Current Knowledge and Future Directions for <i>Cyclospora cayetanensis</i> Research and Its Surrogates

Cyclospora cayetanensis is a foodborne protozoan parasite that causes cyclosporiasis, a disease transmitted by the consumption of sporulated oocysts, often via contaminated produce. Since 2018, outbreaks traced back to domestically grown produce in the United States have raised growing concern. Despite its public health significance, research is hindered by methodological challenges, including inability to culture in vitro/in vivo and limited genomic characterization. This review examines current knowledge on its occurrence and transmission, detection methods, host-parasite interactions, genetics, and remediation strategies, while also evaluating use of surrogate organisms (Eimeria spp. and Cryptosporidium parvum) to address research gaps. Detection remains challenging due to low oocyst concentrations in environmental and food matrices, requiring highly sensitive molecular assays. Additionally, the lack of standardized sampling methods that are representative of an entire batch of produces further complicates reliable detection and surveillance efforts. The recently implemented Food and Drug Administration (FDA) Bacteriological Analytical Manual (BAM) Chapter 19c method has improved sensitivity but still requires refinement. Although Eimeria spp. offer insight into sporulation and environmental behaviors and C. parvum has supported methodological development, neither fully replicates C. cayetanensis biology; limiting the translatability of surrogate-based research. Remediation strategies are underexplored, though research on related coccidia suggests significant resistances to conventional sanitizers. Genomic advancements, including the identification of distinct C. cayetanensis lineages, provide useful insights, though gaps in genome assemblies limit phylogenetic and functional analyses. Emerging tools, such as metagenomics, single-cell sequencing, and AI-driven bioinformatics, may overcome persistent barriers. Addressing these challenges is essential for improving detection, risk assessment, and guiding policy, all of which will mitigate the public health burden of cyclosporiasis.