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Background  Chicken is fast becoming the world’s most consumed meat. As a consequence poultry health is more important now than ever before, with pathogens of chickens recognised as serious threats to food security. One such threat are  Eimeria  species parasites, protozoa which can cause the disease coccidiosis.  Eimeria  can compromise economic poultry production and chicken welfare, and have serious consequences for poor livestock keepers. Seven  Eimeria  species that infect chickens are recognised with a global enzootic distribution. More recently three cryptic Operational Taxonomic Units (OTUx, y and z) have been described in populations of  Eimeria  recovered from chickens in Australia. Two of the three OTUs have also been detected in sub-Saharan Africa, but their occurrence, pathology and the risk they pose is largely unknown.    Results  Nigeria has witnessed a dramatic expansion in poultry production and is now the largest poultry producer in Africa. Here, faecal samples collected from nine of 12 commercial chicken farms sampled in Kaduna state, Nigeria, were found to contain eimerian oocysts. After amplification by in vivo propagation all three cryptic OTU genotypes were detected using polymerase chain reaction (PCR), including OTUy for the first time outside of Australia. Comparison with a widely used, established  Eimeria  species-specific PCR assay revealed failure to detect the OTU genotypes.    Conclusions  All three of the  Eimeria  OTU genotypes appear to be common in north-western Nigeria. The failure of a leading species-specific molecular assay to detect these genotypes indicates a risk of false negative  Eimeria  diagnosis when using molecular tools and suggests that the spatial occurrence of each OTU may be far wider than has been recognised. The risk posed by these novel genotypes is unknown, but it is clear that a better understanding of  Eimeria  occurrence is required together with the validation of effective diagnostics.    Electronic supplementary material  The online version of this article (doi:10.1186/s12917-016-0713-9) contains supplementary material, which is available to authorized users.

Three operational taxonomic units of Eimeria are common in Nigerian chickens and may undermine effective molecular diagnosis of coccidiosis