Discrimination, molecular characterisation and phylogenetic comparison of porcine Eimeria spp. in India

Infections with Eimeria spp. are common in pigs worldwide, occasionally affecting animals clinically after weaning or during the fattening period when diarrhoea and weight loss can be observed upon infection with the more pathogenic species. Molecular characterization of pathogens is valuable to accurately delimit species and development novel diagnostics, although sequences which define Eimeria species that infect pigs are scarce. Only three of the eight common species are currently represented in GenBank. In this study we describe the occurrence of Eimeria species in pigs sampled in Punjab, India; going on to use the samples to generate new species-specific 18S rDNA sequences for all of the previously uncharacterised species. Using these data we report the first phylogenetic analyses to include the eight Eimeria species that commonly infect the domestic pig (Sus scrofa domesticus). Consideration of phylogenetic trees produced using Maximum Likelihood, Neighbour Joining, Maximum Parsimony and Unweighted Pair Group Method with Arithmetic Mean methods indicate that the 18S rDNA sequences present lower levels of genetic diversity than Eimeria which infect avian species and are insufficient to infer stable phylogenies.