Abstract
Eimeria, protozoan parasites from the phylum Apicomplexa, can cause the enteric disease coccidiosis in all farmed animals. Coccidiosis is commonly considered to be most significant in poultry; due in part to the vast number of chickens produced in the World each year, their short generation time, and the narrow profit margins associated with their production. Control of Eimeria has long been dominated by routine chemoprophylaxis, but has been supplemented or replaced by live parasite vaccination in a minority of production sectors. However, public and legislative demands for reduced drug use in food production is now driving dramatic change, replacing reliance on relatively indiscriminate anticoccidial drugs with vaccines that are Eimeria species-, and in some examples, strain-specific. Unfortunately, the consequences of deleterious selection on Eimeria population structure and genome evolution incurred by exposure to anticoccidial drugs or vaccines are unclear. Genome sequence assemblies were published in 2014 for all seven Eimeria species that infect chickens, stimulating the first population genetics studies for these economically important parasites. Here, we review current knowledge of eimerian genomes and highlight challenges posed by the discovery of new, genetically cryptic Eimeria operational taxonomic units (OTUs) circulating in chicken populations. As sequencing technologies evolve understanding of eimerian genomes will improve, with notable utility for studies of Eimeria biology, diversity and opportunities for control.
Highlights
Eimeria are protozoan parasites that generally invade and develop within epithelial cells of the intestinal tract
The term ‘coccidiosis’ can be used to describe any disease caused by coccidian parasites, it is generally used to refer to infection by Eimeria, and those of poultry
The mitochondrial genome sequences contain more than 60% adenine and thymine nucleobases (A + T), and include the protein coding genes cytochrome c oxidase subunits I (COI) and III (COIII), and cytochrome b (CytB)
Summary
Eimeria are protozoan parasites that generally invade and develop within epithelial cells of the intestinal tract. Protozoa in this phylum share a conoid structure in the apical complex that plays a role in host cell invasion [4]. There now is consensus that seven Eimeria species are capable of infecting the domestic chicken, Gallus gallus domesticus [21] These seven species can be divided into two groups—those causing hemorrhagic disease (E. brunetti, E. necatrix, and E. tenella) and those primarily causing malabsorption (E. acervulina, E. maxima, E. mitis, and E. praecox) [10]. Many species of Eimeria cannot reliably be differentiated by microscopy because of similar morphologies and overlapping sizes of the oocyst stage Molecular techniques such as PCR have proven useful to distinguish different Eimeria species. Attempts to resolve questions around the heritage of these and other OTU Eimeria genotypes will benefit from recent and future advances in genomics and genetics
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
