Real-time polymerase chain reaction (PCR) assays for the specific detection and quantification of seven Eimeria species that cause coccidiosis in chickens

Development of a TaqMan polymerase chain reaction detection method for the precise identification and quantification of an attenuated Eimeria maxima vaccine strain in poultry

Avian coccidiosis, a parasitic disease prevalent in poultry, is caused by Eimeria species and leads to significant economic losses. The use of attenuated live oocyst vaccines has been adopted as an alternative to the use of anticoccidial drugs. However, the accurate detection and differentiation of vaccine strains from virulent ones remain challenging. Therefore, this study presents a novel TaqMan polymerase chain reaction (PCR) detection method that offers enhanced sensitivity, specificity, and reproducibility compared with traditional PCR techniques. Through whole-genome resequencing and bioinformatics analysis, we identified a molecular marker gene, Em_marker6, with a unique 21-base pair deletion specific to the Eimeria maxima attenuated vaccine strain. Optimized primers and probes targeting this marker enabled rapid quantification cycle value achievement and high fluorescence intensity. The standard curve's slope of -3.540 and correlation coefficient of 0.9971 confirmed precise quantification capabilities. The TaqMan PCR method detected as few as 30 plasmid DNA copies and 50 oocysts per reaction, outperforming traditional PCR techniques by an order of magnitude. No cross-reactivity was observed with other E. maxima wide-type strains or common intestinal pathogens, ensuring the exclusive detection of the E. maxima EMPY vaccine strain. Weekly testing over 3 weeks demonstrated minimal variability, indicating robust consistency in the method's application. Testing on 61 clinical samples revealed a 57.38% positivity rate for E. maxima species and 13.11% for the vaccine strain. The Em_marker6 gene exhibited genetic stability across multiple generations, confirming the detection method's robust stability for the attenuated E. maxima vaccine strain. This study significantly advances the field of avian coccidiosis research and control by providing a valuable tool for monitoring vaccine purity and preventing inadvertent infections in vaccinated flocks, aligning with global efforts to curb antibiotic use in animal feed.

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.

Molecular Investigation of Eimeria Species in Broiler Farms in the Province of Vojvodina, Serbia

Coccidiosis is a significant poultry disease caused by the Eimeria species. This study aims to determine the prevalence of Eimeria spp. on broiler farms in Vojvodina, along with the identification of parasite species, and assess the implemented biosecurity measures. The study was conducted on 100 broiler chicken farms (28 small-sized; 34 medium-sized; 38 large-sized farms) from June 2018 to December 2021. One pooled sample of faeces was collected from three to six-week-old chickens from each farm, and assessment of biosecurity measures was carried out using a questionnaire. Using the PCR method, DNA of Eimeria was found in 59 samples (59%), while 41 samples (41%) were negative. Four species of Eimeria were identified, and their prevalence was the following: E. acervulina (37%), E. maxima (17%), E. mitis (25%) and E. tenella (48%). A significant difference (p < 0.05) was established in the number of oocysts in flocks from small-sized farms compared to medium-sized farms. It was found that regular implementation of disinfection, disinsection and deratisation measures, as well as all the biosecurity measures, can significantly reduce the occurrence of coccidiosis. These results will help to develop better strategies for the control and prevention of coccidiosis on farms.

Effects of "Shi Ying Zi" powder and osthole on immune and antioxidant function of Eimeria tenella-infected broilers

"Shi Ying Zi" powder is a traditional Chinese herbal formula for preventing and treating coccidiosis. In our previous studies, it showed anticoccidial effects and exhibited the potential to control Eimeria tenella infection. In this research, we evaluated the antioxidation and immune effect of "Shi Ying Zi" powder and its effective active ingredient osthole on coccidiosis-infected broilers to explore the mechanism of its anticoccidial effect. We analyzed changes in the antioxidant index, the pathological changes in cecum, immune index of serum and composition of cecal flora. The results showed that the use of "Shi Ying Zi" powder and osthole alleviated the pathological changes in the cecum, spleen and bursa of Fabricius, upregulated the spleen and bursal weigh index. "Shi Ying Zi" powder of 10 g/kg effectively rocovered the contents of interleukins and immunoglobulin in serum. Osthole increased the proportion of Firmicutes, Actino-bacteria and Lactobacillus in the cecum. In summary, "Shi Ying Zi" powder and osthole have anticoccidial effects, and they also can active the immunity, antioxidant functions and upregulate the beneficial bacteria population in Eimeria tenella-infected broilers.

