Targeting single-nucleotide polymorphisms in the 18S rRNA gene to differentiate Cyclospora species from Eimeria species by multiplex PCR

Morphological and molecular characterization of Eimeria magna infecting local rabbit (Oryctolagus cuniculus) in Alkarg City, Saudi Arabia

Coccidiosis is one of the most prevalent diseases found in local rabbits (Oryctolagus cuniculus), which is caused by the Eimeria. The study aimed to more reliably identify Eimeria species (Eimeria magna) infecting Local Rabbits in Alkarg City, Saudi Arabia, based the method on the molecular properties and morphological and molecular biological techniques. Sub-spheroidal oocysts measuring 21-27 × 12-16 (24 × 14.4) μm (20 n) and with a length/width (L/W) ratio of 0.9-1.1 (1.0) were identified by microscopic analysis of a fecal sample. Oocysts feature a bi-layered wall that is 1.0-1.2 (1.1) μm thick. About two-thirds of the wall's thickness is made up of a smooth outer layer. A polar granule is present, but neither a micropyle nor an oocyst residuum is present. The ovoidal sporozoites measure 15-18 × 8-11 (16.5 × 9.5) μm, have an L/W ratio of 1.6-1.8 (1.7), and take up around 21% of the oocyst's total surface. The mean size of the sub-Stieda body is 1.4 × 2.3 μm, while the average size of the Stieda body is 0.9 × 1.8 μm. The para-Stieda body is lacking. Sporocyst residuum appears membrane-bound and has an uneven form made up of several granules. With two refractile bodies below the striations and pronounced striations at the more pointed end, sporozoites are vermiform, measuring an average of 11.6 × 4.0 μm. The results of the sequencing for the 18S rDNA gene confirmed the species of Eimeria parasites found in the host (rabbits). The current parasite species is closely related to the previously described and deposited E. magna and deeply embedded in the genus Eimeria (family Eimeriidae). According to the findings, single oocyst molecular identification of Eimeria may be accomplished through consistent use of the morphological and molecular results. It is possible to draw the conclusion that the current research supplies relevant facts that help assess the potential infection and future control measures against rabbit coccidiosis to reduce the financial losses that can be incurred by the rabbit industry in Saudi Arabia.

Morphological and molecular identification of Eimeria rajasthani (coccidia: Eimeriidae) in the dromedary camel (Camelus dromedarius) in Riyadh, Saudi Arabia

Introduction

Coccidiosis is a serious parasitic disease in camels caused by an intestinal protozoan parasite of the genus Eimeria, which is linked to significant causes of reduced milk and meat production. In Saudi Arabia, scare literature focused on the coprological investigation of dromedary camels (Camelus dromedarius). To determine the taxonomic status of camel parasite species, we performed morphological characterization of oocysts and genetic analysis (18S rRNA and ITS-1 gene regions) of Eimeria species collected from camels in Riyadh, Saudi Arabia.

Methods

A total of 150 faecal samples were obtained from camels at the old camel market. These samples were tested for the presence of Eimeria oocysts using the conventional floatation technique before being sporulated in a 2.5% potassium dichromate solution. Eimeria oocysts were morphologically and molecularly examined and identified, and the infection rate of parasitic infections was determined.

Results

Our findings revealed that the overall frequency of oocysts was 30%. The identified species was Eimeria rajasthani, which had a typical ellipsoidal oocyst shape. Oocystic polar granule, micropyle, micropylar cap, and oocyst residuum are not visible. Sporocysts are oval with stieda body. Sporocyst residuum contains many granules and sporozoites with refractile bodies and nuclei. Genetic analyses of the sequence data from the partial 18S rRNA and ITS-1 gene regions revealed that the sequences obtained from E. rajasthani oocysts are related to DNA sequences reported from E. lamae from the Alpaca from China, particularly the 18S rRNA sequences.

Conclusion

This study emphasized the need to use molecular phylogenetic tools to describe camel intestinal coccidian parasites with traditional morphology-based approaches to better understand their biology. For camel husbandry and disease control, more studies should be conducted to better understand the epidemiology of these protozoan parasites.

Effects of supplementing direct-fed microbials on health and growth of preweaning Gyr × Holstein dairy calves

