Abstract
Swine coccidiosis is a host-specific protozoan disease caused by Cystoisospora suis and various Eimeria species, leading to diarrhea or subclinical signs in pigs. In this study, 3296 fecal samples from 55 farms across six provinces in China were collected and examined to determine the prevalence and molecular characteristics of swine coccidia. The single oocyst isolation technique (SOIT) and molecular characterization identified nine coccidian species, with an overall infection prevalence of 13.83%. Infection rates varied by locations, host age groups, and sampling seasons. Among the positive swine coccidia samples, Cystoisospora suis showed the highest prevalence at 58.77%, followed by eight Eimeria spp(.) species. SOIT along with molecular characterization of C. suis at the SSU rRNA and ITS rRNA gene loci revealed the sequence homology from 99.8 to 100.0%. Additionally, the eight species of Eimeria(.) exhibited a high degree of sequence homology at the SSU rRNA and COX I gene loci. Due to the limitation of single molecular marker genes, this study introduced SOIT for DNA extraction, followed by nested PCR amplification of the SSU rRNA, ITS rRNA, and COX I gene loci to identify swine coccidia. This study is the first to systematically evaluate the prevalence and genetic diversity of coccidia in Chinese pig farms by SOIT, offering a method for accurately identifying swine coccidiosis and a scientific foundation for its effective prevention and control.