DNA-based quantification and counting of transmission stages provides different but complementary parasite load estimates: an example from rodent coccidia (Eimeria)

Background

Counting parasite transmission stages in faeces is the classical measurement to quantify “parasite load”. DNA-based quantifications of parasite intensities from faecal samples are relatively novel and often validated against such counts. When microscopic and molecular quantifications do not correlate, it is unclear whether oocyst counts or DNA-based intensity better reflects biologically meaningful concepts. Here, we investigate this issue using the example of Eimeria ferrisi (Coccidia), an intracellular parasite of house mice (Mus musculus).

Methods

We performed an infection experiment of house mice with E. ferrisi, in which the intensity of infection correlates with increased health impact on the host, measured as temporary weight loss during infection. We recorded the number of parasite transmissive stages (oocysts) per gram of faeces (OPG) and, as a DNA-based measurement, the number of Eimeria genome copies per gram of faeces for 10 days post-infection (dpi). We assessed weight loss relative to the day of experimental infection as a proxy of host health and evaluated whether DNA or oocyst counts are better predictors of host health.

Results

Absolute quantification of Eimeria DNA and oocyst counts showed similar but slightly diverging temporal patterns during 10 dpi. We detected Eimeria DNA earlier than the first appearance of oocysts in faeces. Additionally, Eimeria OPGs within each dpi did not explain parasite DNA intensity. Early dpi were characterized by high DNA intensity with low oocyst counts, while late infections showed the opposite pattern. The intensity of Eimeria DNA was consistently a stronger predictor of either maximal weight loss (1 value per animal during the infection course) or weight loss on each day during the experiment when controlling for between-dpi and between-individual variance.

Conclusions

Eimeria ferrisi oocyst counts correlate weakly with parasite intensity assessed through DNA quantification. DNA is likely partially derived from life-cycle stages other than transmissive oocysts. DNA-based intensities predict health outcomes of infection for the host more robustly than counts of transmissive stages. We conclude that DNA-based quantifications should not necessarily require validation against counts of transmissive stages. Instead, DNA-based load estimates should be evaluated as complementary sources of information with potential specific biological relevance for each host-parasite system.

Graphical Abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s13071-021-05119-0.

Centennial Review: Factors affecting the chicken gastrointestinal microbial composition and their association with gut health and productive performance

Maintenance of "gut health" is considered a priority in commercial chicken farms, although a precise definition of what constitutes gut health and how to evaluate it is still lacking. In research settings, monitoring of gut microbiota has gained great attention as shifts in microbial community composition have been associated with gut health and productive performance. However, microbial signatures associated with productivity remain elusive because of the high variability of the microbiota of individual birds resulting in multiple and sometimes contradictory profiles associated with poor or high performance. The high costs associated with the testing and the need for the terminal sampling of a large number of birds for the collection of gut contents also make this tool of limited use in commercial settings. This review highlights the existing literature on the chicken digestive system and associated microbiota; factors affecting the gut microbiota and emergence of the major chicken enteric diseases coccidiosis and necrotic enteritis; methods to evaluate gut health and their association with performance; main issues in investigating chicken microbial populations; and the relationship of microbial profiles and production outcomes. Emphasis is given to emerging noninvasive and easy-to-collect sampling methods that could be used to monitor gut health and microbiological changes in commercial flocks.

A flow cytometric method for enumeration and speciation of coccidia affecting broiler chickens

Production losses, mortality, and control measures associated with coccidiosis, caused by Eimera species, cost the broiler industry over $14 billion a year. Current means to distinguish Eimeria species such as oocyst morphology, pre-patent period and site of infection are subjective, labor intensive or unsuitable for high-throughput applications. Although Polymerase Chain Reaction (PCR) techniques have been validated, the target gene cannot differentiate relative abundance of each species in mixed infections. In this study, we developed a non-antibody-based flow cytometry high throughput method to simultaneously enumerate and speciate four Eimeria species, E. acervulina, E. mitis, E. maxima, and E. tenella, using commercial coccidia vaccine as well as field fecal samples. Our findings showed that the four Eimeria oocyst populations could be distinctly speciated based on their size and granularity (shape) via scatter plotting. These distinct populations were sorted and confirmed by quantitative real-time PCR assay. Finally, the flow cytometry findings were applied to enumerate and speciate oocysts from fecal samples collected from commercial broiler flocks vaccinated for coccidiosis at day of hatch and the results were validated against the conventional manual method of floatation and microscopic examination. Collectively, the findings of this study suggested that non-antibody based Flow Cytometry technique can be successful in the simultaneous enumeration and speciation of coccidia. Further development and validation is needed to make this diagnostic tool useful for field applications at a much larger scale as well as to speciate other Eimeria species.

