Molecular Characterization of Giardia duodenalis and Enterocytozoon bieneusi Isolated from Tibetan Sheep and Tibetan Goats Under Natural Grazing Conditions in Tibet

Global prevalence of Giardia infection in nonhuman mammalian hosts: A systematic review and meta-analysis of five million animals

BACKGROUND

Members of the Giardia genus are zoonotic protozoan parasites that cause giardiasis, a diarrheal disease of public and veterinary health concern, in a wide range of mammal hosts, including humans.

METHODOLOGY

We conducted a systematic review and meta-analysis to provide evidence-based data on the worldwide prevalence of Giardia infection in nonhuman mammals that can be used as scientific foundation for further studies. We searched public databases using specific keywords to identify relevant publications from 1980 to 2023. We computed the pooled prevalence estimates utilizing a random-effects meta-analysis model. Animals were stratified according to their taxonomic hierarchy, as well as ecological and biological factors. We investigated the influence of predetermined variables on prevalence estimates and heterogeneity through subgroup and meta-regression analyses. We conducted phylogenetic analysis to examine the evolutionary relationships among different assemblages of G. duodenalis.

PRINCIPAL FINDINGS

The study included 861 studies (1,632 datasets) involving 4,917,663 animals from 327 species, 203 genera, 67 families, and 14 orders from 89 countries. The global pooled prevalence of Giardia infection in nonhuman mammals was estimated at 13.6% (95% CI: 13.4-13.8), with the highest rates observed in Rodentia (28.0%) and Artiodactyla (17.0%). Herbivorous (17.0%), semiaquatic (29.0%), and wild (19.0%) animals showed higher prevalence rates. A decreasing prevalence trend was observed over time (β = -0.1036477, 95% CI -0.1557359 to -0.0515595, p < 0.000). Among 16,479 G. duodenalis isolates, 15,999 mono-infections belonging to eight (A-H) assemblages were identified. Assemblage E was the predominant genotype (53.7%), followed by assemblages A (18.1%), B (14.1%), D (6.4%), C (5.6%), F (1.4%), G (0.6%), and H (0.1%). The highest G. duodenalis genetic diversity was found in cattle (n = 7,651, where six assemblages including A (13.6%), B (3.1%), C (0.2%), D (0.1%), E (81.7%), and mixed infections (1.2%) were identified.

CONCLUSIONS/SIGNIFICANCE

Domestic mammals are significant contributors to the environmental contamination with Giardia cysts, emphasizing the importance of implementing good management practices and appropriate control measures. The widespread presence of Giardia in wildlife suggests that free-living animals can potentially act as sources of the infection to livestock and even humans through overlapping of sylvatic and domestic transmission cycles of the parasite.

Investigation of Cryptosporidium spp. and Enterocytozoon bieneusi in free-ranged livestock on the southeastern Qinghai-Xizang Plateau, China

BACKGROUND

Cryptosporidium spp. and Enterocytozoon bieneusi are zoonotic pathogens with global distribution, infecting humans and various livestock. For yaks, Tibetan sheep and horses, the traditional grazing models still hold a main position. After these animals become infected, it not only hinders the development of animal husbandry but also increases the risk of Cryptosporidium spp. and E. bieneusi transmission between livestock and herdsmen.

METHODS

In the present study, a total of 750 fecal samples were collected from yaks, Tibetan sheep and horses in Shiqu County, Sichuan Province, from July to August 2023, and were analyzed by nested Polymerase chain reaction (PCR) amplification of the small subunit ribosomal RNA (SSU rRNA) gene of Cryptosporidium spp. and internal transcribed spacer (ITS) gene of E. bieneusi.

RESULTS

The prevalence of Cryptosporidium spp., and E. bieneusi were 2.1% (16/750) and 1.5% (11/750), respectively. Mixed infections of Cryptosporidium spp. and E. bieneusi were detected in two samples. Among these positive fecal samples, one Cryptosporidium species (Cryptosporidium suis) was identified in the yaks (n = 11), Tibetan sheep (n = 1), and horses (n = 4). Three E. bieneusi genotypes, including a known genotype BEB4 and two novel ones SQY1 and SQY2, were identified in the yaks (n = 7), while in Tibetan sheep (n = 4) only the known genotype BEB4 was detected. The novel genotype SQY1 was grouped into the human-pathogenic Group 1, and the known genotype BEB4 and the novel genotype SQY2 were grouped into Group 2. Enterocytozoon bieneusi was not detected in horses.

CONCLUSIONS

Cryptosporidium suis was identified in yaks and horses while zoonotic E. bieneusi genotype BEB4 in Tibetan sheep for the first time, expanding their host ranges. These findings suggested that yaks, Tibetan sheep and horses could act as potential sources of human Cryptosporidium spp. and E. bieneusi infections, implying that the presence of zoonotic species/genotypes could pose a threat to public health.

Prevalence and genetic diversity of Giardia duodenalis in sheep from large-scale farms in Southern Xinjiang, China

Giardia duodenalis is a significant zoonotic parasite. In this study, 767 fresh fecal samples were collected randomly from six large-scale sheep farms in Southern Xinjiang, China. Initially, G. duodenalis was screened using PCR at the SSU rRNA gene. Positive samples then underwent PCR amplification at the bg, gdh, and tpi genes. The prevalence of G. duodenalis in sheep was 17.5% (134/767), with the highest prevalence observed in the 3-6 months age group at 26.8% (56/209) and the lowest in the over 12 months age group at 6.8% (14/205). Among the 134 positive samples, only Assemblage E was identified. A total of 106, 92, and 98 sequences of G. duodenalis were obtained at the gdh, tpi, and bg genes, respectively. Fourteen isolates of G. duodenalis were successfully amplified at all three genes, resulting in nine G. duodenalis multilocus genotypes (MLG) named MLG E1-MLG E14, indicating high genetic diversity. In conclusion, G. duodenalis infection in sheep from large-scale farms is common in Southern Xinjiang, China, showing geographical regional distributions and genetic diversity.

