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

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 Molecular Characterization of Cryptosporidium spp., Giardia duodenalis and Enterocytozoon bieneusi in Donkeys of Inner Mongolia, Northern China

BACKGROUND

Cryptosporidium spp., Giardia duodenalis, and Enterocytozoon bieneusi are important zoonotic pathogens. In Inner Mongolia, a single pathogen molecular epidemiological survey of these three protozoa was previously conducted on only 176 fecal samples donkeys. In this study, the purpose is to simultaneously evaluate the zoonotic potential of three protozoa.

METHODS

Small subunit ribosomal RNA (SSU rRNA) and gp60 from Cryptosporidium; SSU rRNA, gdh, tpi, and bg from G. duodenalis; and ITS of E. bieneusi were analyzed in 300 fecal samples collected from donkeys from two intensive farms in Inner Mongolia in 2022. Sample processing, nucleic acid extraction, polymerase chain reaction, sequencing, and sequence analysis were performed to determine the prevalence and genetic characteristics of the protozoans.

RESULTS

Our results revealed that 75.33% (226/300) of the samples were infected with at least one protozoan, whereas 2.33% (7/300) were simultaneously infected with all three genera. Mixed infection was observed in 20.67% (62/300; Cryptosporidium + G. duodenalis), 5.33% (16/300; Cryptosporidium + E. bieneusis), and 5.67% (17/300; G. duodenalis + E. bieneusis) of the samples. Overall prevalence of Cryptosporidium, G. duodenalis, and E. bieneusi was 56.33% (169/300), 36.33% (109/300), and 13.33% (40/300), respectively. Five Cryptosporidium species were identified, with C. andersoni being the predominant species. The C. parvum subtypes identified were IIdA20G1 (66.67%) and IIdA19G1 (33.33%). Three G. duodenalis assemblages were identified, with assemblage B being predominant. Seven isolates formed two different assemblage B MLGs, two different assemblage A MLGs, and two different assemblage B + E MLGs. Three known and eight novel sequences of E. bieneusis were identified in group 1 (including horse1 and NMG6-NMG8) and group 2 (including J, BEB6, and NMG1-NMG5), with horse1 being the predominant genotype.

CONCLUSIONS

To our knowledge, this is the first study to demonstrate that donkeys can be infected with a combination of two or three protozoa, with C. andersoni being the most detected Cryptosporidium species. Meanwhile, assemblage B was predominant among G. duodenalis, whereas horse1 was the dominant genotype for E. bieneusi. Moreover, the prevalence of C. bovis, C. ryanae, C. suis, C. parvum subtype IIdA20G1 and eight novel sequences of E. bieneusis and new features of G. duodenalis assemblages were identified in donkeys for the first time. These findings reconfirmed that donkeys in Inner Mongolia are infected with these three protozoa, emphasizing the risk of disease transmission by these protozoans to humans.

Establishment and preliminary application of PCR-RFLP genotyping method for Giardia duodenalis in goats

BACKGROUND

Giardia duodenalis (G. duodenalis) is a globally distributed zoonotic protozoan that parasitizes the small intestines of humans and various mammals, such as goats and sheep. The objective of this study was to establish a convenient, accurate, and specific method based on restriction fragment length polymorphism (RFLP) for genotyping assemblages A, B and E of G. duodenalis in goats. The β-giardin gene was amplified using primer pairs bgF1, bgR1, bgF2 and bgR2 by nested PCR. The PCR products were digested with the restriction enzymes Hinf I and Bgl I. The established PCR-RFLP method was used to detect and analyze the genetic subtypes of G. duodenalis in 130 fecal samples from goats and compared simultaneously with microscopic examination and nucleic acid sequencing for G. duodenalis.

RESULTS

Genetic sequencing confirmed that the PCR-RFLP method accurately distinguished G. duodenalis assemblages A, B and E, as well as different combinations of mixed infections of these three assemblages. Among the 130 samples tested by PCR-RFLP, a total of 26 samples (20.00%) tested positive for G. duodenalis, a higher sensitivity than microscopic examination at 13.85% (18/130). Sequence alignment analysis revealed that among the 26 PCR-positive samples, two were identified as assemblage AI, while the remaining 24 were identified as assemblage E or E12.

CONCLUSIONS

This study established an accurate, efficient and rapid PCR-RFLP genotyping method using the bg sequence of G. duodenalis, enabling accurate identification and effective differentiation of goat-derived G. duodenalis assemblages without requiring sequencing.

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.

