Multilocus sequence typing of Enterocytozoon bieneusi in nonhuman primates in China

To infer population genetics of Enterocytozoon bieneusi in nonhuman primates (NHPs), 126 positive specimens in 839 fecal specimens from 23 NHP species in China based on ITS locus were used, belonging to genotypes Type IV, D, Peru8, Henan V, Peru11, PigEBITS7 and 3 novel ones (CM1, CM2 and CM3). Multilocus sequence typing employing four micro and minisatellites (MS1, MS3, MS4 and MS7) and ITS were used to analyze population structure of 85 isolates successfully amplified at all five loci, which yielded 59 multilocus genotypes. Linkage disequilibrium (LD) was measured using both multilocus sequences and allelic profile data. The observation of strong and significant LD with limited recombination in multilocus sequence analysis indicated the presence of overall clonal population structure of E. bieneusi, which was supported by allelic profile data analysis. Fu's selective neutrality test demonstrated the absence of neutral mutations and molecular selection. The population structure of common ITS genotypes (CM1, Type IV and D) was compared. Strong LD in multilocus sequence analysis versus insignificant LD and/or LE in allelic profile data analysis implied epidemic population in common ITS genotypes. No significant genetic isolation was evidenced by either phylogenetic or substructural analyses. The population genetics was also compared among the sub-population 1 (contained mainly genotype Type IV), sub-population 2 (contained mainly genotypes CM1 and D), sub-population 3 (contained mixed genotypes) and sub-population 4 (contained genotype Henan V). The presence of strong LD in multilocus data analysis with insignificant LD and/or LE in allele profile data analysis suggested the epidemic population in sub-populations.