leading to serious morbidity–mortality and financial loss in poultry production.

Methods

The present study explored the genetic diversity of E. tenella. Litter slurry was collected from 18 broiler farms located in Mymensingh district, Bangladesh. Litter samples were processed for oocyst isolation–identification using parasitological techniques followed by genomic DNA extraction from sporulated oocysts. For molecular analysis, the internaltranscribedspacer1 gene of E. tenella was amplified using species‐specific primers and sequenced. After editing and alignment, 263 bp sequences were used for analysis.

Results

Genetic analysis showed seven distinct genotypes and detected six single nucleotide polymorphisms among the 18 E. tenella isolates. The nucleotide and genotype diversity were 0.00507 and 0.8235, respectively. A phylogenetic tree was constructed with 66 sequences (seven studied genotypes and 59 reference sequences from GenBank database). The neighbour‐joining tree represented that the studied E. tenella isolates were grouped with reference E. tenella isolates with strong nodal support (100%) and the nucleotide sequences of E. tenella, E. necatrix, E. acervulina, E. brunetti, E. maxima, E. mitis and E. praecox formed separate clusters without any geographical boundaries.

Conclusions

This is the first study on the genetic analysis of E. tenella from Mymensingh district, Bangladesh. These findings will provide baseline data on the species conformation and genetic variations of E. tenella. Further extensive investigation will be needed to reveal the population genetic structure of this parasite and thus will facilitate the planning of effective control strategies.

New data on Henneguya postexilis Minchew, 1977, a parasite of channel catfish Ictalurus punctatus, with notes on resolution of molecular markers for myxozoan phylogeny

Previous morphological and histological data are supplemented with molecular and ultrastructural data for a Henneguya sp. isolated from farm-raised channel catfish Ictalurus punctatus in Mississippi, USA. Myxospores were cryptic, encapsulated within a thin layer of epithelium in the gill lamellae with spore measurements consistent with the original description of Henneguya postexilis Minchew, 1977. Myxospores were 42.7-49.1 µm in total length with spore bodies 12.1-17.2 × 3.6-4.8 × 2.9-3 µm. Polar capsules were of unequal length, with the longer capsule being 4.4-6.7 × 1.1-1.6 µm and the shorter capsule being 4.4-6.4 × 1.1-1.6 µm. Polar tubules had 6-8 turns. Caudal processes were 25.7-38.1 µm in length. Spores were encapsulated in a thin layer of epithelium in the gill lamellae. Molecular data from the most commonly used markers for myxozoan identification and phylogeny, partial 18S small subunit ribosomal gene (SSU), partial 28S large subunit ribosomal gene (LSU), and elongation factor 2 (EF2) were generated for H. postexilis. Additionally, novel data for LSU and EF2 were generated for archived myxozoan specimens from farm-raised catfish (H. mississippiensis, H. ictaluri, H. exilis, H. adiposa, H. sutherlandi, H. bulbosus, Unicauda fimbrethilae), as well as archived specimens from wild fish (H. laseeae [from Pylodictis olivaris], Hennegoides flockae [from Aphredoderus sayanus], Myxobolus cloutmani [from Cycleptus elongatus]. These include the first EF2 sequence data for the genera Hennegoides and Unicauda. Phylogenetic analyses using these data placed H. postexilis in well supported clades with other ictalurid-infecting Henneguya species. Phylogenetic signal assessments on these analyses suggest that while SSU provided the greatest phylogenetic signal, LSU yielded comparable signal, supporting previous work implying this region may be underutilised in reconstructing myxobolid phylogenies.

The genetic and morphological diversity of Haemogregarina infecting turtles in Colombia: Are mitochondrial markers useful as barcodes for these parasites?

