title: Cryptic Eimeria genotypes are common across the southern but not northern hemisphere.
abstract: 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 (FST 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.
authors.affiliation: Department of Pathology and Pathogen Biology, Royal Veterinary College, North Mymms, Hertfordshire, UK.
authors.forename: Emily L
authors.initials: EL
authors.lastname: Clark
authors.affiliation: Department of Pathology and Pathogen Biology, Royal Veterinary College, North Mymms, Hertfordshire, UK.
authors.forename: Sarah E
authors.initials: SE
authors.lastname: Macdonald
authors.affiliation: Department of Veterinary Parasitology, Madras Veterinary College, Tamil Nadu Veterinary and Animal Sciences University, Chennai, India.
authors.forename: V
authors.initials: V
authors.lastname: Thenmozhi
authors.affiliation: Division of Parasitology, Indian Veterinary Research Institute, Izatnagar, Uttar Pradesh, India.
authors.forename: Krishnendu
authors.initials: K
authors.lastname: Kundu
authors.affiliation: Division of Parasitology, Indian Veterinary Research Institute, Izatnagar, Uttar Pradesh, India.
authors.forename: Rajat
authors.initials: R
authors.lastname: Garg
authors.affiliation: Division of Parasitology, Indian Veterinary Research Institute, Izatnagar, Uttar Pradesh, India.
authors.forename: Saroj
authors.initials: S
authors.lastname: Kumar
authors.affiliation: Department of Animal Breeding and Genetics, Federal University of Agriculture, Abeokuta, Ogun State, Nigeria.
authors.forename: Simeon
authors.initials: S
authors.lastname: Ayoade
authors.affiliation: Department of Pathology and Pathogen Biology, Royal Veterinary College, North Mymms, Hertfordshire, UK.
authors.forename: Kimberly M
authors.initials: KM
authors.lastname: Fornace
authors.affiliation: Department of Parasitology and Entomology, Faculty of Veterinary Medicine, Ahmadu Bello University, Zaria, Nigeria.
authors.forename: Isa Danladi
authors.initials: ID
authors.lastname: Jatau
authors.affiliation: School of Agriculture, Food and Rural Development, Newcastle University, Newcastle upon Tyne, UK.
authors.forename: Abdalgader
authors.initials: A
authors.lastname: Moftah
authors.affiliation: Department of Pathology and Pathogen Biology, Royal Veterinary College, North Mymms, Hertfordshire, UK.
authors.forename: Matthew J
authors.initials: MJ
authors.lastname: Nolan
authors.affiliation: Division of Parasitology, Indian Veterinary Research Institute, Izatnagar, Uttar Pradesh, India.
authors.forename: N R
authors.initials: NR
authors.lastname: Sudhakar
authors.affiliation: Department of Animal Breeding and Genetics, Federal University of Agriculture, Abeokuta, Ogun State, Nigeria.
authors.forename: A O
authors.initials: AO
authors.lastname: Adebambo
authors.affiliation: Department of Parasitology and Entomology, Faculty of Veterinary Medicine, Ahmadu Bello University, Zaria, Nigeria.
authors.forename: I A
authors.initials: IA
authors.lastname: Lawal
authors.affiliation: Universidad Central de Venezuela, Facultad de Agronomía Instituto de Producción Animal, Av. Universidad via El Limón, Maracay, Venezuela.
authors.forename: Ramón
authors.initials: R
authors.lastname: Álvarez Zapata
authors.affiliation: Accra Veterinary Laboratory, Accra, Ghana.
authors.forename: Joseph A
authors.initials: JA
authors.lastname: Awuni
authors.affiliation: Department of Poultry Science, University of Arkansas, Fayetteville, AR, USA.
authors.forename: H David
authors.initials: HD
authors.lastname: Chapman
authors.affiliation: Southern African Centre for Infectious Disease Surveillance, Morogoro, Tanzania.
authors.forename: Esron
authors.initials: E
authors.lastname: Karimuribo
authors.affiliation: Department of Biotechnical and Diagnostic sciences College of Veterinary Medicine, Animal resources and Biosecurity, Makerere University, Kampala, Uganda.
authors.forename: Claire M
authors.initials: CM
authors.lastname: Mugasa
authors.affiliation: Department of Paraclinical Studies, University of Zambia, Faculty of Veterinary Medicine, Lusaka, Zambia.
authors.forename: Boniface
authors.initials: B
authors.lastname: Namangala
authors.affiliation: Production and Population Health, Royal Veterinary College, North Mymms, Hertfordshire, UK.
authors.forename: Jonathan
authors.initials: J
authors.lastname: Rushton
authors.affiliation: National Animal Protozoa Laboratory & College of Veterinary Medicine, China Agricultural University, Beijing, China.
authors.forename: Xun
authors.initials: X
authors.lastname: Suo
authors.affiliation: CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India.
authors.forename: Kumarasamy
authors.initials: K
authors.lastname: Thangaraj
authors.affiliation: Augusta University, Augusta, GA, USA.
authors.forename: Arni S R
authors.initials: AS
authors.lastname: Srinivasa Rao
authors.affiliation: Division of Parasitology, Indian Veterinary Research Institute, Izatnagar, Uttar Pradesh, India.
authors.forename: Anup K
authors.initials: AK
authors.lastname: Tewari
authors.affiliation: Division of Parasitology, Indian Veterinary Research Institute, Izatnagar, Uttar Pradesh, India.
authors.forename: Partha S
authors.initials: PS
authors.lastname: Banerjee
authors.affiliation: Department of Animal Biotechnology, Madras Veterinary College, Tamil Nadu Veterinary and Animal Sciences University, Chennai, India.
authors.forename: G
authors.initials: G
authors.lastname: Dhinakar Raj
authors.affiliation: Department of Veterinary Parasitology, Madras Veterinary College, Tamil Nadu Veterinary and Animal Sciences University, Chennai, India.
authors.forename: M
authors.initials: M
authors.lastname: Raman
authors.affiliation: Department of Pathology and Pathogen Biology, Royal Veterinary College, North Mymms, Hertfordshire, UK.
authors.forename: Fiona M
authors.initials: FM
authors.lastname: Tomley
authors.affiliation: Department of Pathology and Pathogen Biology, Royal Veterinary College, North Mymms, Hertfordshire, UK. Electronic address: dblake@rvc.ac.uk.
authors.forename: Damer P
authors.initials: DP
authors.lastname: Blake
mesh_terms: D000818:Animals; D044822:Biodiversity; D002645:Chickens / Q000469:parasitology; D002965:Classification; D003048:Coccidiosis / Q000453:epidemiology / Q000469:parasitology / Q000662:veterinary; D016054:DNA, Protozoan / Q000235:genetics*; D004539:Eimeria / Q000235:genetics*; D005838:Genotype; D010802:Phylogeny; D058974:Phylogeography; D011201:Poultry Diseases / Q000453:epidemiology / Q000469:parasitology*; D017422:Sequence Analysis, DNA
chemical_list: D016054:DNA, Protozoan
keywords: Chicken; Eimeria; Genetic diversity; Operational taxonomic units; Vaccine