Molecular prevalence and genotype identification of Enterocytozoon bieneusi in cattle and goats from Zhejiang Province, China

Introduction

Enterocytozoon bieneusi (E. bieneusi) is a widespread intracellular fungi that poses a significant zoonotic threat due to its infectivity toward both humans and animals.

Methods

To evaluate the zoonotic transmission potential of this fungi, a molecular investigation was undertaken on E. bieneusi in cattle and goats reared across multiple cities in Zhejiang Province, China. A total of 651 fresh samples were collected, consisting of 265 cattle and 386 goats. The presence of E. bieneusi was determined by PCR amplification and sequencing analysis of the internal transcribed spacer (ITS) region of the small subunit ribosomal RNA (SSU rRNA) gene in all collected samples.

Results

The results revealed that 17.1% (111/859) of the animals were afflicted with E. bieneusi, cattle having a prevalence of 14.0% (37/265) and goats displaying a higher rate of 19.2% (74/386). Seventeen E. bieneusi genotypes were identified, including 10 known, CHG5 (n = 30), CHG3 (n = 21), I (n = 14), J (n = 12), CHG2 (n = 11), COS-II (n = 8), D (n = 4), CHG19 (n = 2), ETMK5 (n = 1), and Henan III (n = 1), and seven novel, ZJG-I to ZJG-VI and ZJN-I (one each) genotypes.

Discussion

These findings indicate widespread infection of E. bieneusi among the surveyed animals, thereby raising concerns about zoonotic genotypes that could pose potential threats to public health. Furthermore, the identification of novel genotypes of E. bieneusi offers valuable insights into the genetic diversity of this pathogen.

Unnoticed antimicrobial resistance risk in Tibetan cities unveiled by sewage metagenomic surveillance: Compared to the eastern Chinese cities

Sewage surveillance is a cost-effective tool for assessing antimicrobial resistance (AMR) in urban populations. However, research on sewage AMR in remote areas is still limited. Here, we used shotgun metagenomic sequencing to profile antibiotic resistance genes (ARGs) and ARG-carrying pathogens (APs) across 15 cities in Tibetan Plateau (TP) and the major cities in eastern China. Notable regional disparities in sewage ARG composition were found, with a significantly higher ARG abundance in TP (2.97 copies/cell). A total of 542 and 545 APs were identified in sewage from TP and the East, respectively, while more than 40 % carried mobile genetic elements (MGEs). Moreover, 65 MGEs-carrying APs were identified as World Health Organization (WHO) priority-like bacterial and fungal pathogens. Notably, a fungal zoonotic pathogen, Enterocytozoon bieneusi, was found for the first time to carry a nitroimidazole resistance gene (nimJ). Although distinct in AP compositions, the relative abundances of APs were comparable in these two regions. Furthermore, sewage in TP was found to be comparable to the cities in eastern China in terms of ARG mobility and AMR risks. These findings provide insights into ARGs and APs distribution in Chinese sewage and stress the importance of AMR surveillance and management strategies in remote regions.

Investigation of the Infection of Enterocytozoon bieneusi in Sheep and Goats in Jiangsu, China

In order to investigate the infection status and genotypes of Enterocytozoon bieneusi (E. bieneusi) in sheep and goats in Jiangsu Province, a total of 786 fresh fecal samples from 18 farms across five regions in Jiangsu were collected and examined for the presence of E. bieneusi, and the genotype of E. bieneusi was examined using nested-PCR and sequencing of the ribosomal internal transcribed spacer. The results showed that E. bieneusi was detected in the fecal samples of sheep and goats in all regions, with infection rates ranging from 23.65% to 42.81%. The overall infection rate was 36.51% (287/786). The infection rate of E. bieneusi showed no significant difference between sheep and goats, as well as among different ages of animals (p > 0.05), but showed a significant difference in sheep and goats with different health conditions (p < 0.05). The positive products were amplified and cloned and subjected to sequenced analysis. Six genotypes, BEB6, CHG2, CHG3, CHC8, CHG14, and COS-I, were found. Phylogenetic analysis indicated that the six genotypes belonged to Group 2, which had previously been described as a non-zoonotic group.

Prevalence and Genetic Characterization of Giardia duodenalis and Blastocystis spp. in Black Goats in Shanxi Province, North China: From a Public Health Perspective