Adeleorinid parasites commonly infect turtles and tortoises in nature. Currently, our knowledge about such parasites is extremely poor. Their characterization is based on morphological and molecular approaches using the 18S rDNA molecular marker. However, there is a limitation with the 18S rDNA due to its slow rate of evolution. For that reason, the goals of this study were to 1) design primers for new molecular mitochondrial markers to improve the phylogenetic reconstructions of adeleorinid parasites and 2) to determine the morphological and genetic diversity of Haemogregarina infecting turtles and tortoises in Colombia. Turtles from 16 species representing six families were examined for the presence of haemoparasites. We analyzed 457 samples using PCR, and 203 of them were also analyzed by microscopy. Using a mitochondrial genome of Haemogregarina sequenced in this study, we designed primers to amplify fragments of the cytochrome oxidase I (coxI), cytochrome oxidase III (coxIII), and cytochrome b (cytb) mitochondrial markers in adeleorinid parasites. Lineages obtained from nuclear and mitochondrial molecular markers clustered according to the turtle lineages from which they were isolated. It is noteworthy that we found different evolutionary lineages within the same morphotype, which may indicate heteroplasmy and/or cryptic diversity in Haemogregarina. Due to this situation, we could not make a species delimitation, even when integrating the different lines of evidence we had in this study. However, the primers presented here are useful for diagnosis and, moreover, according to the available information, all three genes retain phylogenetic signals; thereby fragments amplified can be used in reconstructing evolutionary relationships. This effort contributes to the knowledge of the diversity of these parasites infecting continental turtles from Colombia.

Multilocus Genotyping of Sympatric Hepatozoon Species Infecting the Blood of Ontario Ranid Frogs Reinforces Species Differentiation and Identifies an Unnamed Hepatozoon Species

Intraerythrocytic gamonts of at least 2 named Hepatozoon species have been reported to infect the erythrocytes of ranid frogs in Ontario, Canada. Although gamonts of both species are morphometrically similar, the cytopathological changes that 1 of these species, Hepatozoon clamatae, causes to host erythrocytes, manifested by nuclear fragmentation, was used historically to distinguish this parasite from Hepatozoon catesbianae. Molecular characterization of these 2 Hepatozoon species has been equivocal in correlating genotype with gamont morphotype. Amplification and sequencing of multiple potential genotyping loci within the nuclear (18S ribosomal deoxyribonucleic acid [rDNA]; internal transcribed spacer 1), apicoplast (23S rDNA), and mitochondrial genomes (complete genomes, cytochrome c oxidase subunits I and III [COI and COIII], and cytochrome b) were conducted on Hepatozoon species that infect ranid frogs in Ontario. Sequence data were then used to evaluate the diversity of parasites present in these amphibian hosts and to assign genotypes to gamont morphotypes, if possible. Three distinct genotypes were identified at all loci; the data permitted the discovery of a third, formerly unrecognized Hepatozoon species in ranid frogs from Ontario. Although all genetic loci demonstrated differences between Hepatozoon species, mitochondrial COIII sequences were most suitable for genotypic differentiation of these parasites of frogs. Linking genotypes to gamont morphotypes proved impossible; genotypes identified as H. catesbianae and H. clamatae were found in infections with or without nuclear fragmentation of their host erythrocytes. This suggests that differentiating these species must rely on suitable genotyping methods for identification in the blood of their amphibian intermediate hosts.

Eimeria varia Upton, Campbell, Weigel & McKown, 1990 is a Junior Synonym of Eimeria megabubonis Upton, Campbell, Weigel & McKown, 1990

AIM

The present work aims to morphologically and molecularly characterize an Eimeria sp. recovered from an adult, captive barred owl Strix varia in Mississippi, USA. While the owl was shedding oocysts, no clinical signs of coccidiosis were observed.

MATERIALS AND METHODS

Oocysts collected from a barred owl, S. varia were isolated from feces by fecal flotation and characterized by light microscopy. The oocysts were allowed to sporulate in K₂Cr₂O₇ for 7 days and measured for comparison with previously described Eimeria species. Genomic DNA was extracted from measured oocysts and the cytochrome c oxidase subunit 1 mitochondrial gene was amplified and sequenced for comparison and phylogenetic analyses with publicly available sequence data.

RESULTS

Oocysts collected from S. varia were morphologically and molecularly consistent with all previous accounts of Eimeria megabubonis from the great horned owl Bubo virginianus and morphologically consistent with the only account of Eimeria varia from S. varia. Phylogenetic analyses grouped the E. megabubonis sequence from the present study with previously reported sequences from E. megabubonis.

