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Despite their wide occurrence, cryptosporidiosis and giardiasis are considered neglected diseases by the World Health Organization. The epidemiology of these diseases and microsporidiosis in humans in developing countries is poorly understood. The high concentration of pathogens in raw sewage makes the characterization of the transmission of these pathogens simple through the genotype and subtype analysis of a small number of samples. The distribution of genotypes and subtypes of Cryptosporidium spp., Giardia duodenalis, and Enterocytozoon bieneusi in 386 samples of combined sewer systems from Shanghai, Nanjing and Wuhan and the sewer system in Qingdao in China was determined using PCR-sequencing tools. Eimeria spp. were also genotyped to assess the contribution of domestic animals to Cryptosporidium spp., G. duodenalis, and E. bieneusi in wastewater. The high occurrence of Cryptosporidium spp. (56.2%), G. duodenalis (82.6%), E. bieneusi (87.6%), and Eimeria/Cyclospora (80.3%) made the source attribution possible. As expected, several human-pathogenic species/genotypes, including Cryptosporidium hominis, Cryptosporidium meleagridis, G. duodenalis sub-assemblage A-II, and E. bieneusi genotype D, were the dominant parasites in wastewater. In addition to humans, the common presence of Cryptosporidium spp. and Eimeria spp. from rodents indicated that rodents might have contributed to the occurrence of E. bieneusi genotype D in samples. Likewise, the finding of Eimeria spp. and Cryptosporidium baileyi from birds indicated that C. meleagridis might be of both human and bird origins. The distribution of Cryptosporidium species, G. duodenalis genotypes and subtypes, and E. bieneusi genotypes in urban wastewater indicates that anthroponotic transmission appeared to be important in epidemiology of cryptosporidiosis, giardiasis, and microsporidiosis in the study areas. The finding of different distributions of subtypes between Shanghai and Wuhan was indicative of possible differences in the source of C. hominis among different areas in China.

Black skimmers (Rynchops niger niger) are New World coastal seabirds that breed along the Gulf of Mexico, southern Atlantic and Pacific coasts of the United States. Black skimmer populations are declining in North America, and little is known about health and diseases of this species. An outbreak of mortality causing the death of approximately 160 juvenile black skimmers occurred in the West Galveston and East Matagorda Bay populations during the 2022 and 2023 breeding seasons. Necropsy, histopathology, and molecular genetic methods were utilized to investigate the cause of morbidity in six chicks that died or were euthanized. The main gross findings included bilateral renomegaly with multiple pale tan foci. Characteristic histologic findings were granulomatous nephritis and cloacitis with intralesional coccidia. Various developmental stages including immature gamonts, microgamonts, macrogamonts, and oocysts were present extracellularly and in the cytoplasm of epithelial cells of distal tubules, medullary collecting ducts, ureters, and cloacal epithelium. A few oocysts were in the cytoplasm of multinucleated giant cells. Additionally, schizonts were observed in the small intestine of one case. Genetic analysis of partial 18S rRNA gene revealed a previously uncharacterized Eimeria lineage affecting kidney and cloaca and another Eimeria lineage affecting the small intestine. To the best of our knowledge, this is the first report of Eimeria infection in the genus Rynchops. The significance of renal and intestinal coccidiosis in black skimmers is unknown; however, in the present work it appeared to cause morbidity and likely contributed to the recent mortality outbreak.

This study presents the first molecular investigation into the prevalence and risk factors of Eimeria spp. infection among weaned dairy calves in Thessaly, Greece. Utilizing a cross-sectional design, 665 fecal samples were collected from 35 intensive dairy cattle farms and analyzed via genus-specific PCR and species-specific multiplex PCR targeting the internal transcribed spacer 1 (ITS-1) region. The overall molecular prevalence was found to be 46.3%, with Eimeria bovis (24.7%) and Eimeria zuernii (14.0%) emerging as the most prevalent species. Mixed infections were common, occurring in 51.0% of the positive cases. Multivariable analysis revealed that dairy calves aged less than 60 days had 2.15 times higher odds of infection compared to older calves. Environmental factors also significantly influenced infection rates, specifically ground flooring, the use of immovable/concrete water troughs and infrequent cleaning of floors, feeders and water troughs. These results highlight the high burden of pathogenic Eimeria in dairy cattle herds of Thessaly, Greece, and underscore the importance of integrating rigorous hygiene protocols with age-targeted management to control bovine coccidiosis.