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.

Molecular detection of Eimeria species and Clostridium perfringens in poultry dust and pooled excreta of commercial broiler chicken flocks differing in productive performance

Necrotic enteritis and coccidiosis are the most economically detrimental enteric diseases of broiler chickens. This study aimed to investigate the association of DNA load of Clostridium perfringens, netB, and five Eimeria species (E. brunetti, E. maxima, E. necatrix, E. acervulina and E. tenella) in poultry house dust and pooled excreta with flock productive performance. The dust and pooled excreta from the floor were collected weekly at days 7, 14, 21, 28 and 35 of chicken age from 16 flocks of eight farms from two Australian integrator companies. The farms were ranked as high or low performers by each integrator according to the production performance of studied flocks. Eimeria tenella and necatrix were not detected in any farm while E. brunetti was detected in a low-performance farm and netB was detected in a high-performance farm. C. perfringens, E. acervulina and E. maxima DNA were detected on all farms with no significant differences in DNA load between high and low-performance farms or companies. The lack of association of pathogen DNA load and farm performance is possibly due to overall low to moderate pathogen DNA load detected in this study. Further studies on a larger number of farms are needed to determine whether these population level measurements of key pathogens based on PCR detection of nucleic acids are correlated with performance variables.

Genome-wide analysis of differentially expressed profiles of mRNAs, lncRNAs and circRNAs in chickens during Eimeria necatrix infection

BACKGROUND

Eimeria necatrix, the most highly pathogenic coccidian in chicken small intestines, can cause high morbidity and mortality in susceptible birds and devastating economic losses in poultry production, but the underlying molecular mechanisms in interaction between chicken and E. necatrix are not entirely revealed. Accumulating evidence shows that the long-non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) are key regulators in various infectious diseases. However, the expression profiles and roles of these two non-coding RNAs (ncRNAs) during E. necatrix infection are still unclear.

METHODS

The expression profiles of mRNAs, lncRNAs and circRNAs in mid-segments of chicken small intestines at 108 h post-infection (pi) with E. necatrix were analyzed by using the RNA-seq technique.

RESULTS

After strict filtering of raw data, we putatively identified 49,183 mRNAs, 818 lncRNAs and 4153 circRNAs. The obtained lncRNAs were classified into four types, including 228 (27.87%) intergenic, 67 (8.19%) intronic, 166 (20.29%) anti-sense and 357 (43.64%) sense-overlapping lncRNAs; of these, 571 were found to be novel. Five types were also predicted for putative circRNAs, including 180 exonic, 54 intronic, 113 antisense, 109 intergenic and 3697 sense-overlapping circRNAs. Eimeria necatrix infection significantly altered the expression of 1543 mRNAs (707 upregulated and 836 downregulated), 95 lncRNAs (49 upregulated and 46 downregulated) and 13 circRNAs (9 upregulated and 4 downregulated). Target predictions revealed that 38 aberrantly expressed lncRNAs would cis-regulate 73 mRNAs, and 1453 mRNAs could be trans-regulated by 87 differentially regulated lncRNAs. Additionally, 109 potential sponging miRNAs were also identified for 9 circRNAs. GO and KEGG enrichment analysis of target mRNAs for lncRNAs, and sponging miRNA targets and source genes for circRNAs identified associations of both lncRNAs and circRNAs with host immune defense and pathogenesis during E. necatrix infection.

CONCLUSIONS

To the best of our knowledge, the present study provides the first genome-wide analysis of mRNAs, lncRNAs and circRNAs in chicken small intestines infected with E. necatrix. The obtained data will offer novel clues for exploring the interaction mechanisms between chickens and Eimeria spp.

Quantification of Eimeria necatrix, E. acervulina and E. maxima genomes in commercial chicken farms by quantitative real time PCR