This study aimed to evaluate the effects of direct-fed microbials (DFM) on health and growth responses of preweaning Bos indicus × Bos taurus (Gyr × Holstein) crossbred calves. Ninety newborn heifer calves (initial BW of 35 ± 4.0 kg) were used. At birth, calves were ranked by initial BW and parity of the dam and assigned to: (1) whole milk without DFM supplementation (CON; n = 30), (2) whole milk with the addition of 1.0 g/calf per day of a Bacillus-based DFM (BAC; n = 30), or (3) whole milk with the addition of 1.0 g/calf per day of BAC and 1.2 g/calf per day of Enterococcus faecium 669 (MIX; n = 30). Milk was fed individually during the study (77 d), and the BAC and MIX treatments were offered daily throughout the 77-d preweaning period. All calves were offered a starter supplement and corn silage starting on d 1 and 60 of age, respectively. Milk and starter supplement intake were evaluated daily, and BW was recorded on d 0 and at weaning (d 77). Diarrhea and pneumonia were assessed daily, and fecal samples were collected on d 0, 7, 14, 21, and at weaning (d 77) for assessment of the presence of bacterial and protozoal pathogens via qPCR. All data were analyzed using SAS (v. 9.4) with calf as the experimental unit and using single-df orthogonal contrasts (BAC + MIX vs. CON; BAC vs. MIX). Daily feeding of DFM, regardless of type, improved weaning BW. Odds ratio for occurrence of pneumonia was lower for DFM-supplemented calves, but its occurrence did not differ between BAC and MIX calves. No Salmonella spp. or Escherichia coli F41 were detected in any of the calves. The proportion of calves positive for E. coli F17 was greater for DFM calves on d 7 (92% and 96% vs. 81% for BAC, MIX, and CON, respectively), on d 21 (13% and 26% vs. 7% for BAC, MIX, and CON, respectively), and at weaning (48% and 35% vs. 22% for BAC, MIX, and CON, respectively). For Clostridium difficile, more DFM calves were positive on d 7 (65% and 30% vs. 35% for BAC, MIX, and CON, respectively) and 14 (20% and 28% vs. 7% for BAC, MIX, and CON, respectively), but proportion of positive calves was also greater for BAC versus MIX on d 7. More CON calves were positive for Clostridium perfringens on d 14 (14% vs. 3% and 8% for CON, BAC, and MIX, respectively) compared with DFM-fed calves. Incidence of calves positive for C. perfringens was greater in BAC than MIX on d 7 (50% vs. 18%), and greater for MIX than BAC at weaning (9% vs. 0%). For protozoa occurrence, a lower proportion of DFM calves were positive for Cryptosporidium spp. on d 7 (58% and 48% vs. 76% for BAC, MIX, and CON, respectively), but opposite results were observed on d 21 for Cryptosporidium spp. (3% and 11% vs. 0% for BAC, MIX, and CON, respectively) and Eimeria spp. on d 14 (7% and 8% vs. 0% for BAC, MIX, and CON, respectively) and 21 (50% and 59% vs. 38% for BAC, MIX, and CON, respectively). In summary, DFM feeding alleviated the occurrence of pneumonia and improved growth rates, while also modulating the prevalence of bacteria and protozoa in preweaning Gyr × Holstein calves.

Morphology, morphometry, and phylogeny of the protozoan parasite, Eimeria labbeana-like (Apicomplexa, Eimeriidae), infecting Columba livia domestica

Introduction

Eimeria spp. are intracellular protozoan parasites of the phylum Apicomplexa causing economic losses to various wild and domestic animals. An eimerian species infecting Columba livia domestica was identified in this study.

Methods

A total of 15 faecal samples were examined by floatation technique, a prevalence rate of 60% was reported. Eimerian oocysts were sporulated in 2.5% potassium dichromate solution then identified using morphological and molecular (DNA amplification of the 18S rRNA and ITS-1 genes) diagnostic techniques.

Results

Sporulated oocysts were identified as Eimeria labbeana-like, after morphometry with typical bi-layered wall with spherical to subspherical oocysts morphology. A polar granule is present, but no micropyle or oocyst residuum. Sporocysts are elongated ovoidal with stieda body. Sporocyst residuum with many granules and sporozoites with refractile bodies and nucleus. Both 18S rRNA and ITS-1 sequences have been deposited in GenBank database. DNA sequences from the partial 18S rRNA generated from the oocysts were found to be related to eimerian and isosporan parasites found in domestic pigeons. For the first time, ITS-1 sequences for E. labbeana-like were provided.

Conclusion

The necessity of using molecular techniques to describe pigeon intestinal coccidian parasites in conjunction with traditional morphology-based tools was emphasized in this work in order to understand the biology of such parasites.

Identification of Eimeria acervulina (Apicomplexa: Eimeriidae) infecting the broiler chicken Gallus gallus domesticus through morphology and molecular analyses

Coccidiosis is an intestinal protozoan disease that affects the poultry industry worldwide. The severity of this disease varies depending on the identity of the infectious agents. Therefore, this study was carried out to identify the Eimeria species that affect broiler chickens, Gallus gallus domesticus, through morphological and molecular phylogenetic analyses. Twenty-five faecal samples were collected from the broiler chickens in a commercial poultry farm in Riyadh (Saudi Arabia). Using the floatation technique, faeces were examined microscopically for the Eimeria occurrence. Identification of Eimeria species was performed based on morphological criteria and molecular tools (DNA amplification for the partial small subunit ribosomal RNA (18S rRNA), internal transcribed spacer (ITS)-1, and mitochondrial cytochrome c oxidase I (COI) genes. In this study, 32% (8 out of 25) of collected samples were found to be positive for coccidiosis. After sporulation in potassium dichromate (K2Cr2O7), the sporulated oocysts were observed as ovoid and measured 18.37-23.19 µm (19.87) long and 15.07-18.67 µm (16.46) wide, with the anterior location of a polar granule and absence of micropyle. These Eimeria oocysts were assumed to size and shape characteristics of Eimeria acervulina. Molecular analysis was conducted on the sequences of the polymerase chain reaction products from the three genes studied (18S rRNA, ITS-1, and COI). At the three genes, results showed that the resultant sequences clustered with E. acervulina from different regions confirming morphological description. This study highlighted the importance of molecular techniques to detect avian Eimeria species more than the traditional morphology-based tool to optimise the appropriate anticoccidial strategies for long-term control in the studied area.

