Whole Genome Sequencing of Human-Pathogenic Cyclospora cayetanensis Parasites

Introduction: Cyclospora cayetanensis is a human-pathogenic apicocomplexan parasite that infects the gastrointestinal track and causes acute gastrointestinal illness. In recent years, this protozoan parasite has led to several foodborne outbreaks in the United States and Canada associated with imported produce.  To date, a large number of mammalian and avian species have been examined over the years for its presence. Nevertheless, humans are recognized as the host of this coccidian parasite. In our previous studies, we characterized the 70 kDa heat shock protein (HSP70) and the ribosomal RNA (rRNA) loci of C. cayetanensis for their rapid detection and understanding genetic diversity. In this study, we have performed the Whole Genome sequencing for twelve isolates of C. cayetanensis collected from three endemic regions.

Purpose: The major objective of this study was to obtain whole genome sequence of the C. cayetanensis parasite.

Methods: In this study, whole genome sequencing was performed on a total of twelve isolates of C. cayetanensis using Illumina MiSeq Next-Generation Sequencer in our laboratory. The data was analyzed using MiSeq, DNASTAR, and GENEIOUS software.

Results: Whole genome sequences were generated for twelve C. cayetanensis isolates from Nepal, Mexico and Peru using MiSeq Nextera XT DNA Sample Preparation Kit and MiSeq Reagent Kit V2, and de novo assembled into sequence contigs. Using MiSeq sequencer, whole genome sequencing was performed that resulted bases with high quality scores (Q ≥ 30: > 75% bases higher than Q30 at 2 x 250 bp), and with high base call accuracy. This novel tool can be used in understanding the transmission dynamics of C. cayetanensis parasite.

Significance: Our results suggest that the C. cayetanensis is a genetically distinct species. Whole genome sequencing can be used in understanding the species structure of this human-pathogenic parasite of public health importance.