Blastocystis spp. and Giardia duodenalis are two prevalent zoonotic intestinal parasites that can cause severe diarrhea and intestinal diseases in humans and many animals. Black goat (Capra hircus) farming is increasingly important in China due to the remarkable adaptability, high reproductive performance, rapid growth rate, and significant economic value of black goats. A number of studies have indicated that black goats are the potential reservoir of multiple zoonotic protozoans in China; however, the prevalence and zoonotic status of G. duodenalis and Blastocystis spp. in black goats in Shanxi Province is still unknown. Thus, a total of 1200 fecal samples of black goats were collected from several representative regions at different altitudes in Shanxi Province and were examined for the presence and genotypes of G. duodenallis and Blastocystis spp. by amplifying the beta-giardin (bg), glutamate dehydrogenase (gdh), and triosephosphate isomerase (tpi) loci of G. duodenalis and SSU rRNA of Blastocystis spp. using PCR and sequence analysis methods, respectively. The overall prevalence of G. duodenalis and Blastocystis spp. in black goats in Shanxi Province were 7.5% and 3.5%, respectively. Two assemblages (B and E) of G. duodenalis and four subtypes (ST5, ST10, ST14, and ST30) of Blastocystis spp. were identified, with assemblage E and ST10 as the prevalent genotype and subtype in black goats, respectively. One novel multilocus genotype (MLG) was identified in MLG-E and was designated as MLG-E12. For both G. duodenalis and Blastocystis spp., the prevalence was significantly related to the region and age groups (p < 0.05). This is the first report on the prevalence of G. duodenalis and Blastocystis spp. in black goats in Shanxi Province. These results not only provide baseline data for the prevention and control of both parasites in black goats in Shanxi Province, but also enhance our understanding of the genetic composition and zoonotic potential of these two parasites.

Design and evaluation of loop-mediated isothermal amplification for rapid detection of Enterocytozoon bieneusi

Enterocytozoon bieneusi is one of the most prevalent microsporidia species, responsible for more than 90% of human and animal microsporidiosis. Microsporidia species, particularly E. bieneusi, are frequently reported from waterborne and foodborne outbreaks. Therefore, early detection is crucial in clinics and outbreak investigations. This study aimed to design a loop-mediated isothermal amplification (LAMP) for rapid detection of E. bieneusi. Total DNA was extracted from 30 E. bieneusi -positive samples, which had been confirmed with nested PCR. LAMP primers were designed based on the identical fragment of small subunit ribosomal RNA (SSU rRNA) gene. LAMP reactions were performed at 63 °C for 60 min. The sensitivity and specificity of the assay were analyzed and the results of amplification were compared to real-time PCR. Our results showed that the LAMP assay successfully amplified 25/30 (83.3%) samples. The specificity results indicated no false positive with other microorganisms. Furthermore, the LAMP method exhibited a sensitivity (limit of detection, LoD) as low as 34 ag/μL of total DNA. Compared to the LAMP assay, real-time PCR was able to detect all 30 nested PCR-positive samples. Our findings showed that the LAMP assay was able to detect 83.3% of E. bieneusi-positive samples. Although the current assay was not able to detect all nested PCR-positive samples, the lack of need for specific instruments, rapid processes, and high specificity makes LAMP assay a suitable tool for screening.

Occurrence and Phylogenetic Analysis of Zoonotic Enteropathogenic Protist Parasites in Asymptomatic Domestic Ruminants from Portugal

Enteropathogenic parasites are of significant concern for public health due to their zoonotic potential and their impact on human and animal health. In this study, we investigated their occurrence and characterized these enteropathogens in asymptomatic domestic ruminants from Portugal. A total of 302 stool samples were collected from cattle (n = 166), sheep (n = 73), and goats (n = 63) in various regions of Portugal and tested for Cryptosporidium spp., Giardia duodenalis, Enterocytozoon bieneusi, Blastocystis sp., and Balantioides coli by PCR. The occurrence of Cryptosporidium spp. was found to be 12.7% (8/63, 95% confidence interval [CI]: 5.65-23.5) in goats; however, no sample was found to be positive for Cryptosporidium spp. in cattle and sheep. For E. bieneusi, 6.35% (4/63; 95%CI: 1.76-15.47) of goats were found to be positive; however, no cattle or sheep were found to be positive. Blastocystis sp. was found in sheep (9.59%; 7/73; 95% [CI]: 0.394-18.76) and goats (12.70%; 8/63; 95% [CI]: 5.65-23.50) but none was found in cattle. No positive results for G. duodenalis or B. coli were detected in this study. This study provides essential baseline information for understanding the silent shedding and epidemiology of these enteropathogens in Portugal, contributing to overall livestock health and related occupational safety. Raising awareness among consumers, veterinarians, and farm owners is crucial to minimize the risk of transmission and promote effective disease control strategies.

Occurrence and Genotypic Identification of Blastocystis spp., Enterocytozoon bieneusi, and Giardia duodenalis in Leizhou Black Goats in Zhanjiang City, Guangdong Province, China

Blastocystis spp., Enterocytozoon bieneusi, and Giardia duodenalis are three common zoonotic intestinal parasites that cause severe diarrhea and enteric diseases. Leizhou black goats are characterized by a high reproductive rate, fast growth, and good meat quality, making them one of the pre-eminent goat breeds in China. Goats are reportedly common reservoirs of these three intestinal pathogens, but no information on their prevalence or genotypic distributions in black goats in Guangdong Province, China, is available. A total of 226 fecal samples were collected from goats in Zhanjiang city and genomic DNA was extracted from them. The presence of the three pathogens was detected using nested PCR targeting the sequences encoding SSU rRNA (Blastocystis spp.), the internal transcribed spacer of rRNA (ITS; E. bieneusi), as well as beta-giardin, glutamate dehydrogenase, and triosephosphate isomerase (G. duodenalis). All PCR products were sequenced to determine the species and genotypes of the organisms. The total prevalence rates of Blastocystis spp., E. bieneusi, and G. duodenalis were 33.63% (76/226), 17.70% (40/226), and 24.78% (56/226), respectively. Four subtypes of Blastocystis spp. were detected: ST5 (n = 6), ST10 (n = 50), ST14 (n = 14), and ST21 (n = 6). Among them, ST10 was the dominant genotype, accounting for 65.79% of strains, followed by the genotypes ST14 (18.42%), zoonotic ST5 (7.89%), and ST21 (7.89%). Four genotypes of E. bieneusi were detected: CHG3 (n = 32), CM21 (n = 4), CHG1 (n = 2), and ET-L2 (n = 2). Among these, CHG3 was the dominant genotype. Assemblage E (n = 54) and concurrent assemblages A and E (n = 2) were identified in the G. duodenalis-positive goats using multilocus genotyping. Blastocystis spp., E. bieneusi, and G. duodenalis infections were common in Leizhou black goats, all of which have zoonotic genotypes, indicating the potential risk of zoonotic transmission. Our results provide basic data for the prevention and control of these three intestinal pathogens. Further studies are required to better understand their genetic characteristics and zoonotic potential in Guangdong Province.

