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Background   Enterocytozoon bieneusi  and  Cryptosporidium  spp. are prevalent zoonotic parasites associated with a high burden among children. To date only limited molecular epidemiological data on  E. bieneusi  and  Cryptosporidium  spp. in humans living in Thailand has been published.    Methods  PCR-based tools were used to detect and characterize  E. bieneusi  and  Cryptosporidium  spp. The internal transcribed spacer (ITS) region of the rRNA gene was used to investigate  E. bieneusi , and the small subunit (SSU) rRNA gene was used to investigate  Cryptosporidium  spp., and 697 fecal samples from villagers and school children in rural areas in Thailand were analyzed.    Results  The infection rates were 2.15% (15/697) for  E. bieneusi  and 0.14% (1/697) for  Cryptosporidium  spp. The prevalence of  E. bieneusi  was significantly high in Loei province. Sequence analysis indicated that the  Cryptosporidium  isolate was  C. parvum . Nine  E. bieneusi  genotypes were identified, EbpC, Peru12, TMH6, TMH3, TMH7, H, D, and two novel genotypes TMLH1 and TMLH2.  E. bieneusi  prevalence was significantly higher in male participants than in female participants, and in children aged 3–15 years than in participants aged > 15 years.    Conclusions  The prevalence, genotypes, and zoonotic potential of  E. bieneusi  were found to vary significantly high even in one country. Transmission routes and key animal carriers of  E. bieneusi  may be associated with differences in hygiene, sanitation, and cultural behaviors. Further molecular studies including longitudinal studies will be required to unveil epidemiological characteristics of these opportunistic intestinal protozoa in all over the countries.

“Enterocytozoon bieneusi and Cryptosporidium: a cross-sectional study conducted throughout Thailand”