Prevalence and molecular characterization of Cryptosporidium spp., Enterocytozoon bieneusi, and Giardia duodenalis in dairy cattle in Ningxia, northwestern China

Cryptosporidium spp., Enterocytozoon bieneusi, and Giardia duodenalis are common intestinal pathogens that infect humans and animals. To date, research regarding these three protozoa in the Ningxia Hui Autonomous Region (Ningxia) has mostly been limited to a single pathogen, and comprehensive data on mixed infections are unavailable. This study aimed to evaluate the zoonotic potential of these three protozoa. In this study, small subunit ribosomal RNA (SSU rRNA) and 60 kDa glycoprotein (gp60) genes of Cryptosporidium; internal transcribed spacer (ITS) gene of E. bieneusi; and SSU rRNA, glutamate dehydrogenase (gdh), triosephosphate isomerase (tpi), and beta-giardin (bg) genes of G. duodenalis were examined. DNA extraction, polymerase chain reaction, and sequence analysis were performed on fecal samples collected from 320 dairy cattle at three intensive dairy farms in Ningxia in 2021 to determine the prevalence and genetic characteristics of these three protozoa. The findings revealed that 61.56% (197/320) of the samples were infected with at least one protozoan. The overall prevalence of Cryptosporidium was 19.38% (62/320), E. bieneusi was 41.56% (133/320), and G. duodenalis was 29.38% (94/320). This study identified four Cryptosporidium species (C. bovis, C. andersoni, C. ryanae, and C. parvum) and the presence of mixed infections with two or three Cryptosporidium species. C. bovis was the dominant species in this study, while the dominant C. parvum subtypes were IIdA15G1 and IIdA20G1. The genotypes of E. bieneusis were J, BEB4, and I alongside the novel genotypes NX1-NX8, all belonging to group 2, with genotype J being dominant. G. duodenalis assemblages were identified as assemblages E, A, and B, and a mixed infection involving assemblages A + E was identified, with assemblage E being the dominant one. Concurrently, 11 isolates formed 10 different assemblage E multilocus genotypes (MLGs) and 1 assemblage A MLG and assemblage E MLGs formed 5 subgroups. To the best of our knowledge, this is the first report on mixed infection with two or three Cryptosporidium species in cattle in Ningxia and on the presence of the C. parvum subtype IIdA20G1 in this part of China. This study also discovered nine genotypes of E. bieneusis and novel features of G. duodenalis assemblages in Ningxia. This study indicates that dairy cattle in this region may play a significant role in the zoonotic transmission of Cryptosporidium spp., E. bieneusi, and G. duodenalis.

Unveiling the presence and genotypic diversity of Giardia duodenalis on large-scale sheep farms: insights from the Henan and Ningxia Regions, China

BACKGROUND

The parasitic protozoan Giardia duodenalis is an important cause of diarrheal disease in humans and animals that can be spread by fecal-oral transmission through water and the environment, posing a challenge to public health and animal husbandry. Little is known about its impact on large-scale sheep farms in China. In this study we investigated G. duodenalis infection of sheep and contamination of the environment in large-scale sheep farms in two regions of China, Henan and Ningxia.

METHODS

A total of 528 fecal samples, 402 environmental samples and 30 water samples were collected from seven large-scale sheep farms, and 88 fecal samples and 13 environmental samples were collected from 12 backyard farms. The presence of G. duodenalis was detected by targeting the β-giardin (bg) gene, and the assemblage and multilocus genotype of G. duodenalis were investigated by analyzing three genes: bg, glutamate dehydrogenase (gdh) and triphosphate isomerase (tpi).

RESULTS

The overall G. duodenalis detection rate was 7.8%, 1.4% and 23.3% in fecal, environmental and water samples, respectively. On the large-scale sheep farms tested, the infection rate of sheep in Henan (13.8%) was found to be significantly higher than that of sheep in Ningxia (4.2%) (P < 0.05). However, the difference between the rates of environmental pollution in Henan (1.9%) and Ningxia (1.0%) was not significant (P > 0.05). Investigations of sheep at different physiological stages revealed that late pregnancy ewes showed the lowest infection rate (1.7%) and that young lambs exhibited the highest (18.8%). Genetic analysis identified G. duodenalis belonging to two assemblages, A and E, with assemblage E being dominant. A total of 27 multilocus genotypes were identified for members of assemblage E.

CONCLUSIONS

The results suggest that G. duodenalis is prevalent on large-scale sheep farms in Henan and Ningxia, China, and that there is a risk of environmental contamination. This study is the first comprehensive examination of the presence of G. duodenalis on large-scale sheep farms in China. Challenges posed by G. duodenalis to sheep farms need to be addressed proactively to ensure public health safety.

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.

