Prevalence of Enterocytozoon bieneusi and Encephalitozoon spp. in Swedish patients with suspected gastrointestinal parasite infection: a cross-sectional molecular study

Microsporidia are opportunistic fungal parasites that may cause gastrointestinal disease in humans, mainly in immunocompromised individuals; yet contemporary prevalence data from Northern Europe are limited. The purpose of this study was to determine the prevalence of Enterocytozoon bieneusi and Encephalitozoon spp. in fecal samples from immunocompromised patients compared with reference patients without documented immunosuppression in Sweden. In this cross-sectional study, 1,238 fecal samples submitted for routine intestinal parasite diagnostics in 2023 at two Swedish microbiology laboratories were included. Samples originated from 619 immunocompromised patients and 619 age- and sex-matched reference patients. Real-time PCR was used to detect E. bieneusi and Encephalitozoon spp. All samples were additionally analyzed for Entamoeba histolytica, Cryptosporidium spp., and Giardia intestinalis to enable comparison with other intestinal pathogens. Enterocytozoon bieneusi was detected significantly more often in immunocompromised patients than in reference patients (5.0% vs. 2.0%, p = 0.002). No cases of Encephalitozoon spp. were identified. The overall prevalence of E. bieneusi was similar between the two study sites (3.3% and 4.0%). No significant differences between groups were observed for Cryptosporidium spp., G. intestinalis, or E. histolytica. Immunocompromised patients in Sweden have a higher prevalence of E. bieneusi compared with reference patients. These findings provide updated prevalence data from a low-endemic setting and support the consideration of molecular diagnostics for microsporidia in selected patient groups.