A map of the historical spread of Cyclospora cayetanensis with a focus on the United States of America (USA)

Cyclospora cayetanensis causes significant seasonal foodborne illness, characterized by recent large-scale nationwide outbreaks. We are currently experiencing the largest recorded outbreak in USA history during the summer of 2026. The summer 2026 outbreak emphasizes the urgent need for enhanced surveillance of infectious diseases. In this study, we use phylogenetic network analysis via the StrainHub framework to reconstruct the historical spread of C. cayetanensis in the USA using only mitochondrial sequence data and place of isolation metadata collected from 1997 to 2022. By quantifying parasite importation to localities through the metric indegree centrality, we identify Texas as a primary sink for C. cayetanensis introduction. Our finding aligns with historical epidemiologic investigations such as the 2013 multistate outbreak. While our model demonstrates the efficacy of reconstructing transmission pathways from molecular data alone, it also reveals critical surveillance gaps, particularly the masking of geographic origins in public datasets and the current absence of molecular data for the 2026 event. Moving forward, integrating real-time molecular surveillance with robust network analysis is essential to shift from reactive to proactive intervention strategies. We conclude that improved data sharing and reporting across food, clinical, and farm sectors are vital for disrupting transmission cycles of parasites. This work will protect public health and ensure a fresh clean supply of key foods for the nutrition of Americans.