Advent of quantitative polymerase chain reaction and its variants have enabled identification and quantification of seven known Eimeria species of poultry in biological samples. Attempts were made in the present study to identify and quantify three important pathogenic Eimeria species responsible for intestinal coccidiosis in domestic farmed chicken, E. necatrix, E. acervulina and E. maxima in droppings collected from thirty one poultry farms of North Indian states of Haryana, Punjab, Uttar Pradesh and Uttarakhand. The study included broiler, layer and backyard rearing units. Overall occurrence of E. necatrix, E. maxima and E. acervulina was 64.5%. E. necatrix was detected in 55% (11/20) broiler farms, 66.7% (4/6) layer farms and 100% (5/5) backyard rearing units studied. Thus, occurrence of E. necatrix was detected in 64.5% (20/31) farms studied. E. maxima and E. acervulina were detected in droppings of 65% (13/20) broiler farms, 66.7% (4/6) layer farms and 60% (3/5) back yard rearing units. Genome counts of each Eimeria species revealed maximum parasite load of E. necatrix followed by E. acervulina in broiler farms and least in layer farms. The mean parasite load (genome) copies for these parasite species were intermediate for backyard units while E. maxima had the lowest number of genome copies in droppings. Mean E. maxima counts were highest in boiler farms, while it was similar for layer and back yard units. However, statistically no significant differences were observed for parasite load existing either between the broiler, layer or back yard units or between the genome counts of E. necatrix, E. acervulina or E. maxima.

Morphological characterization and first molecular identification of the eleven Eimeria species that infect sheep from Mexico

Within livestock production, enteric diseases play an important role, since they cause severe economic losses due to mortality, growth depression, and reduction in the conversion rate. Coccidiosis caused by Eimeria spp. is a parasitic disease of high morbidity that affects various animal species, including sheep. In sheep, eleven species of Eimeria have been identified mainly through microscopical identification of the oocysts; however, this technique has certain limitations that make it difficult to identify the different Eimeria species. The objective of the present study was to morphologically identify the eleven species of Eimeria that infect sheep in the southeastern region of the State of Mexico, as well as obtain the partial sequence of the ITS-1 rRNA region of each species and analyze it phylogenetically. A total of 412 samples were collected from the 13 municipalities that comprise the region I of the State of Mexico, out of which, 40 had approximately 80% of a single Eimeria species. Among these, the eleven Eimeria species reported in sheep were identified. The phylogenetic analysis showed that the species reported in this study are associated with those reported in rabbits, bovines, and birds. It is suggested that the phylogenetic division of sheep in two clades may be associated with the presence or absence of the residual body. It is proposed that the present methodology can be used effectively for diagnosis and to obtain information about the epidemiology of ovine coccidial infection. The results obtained in this study constitute the first report of the ITS-1 region of the eleven Eimeria species that infect sheep worldwide.

Illumina Next Generation Sequencing for the Analysis of Eimeria Populations in Commercial Broilers and Indigenous Chickens

Eimeria species parasites can cause the enteric disease coccidiosis, most notably in chickens where the economic and welfare implications are significant. Seven Eimeria species are recognized to infect chickens, although understanding of their regional occurrence, abundance, and population structure remains limited. Reports of Eimeria circulating in chickens across much of the southern hemisphere with cryptic genotypes and the capacity to escape current anticoccidial vaccines have revealed unexpected levels of complexity. Consequently, it is important to supplement validated species-specific molecular diagnostics with new genus-level tools. Here, we report the application of Illumina MiSeq deep sequencing to partial 18S rDNA amplicons generated using Eimeria genus-specific primers from chicken caecal contents collected in India. Commercial Cobb400 broiler and indigenous Kadaknath type chickens were sampled under field conditions after co-rearing (mixed type farms, n = 150 chickens for each) or separate rearing (single type farms, n = 150 each). Comparison of MiSeq results with established Internal Transcribed Spacer (ITS) and Sequence Characterised Amplified Region (SCAR) quantitative PCR assays suggest greater sensitivity for the MiSeq approach. The caecal-dwelling Eimeria tenella and E. necatrix dominated each sample set, although all seven species which infect chickens were detected. Two of the three cryptic Eimeria genotypes were detected including OTU-X and OTU-Y, the most northern report for the latter to date. Low levels of DNA representing other Eimeria species were detected, possibly representing farm-level contamination with non-replicating oocysts or Eimeria DNA, or false positives, indicating a requirement for additional validation. Next generation deep amplicon sequencing offers a valuable resource for future Eimeria studies.

Investigations on the Occurrence and Associated Risk Factors of Avian Coccidiosis in Osun State, Southwestern Nigeria

Avian coccidiosis is one of the most important diseases of poultry and it is responsible for a large number of poultry mortalities worldwide. This study was carried out to investigate the occurrence and associated risk factors of avian coccidiosis in Osun State, Nigeria. Fecal samples were collected and examined from 5,544 avian species that were brought for treatment at the state veterinary hospitals over a 10-year period. Parameters such as age, sex, season, and species of birds were determined. Also, the months of the year were taken into consideration. Overall prevalence of 41.3% was recorded. The year specific rate for avian coccidiosis was highest in 2007 (97.9%) and lowest in 2006 (0.4%), while the month-specific rate was highest in November (85.7%) and lowest in July 2006 (13.3%). There was a significantly (P < 0.05) higher prevalence in young birds compared to adults, in males compared to females, and during the wet season compared to the dry season. Broilers (99.8%) and cockerels (81.0%) were the bird types with the highest prevalence rate. The high prevalence of avian coccidiosis in the study area shows that the disease is endemic and there is need to embark on a radical preventive measure to curtail the disease.