Cryptosporidium spp. in large-scale sheep farms in China: prevalence and genetic diversity

Cryptosporidium spp. are significant zoonotic intestinal parasites that induce diarrhea and even death across most vertebrates, including humans. Previous studies showed that sheep are important hosts for Cryptosporidium and that its distribution in sheep is influenced by geography, feeding patterns, age, and season. Environmental factors also influence the transmission of Cryptosporidium. Molecular studies of Cryptosporidium in sheep have been conducted in only a few regions of China, and studies into the effect of sheep-housing environments on Cryptosporidium transmission are even rarer. To detect the prevalence of Cryptosporidium in large-scale sheep-housing farms, a total of 1241 fecal samples were collected from sheep, 727 environmental samples were taken from sheep housing, and 30 water samples were collected in six regions of China. To ascertain the existence of the parasite and identify the species of Cryptosporidium spp., we conducted nested PCR amplification of DNA extracted from all samples using the small-subunit (SSU) rRNA gene as a target. For a more in-depth analysis of Cryptosporidium spp. subtypes, C. xiaoi-and C. ubiquitum-positive samples underwent separate nested PCR amplification targeting the 60 kDa glycoprotein (gp60) gene. The amplification of the Cryptosporidium spp. SSU rRNA gene locus from the whole genomic DNA of all samples yielded a positive rate of 1.2% (20/1241) in fecal samples, 0.1% (1/727) in environmental samples, and no positive samples were found in water samples. The prevalence of Cryptosporidium spp. infection in large-scale housed sheep was 1.7%, which was higher than that in free-ranging sheep (0.0%). The highest prevalence of infection was found in weaning lambs (6.8%). Among the different seasons, the peaks were found in the fall and winter. The most prevalent species were C. xiaoi and C. ubiquitum, with the former accounting for the majority of infections. The distribution of C. xiaoi subtypes was diverse, with XXIIIc (n = 1), XXIIId (n = 2), XXIIIe (n = 2), and XXIIIl (n = 4) identified. In contrast, only one subtype, XIIa (n = 9), was found in C. ubiquitum. In this study, C. xiaoi and C. ubiquitum were found to be the predominant species, and Cryptosporidium was found to be present in the environment. These findings provide an important foundation for the comprehensive prevention and management of Cryptosporidium in intensively reared sheep. Furthermore, by elucidating the prevalence of Cryptosporidium in sheep and its potential role in environmental transmission, this study deepens our understanding of the intricate interactions between animal health, environmental contamination, and public health dynamics.

Molecular evaluation of Cryptosporidium spp. in sheep in southern Xinjiang, China

Cryptosporidium spp. are diarrheagenic intestinal parasites with multiple hosts worldwide. A total of 1252 fresh fecal samples of sheep were collected from 10 large-scale farms in southern Xinjiang. Based on the small subunit ribosomal (SSU rRNA) gene of Cryptosporidium, 100 Cryptosporidium-positive samples (8.0%, 100/1252) were detected by PCR. Nine out of 10 farms were positive for Cryptosporidium, with the highest infection rate being 18.4% (23/125) on farm 9 in Qira. The infection rates of Cryptosporidium in pre-weaned lambs, weaned lambs, fattening sheep, and adult sheep were 20.3% (61/301), 10.3% (34/329), 0.9% (3/327), and 0.7% (2/295), respectively. Three Cryptosporidium species were identified, namely, C. xiaoi (n = 61), C. parvum (n = 22), and C. ubiquitum (n = 17). Of them, C. xiaoi was detected on all positive farms and in different age groups of sheep. The subtypes of C. parvum and C. ubiquitum were identified by PCR at the 60 kDa glycoprotein (gp60) gene. Two C. parvum subtypes were identified: IIdA19G1 (n = 21) and IIdA15G1 (n = 1). One C. ubiquitum subtype was identified with XIIa (n = 17). These results indicated the common transmission and genetic diversity of Cryptosporidium in sheep in southern Xinjiang, and further investigations are needed on the zoonotic potential of C. parvum and C. ubiquitum in this region.

Tubulin as a potential molecular target for resveratrol in Giardia lamblia trophozoites, in vitro and in silico approaches

Giardia lamblia is a globally distributed protozoan parasite that causes intestinal disease. Recently, there is an increase in refractory cases of giardiasis to chemotherapeutic agents, and drugs available cause side effects that may limit its use or cause therapeutic non-compliance. Therefore, search for alternative and less harmful drugs to treat giardiasis is an important task. In this sense, resveratrol (RSV) is a polyphenol with a wide range of pharmacological effects such as antimicrobial, anticarcinogenic and antioxidant. The aim of this study was to evaluate the effects of RSV on Giardia lamblia trophozoites in vitro and in silico, focusing on tubulin affectation, a major protein of the Giardia cytoskeleton which participates in relevant processes for cell survival. In vitro determinations showed that RSV inhibits parasite growth and adherence, causes morphological changes, and induces apoptosis-like cell death through tubulin alterations demonstrated by immunolocalization and Western blot assays. Bioinformatic analysis by molecular docking suggested that RSV binds to Giardia tubulin interface heterodimer, sharing binding residues to those reported with depolymerization inhibitors. These findings suggest that RSV affects microtubular dynamics and make it an interesting compound to study for its safety and antigiardiasic potential.

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.