CONCLUSION

Morphological and molecular data from oocysts collected in this study reveal S. varia is a host for E. megabubonis. Agreement between current data, morphological and molecular data of E. megabubonis, and morphological data from the original description of E. varia indicates E. varia is a junior synonym of E. megabubonis.

Exploiting digital droplet PCR and Next Generation Sequencing technologies to determine the relative abundance of individual Eimeria species in a DNA sample

DNA-based diagnostic assays for detecting infections with Eimeria species have been limited to providing identification and presence/absence data for samples containing oocysts. Modern technologies that generate quantitative data, such as droplet digital PCR (ddPCR) and Next Generation Sequencing (NGS), utilize a relatively short amplicon size containing sufficient species-specific variation for reliable species level identification. Targeting the cytochrome c oxidase subunit III gene in the mitochondrial genome, we established protocols using these technologies to determine the relative abundance of the number of copies/μL of Eimeria species in a sample. Samples from chickens of known and unknown Eimeria species composition were analyzed to determine the suitability of these technologies as diagnostic assays. All technologies demonstrated robust capability of identifying and quantifying the Eimeria species in samples. The new quantitative assays described herein will produce invaluable detail of Eimeria species infections for an array of situations in commercial chicken production systems, enabling further characterization of the disease profile and allowing for the development or enhancement of new intervention strategies.

Detection of Eumonospora henryae (Apicomplexa: Sarcocystidae) from Falco columbarius (Falconiformes: Aves): Comparison of host-parasite phylogram and comments on the family Sarcocystidae Poche, 1913

The genus Eumonospora Allen, 1933 (Apicomplexa: Sarcocystidae), an avian coccidia, is characterized by monosporocystic and octasporozoic oocysts without Stieda and substieda bodies. Some members of Eumonospora, which infect several raptor species, exhibit high levels of pathogenicity, making eumonosporiosis the leading cause of death in captive-bred raptors. The host specificity of these species appears to be mesostenoxenous, as evidenced by unsuccessful transmission between different orders of avian hosts. However, several studies have detected Eumonospora spp. in taxonomically distant avian hosts, indicating that some of these species may be euryxenous. In the current study, diarrheic fecal examination of a captive-bred juvenile merlin (Falconiformes: Aves) in Tokyo, Japan, was conducted, and a large number of oocysts were morphologically and molecularly identified as E. henryae (Yakimoff and Matschulsky, 1932), a coccidia species reported only in Strigiformes. This is a new recorded host for this coccidia. Phylogenetic analyses via Bayesian inference and maximum likelihood methods using concatenated genomic datasets consisting of nuclear 18S rDNA, nuclear 28S rDNA and mitochondrial cytochrome C oxidase subunit 1 gene, revealed a well-supported monophyletic clade of Eumonospora spp. belonging to the family Sarcocystidae Poche 1913, which largely corresponded to the avian host phylogram. Therefore, based on distinguishable oocyst morphology, a new subfamily, Eumonosporinae, within the family Sarcocystidae, is proposed, and a reconsideration of the definition of Sarcocystidae is suggested. Further molecular characterization of this emerging pathogen, as well as clarification of its complete life cycle, including cyst-forming ability, is required for more appropriate generic assessment.

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.

Study on the prevalence and genetic diversity of Eimeria species from broilers and free-range chickens in KwaZulu-Natal province, South Africa

This study was conducted from January to October 2018 with the objective to determine the prevalence and genetic diversity of Eimeria species in broiler and free-range chickens in KwaZulu-Natal province, South Africa. A total of 342 faecal samples were collected from 12 randomly selected healthy broiler chicken farms and 40 free-range chickens from 10 different locations. Faecal samples were screened for the presence of Eimeria oocysts using a standard flotation method. The species of Eimeria isolates were confirmed by amplification of the internal transcribed spacer 1 (ITS-1) partial region and sequences analysis. Among broiler and free-ranging chickens, 19 out of 41 pens (46.3%) and 25 out of 42 faecal samples (59.5%) were positive for Eimeria infection. Molecular detection revealed the following species: Eimeria maxima, Eimeria tenella, Eimeria acervulina, Eimeria brunetti and Eimeria mitis in all the samples screened. Similarly, polymerase chain reaction assays specific for three cryptic Eimeria operational taxonomic units were negative for all the samples. Phylogenetic analysis of the ITS-1 sequences supported species identity with the greatest variation detected for E. mitis. This study provides information on the range and identity of Eimeria species, and their genetic relatedness, circulating in commercially reared broilers and free-ranging chickens from different locations in KwaZulu-Natal province.

