Population genetic analysis of Enterocytozoon bieneusi in humans

► Thirty-nine multilocus genotypes were identified among 72 human Enterocytozoon bieneusi isolates. ► Strong intragenic linkage disequilibria and limited genetic recombination were detected among five genetic loci. ► Enterocytozoon bieneusi was shown to have an overall clonal population structure. ► There were two genetically isolated groups in E. bieneusi: one anthroponotic and one zoonotic. ► MLST analysis of five markers was useful in delineating the population genetic structure of E. bieneusi.