First report on the molecular detection of Enterocytozoon bieneusi in livestock and wildlife around Qinghai Lake in the Qinghai-Tibetan Plateau area, China

Enterocytozoon bieneusi is considered to be a microsporidial species of humans and animals in the worldwide. Limited data have been reported on the prevalence and genotypes of E. bieneusi in livestock and wild animals around Qinghai Lake in the Qinghai-Tibetan Plateau area, which shares water sources, grasslands, and harsh climate with high altitudes. In this study, fecal samples from 110 Tibetan sheep, 128 yaks, 227 wild birds, 96 blue sheep (Pseudois nayaur) and 268 Przewalski's gazelle (Procapra przewalskii) around Qinghai Lake were collected, and then tested for E. bieneusi by PCR and sequencing analysis based on the ribosomal internal transcribed spacer. Among them, ten (9.09%) samples from Tibetan sheep, five (3.91%) from yaks, five (2.20%) from wild birds, one (1.04%) from wild blue sheep and two (0.75%) from Przewalski's gazelle were positive for E. bieneusi. Among sheep, there were nine E. bieneusi genotypes, including two known genotypes (BEB6 and J), and seven novel genotypes (named CHS18-CHS24). From yaks, four genotypes were identified, including two known ones (BEB4 and J) and two novel genotypes (named CHN15 and CHN16). While in wild animals, eight genotypes were found, including five different genotypes from wild bids, with three known genotypes (EbpC, J and NCF2), two novel genotypes (named CHWB1 and CHS24), and two genotypes from Przewalski's gazelle, with one known genotype J and one novel genotype CHWPG1, and one novel genotype CHWBS1 from blue sheep. According to the phylogenetic analysis, five isolates belonged to group 1, and the others were clustered into group 2. This study provides unique data on the epidemiological reports and potential risk factors for E. bieneusi in both domesticated livestock and wild animals around Qinghai Lake in the Qinghai-Tibetan Plateau area; it is important to better understand the molecular epidemiology and zoonotic potential of E. bieneusi in the Qinghai-Tibetan Plateau area.

Seasonal distribution of Cryptosporidium spp., Giardia duodenalis and Enterocytozoon bieneusi in Tibetan sheep in Qinghai, China

Background

Cryptosporidium spp., Giardia duodenalis and Enterocytozoon bieneusi can cause important intestinal diseases in ruminants. However, data on the distribution of these three protozoan pathogens in Tibetan sheep are limited.

Methods

We collected 761 fecal samples from Tibetan sheep across four seasons in Qinghai Province, China, and screened the samples for Cryptosporidium spp., G. duodenalis and E. bieneusi using PCR-based sequence analysis of the genes encoding 18S ribosomal RNA, triosephosphate isomerase and the internal transcribed spacer, respectively.

Results

The positivity rates of Cryptosporidium spp., G. duodenalis and E. bieneusi in Tibetan sheep were 3.68% (28/761 samples), 1.58% (12/761) and 6.44% (49/761), respectively. Four species of Cryptosporidium were identified: C. xiaoi (n = 13 samples), C. ubiquitum (n = 8), C. bovis (n = 6) and C. ryanae (n = 1). Two G. duodenalis assemblages, namely the A (n = 2 samples) and E (n = 10) assemblages, were detected. Five zoonotic E. bieneusi genotypes were found: BEB6 (n = 21 samples), COS-I (n = 14), CHS3 (n = 11) and CGS1 (n = 2) from group 2, and PIGEBITS5 (n = 1) from group 1. Geographic differences in the distribution of E. bieneusi, and seasonal differences for all the three protozoan pathogens were noted.

Conclusions

Our results elucidate the prevalence and genetic diversity of these three pathogens in Tibetan sheep across different regions and seasons, including zoonotic pathogens such as C. ubiquitum, C. ryanae, G. duodenalis assemblage A and five genotypes of E. bieneusi.

Graphical Abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s13071-022-05442-0.

Genotyping of Cryptosporidium spp., Giardia duodenalis and Enterocytozoon bieneusi from sheep and goats in China

Background

Few studies have molecularly characterized the potential zoonotic protozoa, Cryptosporidium spp., Giardia duodenalis and Enterocytozoon bieneusi in sheep and goats in China, therefore total 472 fecal samples were collected from eight provinces and infection rates of three protozoa were determined by PCR analysis of corresponding loci. All PCR positive samples were sequenced to identify the genotype.

Results

The overall infection rates for Cryptosporidium, G. duodenalis, and E. bieneusi were 1.9% (9/472), 20.6% (97/472), and 44.5% (210/472), respectively. C. xiaoi (n = 5), C. ubiquitum (n = 3), and C. anderson (n = 1) were identified in goats. 97 G. duodenalis strains were successfully detected, and assembly E (n = 96) and assembly A (n = 1) were identified. Two novel G. duodenalis multilocus genotype (MLGs) were identified, with one belonging to subgroup AI and the other to subgroup E5. Nine known genotype (BEB6, CD6, CHC8, CHG3, CHG5, Peru6, CHG1, CHG2, and COS-I) and four new genotype (CHG26, CHG27, CHG28, and CHS18) were identified in E. bieneusi, with CHG3 dominant in this group.