Identification of sheep eimerian parasites, Eimeria crandallis and Eimeria faurei, employing microscopic and molecular tools

Coccidiosis, caused by apicomplexan Eimeria species, is a protozoan disease that affects various species of wild and domestic animals. However, data available on Eimeria diversity in ruminants in Saudi Arabia is meagre. Therefore, this study was designed to investigate some eimerian parasites infecting sheep (Sawakni and Harrie breeds) using microscopy and molecular methods for the first time in Saudi Arabia. Twenty-four fecal samples were collected from sheep farms. Based on the floatation technique, eimerian oocysts were observed in 8 of the 24 (33.33%) fecal samples. The coccidian-positive samples were subjected to fecal culture in a shallow layer of 2.5% potassium dichromate (K2 Cr2 O7 ). Detected eimerian oocysts were described micromorphometrically as the basis for traditional oocyst identification. Morphologically, the sporulated oocysts were similar to those of sheep eimerian parasies; Eimeria faurei and Eimeria crandallis. PCR products from the two eimerian species detected from Sawakni and Harrie breeds were sequenced and were found to be distinct from each other with mutations at five positions. One of them clustered with E. crandallis with 99.8%-100% identity with sequences available in GenBank. E. crandallis was obtained from two Sawakni sheep and two Harrie sheep. The other sequences grouped with E. faurei with 99.8% identity with the only sequences available in GenBank. E. crandallis was detected from both Sawakni and Harrie breeds whereas E. faurei was detected only from Sawakni sheep. The findings of this study have implications for the importance of morphometric identification with advanced molecular tools to confirm the identities of sheep Eimeria species and to address the taxonomic study of this eimeriid parasite at the species level.

Detection of Cyclospora cayetanensis, Echinococcus multilocularis, Toxocara spp. and microsporidia in fresh produce using molecular methods: - A review

The current trend for a healthy lifestyle corresponds with a healthy diet, which is associated with regular and frequent consumption of raw fruit and vegetables. However, consumption of ready-to-eat (RTE) food without heat treatment or sufficient washing may pose a risk to consumers. Among the well-known protozoan parasites associated with RTE food and water are Cryptosporidium spp., Giardia duodenalis and Toxoplasma gondii. These belong among prioritized parasitic pathogens, as they are associated with numerous disease outbreaks in humans all around the world. Nevertheless, other parasitic agents such as Cyclospora cayetanensis, Toxocara cati, Toxocara canis, Echinococcus multilocularis and zoonotic microsporidia should not be neglected. Although these selected parasites belong to phylogenetically diverse groups, they have common characteristics associated with fresh produce and each of them poses a health risk to humans. Ensuring healthy food is produced requires the standartization of laboratory methods for the detection of parasitic agents. This article reviews the molecular methods currently used in laboratories for detection of Cyclospora cayetanensis, Toxocara cati, Toxocara canis, Echinococcus multilocularis and zoonotic microsporidia in fresh produce.

Subterranean Waters of Yucatán Peninsula, Mexico Reveal Epigean Species Dominance and Intraspecific Variability in Freshwater Ostracodes (Crustacea: Ostracoda)

The Yucatán Peninsula is a karstic region, rich in subterranean environments with a diverse crustacean stygobiont fauna. In order to gain insights into the biological evolution of the subterranean environments of this region, we evaluated the ostracode species composition of caves and cenotes in five independent sampling campaigns (2008, 2013, 2017–2019). Using morphometric analyses, we evaluated inter-population morphological variability; using molecular analysis based on mitochondrial COI and nuclear 18S rDNA, we evaluated genetic differentiation in selected species. The observed fauna is composed of 20 (epigean) species, presenting a lack of strict stygobionts. Morphometric analyses discriminated up to three morphotypes in each of the three most abundant species: Cytheridella ilosvayi, Alicenula sp. and Cypridopsis vidua. High intraspecific morphological variability was found either in shape or size. Phylogenetic analysis based on COI demonstrated the existence of three lineages on C. ilosvayi, with high support (>0.9). The 18S rDNA sequences were identical among individuals of different populations. A lack of congruence between the genetic markers precluded us from postulating speciation in subterranean environments. It is likely that Late Pleistocene—Early Holocene climate variation related to sea level and precipitation was forcing agent for epigean ostracode dominance in subterranean environments of the Peninsula.

