Comparative analysis of genotypic diversity in Entamoeba nuttalli isolates from Tibetan macaques and rhesus macaques in China

Epidemiological investigation of Entamoeba in wild rhesus macaques in China: A novel ribosomal lineage and genetic differentiation of Entamoeba nuttalli

Wild rhesus macaques are a potential source of zoonotic parasites for humans, and Entamoeba spp. are common intestinal parasites. To investigate the prevalence of Entamoeba in wild rhesus macaques in China and explore the genetic differentiation of the potentially pathogenic species Entamoeba nuttalli, a total of 276 fecal samples from five populations at high altitudes (HAG, 2,800-4,100 m above sea level) and four populations at low altitudes (LAG, 5-1,000 m above sea level) were collected. PCR methods based on the ssrRNA gene were used to detect Entamoeba infection. Genotyping of E. nuttalli was performed based on six tRNA-linked short tandem repeat (STR) loci for further genetic analyses. The results revealed that Entamoeba infection (69.2%) was common in wild rhesus macaques in China, especially in LAG which had a significantly higher prevalence rate than that in HAG (P < 0.001). Three zoonotic species were identified: Entamoeba chattoni (60.9%) was the most prevalent species and distributed in all the populations, followed by Entamoeba coli (33.3%) and Entamoeba nuttalli (17.4%). In addition, a novel Entamoeba ribosomal lineage named RL13 (22.8%) was identified, and phylogenetic analysis revealed a close genetic relationship between RL13 and Entamoeba. hartmanni. Genotyping of E. nuttalli obtained 24 genotypes from five populations and further analysis showed E. nuttalli had a high degree of genetic differentiation (FST > 0.25, Nm < 1) between the host populations. The result of analysis of molecular variance (AMOVA) revealed that observed genetic differences mainly originate from differences among populations (FST = 0.91). Meanwhile, the phylogenetic tree showed that these genotypes of E. nuttalli were clustered according to geographical populations, indicating a significant phylogeographic distribution pattern. Considering the potential pathogenicity of E. nuttalli, attention should be paid to its risk of zoonotic transmission.

Feeding sites promoting wildlife-related tourism might highly expose the endangered Yunnan snub-nosed monkey (Rhinopithecus bieti) to parasite transmission

An increasing number of studies have found that the implementation of feeding sites for wildlife-related tourism can affect animal health, behaviour and reproduction. Feeding sites can favour high densities, home range overlap, greater sedentary behaviour and increased interspecific contacts, all of which might promote parasite transmission. In the Yunnan snub-nosed monkey (Rhinopithecus bieti), human interventions via provisioning monkeys at specific feeding sites have led to the sub-structuring of a group into genetically differentiated sub-groups. The fed subgroup is located near human hamlets and interacts with domesticated animals. Using high-throughput sequencing, we investigated Entamoeba species diversity in a local host assemblage strongly influenced by provisioning for wildlife-related tourism. We identified 13 Entamoeba species or lineages in faeces of Yunnan snub-nosed monkeys, humans and domesticated animals (including pigs, cattle, and domestic chicken). In Yunnan snub-nosed monkeys, Entamoeba prevalence and OTU richness were higher in the fed than in the wild subgroup. Entamoeba polecki was found in monkeys, pigs and humans, suggesting that this parasite might circulates between the wild and domestic components of this local social–ecological system. The highest proportion of faeces positive for Entamoeba in monkeys geographically coincided with the presence of livestock and humans. These elements suggest that feeding sites might indirectly play a role on parasite transmission in the Yunnan snub-nosed monkey. The implementation of such sites should carefully consider the risk of creating hotspots of disease transmission, which should be prevented by maintaining a buffer zone between monkeys and livestock/humans. Regular screenings for pathogens in fed subgroup are necessary to monitor transmission risk in order to balance the economic development of human communities dependent on wildlife-related tourism, and the conservation of the endangered Yunnan snub-nosed monkey.