Cryptic Eimeria genotypes are common across the southern but not northern hemisphere

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The seven Eimeria spp. recognised to infect chickens are present globally.

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Cryptic Eimeria operational taxonomic units (OTUs) are common in the southern but not northern hemisphere.

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Parasite population structure appears to vary between Eimeria spp.

The phylum Apicomplexa includes parasites of medical, zoonotic and veterinary significance. Understanding the global distribution and genetic diversity of these protozoa is of fundamental importance for efficient, robust and long-lasting methods of control. Eimeria spp. cause intestinal coccidiosis in all major livestock animals and are the most important parasites of domestic chickens in terms of both economic impact and animal welfare. Despite having significant negative impacts on the efficiency of food production, many fundamental questions relating to the global distribution and genetic variation of Eimeria spp. remain largely unanswered. Here, we provide the broadest map yet of Eimeria occurrence for domestic chickens, confirming that all the known species (Eimeria acervulina, Eimeria brunetti, Eimeria maxima, Eimeria mitis, Eimeria necatrix, Eimeria praecox, Eimeria tenella) are present in all six continents where chickens are found (including 21 countries). Analysis of 248 internal transcribed spacer sequences derived from 17 countries provided evidence of possible allopatric diversity for species such as E. tenella (F_ST values ⩽0.34) but not E. acervulina and E. mitis, and highlighted a trend towards widespread genetic variance. We found that three genetic variants described previously only in Australia and southern Africa (operational taxonomic units x, y and z) have a wide distribution across the southern, but not the northern hemisphere. While the drivers for such a polarised distribution of these operational taxonomic unit genotypes remains unclear, the occurrence of genetically variant Eimeria may pose a risk to food security and animal welfare in Europe and North America should these parasites spread to the northern hemisphere.

Evaluation of ionophore sensitivity of Eimeria acervulina and Eimeria maxima isolated from the Algerian to Jijel province poultry farms

The present study represents the first description of ionophore resistance in recovered from commercial Algerian (Jijel-Algeria) broiler farms. Microscopy and intervening transcribed sequence 1 PCR (ITS1 PCR) revealed only 2 Eimeria species present in litter from these farms- namely Eimeria acervulina and Eimeria maxima. A pool of these isolates were evaluated in broiler chickens (Cobb 500) for sensitivity to 5 anticoccidial compounds-diclazuril (1ppm), lasalocid (125ppm), monensin (125ppm), narasin (70ppm) and salinomycin (60ppm). As indicated by anticoccidial sensitivity profiles based on lesion scores and anticoccidial index (ACI), complete resistance to monensin and narasin, partial resistance to salinomycin and lasalocid, and complete sensitivity to diclazuril was observed. While lack of sensitivity to monensin is not surprising given its use for years as the sole anticoccidial compound, the resistance to monoether (narasin) and polyether (lasalocid) ionophores suggests that cross-resistance has developed in a segment of the Eimeria population. The fairly uniform Eimeria species composition among all poultry farms suggests that E. acervulina and E. maxima more rapidly develop resistance to ionophore drugs.

Quantitative real-time PCR (qPCR) for Eimeria tenella replication--Implications for experimental refinement and animal welfare