A novel coccidian (Apicomplexa: Eimeriidae) from Scotophilus leucogaster (Chiroptera: Vespertilionidae) in southern Saudi Arabia

A novel species of coccidia, resembling a member of the genus Eimeria, was found in bats, Scotophilus leucogaster, collected in southern Saudi Arabia has been described on the basis of unsporulated oocysts and DNA sequencing of the Internal Transcribed Spacer 1 (ITS1) and partial 18S rDNA regions. Unsporulated oocysts of this form are ovoidal to spheroidal and had a 2-layered wall, 1.5-2.0 (1.9 ± 0.2); the outer layer was light blue with striations, and thicker than the inner, darker layer. No micropyle was present. Unsporulated oocysts (N = 150) measured 27.2 × 22.1 (25-30 × 20-25), length width ratio, 1.2 (1.1-1.4). There was no evidence of an oocyst residuum and/or polar granule. This parasite was detected in 2/7 (29%) S. leucogaster collected from southern Saudi Arabia. Oocysts incubated at 25 °C in 2.5% K₂Cr₂O₇ did not sporulate after > 1 month. Unsporulated oocyst measurements were compared with other coccidian parasites of bats that discharge oocysts in their feces. Sequences of the ITS1 and the 18S rDNA regions obtained from the unsporulated oocysts grouped this coccidium from S. leucogaster with eimerian species from various rodent and squirrel species. It is critical that future investigators obtain fully sporulated oocysts of this coccidium for full description of the parasite recovered in our study so it can be correctly assigned to genus and given an accurate binomial.

Diagnosis of sub-clinical coccidiosis in fast growing broiler chickens by MicroRNA profiling

Coccidiosis in broiler chickens, caused by infection with Eimeria spp. remains one of the most economically important production diseases. Development of a genetic biomarker panel of sub-clinical infection would be an important biological tool for the management of broiler flocks. We analysed expression of MicroRNAs (miRNAs) to determine the potential for these in diagnosing coccidiosis in broiler flocks. miRNA expression, in the ilea of Ross 308 broilers, was compared between chickens naturally clinically or sub-clinically infected with Eimeria maxima and Eimeria acervulina using NextSeq 500 sequencing. 50 miRNAs with greatest coefficient of variance were determined and principal component analysis showed that these miRNAs clustered within the clinical and sub-clinical groups much more closely than uninfected controls. Following false detection rate analysis and quantitative PCR we validated 3 miRNAs; Gallus gallus (gga)-miR-122-5p, gga-miR-205b and gga-miR-144-3p, which may be used to diagnose sub-clinical coccidiosis.

A Molecular Tool for Rapid Detection and Traceability of Cyclospora cayetanensis in Fresh Berries and Berry Farm Soils

Due to recent outbreaks of cyclosporiasis associated with consumption of fresh berries, producers are demanding modern microbiological tools for the rapid and accurate identification of the human pathogen Cyclospora cayetanensis in berries and environmental samples. The aim of the present work was to develop a molecular tool based on a PCR approach for the rapid and accurate detection of C. cayetanensis. A nested PCR assay was validated for the amplification of a 294 bp size region of the 18S rRNA gene from C. cayetanensis. The limit of detection for the nested PCR assay was validated using 48 berry samples spiked with ~0, 10, 100, and 1000 oocyst per gram of sample. With this assay, it was possible to detect as few as 1 oocyst per gram of berry, in a 50 g sample. Sanger DNA sequencing and phylogenetic analysis were carried out to confirm the presence of C. cayetanensis in berry (n = 17) and soil (n = 5) samples. The phylogenetic analysis revealed that the C. cayetanensis sequences obtained from Mexico clustered within a group recovered from China, Peru, Guatemala-Haiti, and Japan. The PCR protocol designed in the present study could be an important tool for the rapid and accurate detection of this human pathogen in environmental and food samples.

Eimeria tamimi sp. n. (Apicomplexa: Eimeriidae) from the rock hyrax (Procavia capensis jayakari) in central Saudi Arabia

Faecal samples from the rock hyrax (Procavia capensis jayakari Thomas) were collected from the Ibex Reserve in central Saudi Arabia. Eimerian oocysts, which are believed to represent a new species described here as Eimeria tamimi sp. n., were detected in 40 out of 93 samples. Oocysts were fully sporulated in 24-48 hours at 25 ± 2 °C. Sporulated oocysts of E. tamimi sp. n. were ovoid, measuring 35-42 × 19-25 μm (39 × 23 μm), a length/width ratio 1.5-2 (1.7). Oocyst wall was bilayered and measured 1.5 μm in thickness. Micropyle, oocyst residuum and polar granules were not present. Sporocysts are elongate, measuring 12-18 × 9-12 μm (15 × 10 μm), with a length/width ratio 1.1-1.8 (1.5) prominent Stieda bodies and sporocyst residuum. Experimental infection of two clinically healthy rock hyraxes with sporulated oocysts of E. tamimi sp. n. resulted in shedding unsporulated oocysts 5-10 days post infection. Partial sequences of 18S ribosomal RNA (18S rDNA) and cytochrome C oxidase subunit 1 (COI) regions were amplified using the polymerase chain reaction (PCR) and sequenced. Phylogenetic analysis based on 18S rDNA using maximum likelihood (ML) and Bayesian inference (BI) methods revealed that E. tamimi sp. n. grouped with Eimeria quokka Barker, O'Callaghan et Beveridge, 1988, E. mundayi Barker, O´Callaghan et Beveridge, 1988, E. potoroi Barker, O'Callaghan et Beveridge, 1988 and E. gaimardi Barker, O'Callaghan et Beveridge, 1988 marsupials. Eimerian species have been regarded as a paraphyletic group and the present investigation confirmed the conflict between phenotypic traits, used widely in the classification of this group of parasites.

