Molecular characterization of Enterocytozoon bieneusi has led to better understanding of microsporidiosis transmission in humans. This study aimed to detect and genotype E. bieneusi in human immunodeficiency virus (HIV)-infected persons. Stool specimens were collected from 463 HIV-infected patients and analyzed for E. bieneusi by polymerase chain reaction (PCR) and DNA sequence analysis of the internal transcribed spacer. E. bieneusi was detected in 77 HIV patients. CD4 cell counts < 200 cells/μL was associated with E. bieneusi infection (P = 0.09). E. bieneusi was significantly associated with weight loss (P < 0.0001), diarrhea (P = 0.006), fever (P < 0.0001), not being married (P < 0.0001), and flush type of toilet (P = 0.0007). Six known genotypes of D, A, IV, CAF2, EbpA, and Peru 8 in 31, 22, 14, 2, 1, and 1 patients, respectively, five novel genotypes of E. bieneusi, and one infection with mixed genotypes were observed in this study. Three of the novel genotypes were genetically distant to the genotypes commonly found in humans.
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