The Eimeria species are highly pathogenic parasites of chickens. Research aimed at reducing their impact is hindered by a lack of non-subjective, quantitative, tools to measure parasite replication in the host. The time-consuming, and often time-sensitive, nature of existing approaches precludes their use in large-scale genetic, epidemiological, and evolutionary analyses. We have used quantitative real-time PCR (qPCR) to accurately quantify Eimeria tenella in chicken tissue and shown this to be more efficient and sensitive than traditional methodologies. We tested four chicken-specific reference qPCR assays and found beta-actin (actb) to be optimal for sample normalisation. In an experimental setting, chickens were inoculated with 500, 1500, or 4500 E. tenella oocysts and parasite replication and the impact of infection measured by i) qPCR analysis of DNA extracted from caecal tissues collected at five and eight days post-infection (dpi), ii) faecal oocyst counts (FOCs) on samples taken from six to eight dpi, and iii) lesion scoring on caeca collected post-mortem at five and eight dpi. Quantitative real-time PCR test results indicated a significant dose-dependent increase in parasite numbers among study groups for samples collected five dpi (i.e., prior to gametogony) (R² = 0.994) (p < 0.002) but not in those from day eight (after most oocyst shedding) (R² = 0.006) (p > 0.379). A strong dose-dependent increase in parasite replication and severity of infection was also revealed by FOC (R² = 0.997) and lesion scoring. Importantly, qPCR offers substantial improvements for animal welfare via improved statistical power and reduced group sizes in experimental studies. The described qPCR method overcomes subjective limitations of coproscopic quantification, allows reproducible medium- to high-throughput examination of tissues, faeces, and oocysts, and is a valuable tool for determining the impact of Eimeria infections in both experimental and field settings.

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Quantitative PCR indicates significant dose-dependent increases in parasites.

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More sensitive measure of parasite replication than faecal oocyst count/lesion score

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Significant implications for animal welfare and experiment refinement (3R's)

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Support studies focusing on the genetic basis of resistance/susceptibility

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Major implications for investigations of key aspects of Eimeria biology and control

Control of avian coccidiosis: future and present natural alternatives

Numerous efforts to date have been implemented in the control of avian coccidiosis caused by the Eimeria parasite. Since the appearance of anticoccidial chemical compounds, the search for new alternatives continues. Today, no product is available to cope with the disease; however, the number of products commercially available is constantly increasing. In this review, we focus on natural products and their anticoccidial activity. This group comprises fatty acids, antioxidants, fungal and herbal extracts, and immune response modulators with proven anticoccidial activity, many of which exist as dietary supplements. Additionally, we offer an overview of the poultry industry and the economic cost of coccidiosis as well as the classical strategies used to control the disease.

A rapid method for determining salinomycin and monensin sensitivity in Eimeria tenella

Standard methods of determining the ionophore sensitivity of Eimeria rely on infecting chickens with an isolate or a mixture of Eimeria spp. oocysts in the presence of different anti-coccidial drugs. The purpose of this study was to develop a rapid in vitro method for assessing salinomycin and monensin sensitivity in Eimeria tenella. Cultures of MDBK cells were grown to 85% confluency, and then inoculated with excysted E. tenella laboratory strain (APU-1) sporozoites in the presence of different concentrations of salinomycin or monensin. At various timepoints, the monolayers were fixed for counting intraceullar sporozoites, or were subjected to DNA extraction, followed by molecular analysis using quantitative (qPCR) or semi-quantitative PCR (sqPCR). Preliminary experiments showed that 24h was the optimum time for harvesting the E. tenella-infected cell cultures. The average number of E. tenella sporozoites relative to untreated controls displayed a linear decrease between 0.3 and 33.0 μg/ml salinomycin and between 0.3 and 3.3 μg/ml monensin. A similar pattern was observed in the relative amount of E. tenella DNA as measured by sqPCR. A linear decrease in the relative amount of E. tenella DNA was observed over the entire range of salinomycin and monensin concentrations as measured by qPCR possibly reflecting the greater sensitivity of this assay. Comparison of sporozoite counting, sqPCR, and qPCR signals using a criterion of 50% inhibition in sporozoite numbers or level of PCR amplification product showed good agreement between the three assays. E. tenella field isolates (FS-1 and FS-2) displaying resistance to salinomycin and monensin were evaluated in the in vitro assay using qPCR and sqPCR. Compared to E. tenella APU-1, the E. tenella FS-1 and FS-2 isolates showed higher levels of E. tenella DNA at 24h by both qPCR and sqPCR. This in vitro assay represents a significant advance in developing rapid, cost-effective methods for assessing ionophore sensitivity in E. tenella.

A selective review of advances in coccidiosis research

Coccidiosis is a widespread and economically significant disease of livestock caused by protozoan parasites of the genus Eimeria. This disease is worldwide in occurrence and costs the animal agricultural industry many millions of dollars to control. In recent years, the modern tools of molecular biology, biochemistry, cell biology and immunology have been used to expand greatly our knowledge of these parasites and the disease they cause. Such studies are essential if we are to develop new means for the control of coccidiosis. In this chapter, selective aspects of the biology of these organisms, with emphasis on recent research in poultry, are reviewed. Topics considered include taxonomy, systematics, genetics, genomics, transcriptomics, proteomics, transfection, oocyst biogenesis, host cell invasion, immunobiology, diagnostics and control.