Conclusions

The present results highlight the role of sheep and goats as reservoir hosts for this three gastrointestinal pathogens. In summary, we provided a platform for more detailed research on genotyping or subtyping intestinal pathogens to better understand their risks and modes of transmission.

Prevalence and new genotypes of Enterocytozoon bieneusi in wild rhesus macaque (Macaca mulatta) in China: A zoonotic concern

Enterocytozoon bieneusi is a zoonotic pathogen with a wide range of animal host. There are only few reports of E. bieneusi infection in wild Chinese rhesus macaques. Here, we determined the prevalence of E. bieneusi in nine wild rhesus macaque populations and assessed their zoonotic potential by performed genotype of ITS gene. A total of 324 fecal samples of rhesus macaque were collected in nine geographical populations from five Chinese provinces (Sichuan, Chongqing, Qinghai, Tibet and Hainan). 38 samples (11.7%) were found to be infected with E. bieneusi, and 11 genotypes were identified including three known genotypes (D, EbpC and SCC-2) and eight novel genotypes named Mul6∼13. Genotype D (63.2%) was the most prevalent, being observed in seven populations except XZ-2 and QH, and other genotypes were identified only in a single area. According to the phylogenetic analysis, Mul6∼9, Mul11∼13 and zoonotic genotype D were clustered into Group 1, indicating that these genotypes may be potentially zoonotic. Among nine populations, population SC-3 had the highest infection rate (26.3%), and the lowest was the wild QH population without infection, but the difference of infection rate among the nine populations is not significant. It is concluded that, rhesus macaque populations are generally infected E. bieneusi in many areas of China, and there may be a risk of cross infection with E. bieneusi in some areas found having zoonotic genotypes, and these areas should be paid more attention to prevent.

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Nine geographical populations (3 semi-wild and 6 wild) from five Chinese provinces (Sichuan, Chongqing, Qinghai, Tibet and Hainan).

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11 genotypes of Enterocytozoon bieneusi were identified.

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Three known genotypes (D, EbpC and SCC-2) and eight novel genotypes (Mul6∼13).

Molecular Identification and Genotyping of Enterocytozoon bieneusi in Sheep in Shanxi Province, North China

Enterocytozoon bieneusi is a fungus-like protist that can cause malabsorption and diarrhea in sheep, other animals, and humans, threatening the development of animal husbandry and public health. To date, there are no data about the prevalence and genotypes of E. bieneusi in sheep in Shanxi Province, North China. In this study, 492 fecal samples were collected from sheep in three representative counties in northern, central, and southern Shanxi Province. Nested PCR amplification was performed to detect the prevalence and identify the genotypes of E. bieneusi based on the internal transcribed spacer (ITS) region of the rRNA gene. Overall, 168 of 492 examined samples were E. bieneusi-positive, with a prevalence of 34.2% (168/492). Significant differences in the prevalence of E. bieneusi were observed among the three sampled regions (χ2 = 95.859, df = 2, p < 0.001), but the differences in E. bieneusi prevalence were not statistically significant between different genders and age groups (p > 0.05). Sequence analysis showed that four known genotypes (BEB6, COS-I, CHS7, and CHC8) and one novel genotype (named SY-1) were identified. BEB6 was the prevalent genotype found within the three counties. Phylogenetic analysis revealed that the five genotypes observed in this study belong to Group 2. The present study reported the presence and genotypes of E. bieneusi infection in sheep in Shanxi Province for the first time, which enriches the knowledge of the genetic diversity of E. bieneusi and provides baseline data for the prevention and control of E. bieneusi infection in animals and humans.

Molecular Detection and Genotyping of Enterocytozoon bieneusi in Black Goats (Capra hircus) in Yunnan Province, Southwestern China

Simple Summary

Enterocytozoon bieneusi is one of the most common parasites in human and animals, and a threat to public health. So far, no data are available for E. bieneusi prevalence and genotypes in black goats in Yunnan Province, Southwestern China. Therefore, the objective of this study was to detect the prevalence and genotypes of E. bieneusi by examining 907 fecal samples collected from 5 counties in Yunnan Province. Ninety-three fecal samples (10.3%) were E. bieneusi-positive by PCR amplification. Four new genotypes and 11 known genotypes were identified, and all genotypes considered to be the zoonotic potential. Phylogenetic analysis showed that all of these genotypes were allocated into the zoonotic groups of E. bieneusi indicating its zoonotic potential. These results indicated that effective strategies and measures must be taken to prevent and control E. bieneusi transmission to other animals and humans.

Abstract

Enterocytozoon bieneusi is a fungus-like protist that can parasitize in the intestines of humans and various animals causing a threat to public health. However, there has been no data for E. bieneusi prevalence and genotypes in black goats in Yunnan Province, Southwestern China. In this study, 907 fecal samples were collected from black goats in 5 counties from Yunnan Province. The prevalence and genotypes of E. bieneusi were examined by nested PCR amplification targeting the nuclear internal transcribed spacer (ITS). Multi-locus sequence typing (MLST) was used to further examine the potential occurrence of genetic segregation. The overall prevalence of E. bieneusi in black goats in Yunnan Province was 10.3% (93/907). Statistical analysis revealed that E. bieneusi prevalence was significantly associated with the region, age and gender of black goats (p < 0.001). Four new genotypes (CYG-1, CYG-2, CYG-3, CYG-4) and 11 known genotypes (CHG1, CHG2, CHG3, CHG5, CHG28, J, D, BEB6, Wildboar3, CD6, SDD1) of E. bieneusi were identified. At the microsatellite and minisatellite loci, 15, 2, 17, and 33 sequences were obtained, respectively, forming one new multi-locus genotype (MLG27). Phylogenetic analysis revealed that all 15 genotypes were clustered into group 1 and group 2, with zoonotic potential. This is the first report of E. bieneusi prevalence and genotypes in black goats in Yunnan Province, China. Effective control strategies and measures should be taken to reduce the risk of E. bieneusi transmission between black goats, other animals, and humans.

