Molecular Detection, Multilocus Genotyping, and Population Genetics of Enterocytozoon bieneusi in Pigs in Southeastern China

Abstract

Enterocytozoon bieneusi is an important opportunistic pathogen widely distributed in humans and animals that causes diarrhea or fatal diarrhea in immunocompromised hosts. To examine the infection status and molecular characteristics of E. bieneusi in pigs, 725 fecal samples were collected from pigs in six areas of Fujian Province. The E. bieneusi genotypes were identified based on the internal transcribed spacer (ITS) regions of the ribosomal RNA (rRNA) gene by nested PCR, and its population genetics were analyzed by multilocus sequence typing (MLST). The results showed that the infection rate of E. bieneusi was 24.4% (177/725), and 11 known genotypes (EbpC, EbpA, CHN‐RR2, KIN‐1, CHG7, CHS5, CM11, CHG23, G, PigEBITS, and D) and 2 novel genotypes (FJF and FJS) were identified. All the genotypes were found to be clustered into zoonotic Group 1. Moreover, 52 positive samples were successfully amplified at minisatellite and microsatellite loci and formed 48 distinct multilocus genotypes (MLGs). Further population structure analyses showed strong genetic linkage disequilibrium (LD) and several recombination events (Rm), indicating that E. bieneusi has a clonal population structure. This study is the first to investigate the prevalence and molecular characteristics of E. bieneusi in Fujian Province and could provide baseline data to control E. bieneusi infection in pigs and humans and deepen our understanding of the zoonotic risk of E. bieneusi and its distribution in China.

Multilocus sequence typing of Enterocytozoon bieneusi in crab-eating macaques (Macaca fascicularis) in Hainan, China

“…Currently, multilocus sequence typing has been used to analyze the genetic diversity of E. bieneusi around the world [15,42,43]. In Peru, India and Nigeria, 66 MLGs were identified in HIV-infected individuals [33,37].…”

“…In Peru, India and Nigeria, 66 MLGs were identified in HIV-infected individuals [33,37]. In China, 59 and 44 MLGs were identified in NHPs and pigs, respectively, while some genetic diversity based on MLST data was also observed in E. bieneusi isolates from domestic, wild, and zoo animals [29,36,[42][43][44][45][46][47][48]. However, few studies analyzed the MLGs of this pathogen in NHPs in China.…”

Multilocus Sequence Typing of Enterocytozoon bieneusi Isolates From Various Mammal and Bird Species and Assessment of Population Structure and Substructure

“…2013) and from animals in China (Li et al, 2017;Wang et al, 2019;Zhang et al, 2020). However, genetic segregation at some geographical level appeared in the other studies conducted in China (Wan et al, 2016;Wang et al, 2018a;.…”

“…Five genotypes in Table 4 have been changed to the first published names instead of genotype names described in original papers: CM1 to Macaque3 (Karim et al, 2014); Henan-I to LW1 (Wan et al, 2016); CHG19 to PigEBITS4 (Wang et al, 2018a;; CHS5 to EbpA (Wang et al, 2018a;Zhang et al, 2020); CM6 to CS-4 (Wang et al, 2018a). a 39 E. bieneusi isolates are derived from foxes (n = 30) and raccoon dogs (n = 9).…”

“…To date, MLST analysis have been performed in at least 167 ITS genotypes of E. bieneusi in at least ten countries, with 23 from humans and 151 from animals ( Supplementary Table S1 ). Some MLST data have been used to assess population structures of E. bieneusi isolates derived from different hosts: AIDS patients ( Li et al, 2012 , 2013 ), non-human primates (NHPs) ( Karim et al, 2014 ), pigs ( Wan et al, 2016 ; Wang et al, 2018a ; Li et al, 2019 ; Zhang et al, 2020 ), foxes and raccoon dogs ( Li et al, 2016b ), captive giant pandas ( Li et al, 2017 ), and dairy cattle ( Wang et al, 2019 ). Meanwhile, some studies also explored the issues of E. bieneusi population genetics in relation to geographical origins and host origins ( Li et al, 2013 , 2016b , 2017 , 2019 ; Wan et al, 2016 ; Wang et al, 2018a , 2019 ; Zhang et al, 2020 ).…”