An optimised protocol for molecular identification of Eimeria from chickens

Molecular approaches supporting identification of Eimeria parasites infecting chickens have been available for more than 20 years, although they have largely failed to replace traditional measures such as microscopy and pathology. Limitations of microscopy-led diagnostics, including a requirement for specialist parasitological expertise and low sample throughput, are yet to be outweighed by the difficulties associated with accessing genomic DNA from environmental Eimeria samples. A key step towards the use of Eimeria species-specific PCR as a sensitive and reproducible discriminatory tool for use in the field is the production of a standardised protocol that includes sample collection and DNA template preparation, as well as primer selection from the numerous PCR assays now published. Such a protocol will facilitate development of valuable epidemiological datasets which may be easily compared between studies and laboratories. The outcome of an optimisation process undertaken in laboratories in India and the UK is described here, identifying four steps. First, samples were collected into a 2% (w/v) potassium dichromate solution. Second, oocysts were enriched by flotation in saturated saline. Third, genomic DNA was extracted using a QIAamp DNA Stool mini kit protocol including a mechanical homogenisation step. Finally, nested PCR was carried out using previously published primers targeting the internal transcribed spacer region 1 (ITS-1). Alternative methods tested included sample processing in the presence of faecal material, DNA extraction using a traditional phenol/chloroform protocol, the use of SCAR multiplex PCR (one tube and two tube versions) and speciation using the morphometric tool COCCIMORPH for the first time with field samples.

Application of a qPCR assay with melting curve analysis for detection and differentiation of protozoan oocysts in human fecal samples from Dominican Republic

A quantitative polymerase chain reaction assay with melt curve analysis (qPCR-MCA) was applied for the detection of protozoan oocysts in 501 human fecal samples collected in Dominican Republic. Samples were subjected to qPCR using universal coccidia primers targeting 18S rDNA to detect oocysts followed by MCA to identify oocyst species based on amplicon melting temperature. Putative positive samples were also tested by conventional PCR and microscopy. Cystoisospora belli (×3), Cryptosporidium parvum (×3), Cryptosporidium hominis (×5), Cryptosporidium meleagridis (×1), Cryptosporidium canis (×1), and Cyclospora cayetanensis (×9) were detected by qPCR-MCA and confirmed by sequencing. This assay consistently detected 10 copies of the cloned target fragment and can be considered more efficient and sensitive than microscopy flotation methods for detecting multiple species of oocysts in human feces. The qPCR-MCA is a reliable protozoan oocyst screening assay for use on clinical and environmental samples in public health, food safety and veterinary programs.

Real-time PCR-based quantification of Eimeria genomes: a method to outweigh underestimation of genome numbers due to PCR inhibition

Eimeria species parasites can cause the disease coccidiosis in all livestock species, most notably poultry. Traditional diagnostics such as faecal microscopy have now been supplemented by molecular assays including genus-specific and species-specific quantitative polymerase chain reaction (qPCR), although DNA extracted from faecal samples is commonly affected by PCR inhibition. This was confirmed when genomic DNA extracted from chicken faeces inhibited the threshold cycle value of internal positive control (IPC) DNA amplification by 15.33%. Hence, the objective of the present study was to use IPC qPCR to determine PCR inhibition in a series of experimental samples and use the increase in IPC qPCR threshold cycle value as an individual (sample-specific) correction factor for an established 5S rDNA qPCR used to estimate total Eimeria genome numbers. IPC-corrected genome counts were correlated with conventional oocyst per gram counts and compared with non-corrected counts, revealing a 0.1769 increase in correlation coefficient to outweigh underestimation of oocyst counts. Though the sample size used in this study is small, this limitation would be offset by the sample-specific correction factor determined using the IPC along with each sample.

Control of poultry coccidiosis: changing trends

Coccidiosis is the most important protozoan disease affecting the poultry industry worldwide. Control of poultry coccidiosis is presently based on managerial skills and the use of prophylactic coccidiostatic drugs. With the emergence of drug resistant Eimeria strains, emphasis has been laid on development and use of safer vaccines; some of them have been commercialized successfully. The present review deals with the various factors responsible for the development of clinical coccidiosis in poultry as well as an overview of the currently available inducers and boosters of immunity against coccidiosis. There are three groups of vaccines currently available against coccidiosis which can be distinguished on the basis of characteristics of the Eimeria species included in the respective products, viz. vaccines based on live virulent strains, vaccines based on live attenuated strains, and vaccines based on live strains that are relatively tolerant to the ionophore compounds. The latter vaccine combines the early chemotherapeutic effect of ionophores with the late prophylactic effect of vaccination. Although in the near future more varieties of oocyst based live vaccines are expected, identification of selective coccidian-specific immunoprotective molecules is likely to get more attention to facilitate the sustainable control of poultry coccidiosis.