Molecular-Based Detection of Enterocytozoon bieneusi in Farmed Masked Palm Civets (Paguma larvata) in Hainan, China: A High-Prevalence, Specificity, and Zoonotic Potential of ITS Genotypes

Enterocytozoon bieneusi is a microsporidian and zoonotic species. This study investigated the prevalence and distribution of E. bieneusi genotypes in farmed masked palm civets using nested PCR, as well as assessed their zoonotic potential by phylogenetic analysis of the ITS region of the rRNA region. Here, we collected 251 fecal specimens from farmed masked palm civets (Paguma larvata) from the Hainan Island, China. In total, 128 of 251 samples were positive for E. bieneusi, with an average infection rate of 51.0%. Seventeen genotypes were identified including 12 known genotypes—HNR-VI (n = 56), SHR1 (n = 45), SHW7 (n = 6), KIN-1 (n = 3), D (n = 3), New1 (n = 3), EbpC (n = 2), CHC5 (n = 1), CHG19 (n = 1), CHN4 (n = 1), EbpA (n = 1), and Henan-III (n = 1)—and five novel genotypes (HNPL-I to HNPL-II; one each). Phylogenetic analysis categorized these genotypes into two groups. Thirteen of them were members of the zoonotic group 1, and the remaining four genotypes were in group 12. This study has shown that the infection rates of E. bieneusi in masked palm civets from Hainan were relatively high and provide baseline data to control and prevent microsporidiosis in farm-related communities. Therefore, infections in masked palm civets with zoonotic genotypes D, EbpC, CHN4, EbpA, KIN-1, and Henan-III should be considered potential threats to public health.

Common occurrence of Enterocytozoon bieneusi genotypes SHR1 and PL2 in farmed masked palm civet (Paguma larvata) in China

Enterocytozoon bieneusi is a common pathogen in a broad range of vertebrate hosts. To assess the prevalence and genotypes of E. bieneusi in farmed masked palm civet (Paguma larvata), 537 fecal samples from seven provinces in China were tested by nested PCR of the polymorphic internal transcribed spacer (ITS) region. Among of all the samples, 60.0% (325/531) were positive for E. bieneusi, with the highest prevalence in Hebei province (85.0%). Sequence analysis revealed the presence of nine E. bieneusi genotypes, including four known genotypes (SHR1, PL2, PL4, CHG19) and five novel genotypes (PL12 to PL16). Genotypes SHR1 and PL2 were the most common genotypes in seven provinces. Phylogenetic analysis showed that three genotypes (CHG19, PL4 and PL16) were distributed to Group 1, and six genotypes (SHR1, PL2, PL12, PL13, PL14 and PL15) formed a novel clade, which was named group 12. Findings highlight the need to conduct additional research to elucidate the epidemiology of E. bieneusi in farmed masked palm civet.

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The overall infection rate of Enterocytozoon bieneusi was 60.0% (325/537) in farmed masked palm civet (Paguma larvata) in China.

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Nine genotypes were identified, including four known genotypes (SHR1, PL2, PL4, CHG19) and five novel genotypes (named as PL12 to PL16).

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Genotypes in farmed masked palm civet formed a novel clade which was named as group 12.

Molecular epidemiology and genotype/subtype distribution of Blastocystis sp., Enterocytozoon bieneusi, and Encephalitozoon spp. in livestock: concern for emerging zoonotic infections

Intestinal parasitic infections have high prevalence rate in many regions especially in developing countries. The aim of this study was to determine the presence and genotype/subtype of some intestinal protozoa in livestock in Iran. Stool samples were collected from cattle, sheep, chickens, and horses. The presence of targeted parasites was evaluated using real-time PCR. Genotyping/subtyping of positive samples was characterized using sequencing of the ITS and barcoding region, respectively. Blastocystis sp., 27.7% (48/173) and Enterocytozoon bieneusi 26.0% (45/173) were the most frequent protozoa followed by Encephalitozoon spp., 0.57% (1/173). Cryptosporidium spp. were not detected among samples. Encephalitozoon spp., was detected only in chickens 2.2% (1/45). A statistically correlation was seen between animals and the prevalence of targeted protozoa. E. bieneusi genotypes I (9/38; 23.68%), BEB6 (22/38; 57.89%), D (6/38; 15.79%), and horse1 (1/38; 2.63%) were detected among samples. A statistically significant correlation was seen between the genotypes and animals (P ≤ 0.05). Blastocystis sp., ST1 (1/45; 2.22%), ST5 3/45; 6.66%), ST7 (1/45; 2.22%), ST10 (24/45; 53.33%), and ST14 (16/45; 35.55%) were characterized among samples. There was no significant correlation between certain subtypes and animals (P = 0.173). The presence of zoonotic potential genotypes of E. bieneusi in animals and zoonotic potential subtypes ST1 and ST7 among our samples provide a clue about the transmission dynamic of E. bieneusi and Blastocystis sp. between animals–animals and humans–animals.

