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This study aimed to genotype and analyze the phylogeny ofEnterocytozoon bieneusi along with its prevalence in nonhuman primates (NHPs) based on ITS marker.A total of 1386 fecal specimens from 23 NHP species from five provinces in China were examined by PCR amplification of ITS locus.E.bieneusi was detected in 158(11.40%)specimens of only five NHP species including cynomolgus monkey(67.74%),rhesus macaque(8.78%),Japanese macaque (33.33 %),whitE-headed langur (13.61%) and golden snub:nosed monkey(3 A5%) (P<0.0001).The infection rates were 70.18%,21.53%,8.54%,7.53% and 5.59% in Guangdong,Yunnan,Guangxi,Henan and Sichuan Provinces,respectively (P<0.0001).The prevalence was significantly higher in captive NHPs (13.65%) than those in free range (5%) (P<0.0001).Altogether,16 E.bieneusi ITS genotypes were observed,consisting of nine known ones (Type Ⅳ,D,Henan Ⅴ,Peru8,PigEBITS7,EbpC,Peru11,BEB6 and Ⅰ) and seven new genotypes (CM1 to CM7).The major genotypes were CM1,Type Ⅳ and D,being detected in 43,31 and 30 specimens,res pectively.Phylogenetic analysis revealed that seven known genotypes (except BEB6 and Ⅰ) and four new genotypes (CM 1,CM2,CM3 and CM6) belonged to previously described human pathogenic group having zoonotic potentials.Genotypes CM5 and CM7 clustered with cattle specific genotypes whereas genotype CM4 was placed out of any of previously proposed groups.It was concluded that the presence of same major genotypes in both humans andnonhuman primatesresiding in the samegeographical location signified the role ofnonhuman primates in zoonotic transmission ofE.bieneusi.