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

Abstract

BackgroundChicken 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.ResultsNigeria 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.ConclusionsAll 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 materialThe online version of this article (doi:10.1186/s12917-016-0713-9) contains supplementary material, which is available to authorized users.

Application of a new PCR-RFLP panel suggests a restricted population structure for Eimeria tenella in UK and Irish chickens

“…The E. tenella Houghton, Nippon-2, Weybridge and Wisconsin reference isolates (Shirley and Harvey, 2000, Reid et al, 2014) and a Nigerian field isolate (Jatau et al, 2016) were maintained, purified, and propagated as described previously using specific pathogen-free White Leghorn chickens (Long et al, 1976, MAFF, 1986). Genomic DNA was isolated and purified using a QIAamp DNA Stool mini kit as recommended by the manufacturer (Qiagen, Hilden, Germany), including an additional initial mechanical disruption step (Kumar et al, 2014).…”

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“…However, Eimeria parasites remain widespread and drug resistance is common ( 3 , 4 ), resulting in very high levels of sub-clinical infection as well as outbreaks of clinical disease. Seven Eimeria species have long been recognized to infect chickens; but the recent detection of Eimeria circulating in chickens across much of the southern hemisphere with cryptic genotypes and the capacity to escape current anticoccidial vaccines has revealed unexpected levels of complexity ( 3 , 5 , 6 ). As a consequence understanding Eimeria occurrence, abundance and population structure is increasingly important ( 7 ).…”

Comparison of Molecular Methods for the Detection of Eimeria in Domestic Chickens in Malaysia

“…Alternatively, it may be that oocysts of the cryptic operational taxonomic units (OTUs) x, y and/or z were recovered from these samples (Clark et al 2016). Recent studies with DNA extracted from Nigerian OTU samples have suggested that molecular diagnostic tools designed to target the seven recognised Eimeria species that infect chickens may not be capable of detecting these cryptic parasites (Jatau et al 2016).…”