Juvenile kiwi ( Apteryx spp.) within captive-rearing programmes commonly suffer from coccidiosis, which primarily affects the intestine but can also impact other organs, such as the kidneys, liver, lung, and spleen (Morgan  et al. Avian Pathol 42:137–146 2013 ). In some immune-compromised birds, disease causes significant morbidity and, occasionally, mortality (Morgan et al. NZVJ 62:315–320 2014 ); however, understanding of the biology of disease-causing Eimeria species in kiwi is limited. A probe-based qPCR assay targeting a 115-bp fragment of the Eimeria mitochondrial cytochrome c oxidase I (CO1) gene was developed to identify three distinct kiwi Eimeria species: the two species most commonly recovered from faeces, Eimeria kiwii and Eimeria apteryxii , as well as the newly described species, Eimeria koka (Scheltema et al. Syst Parasitol 102:30  2025 ). The qPCR assay was then applied to retrospectively analyse formalin-fixed paraffin-embedded intestine, kidney, liver, lung, and spleen tissues from ten historic post-mortem cases from kiwi diagnosed with extraintestinal coccidiosis. This novel assay detected infection more often (33/47 tissues) than manual histopathological identification (25/47 tissues). Only one species, E. koka , was detected in extraintestinal tissues with the highest prevalence (9/10) in kidney tissues. In contrast, E. kiwii was reliably detected in 8/9 intestinal tissues but was not detected in the other tissues tested. E. apteryxii was not detected in any of the tissues analysed. These findings suggest that kiwi are infected by at least one intestinal and one renal-specific species, the latter of which is suspected to disseminate under certain conditions to other organs of the body.

Coccidiosis is a common disease of camels, and camels are important for the economy of Asia and the Arabian Peninsula. Little is known regarding the prevalence of coccidian parasites in camels in Egypt. Fecal samples collected from the rectums of 200 camels at the Cairo slaughterhouse were processed using the sucrose flotation technique. Eimeria species oocysts were found in 38%. Three Eimeria species were identified: Eimeria cameli–like in 31%, Eimeria rajasthani in 18%, and Eimeria dromedarii in 14%. The morphology of E. rajasthani and E. dromedarii oocysts was identical to that in literature. However, there was great variability in size and structure among E. cameli oocysts; oocysts were 70–100 lm long and truncate to ovoid. Four morphotypes (types 1 to 4) were recognized. Types 1 and 2 oocysts had similar truncate ovoid shape and were dark brown, but their shape indices were different. Both types could be easily distinguished from type 3 (elongate ovoid and light brown). All oocysts were enclosed in a transparent outer covering (capsule), although this capsule was barely seen in types 3 and 4. An extension from the capsule situated in front of the micropyle, referred to as polar cap–like structure (PCL), was characteristic for types 1 and 2. The PCL of type 1 resembled the crown, while in type 2 it looked like a small thickening with a smooth top. The PCL was absent in types 3 and 4 oocysts. The latter was found only in a single oocyst. Experimental infections with E. cameli oocysts and molecular studies are needed to determine whether the monotypes described here are different species or strain variations or both.

Swine coccidiosis is a host-specific protozoan disease caused by Cystoisospora suis and various Eimeria species, leading to diarrhea or subclinical signs in pigs. In this study, 3296 fecal samples from 55 farms across six provinces in China were collected and examined to determine the prevalence and molecular characteristics of swine coccidia. The single oocyst isolation technique (SOIT) and molecular characterization identified nine coccidian species, with an overall infection prevalence of 13.83%. Infection rates varied by locations, host age groups, and sampling seasons. Among the positive swine coccidia samples, Cystoisospora suis showed the highest prevalence at 58.77%, followed by eight Eimeria spp . species. SOIT along with molecular characterization of C. suis at the SSU rRNA and ITS rRNA gene loci revealed the sequence homology from 99.8 to 100.0%. Additionally, the eight species of Eimeria . exhibited a high degree of sequence homology at the SSU rRNA and COX I gene loci. Due to the limitation of single molecular marker genes, this study introduced SOIT for DNA extraction, followed by nested PCR amplification of the SSU rRNA, ITS rRNA, and COX I gene loci to identify swine coccidia. This study is the first to systematically evaluate the prevalence and genetic diversity of coccidia in Chinese pig farms by SOIT, offering a method for accurately identifying swine coccidiosis and a scientific foundation for its effective prevention and control. Graphical Abstract

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.

