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Notes: Intestinal microsporidiosis caused by Enterocytozoon bieneusi and Encephalitozoon intestinalis are opportunistic infections occurring in severely immuno-depressed patients, and may cause severe chronic diarrhea. Due to the extent of the HIV pandemic, microsporidia could pose a serious threat to public health in Africa. This study was conducted in Libreville, Gabon, central Africa, among HIV-positive patients between September 2002 and December 2003. Criteria for inclusion were being HIV positive (HIV1 and/or HIV2), regardless of the CD4 cell count, stage of the disease or gastrointestinal symptoms. Nine hundred and ninety-tree stool samples from 836 patients (mean age 38 years, range 18 months-74 years) were screened for microsporidia by immunofluorescence using species-specific monoclonal antibodies and confirmed by PCR. Twenty seven cases of E. bieneusi infection were found in the cohort, a prevalence of 2.7%. These patients were in the most severely immuno-depressed group, 84% had a CD4 cell count below 200/mm3 compared to 57% of the cohort (mean=55 CD4+cells/mm3 compared to a mean of 88/mm3 for the microsporidia negative patients with less than 200 CD4/mm3).The ribosomal DNA ITS sequence has been determined for several E. bieneusi isolates. A very high diversity of genotypes wasfound: eight different sequences were found from only 12 samples. This is surprisingly high since in previous studies conducted in Europe and America only 15 of the 49 E. bieneusi genotypes described have been found to infect humans. Only three genotypes from our samples have already been described: type K (two specimens). previously reported in human and cat, type D (one specimen) in human, pig and rhesus monkey, type E (1 specimen) in man, pig, racoon and muskrat. The five other genotypes are new and have been named Gabon-1 to 5. The phylogenetic analysis of the sequences shows that genotypes Gabon-1,2,3 and 4 (one specimen each) are close to types E, WL12, D and K, respectively, which belong to a group comprising most genotypes described so far. However, the Gabon-5 genotype (four specimens) is only distantly related to this group and is most apparent to the group of genotypes (WL1-3) recently described from racoons in North America. It was thus suggested that this group could represent another species or subspecies of E. bieneusi which are host-adapted and do not infect humans. However, the finding of genotype Gabon-5 shows that even distantly related genotypes infect severely immuno-depressed humans.This work was supported by the French National Agency for AIDS Research (ANRS-1264).