Identification of Mamu-DRB1 gene as a susceptibility factor for Entamoeba nuttalli infection in Chinese Macaca mulatta

Entamoeba nuttalli infection is highly prevalent in captive and wild macaques. A recent study suggested that the genetic factor of host macaques was correlated with the genotypes of E. nuttalli isolates. This study focused on the correlation between the rhesus macaque host major histocompatibility complex gene and E. nuttalli infection. Thirty-nine stool samples were obtained from Mount Qing-ling (Guizhou Province, China). Polymerase chain reaction analysis detected the infection rate of E. nuttalli, Entamoeba coli, and Entamoeba chattoni as 69.23%, 69.23%, and 87.18%, respectively. A new Serine-rich Protein genotype was detected, and the rRNA of E. nuttalli isolates from Mount Qian-ling was completely identical to the GY4 strain. In the distance-based neighbor-joining tree, Mamu-DRB1, not Mamu-DPB or Mamu-B gene, was related to E. nuttalli infection. Mamu-DRB1 genes of rhesus macaques in Mounts Qian-ling and Long-hu were highly polymorphic, and the rhesus macaques with two major types of Mamu-DRB1 showed susceptibility to E. nuttalli infection. The Mamu-DRB1 gene analysis in this study indicated that the Mamu-DRB1 gene is an important factor that influences the susceptibility of E. nuttalli infection in Chinese Macaca mulatta. This study contributes to a better understanding of host susceptibility to Entamoeba.

Genotyping of Entamoeba nuttalli strains from the wild rhesus macaques of Myanmar and comparison with those from the wild rhesus macaques of Nepal and China

Entamoeba nuttalli found in macaques is phylogenetically the closest species to Entamoeba histolytica and is potentially pathogenic. In this study, the prevalence of Entamoeba infections was examined in wild rhesus macaques by examining 73 and 90 fecal samples collected from two sites, Popa Taung Kalat (PTK) and Pho Win Taung (PWT), in Myanmar. The positive rates of E. nuttalli detected using PCR were 49% and 31% in PTK and PWT, respectively, but no infections of E. histolytica and E. moshkovskii were found. Entamoeba dispar was detected in 6% of samples only from PWT. Positive rates of E. chattoni and E. coli were both 70% in PWT and 67% and 79% in PTK, respectively. Six E. nuttalli strains from PTK and eight from PWT were obtained in the culture with xenic medium and then, one and two strains, respectively, were axenized and finally cloned. The genotypic analysis of serine-rich protein genes revealed two genotypes each in both sites. The genotypes found in five of six strains from PTK were similar to those from the strains found in Nepal, whereas the remaining one from PTK and two from PWT were similar to those obtained from macaques in China. The sequence of the 18S rDNA of strains with these four genotypes was identical to that of the strains from China. Six loci of tRNA-linked short tandem repeats were analyzed for further genotyping of the strains. Although there were two types in locus A-L in PTK isolates, one of each type for PTK and PWT was found in the other loci, including locus A-L in PWT strains. These results demonstrated that the E. nuttalli strains from Myanmar are closer to the strains from macaques in China rather than those from macaques in Nepal.

First Detection and Molecular Identification of Entamoeba in Yaks from China

BACKGROUND

Yak, a predominant livestock of plateau areas, is known as a host to many parasites. And the genus Entamoeba, the third-common cause of the mortality worldwide from parasitic diseases, was discovered in yaks once.

METHODS

We investigated the distribution and species of Entamoeba spp. from yaks in Qinghai province, northwestern China, by collecting 1027 yak fecal samples. All samples were divided according to seven geographical sites, four seasons, and two age groups of yaks. After extracting DNA, polymerase chain reaction (PCR) was performed to amplify the 18S rRNA gene, and sequences were analyzed with phylogenetic method.

