Evaluation of nuclear and mitochondrial phylogenetics for the subtyping of Cyclospora cayetanensis

Cyclospora cayetanensis is an enteric coccidian parasite responsible for gastrointestinal disease transmitted through contaminated food and water. It has been documented in several countries, mostly with low-socioeconomic levels, although major outbreaks have hit developed countries. Detection methods based on oocyst morphology, staining, and molecular testing have been developed. However, the current MLST panel offers an opportunity for enhancement, as amplification of all molecular markers remains unfeasible in the majority of samples. This study aims to address this challenge by evaluating two approaches for analyzing the genetic diversity of C. cayetanensis and identifying reliable markers for subtyping: core homologous genes and mitochondrial genome analysis. A pangenome was constructed using 36 complete genomes of C. cayetanensis, and a haplotype network and phylogenetic analysis were conducted using 33 mitochondrial genomes. Through the analysis of the pangenome, 47 potential markers were identified, emphasizing the need for more sequence data to achieve comprehensive characterization. Additionally, the analysis of mitochondrial genomes revealed 19 single-nucleotide variations that can serve as characteristic markers for subtyping this parasite. These findings not only contribute to the selection of molecular markers for C. cayetanensis subtyping, but they also drive the knowledge toward the potential development of a comprehensive genotyping method for this parasite.