The global molecular epidemiology of microsporidia infection in sheep and goats with focus on Enterocytozoon bieneusi: a systematic review and meta-analysis

BACKGROUND

Microsporidia is a zoonotic pathogen with health consequences in immunocompromised patients. Small ruminants are a potential reservoir of microsporidia for humans in their vicinity. Hence, we aimed to evaluate the molecular prevalence of microsporidian infections with emphasis on Enterocytozoon bieneusi genotypes among sheep and goats at a global scale through systematic review and meta-analysis approach.

METHODS

The standard protocol of preferred reporting items for systematic reviews and meta-analyses (PRISMA) guidelines were followed. Eligible prevalence studies on small ruminant microsporidiosis, published from 1 January 2000 until 15 April 2021 were gathered using systematic literature search in PubMed, Scopus, Web of Science and Google Scholar databases. Inclusion and exclusion criteria were applied. The point estimates and 95% confidence intervals were calculated using a random-effects model. The variance between studies (heterogeneity) was quantified by I2 index.

RESULTS

In total, 25 articles (including 34 datasets) were included for final meta-analysis. The pooled molecular prevalence of microsporidia in sheep and goats was estimated to be 17.4% (95% CI: 11.8-25%) and 16% (95% CI: 11.2-22.4%), respectively. Likewise, the overall prevalence of E. bieneusi was estimated to be 17.4% (95% CI: 11.8-25%) for sheep and 16.3% (95% CI: 11.3-22.8%) for goats. According to internal transcribed spacer (ITS) gene analysis, E. bieneusi with genotypes BEB6 (15 studies) and COS-1 (nine studies) in sheep, and CHG3 (six studies) and BEB6 (five studies) in goats were the highest reported genotypes.

CONCLUSION

The present results highlight the role of sheep and goats as reservoir hosts for human-infecting microsporidia. Therefore, this global estimate could be beneficial on preventive and control measures.

Diagnosis and molecular typing of Enterocytozoon bieneusi: the significant role of domestic animals in transmission of human microsporidiosis

Enterocytozoon bieneusi is an obligate intracellular fungus-like parasite with high genetic diversity among mammalian and avian hosts. Based on polymorphism analysis of the ribosomal internal transcribed spacer (ITS), nearly 500 genotypes were identified within E. bieneusi. Those genotypes form several genetic groups that exhibit phenotypic differences in host specificity and zoonotic potential and probably have varying public health implications. Some of the genotypes in Group 1 (e.g., D, EbpC, and Type IV) and Group 2 (e.g., BEB4, BEB6, I, and J) are the most common ones that infect a variety of hosts including humans and thus are of public health importance. By contrast, those genotypes in other genetic groups (Groups 3-11) are mostly restricted to the hosts from which they were originally isolated, which would have unknown or limited impacts on public health. Advances on diagnosis and molecular typing of E. bieneusi are introduced in this review. Genotype distribution pattern of E. bieneusi in major domestic animal groups (pigs, cattle, sheep, goats, cats, and dogs), the role of those animals in zoonotic transmission of microsporidiosis, and food and water as potential vehicles for transmission are interpreted here as well. This review highlights the importance of including more genetic or epidemiological data obtained in the same geographical areas and using more reliable genetic markers to analyze the actual extent of host specificity in E. bieneusi, for the purpose of fully appreciating zoonotic risks of those domestic animals in close contacts with men and enhancing our understanding of the modes of transmission.

Enterocytozoon bieneusi genotypes in farmed goats and sheep in Ningxia, China

Enterocytozoon bieneusi is reported to be a common microsporidian of humans and animals in various countries. However, scarce information on E. bieneusi has been recorded in farmed goats and sheep in China. As such, we undertook molecular epidemiological investigation of E. bieneusi in farmed goats (Capra aegagrus hircus) and sheep (Ovis aries) in Ningxia, China. A total of 660 genomic DNAs were extracted from individual faecal samples from famed goats (n = 300) and sheep (n = 360), and then tested using a nested PCR-based sequencing approach employing internal transcribed spacer (ITS) of nuclear ribosomal DNA as the genetic marker. Enterocytozoon bieneusi was detected in 237 of all 660 (36%) faecal samples from goats (n = 89) and sheep (n = 148). Correlation analyses revealed that E. bieneusi positive rates were significantly associated with age-groups, seasons and locations (P < 0.05). The analysis of ITS sequence data revealed the presentation of eight known genotypes (BEB6, CD6, CHG1, CHG3, CHG5, CHS8, CM7 and SX1). Phylogenetic analysis of ITS sequence data sets showed that they clustered within Group 2, showing zoonotic potential. These findings suggested that goats and sheep in Ningxia harbor zoonotic genotypes of E. bieneusi and may have a significant risk for zoonotic transmission. Further insight into the epidemiology of E. bieneusi in farmed animals, water and the environment from other areas in China will be important to have an informed position on the public health significance of microsporidiosis caused by this microbe.