A Host-Specific Blocking Primer Combined with Optimal DNA Extraction Improves the Detection Capability of a Metabarcoding Protocol for Canine Vector-Borne Bacteria

Bacterial canine vector-borne diseases are responsible for some of the most life-threatening conditions of dogs in the tropics and are typically poorly researched with some presenting a zoonotic risk to cohabiting people. Next-generation sequencing based methodologies have been demonstrated to accurately characterise a diverse range of vector-borne bacteria in dogs, whilst also proving to be more sensitive than conventional PCR techniques. We report two improvements to a previously developed metabarcoding tool that increased the sensitivity and diversity of vector-borne bacteria detected from canine blood. Firstly, we developed and tested a canine-specific blocking primer that prevents cross-reactivity of bacterial primer amplification on abundant canine mitochondrial sequences. Use of our blocking primer increased the number of canine vector-borne infections detected (five more Ehrlichia canis and three more Anaplasma platys infections) and increased the diversity of bacterial sequences found. Secondly, the DNA extraction kit employed can have a significant effect on the bacterial community characterised. Therefore, we compared four different DNA extraction kits finding the Qiagen DNeasy Blood and Tissue Kit to be superior for detection of blood-borne bacteria, identifying nine more A. platys, two more E. canis, one more Mycoplasma haemocanis infection and more putative bacterial pathogens than the lowest performing kit.

The common gallinule, Gallinula galeata (Aves: Gruiformes: Rallidae), as a new host for Eimeria paludosa (Apicomplexa: Eimeriidae) in Mexico

Up to now, four coccidian species have been identified in Rallidae (Aves: Gruiformes): Eimeria mongolica, E. alakuli, E. paludosa and E. porphyrulae. Here, we described an Eimeria species, E. paludosa, from a common gallinule (Gallinula galeata) in Mexico. Oocysts were ovoid and wall pitted single-layered. A prominent micropyle was present, the oocyst residuum absent and the polar granule was present. On histological examination of tissues, endogenous stages (meronts, microgametocytes and macrogametocytes) were seen in the epithelial cells of the small intestine (upper and lower intestine). In addition to a new locality, this is the first description of E. paludosa from G. galeata and is the third description of a coccidian infecting Rallidae in the Americas.

Generalist Eimeria species in rodents: Multilocus analyses indicate inadequate resolution of established markers

Intracellular parasites of the genus Eimeria are described as tissue/host-specific. Phylogenetic classification of rodent Eimeria suggested that some species have a broader host range than previously assumed. We explore whether Eimeria spp. infecting house mice are misclassified by the most widely used molecular markers due to a lack of resolution, or whether, instead, these parasite species are indeed infecting multiple host species.With the commonly used markers (18S/COI), we recovered monophyletic clades of E. falciformis and E. vermiformis from Mus that included E. apionodes identified in other rodent host species (Apodemus spp., Myodes glareolus, and Microtus arvalis). A lack of internal resolution in these clades could suggest the existence of a species complex with a wide host range infecting murid and cricetid rodents. We question, however, the power of COI and 18S markers to provide adequate resolution for assessing host specificity. In addition to the rarely used marker ORF470 from the apicoplast genome, we present multilocus genotyping as an alternative approach. Phylogenetic analysis of 35 nuclear markers differentiated E. falciformis from house mice from isolates from Apodemus hosts. Isolates of E. vermiformis from Mus are still found in clusters interspersed with non-Mus isolates, even with this high-resolution data.In conclusion, we show that species-level resolution should not be assumed for COI and 18S markers in coccidia. Host-parasite cospeciation at shallow phylogenetic nodes, as well as contemporary coccidian host ranges more generally, is still open questions that need to be addressed using novel genetic markers with higher resolution.

