Clonal Evolution of Enterocytozoon bieneusi Populations in Swine and Genetic Differentiation in Subpopulations between Isolates from Swine and Humans.

Yijing Li,Xichen Zhang,Yixin Lu,Wei Li,Lihua Xiao,Qiang Wan,Mingxin Song

doi:10.1371/journal.pntd.0004966

Abstract

Enterocytozoon bieneusi is a widespread parasite with high genetic diversity among hosts. Its natural reservoir remains elusive and data on population structure are available only in isolates from primates. Here we describe a population genetic study of 101 E. bieneusi isolates from pigs using sequence analysis of the ribosomal internal transcribed spacer (ITS) and four mini- and microsatellite markers. The presence of strong linkage disequilibrium (LD) and limited genetic recombination indicated a clonal structure for the population. Bayesian inference of phylogeny, structural analysis, and principal coordinates analysis separated the overall population into three subpopulations (SP3 to SP5) with genetic segregation of the isolates at some geographic level. Comparative analysis showed the differentiation of SP3 to SP5 from the two known E. bieneusi subpopulations (SP1 and SP2) from primates. The placement of a human E. bieneusi isolate in pig subpopulation SP4 supported the zoonotic potential of some E. bieneusi isolates. Network analysis showed directed evolution of SP5 to SP3/SP4 and SP1 to SP2. The high LD and low number of inferred recombination events are consistent with the possibility of host adaptation in SP2, SP3, and SP4. In contrast, the reduced LD and high genetic diversity in SP1 and SP5 might be results of broad host range and adaptation to new host environment. The data provide evidence of the potential occurrence of host adaptation in some of E. bieneusi isolates that belong to the zoonotic ITS Group 1.

Highlights

Microsporidia are obligate intracellular eukaryotic parasites that infect a wide range of animals and are closely related to fungi [1,2]
This study explored the genetic characteristics of the internal transcribed spacer (ITS) and four mini- and microsatellite markers and assessed the population structure and substructures in 101 E. bieneusi isolates from pigs in China
The measures of linkage disequilibrium (LD) and recombination events supported the occurrence of clonal evolution among the isolates from four study areas of China

Summary

Introduction

Microsporidia are obligate intracellular eukaryotic parasites that infect a wide range of animals and are closely related to fungi [1,2]. E. bieneusi is the most common human microsporidian species and can colonize a variety of other mammals and birds [2,9]. This ubiquitous pathogen causes diarrhea of various severity and duration in relation to host immune status [2,10]. Genotyping of isolates has improved our understanding of the genetic characteristics and the potential transmission modes of E. bieneusi among hosts. Over 200 E. bieneusi genotypes have been identified in humans, companion animals, livestock, horses, birds, and wildlife based on DNA sequence analysis of the ribosomal internal transcribed spacer (ITS) and the established naming convention [13,14]. Humans and pigs are mainly infected with the zoonotic Group 1 genotypes, ruminants with host-adapted Group 2 genotypes, and dogs with the genotypes in an outlier group [2,16,17,18,19,20,21,22]

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