SNPs and sequence repeats identified in this study may be useful as genetic markers for identification and differentiation of C. cayetanensis apicoplast genomes revealed a familiar pattern of tight grouping with Eimeria and Toxoplasma, separated from distant species such as Plasmodium and Babesia. The predicted proteome consists of 29 core apicomplexan peptides found in most of the apicomplexans. We identified several high quality single nucleotide polymorphisms (SNPs) and small insertion/deletions spanning the apicoplast genome supported by extensive sequencing reads data, and a 30 bp sequence repeat at the terminal spacer region in a Nepalese sample. To initialize the search for genetic markers, we mapped the raw sequence reads from an additional 11 distinct clinical stool samples originating from Nepal, New York, Texas, and Indonesia to the apicoplast reference genome. We compared the genome and the predicted proteome to the data available from other apicomplexan parasites. cayetanensis genomic DNA extracted from clinical stool samples, assembled and annotated a 34,146 bp-long circular sequence, and used this sequence as a reference genome in this study. cayetanensis apicoplast, we sequenced the C. cayetanensis could be useful in designing advanced molecular methods for rapid detection and, subtyping and geographical source attribution, which would aid outbreak investigations and surveillance studies. Distinct differences in the apicoplast genomes of C. cayetanensis, a relict non-photosynthetic plastid with an independent genome, provides an attractive target to discover sequence polymorphisms useful as genetic markers for detection and trace back analysis of the parasite. Investigations of these outbreaks are currently hampered due to lack of molecular epidemiological tools for trace back analysis. Food-borne outbreaks of cyclosporiasis have occurred almost every year in the USA since the 1990s.

Cyclospora cayetanensis is an emerging coccidian parasite that causes endemic and epidemic diarrheal disease called cyclosporiasis, and this infection is associated with consumption of contaminated produce or water in developed and developing regions.

Comparative sequence analysis