Abstract Background Cryptosporidium and Microsporidia are major opportunistic pathogens in individuals with HIV, frequently causing gastrointestinal manifestations. Molecular identification of these parasites provides crucial insights into their transmission dynamics, clinical relevance, and zoonotic potential. Methods This cross-sectional study investigated 275 HIV-infected patients in Alborz Province, Iran (2018–2020). Stool samples were examined using Ziehl–Neelsen and modified trichrome staining, followed by PCR amplification and sequencing of the 18 S rRNA and GP60 genes for Cryptosporidium spp., and the ITS region for Enterocytozoon bieneusi and Encephalitozoon intestinalis . Associations between parasitic infections and demographic/clinical variables were analyzed using univariate and multivariable methods. Results Molecular analysis identified Cryptosporidium spp. in 7.6% and Microsporidia in 9.1% of patients, including E. bieneusi (6.5%), E. intestinalis (2.5%), and mixed infections (1.8%). Subtyping revealed that C. parvum (5.8%) predominantly belonged to subtype family IId (IIdA20G1, IIdA19G1), while C. hominis (1.8%) was IdA15G1. E. bieneusi genotypes D, Peru6, and J were detected—genotype J being reported for the first time in Iranian HIV-positive patients. Infections were significantly associated with clinical symptoms including chronic diarrhea, abdominal pain, vomiting, and fever. The highest rates of infection were found among patients with CD4 + counts < 200 cells/µL, no history of ART, animal contact, and use of well water. Conclusions This study highlights the clinical and epidemiological significance of Cryptosporidium , E. bieneusi , and E. intestinalis in HIV-infected individuals. The identification of zoonotic genotypes and their association with gastrointestinal symptoms and immunosuppression emphasizes the need for routine molecular screening, targeted public health interventions, and adoption of One Health strategies to control transmission.
Djawadi et al. (Thu,) studied this question.