Multilocus sequence typing of Enterocytozoon bieneusi: Lack of geographic segregation and existence of genetically isolated sub-populations

Wei Li, Vitaliano Cama, Frederick O. Akinbo, Sandipan Ganguly, Nicholas M. Kiulia, Xichen Zhang, Lihua Xiao

Research output: Contribution to journalArticlepeer-review

43 Scopus citations


The population structure of Enterocytozoon bieneusi was examined by multilocus sequence typing (MLST) of 64 specimens from AIDS patients in Peru, Nigeria, and India and five specimens from captive baboons in Kenya using a combination of the ribosomal internal transcribed spacer (ITS) and four microsatellite and minisatellite markers. Parasites in different geographic locations (Peru, India, and Nigeria) all had strong and significant linkage disequilibrium (LD) and only limited recombination, indicative of a clonal population structure in E. bieneusi from each location. When isolates of various geographical areas were treated as a single population, phylogenetic analysis and substructural analysis using STRUCTURE found no evidence for the existence of geographically segregated sub-populations. Nevertheless, both analyses revealed the presence of two major genetically isolated groups of E. bieneusi: one (sub-population 1) contained all isolates of the anthroponotic ITS genotype A, whereas the other (sub-population 2) harbored isolates of multiple ITS genotypes with zoonotic potential. This was also supported by FST analysis. The measurement of LD and recombination rates indicated that sub-population 2 had a clonal population structure, whereas sub-population 1 had an epidemic population structure. The data confirmed the existence of genetic sub-populations in E. bieneusi that may be transmitted differently in humans.

Original languageEnglish (US)
Pages (from-to)111-119
Number of pages9
JournalInfection, Genetics and Evolution
Issue number1
StatePublished - 2013
Externally publishedYes


  • Enterocytozoon bieneusi
  • Gene diversity
  • Linkage disequilibrium
  • Multilocus sequence typing
  • Population genetics
  • Population structure

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Molecular Biology
  • Microbiology
  • Infectious Diseases
  • Microbiology (medical)


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