Molecular and Histopathological Data on Levisunguis subaequalis Curran, Overstreet, Collins & Benz, 2014 (Pentastomida: Eupentastomida: Porocephalida: Porocephaloidea: Sebekidae: Sebekinae) from Gambusia affinis in Alabama, USA

Levisunguis subaequalis Curran, Overstreet, Collins & Benz, 2014 , was recently described from the lungs of the definitive hosts, softshell turtles, Apalone ferox (Schneider, 1783), and Apalone spinifera aspera (Agassiz, 1857) as well as the viscera of an intermediate host, the western mosquitofish, Gambusia affinis (Baird and Girard, 1853). However, the original account lacked molecular data. Furthermore, histological examination of infected host tissues in the original account of L. subaequalis did not reveal any pathological changes in the intermediate host. The present work provides a robust morphological description of the nymph and novel molecular data from the 18S and 28S ribosomal gene regions and the cytochrome c oxidase subunit 1 (COI) mitochondrial gene. Phylogenetic analyses using Bayesian inference and maximum likelihood analysis with concatenated sequence data from these 3 regions, as well as each region individually, placed the turtle pentastomid L. subaequalis as a sister clade to the crocodilian pentastomids of the genus Sebekia Sambon, 1922. While only concatenated phylogenetic analyses agreed with the currently accepted classification of the Eupentastomida and phylogenetic signal assessment indicated that the concatenated data set yielded the most phylogenetic signal, data from more taxa are still needed for robust phylogenetic inferences to be made. The intensity of infection ranged from 2 to 171 nymphs per fish, compared with the highest previously reported intensity of 6. These high-intensity infections with L. subaequalis were characterized by the nymphs occupying 5-50% of the coelomic cavity of G. affinis. However, despite this heavy parasite infection, fish exhibited minimal pathology. Observed pathology was characterized by compression or effacement of organs adjacent to the nymphs, particularly liver, swim bladder, and intestines, as well as the formation of granulomas around shed pentastomid cuticles. Nonetheless, the morphological and molecular data provided in the present work will bolster future efforts to identify this pentastomid in other hosts where pathology may be present in addition to aiding in the advancement of the field of molecular pentastomid systematics.

Isospora phainopepla n. sp. (Apicomplexa: Eimeriidae) from Phainopepla nitens (Swainson) (Passeriformes: Ptiliogonatidae) in the Joshua Tree National Park, USA

Isospora phainopepla n. sp. is described from the faeces of Phainopepla nitens (Swainson) collected in Joshua Tree National Park, California, USA. To our knowledge, there are no metazoan or protist parasites described yet from any species in the Ptiliogonatidae of the Americas. Sporulated oöcysts of the isosporan are ellipsoidal, 30-35 × 22-29 (32.9 × 25.4) μm, with a length/width (L/W) ratio 1.20-1.35 (1.30); one rice-shaped polar granule is present, but both oöcyst residuum and micropyle are absent. Sporocyts are elongate-ellipsoidal, 22-27 × 11-14 (23.9 × 12.0) μm, with L/W ratio 1.97-2.02 (2.00); prominent Stieda and sub-Stieda bodies are both present, but para-Stieda body is absent. Sporocyst residuum of many scattered granules is present and the sporozoites have prominent anterior and posterior refractile bodies. This parasite is clearly new to science and represents the first species of Isospora hosted by a New World bird species from this small family of silky flycatchers (Ptiliogonatidae). This article was registered in the Official Register of Zoological Nomenclature (ZooBank) as 7F664B0D-DF0E-4CAD-8CEA-45D79C8BBF92. This article was published as an Online First article on the online publication date shown on this page. The article should be cited by using the doi number. This is the Version of Record.

A novel metabarcoding diagnostic tool to explore protozoan haemoparasite diversity in mammals: a proof-of-concept study using canines from the tropics

Haemoparasites are responsible for some of the most prevalent and debilitating canine illnesses across the globe, whilst also posing a significant zoonotic risk to humankind. Nowhere are the effects of such parasites more pronounced than in developing countries in the tropics where the abundance and diversity of ectoparasites that transmit these pathogens reaches its zenith. Here we describe the use of a novel next-generation sequencing (NGS) metabarcoding based approach to screen for a range of blood-borne apicomplexan and kinetoplastid parasites from populations of temple dogs in Bangkok, Thailand. Our methodology elucidated high rates of Hepatozoon canis and Babesia vogeli infection, whilst also being able to characterise co-infections. In addition, our approach was confirmed to be more sensitive than conventional endpoint PCR diagnostic methods. Two kinetoplastid infections were also detected, including one by Trypanosoma evansi, a pathogen that is rarely screened for in dogs and another by Parabodo caudatus, a poorly documented organism that has been previously reported inhabiting the urinary tract of a dog with haematuria. Such results demonstrate the power of NGS methodologies to unearth rare and unusual pathogens, especially in regions of the world where limited information on canine vector-borne haemoparasites exist.

