Genomic Analysis of Eimeria spp. Populations in Relation to Performance Levels of Broiler Chicken Farms in Arkansas and North Carolina

Schwarz, Ryan S.; Jenkins, Mark C.; Klopp, Spangler; Miska, Katarzyna B.

doi:10.1645/ge-1898.1

Cited by 76 publications

(52 citation statements)

References 28 publications

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“…33). ITS sequences often are used for molecular diagnostics and phylogenetic analyses because of the sensitivity and specificity provided by their high copy number and relatively rapid evolution, although intraclonal polymorphism has proven limiting (33,34). Here, multiplex SNP genotyping for E. tenella provided far greater genetic power.…”

Section: Discussionmentioning

confidence: 99%

Population, genetic, and antigenic diversity of the apicomplexanEimeria tenellaand their relevance to vaccine development

Blake

Clark

Macdonald

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

103

102

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The phylum Apicomplexa includes serious pathogens of humans and animals. Understanding the distribution and population structure of these protozoan parasites is of fundamental importance to explain disease epidemiology and develop sustainable controls. Predicting the likely efficacy and longevity of subunit vaccines in field populations relies on knowledge of relevant preexisting antigenic diversity, population structure, the likelihood of coinfection by genetically distinct strains, and the efficiency of cross-fertilization. All four of these factors have been investigated for Plasmodium species parasites, revealing both clonal and panmictic population structures with exceptional polymorphism associated with immunoprotective antigens such as apical membrane antigen 1 (AMA1). For the coccidian Toxoplasma gondii only genomic diversity and population structure have been defined in depth so far; for the closely related Eimeria species, all four variables are currently unknown. Using Eimeria tenella, a major cause of the enteric disease coccidiosis, which exerts a profound effect on chicken productivity and welfare, we determined population structure, genotype distribution, and likelihood of crossfertilization during coinfection and also investigated the extent of naturally occurring antigenic diversity for the E. tenella AMA1 homolog. Using genome-wide Sequenom SNP-based haplotyping, targeted sequencing, and single-cell genotyping, we show that in this coccidian the functionality of EtAMA1 appears to outweigh immune evasion. This result is in direct contrast to the situation in Plasmodium and most likely is underpinned by the biology of the direct and acute coccidian life cycle in the definitive host.Eimeria | coccidiosis | population structure | chickens | food security

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Section: Discussionmentioning

confidence: 99%

Population, genetic, and antigenic diversity of the apicomplexanEimeria tenellaand their relevance to vaccine development

Blake

Clark

Macdonald

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

103

102

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“…These assays have been utilised in commercial poultry flocks (Ogedengbe et al 2011), where it is relatively cost effective because tests for seven species of Eimeria can be carried out as a single PCR reaction. Schwarz et al (2009) examined the relationship between the genetic diversity of Eimeria infection with flock performance (measured as cost-per-mass produced), and found that more pathogenic species were associated with lower performance farms. DNA barcoding of some parasitic taxa has been problematic; for example, high nucleotide diversity in the COI region of platyhelminths made it difficult to design primers to amplify the entire phylum (Moszczynska et al 2009).…”

Section: Identification Of Agricultural Parasitesmentioning

confidence: 99%

Barcoding the food chain: from Sanger to high-throughput sequencing

Littlefair

Clare

2016

Genome

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Society faces the complex challenge of supporting biodiversity and ecosystem functioning, while ensuring food security by providing safe traceable food through an ever-more-complex global food chain. The increase in human mobility brings the added threat of pests, parasites, and invaders that further complicate our agro-industrial efforts. DNA barcoding technologies allow researchers to identify both individual species, and, when combined with universal primers and high-throughput sequencing techniques, the diversity within mixed samples (metabarcoding). These tools are already being employed to detect market substitutions, trace pests through the forensic evaluation of trace "environmental DNA", and to track parasitic infections in livestock. The potential of DNA barcoding to contribute to increased security of the food chain is clear, but challenges remain in regulation and the need for validation of experimental analysis. Here, we present an overview of the current uses and challenges of applied DNA barcoding in agriculture, from agro-ecosystems within farmland to the kitchen table.

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“…Several techniques based on the polymerase chain reaction using primers that specifically targeting different regions of the Eimeria genome have been described (6,7,20,22,25,30). For molecular detection of Eimeria species in chickens, the DNA sequence of the first and second internal transcribed spacers (ITS-1 and ITS-2) of the nuclear DNA, which separate the ribosomal genes, is used most frequently.…”

Section: Acervulina E Brunetti E Maxima E Mitis E Necatrix Ementioning

confidence: 99%

Molecular identification of Eimeria species of broiler chickens in Turkey

BECKSTEAD

2013

Ankara Üniversitesi Veteriner Fakültesi Dergisi

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Summary:The objective of this study was to determine whether seven Eimeria species involved in chicken coccidiosis are present in Turkey and to assess their prevelance in commercial flocks. Litter and faecal samples were collected from 1110 broiler flocks housed in 817 farms (about 12% of all broiler farms in Turkey) between September 2006 and September 2007. Coccidian oocysts were found in 624 (56.2 %) of the samples examined. Species-specific polymerase chain reaction (PCR) and nested PCR tests targeting the internal transcribed spacer-1 (ITS-1) sequences of the genomic rDNA were performed for all seven Eimeria species. The results of species-specific PCR assays confirmed the presence of E. maxima, E. tenella, E. acervulina and E. praecox, and nested PCR results showed the presence of E. mitis and E. brunetti. Although morphologic and morphometric observations revealed the presence of oocysts resembling E. necatrix; it was not confirmed by species specific or nested PCR. Nucleotide sequences of Turkish Eimeria isolates obtained by sequencing of the PCR products from 6 Eimeria species have been entered into the GenBank sequence database under accession numbers HQ680469 through HQ680474.

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Genomic Analysis of Eimeria spp. Populations in Relation to Performance Levels of Broiler Chicken Farms in Arkansas and North Carolina

Cited by 76 publications

References 28 publications

Population, genetic, and antigenic diversity of the apicomplexanEimeria tenellaand their relevance to vaccine development

Population, genetic, and antigenic diversity of the apicomplexanEimeria tenellaand their relevance to vaccine development

Barcoding the food chain: from Sanger to high-throughput sequencing

Molecular identification of Eimeria species of broiler chickens in Turkey

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