Evaluation of an Improved U.S. Food and Drug Administration Method for the Detection of Cyclospora cayetanensis in Produce Using Real-Time PCR

Cyclospora cayetanensis is a protozoan parasite that causes human diarrheal disease associated with the consumption of fresh produce or water contaminated with C. cayetanensis oocysts. In the United States, foodborne outbreaks of cyclosporiasis have been linked to various types of imported fresh produce, including cilantro and raspberries. An improved method was developed for identification of C. cayetanensis in produce at the U.S. Food and Drug Administration. The method relies on a 0.1% Alconox produce wash solution for efficient recovery of oocysts, a commercial kit for DNA template preparation, and an optimized TaqMan real-time PCR assay with an internal amplification control for molecular detection of the parasite. A single laboratory validation study was performed to assess the method's performance and compare the optimized TaqMan real-time PCR assay and a reference nested PCR assay by examining 128 samples. The samples consisted of 25 g of cilantro or 50 g of raspberries seeded with 0, 5, 10, or 200 C. cayetanensis oocysts. Detection rates for cilantro seeded with 5 and 10 oocysts were 50.0 and 87.5%, respectively, with the real-time PCR assay and 43.7 and 94.8%, respectively, with the nested PCR assay. Detection rates for raspberries seeded with 5 and 10 oocysts were 25.0 and 75.0%, respectively, with the real-time PCR assay and 18.8 and 68.8%, respectively, with the nested PCR assay. All unseeded samples were negative, and all samples seeded with 200 oocysts were positive. Detection rates using the two PCR methods were statistically similar, but the real-time PCR assay is less laborious and less prone to amplicon contamination and allows monitoring of amplification and analysis of results, making it more attractive to diagnostic testing laboratories. The improved sample preparation steps and the TaqMan real-time PCR assay provide a robust, streamlined, and rapid analytical procedure for surveillance, outbreak response, and regulatory testing of foods for detection of C. cayetanensis.

Multiplex-Touchdown PCR to Simultaneously Detect Cryptosporidium parvum, Giardia lamblia, and Cyclospora cayetanensis, the Major Causes of Traveler's Diarrhea

This study aimed to develop a multiplex-touchdown PCR method to simultaneously detect 3 species of protozoan parasites, i.e., Cryptosporidium parvum, Giardia lamblia, and Cyclospora cayetanensis, the major causes of traveler’s diarrhea and are resistant to standard antimicrobial treatments. The target genes included the Cryptosporidium oocyst wall protein for C. parvum, Glutamate dehydrogenase for G. lamblia, and 18S ribosomal RNA (18S rRNA) for C. cayetanensis. The sizes of the amplified fragments were 555, 188, and 400 bps, respectively. The multiplex-touchdown PCR protocol using a primer mixture simultaneously detected protozoa in human stools, and the amplified gene was detected in >1×10³ oocysts for C. parvum, >1×10⁴ cysts for G. lamblia, and >1 copy of the 18S rRNA gene for C. cayetanensis. Taken together, our protocol convincingly demonstrated the ability to simultaneously detect C. parvum, G. lamblia, and C. cayetanenesis in stool samples.

Molecular testing for clinical diagnosis and epidemiological investigations of intestinal parasitic infections

Over the past few decades, nucleic acid-based methods have been developed for the diagnosis of intestinal parasitic infections. Advantages of nucleic acid-based methods are numerous; typically, these include increased sensitivity and specificity and simpler standardization of diagnostic procedures. DNA samples can also be stored and used for genetic characterization and molecular typing, providing a valuable tool for surveys and surveillance studies. A variety of technologies have been applied, and some specific and general pitfalls and limitations have been identified. This review provides an overview of the multitude of methods that have been reported for the detection of intestinal parasites and offers some guidance in applying these methods in the clinical laboratory and in epidemiological studies.