Isospora svecica sp. n. (Apicomplexa: Eimeriidae), a new species of coccidium from the white-spotted bluethroat Luscinia svecica cyanecula (Aves: Passeriformes: Muscicapidae)

Using a combination of morphological and molecular data, we describe a new apicomplexan parasite, Isospora svecica sp. n., from the white-spotted bluethroat, Luscinia svecica cyanecula, from the Czech Republic. Oocysts were found in its intestinal tract. Sporulation was exogenous and took 1-3 days. The oocysts were slightly ellipsoidal, of average size 26.17 × 20.33 μm, with a smooth bilayered wall. Micropyle, oocyst residuum, and polar granules were absent. Sporocysts were bottle-shaped, of an average size of 18.82 × 8.82 μm, with a thin, colourless wall. A conspicuous knob-like Stieda body was present. Substieda body was barely visible. Sporocyst residuum was present in the form of granules of various sizes. Sporozoites were banana-shaped and contained large anterior and small posterior refractile bodies. Partial DNA sequences of three genes were obtained from oocysts of Isospora svecica sp. n., being most closely related to other isosporans described from passerines. Little is known about the parasites of the avian family Muscicapidae, including coccidia, a highly prevalent parasitic protist group in all vertebrate classes. Only six species of the genus Isospora have so far been described in Muscicapidae, together with several "Isospora sp." that in fact most likely represent Isospora lacazei. The newly described Isospora svecica sp. n. differs morphologically from other coccidia reported from muscicapid birds, and represents the first coccidian species described from Luscinia svecica.

Babesia odocoilei and zoonotic pathogens identified from Ixodes scapularis ticks in southern Ontario, Canada

Cervid babesiosis, caused by the protozoan hemoparasite Babesia odocoilei and transmitted by the blacklegged tick Ixodes scapularis, is an emerging disease of Canadian cervids. This pathogen has not yet been described in humans. Data are lacking on the role of migratory birds in the adventitious spread of Ba. odocoilei-infected ticks, as well as on the infection status of I. scapularis in environments used by susceptible wildlife hosts. Following a high-mortality outbreak of cervid babesiosis at the Toronto Zoo [TZ], the present study was initiated to investigate Ba. odocoilei and other tick-borne pathogens of veterinary and public health importance (Borrelia burgdorferi sensu stricto (s.s.), Anaplasma phagocytophilum, Borrelia miyamotoi, and Babesia microti) in I. scapularis at three sites in southern Ontario, Canada. Blanket dragging for questing ticks yielded I. scapularis from the three sites evaluated: TZ, Point Pelee National Park, and Long Point Bird Observatory [LPBO]. Babesia odocoilei was identified in I. scapularis collected by dragging at the TZ and at LPBO. Borrelia burgdorferi s.s. was identified in I. scapularis at all three sites. Anaplasma phagocytophilum was identified in I. scapularis collected from the TZ. During the springs of 2016 and 2017, 1102 northward-migrating birds were examined for ticks at LPBO. One or more I. scapularis were found on 3.2% of birds (n = 595) in 2016, and 6.7% (n = 507) of birds in 2017. Overall, across both years, 0.2% and 0.5% of birds carried one or more I. scapularis ticks that tested PCR-positive for Ba. odocoilei and Bo. burgdorferi s.s., respectively. These data indicate that Ba. odocoilei-positive I. scapularis are found in southern Ontario, and suggest that bird-borne ticks have the potential to contribute to range expansion of both Ba. odocoilei and Bo. burgdorferi s.s. in Canada.