Comparison of Eimeria species distribution and salinomycin resistance in commercial broiler operations utilizing different coccidiosis control strategies

The purpose of the present study was to evaluate the species composition and salinomycin sensitivity of Eimeria oocysts isolated from commercial broiler farms that differed by means of coccidiosis control (anticoccidial drugs [ACD] vs. live oocyst vaccines [VAC]). A comparison of Eimeria species composition and salinomycin sensitivity was also made before and after a producer switched from salinomycin to live oocyst vaccines. In general, no significant difference was observed in the concentration of Eimeria spp. oocysts in litter from VAC-utilizing farms compared to litter from ACD-utilizing farms. Application of PCR-based methods to detect coccidia found that Eimeria species distribution in litter from VAC operations more closely resembled the species composition in the live oocyst vaccines. Drug sensitivity testing found that Eimeria oocysts from VAC operations displayed greater salinomycin sensitivity as measured by weight gain and feed conversion efficiency compared to oocysts from ACD farms. These findings provide additional evidence for the usefulness of live oocyst vaccines to restore ionophore sensitivity in poultry operations that contain an ionophore-resistant population of Eimeria spp. oocysts.

Effect of Eimeria acervulina infection history on the immune response and transmission in broilers

Heterogeneity in exposure to Eimeria spp. of chickens in a flock will result in differences between individual birds in oocyst output and acquired immunity, which subsequently affects transmission of the parasite in the population. The aim of this study was to quantify effects of previous infection of broilers with Eimeria acervulina on immune responses, oocyst output and transmission. A transmission experiment was carried out with pair-wise housed broilers, that differed in infection history. This "infection history" was achieved by establishment of a primary infection by inoculation of birds with 50,000 sporulated E. acervulina oocysts at day 6 of age ("primed"); the other birds did not receive a primary infection ("naïve"). The actual transmission experiment started at day 24 of age: one bird (I) was inoculated with 50,000 sporulated oocysts and was housed together with a non-inoculated contact bird (C). Oocyst excretion and parameters describing transmission, i.e. the number of infected C birds and time passed before start of excretion of C birds, were determined from day 28 to day 50 for six pairs of four different combinations of I and C birds (I-C): naïve-naïve, naïve-primed, primed-naïve and primed-primed. Immune parameters, CD4(+), CD8(+), αβTCR(+) and γδTCR(+) T cells and macrophages in duodenum, were determined in an additional 25 non-primed, non-inoculated control birds, and in the naïve-naïve and naïve-primed groups, each group consisting of 25 pairs. Although the numbers of CD4(+) T cells and γδTCR(+) T cells increased after primary infection, none of the immunological cell types provided an indication of differences in infectivity, susceptibility or transmission between birds. Oocyst output was significantly reduced in primed I and C birds. Transmission was reduced most in the primed-primed group, but nonetheless transmission occurred in all groups. This study also showed that acquired immunity significantly reduced oocyst output after inoculation and contact-infection, but not sufficiently to prevent transmission to contact-exposed birds.

Prevalence and cross-immunity of Eimeria species on Korean chicken farms

Epidemiology of Eimeria species in poultry flocks is important to increase the effectiveness of vaccinations and prophylactic strategies on chicken farms. In this study, fecal samples from 356 chicken farms were collected randomly and examined for the prevalence of Eimeria species. Through microscopic examination, it was determined that 78.7% of the tested farms were positive in Eimeria-infection. Seven Eimeria species were detected in all the positive farms by PCR amplification of the internal transcribed spacer 1 (ITS-1) region with species-specific primers. E. acervulina and E. tenella were the most prevalent, followed by E. brunetti and E. praecox (87.5, 62.5, 59.3, and 37.5% of the farms, respectively). Each of E. maxima, E. mitis, and E. necatrix was identified in 31.3% of the farms. Individual positive fecal samples contained multiple Eimeria species (mean=3.4). Since E. maxima is known to generate antigenic variants, cross-immunity was investigated for four isolates of E. maxima from the poultry farms in different regions of Korea. The extent of cross-protection varied from 54.3 to 100% against the heterologous isolates. The results obtained from this large-scale survey will be a useful reference for controlling coccidiosis in the poultry industry.