Molecular characterization of clinical isolates of Cyclospora cayetanensis from patients with diarrhea in India

PURPOSE

Cyclospora cayetanensis is an intestinal coccidian protozoan that has emerged as an important cause of both epidemic and endemic protracted diarrhea worldwide. Though humans appear to be the only natural hosts; the role of animals as natural reservoir is uncertain but of increasing concern. The present study aimed to study the prevalence of coccidian in different groups such as immunocompromised, clinically apparent immunocompetent and healthy individuals. Also, the study isolates were assessed for heterogeneity among the sequences.

MATERIALS AND METHODS

Stool samples from different groups of patients were collected. The parasite was detected in stool by different diagnostic tools such as light microscopy and nested PCR-restriction fragment length polymorphism using 18S ribosomal RNA as the target gene.

RESULTS

The prevalence of C. cayetanensis was 2.4% (19/800) in the present study. The PCR assay amplified Cyclospora cayetanensis DNA in only 89% (17/19) isolates. Further, sequencing revealed no significant difference among the study isolates and the non-primates. Phylogenetic analysis of the study isolates however, formed two clusters. While one cluster showed close evolutionary association with the C. cayetanensis strains, the other cluster showed evolutionary association with the two non-primate species.

CONCLUSION

The methods described here for detection of C. cayetanensis oocysts are simple, efficient, specific, and sensitive and therefore can be effectively applied for laboratory diagnosis and environmental assessment of fresh produce and water sources. Clinicians should include Cyclospora infection in the differential diagnosis of prolonged or relapsing diarrheal illness even in clinically apparent immunocompetent individuals.

Taxonomic resolutions based on 18S rRNA genes: a case study of subclass copepoda

Biodiversity studies are commonly conducted using 18S rRNA genes. In this study, we compared the inter-species divergence of variable regions (V1-9) within the copepod 18S rRNA gene, and tested their taxonomic resolutions at different taxonomic levels. Our results indicate that the 18S rRNA gene is a good molecular marker for the study of copepod biodiversity, and our conclusions are as follows: 1) 18S rRNA genes are highly conserved intra-species (intra-species similarities are close to 100%); and could aid in species-level analyses, but with some limitations; 2) nearly-whole-length sequences and some partial regions (around V2, V4, and V9) of the 18S rRNA gene can be used to discriminate between samples at both the family and order levels (with a success rate of about 80%); 3) compared with other regions, V9 has a higher resolution at the genus level (with an identification success rate of about 80%); and 4) V7 is most divergent in length, and would be a good candidate marker for the phylogenetic study of Acartia species. This study also evaluated the correlation between similarity thresholds and the accuracy of using nuclear 18S rRNA genes for the classification of organisms in the subclass Copepoda. We suggest that sample identification accuracy should be considered when a molecular sequence divergence threshold is used for taxonomic identification, and that the lowest similarity threshold should be determined based on a pre-designated level of acceptable accuracy.

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.

Detection of Cyclospora, Cryptosporidium, and Giardia in ready-to-eat packaged leafy greens in Ontario, Canada

Numerous foodborne outbreaks of diarrheal illness associated with the consumption of produce contaminated with protozoan parasites have been reported in North America in recent years. The present study reports on the presence of Cyclospora, Cryptosporidium, and Giardia in precut salads and leafy greens purchased at retail in Ontario, Canada. A total of 544 retail samples were collected between April 2009 and March 2010 and included a variety of salad blends and individual leafy greens. Most of these products were grown in the United States, with some from Canada and Mexico. Parasites were eluted and concentrated before detection by PCR and immunofluorescence microscopy. DNA sequences were aligned with reference sequences in GenBank. Cyclospora spp. were identified by PCR-restriction fragment length polymorphism in nine (1.7 % ) samples and by DNA sequence analysis. Cryptosporidium spp. were identified in 32 (5.9%) samples; 29 were sequenced and aligned with the zoonotic species Cryptosporidium parvum. Giardia duodenalis was identified in 10 (1.8%) samples, and of the 9 samples successfully sequenced, 7 aligned with G. duodenalis assemblage B and 2 with assemblage A, both of which are also zoonotic. The presence of Cryptosporidium oocysts and Giardia cysts was confirmed in some of the PCR-positive samples using microscopy, while Cyclospora -like oocysts were observed in most of the Cyclospora PCR-positive samples. The relatively high prevalence of these parasites in packaged salads and leafy greens establishes a baseline for further studies and suggests a need for additional research with respect to the possible sources of contamination of these foods, the determination of parasite viability and virulence, and means to reduce foodborne transmission to humans.