Paralogs vs. genotypes? Variability of Babesia canis assessed by 18S rDNA and two mitochondrial markers

Canine babesiosis caused by Babesia canis sensu stricto became an emerging disease of dogs across Europe calling for attention also in countries where it was an only rare imported disease. An easy accessibility of molecular methods and the growing amount of sequencing data led to the description of intraspecific variability in 18S rDNA sequences designated as "genotypes". Using material from a homogenous cohort of dogs with microscopically confirmed canine babesiosis caused by B. canis, we evaluated Babesia intraspecific variability and amplification sensitivity of three different genes (18S rDNA, COI, Cytb) to assess their potential as diagnostic or phylogenetic markers. In raw sequencing data obtained, we observed at least 3 ambiguous positions in up to 86% of chromatograms within the ∼560 bp fragment of 18S rDNA suggesting the existence of several, not identical copies of this gene. Our COI haplotype analysis resulted in a star-like pattern indicating a recent origin of most haplotypes, but not supporting the existence of two dominant haplotypes. Similarly, the Cytb sequences obtained from samples with all variants of 18S rDNA were identical. We corroborate previous observations from three other European countries and bring the evidence of the existence of 18S rDNA paralogs in B. canis genome replacing currently used "genotype" theory.

Molecular analysis of cox-1 and 18S rRNA gene fragments of Eimeria species isolated from endangered grouse: capercaillie (Tetrao urogallus) and black grouse (Tetrao tetrix)

This paper is the first record describing the molecular analysis of Eimeria species occurring in capercaillie (Tetrao urogallus) and black grouse (Tetrao tetrix) which inhabit northern Eurasia and are species critically endangered of extinction. Actions undertaken to protect endangered species, such as breeding individuals in closed aviaries, could allow saving those birds, but they also pose risk of accidental healing of invasive diseases, like coccidiosis. Therefore, an investigation was conducted on fecal samples collected from the capercaillies and black grouse originating from the Kirov region (Russia) and breeding centers located in Poland. Results indicate that the average prevalence of Eimeria revealed 72% (average OPG = 3548) and 80% (average OPG = 5220) in capercaillies and black grouse respectively. Most of the Eimeria spp. oocysts were non-sporulated; however, two different morphological types were observed. The phylogenetic analysis of cox-1 and 18S rRNA genes revealed the analyzed Eimeria sequences to belong to two species. In addition, it showed some similarities between both analyzed genes. Most of the sequences obtained from both grouse species coccidia belonged to one species partially homologous to the Eimeria spp. isolated from ring-necked pheasant (approx. 94 and 96% for cox-1 and 18S rRNA genes, respectively). Two strains isolated from capercaillies imported from Russia were related to turkey coccidia: E. innocua and E. dispersa (97-99% homology) in the cox-1 gene analysis and only one of them was related to those Eimeria species in the 18S rRNA gene analysis (98-99% homology).

Diagnosis and control of chicken coccidiosis: a recent update

Coccidiosis is a deadly disease that hampers chicken's productivity and welfare. Thus, the disease is a major menace to the global poultry industry. Coccidiosis which is caused by the apicomplexan parasite of the genus Eimeria has seven known species which affect the different parts of the intestinal tract of chickens. The disease which occurs by ingestion of sporulated oocyst has been associated with poor poultry management system. Mixed infection among the species of this parasite contributes to both pathogenicity and misdiagnosis of the disease. A progress in identification and diagnosis approach which cuts across pathological, morphological and molecular has been reported for this parasite. Control measures which include anticoccidial drugs, vaccines and natural products have dominated literature for this disease. However, the emergence of genetic and antigenic diversity with implication on resistance to anticoccidials among different strains of Eimeria parasite has generated concerns on the effectiveness of the current anticoccidial vaccines. A new look on the control strategy therefore becomes imperative. This study reviews the current trends on the identification and control of chicken coccidiosis with focus on (1) Avian coccidiosis (2) Epidemiology of chicken coccidiosis (3) Eimeria parasite and distribution in poultry (4) Diagnosis of Eimeria parasite (5) Control measures of coccidiosis (6) Threats posed by genetic and antigenic diversity of Eimeria parasite on coccidiosis control. Genomic study on diversity of Eimeria parasite becomes imperative for effective vaccine design against coccidiosis.

