PREVALENCE, IDENTIFICATION AND GENETIC DIVERSITY OF EIMERIA SPECIES IN COMMERCIAL POULTRY FARMS IN ZARIA AND ENVIRONS, KADUNA STATE, NIGERIA

PREVALENCE, IDENTIFICATION AND GENETIC DIVERSITY OF EIMERIA SPECIES IN COMMERCIAL POULTRY FARMS IN ZARIA AND ENVIRONS, KADUNA STATE, NIGERIA

Abstract

The use of molecular technique is the most accurate and reliable way of identification and characterization of natural infection by Eimeria species in chickens. In Nigeria, information on the characterization of chicken Eimeria are mainly based on the subjective and unreliable parasitological methods. This study determined the prevalence and identify the Eimeria species occurring in commercial poultry farms in Zaria and environs using oocysts morphometric and molecular techniques. It also determined the extent of genetic diversity in the internal transcribed spacer-1 and -2 (ITS-1 and -2) of the isolated Eimeria species, apical membrane antigene-1 coding gene of Eimeria tenella isolates (EtAMA-1) and whole genome of an E. tenella isolate. Litter samples were collected from 123 farms to survey for Eimeria oocysts. Out of the 37 (30.1%) positive samples, 14 were selected for morphometric and molecular identification of Eimeria species and the genetic diversity determination. The morphometric identification was done by the determination of shape index (length/width) of randomly selected oocysts. A nested PCR was used for the molecular identification of common chicken Eimeria (ChE) while the new operational taxonomic units (OTUs) of ChE were surveyed using ITS-2 based PCR. Amplification by PCR, cloning and sequencing of ITS -1 and -2 loci was also done for molecular identification of ChE including the OTUs. Genetic diversity among the ITS -1 and -2 sequences of the isolated Eimeria species were determined using phylogenetic and principal co-ordinate analyses in comparison with sequences of isolates from different parts of the world. Species-specific characterisation focused on the EtAMA-1 coding locus was done by the amplification, cloning and sequencing of the targeted locus for determination of genetic polymorphism among the local clones in comparison with isolates from different parts of the world. Whole genome next generation sequencing of an Eimeria tenella isolate was carried out using Illumina Hiseq2000 technology. The sequence data generated were added to those generated vii elsewhere from Wisconsin (US) and Nippon (Japan) strains of E. tenella and then compared with the 2007 E. tenella Houghton strain reference genome assembly. There was no statistically significant association between the prevalence of the Eimeria infection and specific locations of the flocks (χ2 = 7.587, P > 0.05) and flock type (χ2 = 1.856, P > 0.05). The prevalence of the infection was statistically associated with flock age (χ2 = 6.406, P < 0.05); flock size (χ2 = 9.162, P < 0.05) and management system (χ2 = 4.579, P < 0.05). The morphometric identification method revealed all the seven ChE, while the presence of E. tenella, E. maxima, E. necatrix, E. acervulina, E. mitis and OTUs (OTU-X, OTU-Y and OTU-Z) were confirmed for the first time using molecular diagnostic tools in the study area. Eimeria brunetti and E. praecox were not detected using the molecular techniques. There was widespread occurrence of inter- and intra-specific genetic diversity among the ITS sequences of the isolated Eimeria species and in comparison with isolates from different parts of the world, apparently independent of geographic origin. Genetic diversity was more limited among EtAMA-1 alleles of wild E. tenella isolates from within and outside the country, with minimal diversity compared to archived laboratory strains. The whole genome sequence of the wild Nigerian strain of E. tenella was more genetically diverse from the reference H strain than either of the other laboratory strains (Wisconsin and Nippon). The implications of the observed genetic diversity among the studied Eimeria species on the prospect of future development of recombinant anticoccidia vaccines were discussed. It is recommended that poultry farmers in the study area should imbibe the practice of proper biosecurity, good sanitation and litter management as well as avoidance of other factors that will favour sporulation and dissemination of Eimeria oocysts in order to prevent outbreak of coccidiosis. Further detailed study on the identified OTUs is recommended to established their specific status and importance as pathogens in chickens.

PREVALENCE, IDENTIFICATION AND GENETIC DIVERSITY OF EIMERIA SPECIES IN COMMERCIAL POULTRY FARMS IN ZARIA AND ENVIRONS, KADUNA STATE, NIGERIA

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