Diarrhea outbreak during U.S. military training in El Salvador

Infectious diarrhea remains a major risk to deployed military units worldwide in addition to their impact on travelers and populations living in the developing world. This report describes an outbreak of diarrheal illness in the U.S. military’s 130^th Maneuver Enhancement Brigade deployed in San Vicente, El Salvador during a training and humanitarian assistance mission. An outbreak investigation team from U.S. Naval Medical Research Unit – Six conducted an epidemiologic survey and environmental assessment, patient interviews, and collected stool samples for analysis in an at risk population of 287 personnel from May 31^st to June 3^rd, 2011. Personnel (n = 241) completed an epidemiological survey (87% response rate) and 67 (27%) reported diarrhea and/or vomiting during the past two weeks. The median duration of illness was reported to be 3 days (IQR 2–4 days) and abdominal pain was reported among 30 (49%) individuals. Presentation to the medical aid station was sought by (62%) individuals and 9 (15%) had to stop or significantly reduce work for at least one day. Microscopy and PCR analysis of 14 stool samples collected from previously symptomatic patients, Shigella (7), Cryptosporidium (5), and Cyclospora (4) were the most prevalent pathogens detected. Consumption of food from on-base local vendors (RR = 4.01, 95% CI = 1.53–10.5, p-value <0.001) and arriving on base within the past two weeks (RR = 2.79, 95% confidence [CI] = 1.35–5.76, p-value = 0.001) were associated with increased risk of developing diarrheal disease. The risk of infectious diarrhea is great among reserve military personnel during two week training exercises. The consumption of local food, prepared without proper monitoring, is a risk factor for deployed personnel developing diarrheal illness. Additional information is needed to better understand disease risks to personnel conducting humanitarian assistance activities in the Latin America Region.

Development of allele-specific single-nucleotide polymorphism-based polymerase chain reaction markers in cytochrome oxidase I for the differentiation of Bactrocera papayae and Bactrocera carambolae (Diptera: Tephritidae)

Differentiation of Bactrocera papayae Drew & Hancock and Bactrocera carambolae Drew & Hancock (Diptera: Tephritidae) based on morphological characters has often been problematical. We describe here a single-nucleotide polymorphism (SNP)-based polymerase chain reaction (PCR) assay to differentiate between these two species. For detection of SNPs, fragments derived from each species were amplified using two primer pairs, COIF/COIR and UEA7/UEA10, sequenced, and aligned to obtain a contiguous 1,517-bp segment. Two new sets of primers were designed based on the 11 SNPs identified in the region. Results of the SNP-PCR test using any one of these species-specific primer sets indicate that these two species could be differentiated on basis of presence or absence of a band in the gel profile. We also tested the SNP-PCR primers on Bactrocera umbrosa F., Bactrocera cucurbitae Coquillett, Bactrocera latifrons Hendel, and Bactrocera tau (Walker) but did not detect any band in the gel, indicating the likelihood of a false positive for B. papayae is nil. This SNP-PCR method is efficient and useful, especially for immature life stages or when only adult body parts of the two species are available for identification, as encountered often in quarantine work.

Update on Cyclospora cayetanensis, a food-borne and waterborne parasite

The coccidian parasite Cyclospora cayetanensis is recognized as an emerging pathogen that causes protracted diarrhea in humans. The first cases of Cyclospora infection were reported in the late 1970s and were observed among expatriates and travelers in regions where infections are endemic. Since then, Cyclospora has been considered a cause of traveler's diarrhea. Epidemiological investigations were reported and examined in areas of endemicity even before the true identity of Cyclospora was elucidated. Cyclospora was fully characterized in the early 1990s, but it was not until the 1995 Cyclospora outbreak in the United States and Canada that it caught the attention of the public and physicians. The biology, clinical presentation, epidemiology, diagnosis, treatment, and control of cyclosporiasis are reviewed, with a focus on diagnostic assays currently being used for clinical and environmental samples. Challenges and limitations in working with Cyclospora are also discussed.

From parasite genomes to one healthy world: Are we having fun yet?

In 1990, the Human Genome Sequencing Project was established. This laid the ground work for an explosion of sequence data that has since followed. As a result of this effort, the first complete genome of an animal, Caenorhabditis elegans was published in 1998. The sequence of Drosophila melanogaster was made available in March, 2000 and in the following year, working drafts of the human genome were generated with the completed sequence (92%) being released in 2003. Recent advancements and next-generation technologies have made sequencing common place and have infiltrated every aspect of biological research, including parasitology. To date, sequencing of 32 apicomplexa and 24 nematode genomes are either in progress or near completion, and over 600k nematode EST and 200k apicomplexa EST submissions fill the databases. However, the winds have shifted and efforts are now refocusing on how best to store, mine and apply these data to problem solving. Herein we tend not to summarize existing X-omics datasets or present new technological advances that promise future benefits. Rather, the information to follow condenses up-to-date-applications of existing technologies to problem solving as it relates to parasite research. Advancements in non-parasite systems are also presented with the proviso that applications to parasite research are in the making.

