We identified genotypes of Enterocytozoon bieneusi from 33 stool samples of Thai human immunodeficiency virus (HIV)-infected adult patients. Genotype D was identified at the highest frequency (36.4%), while genotype E was the second most common (15.1%). Genotypes O and PigEBITS 7, previously found only in pigs, were observed in Thai HIV-infected patients. Phylogenetic analysis supported a zoonotic nature for E. bieneusi.

An evaluation of the sensitivities of three DNA extraction methods, i.e., FTA filter paper, a QIAamp stool mini kit, and a conventional phenol-chloroform method, by using specimens with known concentrations of Enterocytozoon bieneusi spores was performed. FTA filter paper and the QIAamp stool mini kit were the most sensitive methods, which could detect E. bieneusi in specimens with a concentration of 800 spores/ml. We also compared five previously described PCR methods that use five different primer pairs for the detection of E. bieneusi and showed that MSP3-MSP4B and EBIEF1-EBIER1 were the most sensitive primers. Although both sets of primers showed the same sensitivity, using the MSP3-MSP4B primers can directly provide genotypic information by sequencing. A blinded diagnostic test to compare PCR and light microscopy methods for the detection of E. bieneusi in stool specimens was also conducted. The use of FTA filter paper for DNA extraction together with the PCR method using the primer pair MSP3-MSP4B showed 100% sensitivity and 100% specificity for the detection of E. bieneusi in stool specimens, while the light microscopy method gave a sensitivity of 86.7% and a specificity of 100%.

A cross-sectional study of Enterocytozoon bieneusi infection in children who lived in an orphanage in Bangkok, Thailand was conducted in April 2003. Two hundred ninety stool specimens were collected and examined under light microscopy after staining with gram-chromotrope. Confirmation of E. bieneusi was done using transmission electron microscopy. Of 290 samples, 12 (4.1%) were positive for E. bieneusi. Genotypic characterization of 10 E. bieneusi showed that all were genotype A, which might indicate the same source of infection. Multivariate analysis showed that orphans who were 12-23 months old, girls, and living in one particular house were independently associated with E. bieneusi infection. Our study suggests that E. bieneusi infection in this orphanage might be transmitted person to person.

We determined that 15.7% of pigs and 1.4% of humans in a pig farm community in central Thailand harbored Enterocytozoon bieneusi. Genotyping of E. bieneusi from pigs showed genotypes O, E, and H. However, only genotype A was found in human subjects. This indicates nonzoonotic transmission of E. bieneusi in this community.

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Stool samples from seven human immunodeficiency virus (HIV)-negative and two HIV-positive children with asymptomatic Enterocytozoon bieneusi infections were daily examined to quantify spore shedding using Gram-chromotrope staining under light microscopy. The spore shedding pattern and intensity in these children was variable. Mean spore concentrations in the stool samples from these children ranged from 2.4 × 102 to 1.2 × 105 spores per gram. Light microscopy could detect spores in stool specimens for 9–33 days, while PCR was able to detect E. bieneusi in stool specimens for 3–40 days longer. This suggests that light microscopy may not detect low levels of spore shedding. Considering that the asymptomatic group are a potential source of infection, detection methods with a higher sensitivity should be used.

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