Enterocytozoon bieneusi in raw milk of cattle, sheep and water buffalo in Turkey: Genotype distributions and zoonotic concerns

Raw milk is a continued threat to public health due to possible contamination with zoonotic pathogens. Enterocytozoon bieneusi is one of the most prevalent pathogenic fungi in a wide range of vertebrate hosts, causing diarrheal disease. Although there has been some evidence, the role and potential risk of raw milk of dairy animals in the transmission dynamics of E. bieneusi is not clear. Therefore, we aimed to determine the occurrence and genotypes of E. bieneusi in raw milk of dairy animals in several farms of the Central Anatolia Region. We also investigated if there is a relation between the presence of E. bieneusi and mastitis. Genomic DNAs from a total of 450 raw milk including 200, 200 and 50 samples from cattle, sheep and water buffalo respectively were analyzed using nested PCR, targeting the internal transcribed spacer of E. bieneusi. Totally milk samples of 9 (4.5%) dairy cattle, 36 (18.0%) sheep, and 1 (2.0%) water buffalo were PCR-positive. A significant relationship was determined between mastitis and the presence of E. bieneusi. Sequence analysis revealed the presence of eight genotypes: two known (ERUSS1, BEB6) and six novel genotypes (named as TREb1 to TREb6). The genotype ERUSS1 and BEB6 were the most common genotypes, found in all cattle and sheep farms. Phylogenetic analysis clustered all the identified genotypes in Group 2. This study provides novel findings that contribute to the transmission dynamics and molecular epidemiology of E. bieneusi. Our study also highlighted the potential risk of raw milk for public health with respect to microsporidia infections.

Molecular detection and genotyping of microsporidia species in chickens in Turkey

Microsporidia are obligate intracellular pathogens that infect various hosts including invertebrates and vertebrates. Despite the importance, knowledge on the prevalence and molecular characteristics of microsporidia in chickens is limited, and no data are available for Turkey. A total of 300 fecal samples from chickens in the Central Anatolia Region of Turkey were analyzed by using a nested polymerase chain reaction assay targeting the rRNA internal transcribed spacer (ITS) region for the common microsporidia species. Corresponding PCR amplicons from the positive samples were sequenced for genotyping. Enterocytozoon bieneusi was identified in 22 (7.3 %) samples, whereas Encephalitozoon spp. was not detected. The prevalence of E. bieneusi was 63.6 % in Kayseri and 36.4 % in Nevsehir provinces, and 8.8 % in soft fecal samples and 9.7 % in diarrhoeic samples. No infections were found in Kirsehir Province. Significant differences were found for the distribution of E. bieneusi among provinces and fecal conditions. Infections were found only in free-range chickens. As a result of ITS region sequencing, two genotypes were characterized. The novel genotype ERUNT1 (n = 21), belonging to zoonotic group 1, was the most common genotype throughout the study area. The other known genotype, ERUSS1 (n = 1), had a restricted distribution and was previously detected in cattle and sheep in the same region. Our study provides the first data on microsporidia species from chickens in Turkey. None of these genotypes have been reported in humans; thus, the risk potential for public health is limited but needs further investigation.

Prevalence and genotype distribution of Enterocytozoon bieneusi in farmed raccoon dogs (Nyctereutes procyonoides) in Shandong Province, eastern China

Enterocytozoon bieneusi is a common microsporidian species, which can infect humans and various species of animals. However, little is known about E. bieneusi prevalence and genotypes in farmed raccoon dogs (Nyctereutes procyonoides) in Shandong Province, China. In this study, a total of 356 fecal samples were collected from farmed raccoon dogs in Weihai, Weifang, and Yantai cities in Shandong Province, China. A total of 23 (6.5%) samples were E. bieneusi-positive by nested PCR amplification of the internal transcribed spacer (ITS) region of ribosomal DNA. Statistical analysis showed that E. bieneusi prevalence in male raccoon dogs was higher than that in female raccoon dogs, and the highest E. bieneusi prevalence was detected in adult raccoon dogs. Sequence analysis revealed four known E. bieneusi genotypes (D, type IV, CHG1, and Peru8), and type IV (11/23) was the predominant genotype. The genotypes type IV, Peru8, and CHG1 were reported in raccoon dogs for the first time in China. Phylogenetic analysis showed that three human-pathogenic genotypes (D, type IV, and Peru8) were clustered into group 1, and the CHG1 belonged to group 2. These findings expand the current understanding of E. bieneusi prevalence and genotype distribution in raccoon dogs in China. Our study also shows that raccoon dogs are hosts for E. bieneusi belonging to several genotypes, including zoonotic ones, highlighting the possibility of transmission of this pathogen between raccoon dogs and humans.

Genotype identification and phylogenetic analysis of Enterocytozoon bieneusi in farmed black goats (Capra hircus) from China's Hainan Province

Enterocytozoon bieneusi is an important pathogen commonly found in humans and animals. Farmed animals with close contact to humans are important hosts of E. bieneusi. The role of goats in the transmission of E. bieneusi, however, remains unclear. In this study, 341 fresh fecal samples of black goats were collected from five locations in Hainan Province, China. Enterocytozoon bieneusi was identified and genotyped by sequences of the internal transcribed spacer (ITS) region. Phylogenetic analysis was performed by constructing a neighbor-joining tree of the ITS gene sequences. The average prevalence of E. bieneusi in black goats was 24.0% (82/341) with rates ranging from 6.3% (4/63) to 37.2% (32/86) across the locations (χ² = 17.252, p < 0.01). Eight genotypes of E. bieneusi were identified, including six known genotypes: CHG5 (n = 47); CHG3 (n = 23); CHG2 (n = 4); CM21 (n = 3); D (n = 2); and AHG1 (n = 1), and two novel genotypes termed HNG-I (n = 1) and HNG-II (n = 1). In the phylogenetic tree, genotype D was clustered into Group 1 and the other identified genotypes were included in Group 2. This represents the first report identifying E. bieneusi in black goats from Hainan Province, with a high prevalence and wide occurrence demonstrated. The two new genotypes identified provide additional insights into the genotypic variations in E. bieneusi. Due to the small percentage of zoonotic genotypes in these animals, there is minimal risk of zoonotic transmission of E. bieneusi.