With the Eimeria spp. populations that infect chickens used as a model for coccidian biology, we aimed to survey the transcriptome of Eimeria maxima and contrast it to the 2 other Eimeria spp. for which transcriptome data are available, i.e., Eimeria tenella and Eimeria acervulina. The asexual intracellular development stage, the merozoite, was specifically examined, and we used expressed sequence tag (EST) analysis to provide experimental evidence of transcription and a framework for understanding the merozoite stage of E. maxima. Of 2,680 individual ESTs obtained, 48.2% shared most significant (E < 10−5) homology to sequences from other apicomplexan species, primarily other Eimeria spp. and Toxoplasma gondii, and 47.5% were unique. Annotation of these ESTs enabled categorization to putative biological function and revealed an emphasis on translation, cytoskeleton, metabolism, signaling, transport, and protein folding, as well as the apicomplexan specific surface antigens and micronemes. Comparative analysis of abundantly expressed transcripts from merozoites of the 3 Eimeria spp. revealed a novel transcript common to all 3. Sharing no significant homology to any other sequence in public databases, this transcript was predicted to encode an Eimeria-specific protein (ESP) with 166–178 amino acids and 58.9–65.1% interspecific identity. A predicted signal peptide was identified, consistent with the assumption that ESP is a secreted protein. These annotated ESTs from E. maxima merozoites provide a resource for intra- and interspecific comparative analyses that will be useful in distinguishing the unique biology of coccidian parasites in relation to the diverse phylum of Apicomplexa.

Pigeon coccidiosis caused by Eimeria spp. is an important veterinary disease with a significant economic impact on the pigeon industry. Preventive measures for Eimeria columbarum in pigeons have been hampered by the lack of extensive genetic, morphological, and biological data on the oocysts. In this study, we examined the prevalence and identity of Eimeria spp. in domestic pigeons from seven cities in Guangdong Province, China. Data show that coccidiosis was prevalent in domestic pigeons in Guangdong Province, with an overall Eimeria spp. detection rate of 73.4%. Five Eimeria species were identified, including E. columbarum (73.4%), Eimeria kapotei (25.6%), Eimeria labbeana (19.6%), Eimeria duculai (19.6%), and Eimeria tropicalis (6.7%). We obtained single oocyst-derived lines of the dominant E. columbarum from fecal specimens. E. columbarum oocysts measured 20.06 ± 0.69 μm × 18.63 ± 1.03 μm, and sporocysts measured 10.29 ± 0.82 μm × 85.38 ± 0.46 μm. In infection experiment using obtained E. columbarum isolates, 60-day-old coccidia-free pigeons exhibited a prepatent period of 105 h and patent period of 9-10 days followed by severe diarrhea, depression, anorexia, and emaciation. Endogenous development of the parasite was observed mainly in the cytoplasm of epithelial cells in the duodenum, jejunum, ileum, and rectum. Two generations of meronts developed on days 3 and 4 after infection, respectively, while gamont and gamete developed on day 5 after infection. The morphological, genetic, and biological data are expected to be useful in elucidating the biological characterization of pigeon coccidiosis to develop measures against the treatment and containment of this disease.

Forty-nine olive-backed pocket mice, Perognathus fasciatus were collected during 2011 and 2012 from 4 sites in Wyoming and examined for coccidian parasites. Fifteen (31%) were found to be passing oocysts of a new species of Eimeria Schneider, 1875. Sporulated oocysts of Eimeria fasciata n. sp. are ellipsoidal to ovoidal, 23.3 × 20.7 (19–27 × 17–25) µm, with a shape index of 1.1; they typically contain a single, smooth, bubble-like oocyst residuum. Oocysts possess 1–2 polar granules, lack a micropyle, and are bilayered with a thickness of 1.3 µm. Sporocysts are ovoidal, 10.0 × 8.2 (8–12 × 7–10) µm, with a shape index of 1.2; they contain a sporocyst residuum that appears similar to a cluster of 1–8 grapes. The Stieda body is small, appearing flattened to knobby, and there are no subStieda or paraStieda bodies. This new eimerian represents the only coccidian, to date, reported from P. fasciatus, as well as the only species from any heteromyid rodent in Wyoming.