Novel insights on the genetic population structure of human-infecting spp. and evidence for rapid subtype selection among isolates from the USA.

Human-infecting was recently characterized as three species, two of which ( and ) are currently responsible for all known human infections in the USA, yet much remains unknown about the genetic structure within these two species. Here, we investigate genotyping data from 2018 through 2022 to ascertain if there are temporal patterns in the genetic structure of parasites that cause infections in US residents from year to year. First, we investigate three levels of genetic characterization: species, subpopulation, and strain, to elucidate annual trends in infections. Next, we determine if shifts in genetic diversity can be linked to any of the eight loci used in our genotyping approach. We observed fluctuations in the abundance of types at the species and subpopulation levels, but no significant temporal trends were identified; however, we found recurrent and sporadic strains within both and . We also uncovered major shifts in the mitochondrial genotypes in both species, where there was a universal increase in abundance of a specific mitochondrial genotype that was relatively abundant in 2018 but reached near fixation (was observed in over 96% of isolates) in by 2022. Similarly, this allele jumped from 29% to 82% relative abundance of isolates belonging to . Overall, our analysis uncovers previously unknown temporal-genetic patterns in US types from 2018 through 2022 and is an important step to presenting a clearer picture of the factors influencing cyclosporiasis outbreaks in the USA.