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This study analyzed 893 fecal specimens of diarrheic and nondiarrheic pigs from 17 cities,northeast China for the prevalence and genetic characteristics of Enterocytozoon bieneusi.The parasite was detected in 422 of 893(47.3%)pigs by nested PCR of the ribosomal intemal transcribed spacer(ITS),giving a prevalence of 35.1%in diarrheic animals(61/174)and 50.2%in nondiarrheic animals(361/719).The difference in prevalence between preweaned(50.4%,141/280)and growing pigs(37.5%,141/376)and between weaned(59.1%,140/237)and growing pigs is significant(p < 0.05).Genotypic typing and phylogenetic analysis facilitated identification of 15 known genotypes CC-1,CHN7,D,EbpA,EbpB,EbpC,EbpD,G,H,Henan-Ⅰ,Henan-Ⅲ,Henan-Ⅳ,O,PigEBITS3,and PigEBITS5 and 10 novel genotypes CS-1 to CS-10.Among those,CS-4,D,EbpA,EbpC,EbpD,H,Henan-Ⅰ,Henan-Ⅲ,Henan-Ⅳ,O,and PigEBITS5 are human-pathogenic genotypes and CS-8,D,EbpA,EbpB,EbpC,EbpD,G,Henan-Ⅰ,and O are the contributors to water contamination.This study also investigated fecal specimens from children of various age groups and clinic presentations for the E.bieneusi prevalence(7.5%,19/255)and genotypes(CS-4,EbpC,Henan-Ⅳ,and NEC1 to NEC5).The most dominant genotype EbpC found in pigs from Changchun,Songyuan,Daqing,and Qiqihar contributed significantly to human infections in Daqing and Harbin.Genotypes CS-4 and EbpC from Harbin and Henan-Ⅳ from Qiqihar,Suihua,and Changchun determined in pigs herein represented the main causative agents of human microsporidiosis in Harbin.This study provided robust evidence that pigs could be an outstanding source of human microsporidiosis and water contamination in China.