Highly sensitive and specific PCR assay for reliable detection of Cyclospora cayetanensis oocysts

Multiple outbreaks of food-borne gastroenteritis caused by the coccidian parasite Cyclospora cayetanensis have been reported annually in North America since 1995. Detection of C. cayetanensis contamination typically relies on laborious and subjective microscopic examination of produce washes. Molecular detection methods based on nested PCR, restriction fragment length polymorphism, or multiplex PCR have been developed for C. cayetanensis; however, they have not been adequately validated for use on food products. Further challenges include reliably extracting DNA from coccidian oocysts since their tough outer wall is resistant to lysis and overcoming PCR inhibitors in sample matrices. We describe preliminary validation of a reliable DNA extraction method for C. cayetanensis oocysts and a sensitive and specific novel PCR assay. The sensitivity and repeatability of the developed methods were evaluated by multiple DNA extractions and PCR amplifications using 1,000-, 100-, 10-, or 1-ooycst aliquots of C. cayetanensis oocysts in water or basil wash sediment. Successful PCR amplification was achieved on 15 and 5 replicates extracted from aliquots containing 1,000 oocysts in water and basil wash, respectively. All 45 replicates of the 100-oocyst aliquots in water and 5 in basil wash were amplified successfully, as were 43/45 and 41/45 of the 10- and 1-oocyst aliquots in water and 9/15 and 2/15 in basil wash, respectively. The developed primers showed no cross-reactivity when tested against bacteria, nematodes, and protozoans, including Eimeria, Giardia, and Cryptosporidium. Our results indicate that these methods are specific, can reliably detect a single oocyst, and overcome many of the limitations of microscopic diagnosis.

A multiplex PCR that discriminates between Trypanosoma brucei brucei and zoonotic T. b. rhodesiense

Two subspecies of Trypanosoma brucei s.l. co-exist within the animal populations of Eastern Africa; T. b. brucei a parasite which only infects livestock and wildlife and T. b. rhodesiense a zoonotic parasite which infects domestic livestock, wildlife, and which in humans, results in the disease known as Human African Trypanosomiasis (HAT) or sleeping sickness. In order to assess the risk posed to humans from HAT it is necessary to identify animals harbouring potentially human infective parasites. The multiplex PCR method described here permits differentiation of human and non-human infective parasites T. b. rhodesiense and T. b. brucei based on the presence or absence of the SRA gene (specific for East African T. b. rhodesiense), inclusion of GPI-PLC as an internal control indicates whether sufficient genomic material is present for detection of a single copy T. brucei gene in the PCR reaction.

Genetic identification of antigens protective against coccidia

The Eimeria species, causative agents of the disease coccidiosis, are genetically complex protozoan parasites endemic in livestock. Drug resistance remains commonplace among the Eimeria, and alternatives to chemotherapeutic control are being sought. Vaccines based upon live formulations of parasites are effective, but production costs are high, stimulating demand for a recombinant subunit vaccine. The identity of antigens suitable for inclusion in such vaccines remains elusive. Selection of immunoprotective antigens of the Eimeria species as vaccine candidates based upon recognition by the host immune system has been unsuccessful, obscured by the considerable number of molecules that are immunogenic but not immunoprotective. This is a common problem which characterizes work with most eukaryotic parasites. The identification of a selective criterion to directly access genetic loci that encode immunoprotective antigens of Eimeria maxima using a mapping strategy based upon parasite genetics, immune selection and DNA fingerprinting promises to revolutionize the process of antigen discovery. Linkage analyses of DNA markers amplified from populations of recombinant parasites defined by an ability to escape parent-specific deleterious selection by strain-specific immunity and chemotherapy has revealed four discrete regions within the E. maxima genome linked to escape from a protective immune response. These regions now form the basis of detailed study to identify antigens as candidates for inclusion in future vaccination strategies.

Cyclospora cayetanensis, a food- and waterborne coccidian parasite

Food- and waterborne coccidia including Cryptosporidium parvum, Cyclospora cayetanensis, Sarcocystis hominis and Sarcocystis suihominis, and Isospora belli are cyst-forming apicomplexan protozoa that cause intracellular infections, predominantly in the epithelial cells of the intestine. They are transmitted by oocysts from person-to-person by the fecal-oral route or via contaminated water or food. The most common symptom of infection is diarrhea, however, asymptomatic infections occur. Infections are associated with intestinal inflammation, with pathological lesions such as villus blunting, and abnormal function such as malabsorption. Mild-to-moderate, self-limiting diarrhea is common in healthy individuals ingesting infective stages of these organisms. However, patients with immune dysfunction can have severe intestinal injury and prolonged diarrhea. Diagnosis in many cases is made by a microscopic examination of the stool, and the use of appropriate staining techniques, but more recently molecular methods for detection are used increasingly. Effective antimicrobial treatment for prolonged infection in immunocompromised patients is available for most of these infections. These gastrointestinal coccidial pathogens have important similarities in epidemiology, disease pathogenesis, clinical manifestations, diagnosis, and treatment. Although there are many other cyst-forming coccidia of public health, veterinary and/or economic importance, discussion in this chapter will be limited to C. cayetanensis, as an important example of the group. Aspects of the biology, epidemiology, diagnosis, disease, treatment and control are considered. This parasite is considered to be an emerging pathogen. From 1990 to 2000, there were 11 foodborne outbreaks of cyclosporosis in North America that affected at least 3600 people. There are many outstanding questions regarding this parasite and under-reporting is common because general diagnostic methods for intestinal parasites are inadequate for detection of Cyclospora.