Mysteries of host switching: Diversification and host specificity in rodent-coccidia associations

Recent studies show that host switching is much more frequent than originally believed and constitutes an important driver in evolution of host-parasite associations. However, its frequency and ecological mechanisms at the population level have been rarely investigated. We address this issue by analyzing phylogeny and population genetics of an extensive sample, from a broad geographic area, for commonly occurring parasites of the genus Eimeria within the abundant rodent genera Apodemus, Microtus and Myodes, using two molecular markers. At the most basal level, we demonstrate polyphyletic arrangement, i.e. multiple origin, of the rodent-specific clusters within the Eimeria phylogeny, and strong genetic/phylogenetic structure within these lineages determined at least partially by specificities to different host groups. However, a novel and the most important observation is a repeated occurrence of host switches among closely related genetic lineages which may become rapidly fixed. Within the studied model, this phenomenon applies particularly to the switches between the eimerians from Apodemus flavicollis/Apodemus sylvaticus and Apodemus agrarius groups. We show that genetic differentiation and isolation between A. flavicollis/A. sylvaticus and A. agrarius faunas is a secondary recent event and does not reflect host-parasite coevolutionary history. Rather, it provides an example of rapid ecology-based differentiation in the parasite population.

Eimeria spp. in captive-reared corncrakes (Crex crex): results of a GeneScan assay consistent with high prevalence of infection and extra-intestinal life stages

Eimeria crecis and Eimeria nenei have been detected in association with enteric disease ("coccidiosis") in the corncrake (Crex crex: Family Rallidae, Order Gruiformes). Both parasite species are common in apparently healthy free-living corncrakes, but captive-bred juvenile birds reared for reintroduction appeared particularly susceptible to clinical coccidiosis. We investigated the occurrence and relative pathogenicity of these Eimeria species in this juvenile corncrake population and developed a diagnostic species-specific polymerase chain reaction (PCR) for their identification. PCR amplification and sequencing of 18S rDNA were performed on genomic DNA extracted from samples of corncrake intestine, liver and spleen. Sequences generated were used to design a GeneScan diagnostic PCR assay targeting a species-specific TTA indel located within the 18S rDNA - the results suggested this assay was more sensitive than the 18S rDNA/amplicon sequencing approach. Eimeria sp. DNA (consistent with Eimeria sp. infection) was detected at a high prevalence and E. crecis was the predominant species. Each Eimeria species was detected in cases with and without histological evidence of coccidiosis: parasite detection was not statistically associated with disease. In addition to intestinal tissue, liver and spleen samples were positive for Eimeria sp. DNA. Its detection in tissues other than intestine is unusual and a novel finding in corncrakes, although extra-intestinal infection occurs with closely related Eimeria species in cranes (Family Gruidae, Order Gruiformes). Eimeria sp. infection of corncrakes appears typically to be chronic, and to exhibit extra-intestinal spread: as in cranes, these characteristics may be adaptations to the host's migratory nature.

Wildlife parasitology in Australia: past, present and future

Wildlife parasitology is a highly diverse area of research encompassing many fields including taxonomy, ecology, pathology and epidemiology, and with participants from extremely disparate scientific fields. In addition, the organisms studied are highly dissimilar, ranging from platyhelminths, nematodes and acanthocephalans to insects, arachnids, crustaceans and protists. This review of the parasites of wildlife in Australia highlights the advances made to date, focussing on the work, interests and major findings of researchers over the years and identifies current significant gaps that exist in our understanding. The review is divided into three sections covering protist, helminth and arthropod parasites. The challenge to document the diversity of parasites in Australia continues at a traditional level but the advent of molecular methods has heightened the significance of this issue. Modern methods are providing an avenue for major advances in documenting and restructuring the phylogeny of protistan parasites in particular, while facilitating the recognition of species complexes in helminth taxa previously defined by traditional morphological methods. The life cycles, ecology and general biology of most parasites of wildlife in Australia are extremely poorly understood. While the phylogenetic origins of the Australian vertebrate fauna are complex, so too are the likely origins of their parasites, which do not necessarily mirror those of their hosts. This aspect of parasite evolution is a continuing area for research in the case of helminths, but remains to be addressed for many other parasitic groups.