RESULTS

We observed an overall Entamoeba positive rate of 36.32% (373/1027) in yaks from Qinghai province. The common species included Entamoeba bovis (284/373), Entamoeba sp. MG107/BEL (79/373), Entamoeba sp. ribosomal lineage (RL) two (8/373), and Entamoeba sp. RL9 (2/373). According to the result of statistical analysis, Entamoeba infection rate was the highest in summer and significantly differed from that observed during other seasons (P < 0.05). The yaks from Golog had the highest prevalence of Entamoeba among all geographical origins in Qinghai province (P < 0.05). However, no significant difference was observed (P > 0.05) among different age groups, as evident from a positive rate of 39.58% in ≤ 6-month and 36.16% in > 6-month yaks.

CONCLUSION

These results indicate the prevalence and predominant species of Entamoeba in yaks. To our knowledge, this is the first study to report E. bovis, Entamoeba sp. RL2, and Entamoeba sp. RL9 in Chinese yaks.

Whole genome sequencing of Entamoeba nuttalli reveals mammalian host-related molecular signatures and a novel octapeptide-repeat surface protein

The enteric protozoa Entamoeba histolytica is the causative agent of amebiasis, which is one of the most common parasitic diseases in developed and developing countries. Entamoeba nuttalli is the genetically closest species to E. histolytica in current phylogenetic analyses of Entamoeba species, and is prevalent in wild macaques. Therefore, E. nuttalli may be a key organism in which to investigate molecules required for infection of human or non-human primates. To explore the molecular signatures of host-parasite interactions, we conducted de novo assembly of the E. nuttalli genome, utilizing self-correction of PacBio long reads and polishing corrected reads using Illumina short reads, followed by comparative genomic analysis with two other mammalian and a reptilian Entamoeba species. The final draft assembly of E. nuttalli included 395 contigs with a total length of approximately 23 Mb, and 9,647 predicted genes, of which 6,940 were conserved with E. histolytica. In addition, we found an E. histolytica-specific repeat known as ERE2 in the E. nuttalli genome. GO-term enrichment analysis of mammalian host-related molecules indicated diversification of transmembrane proteins, including AIG1 family and BspA-like proteins that may be involved in the host-parasite interaction. Furthermore, we identified an E. nuttalli-specific protein that contained 42 repeats of an octapeptide ([G,E]KPTDTPS). This protein was shown to be localized on the cell surface using immunofluorescence. Since many repeat-containing proteins in parasites play important roles in interactions with host cells, this unique octapeptide repeat-containing protein may be involved in colonization of E. nuttalli in the intestine of macaques. Overall, our draft assembly provides a valuable resource for studying Entamoeba evolution and host-parasite selection.

Molecular epidemiology, evolution, and phylogeny of Entamoeba spp

Entamoeba histolytica is a protozoan parasite and the causative agent of amoebiasis in humans. The estimations of the worldwide burden of amoebiasis by the WHO indicated that approximately 500 million people were infected with the parasite and 10% of these individuals had invasive amoebiasis. However, our understanding of the disease burden and epidemiology of human amebiasis has undergone dramatic changes over the last two decades based on molecular analyses. The development of Entamoeba genomics has also provided some interesting and valuable information on the evolution and population structure of this parasite. In addition, the use of a number of molecular markers has greatly expanded our understanding of Entamoeba host range and genetic diversity. In this review, we re-assessed Entamoeba prevalence and species in humans, non-human primates, other animals, and the environment in the context of molecular data. Some issues regarding the evolution and phylogeny of different Entamoeba species lineages are also discussed.

Are molecular tools clarifying or confusing our understanding of the public health threat from zoonotic enteric protozoa in wildlife?

Emerging infectious diseases are frequently zoonotic, often originating in wildlife, but enteric protozoa are considered relatively minor contributors. Opinions regarding whether pathogenic enteric protozoa may be transmitted between wildlife and humans have been shaped by our investigation tools, and have led to oscillations regarding whether particular species are zoonotic or have host-adapted life cycles. When the only approach for identifying enteric protozoa was morphology, it was assumed that many enteric protozoa colonized multiple hosts and were probably zoonotic. When molecular tools revealed genetic differences in morphologically identical species colonizing humans and other animals, host specificity seemed more likely. Parasites from animals found to be genetically identical - at the few genes investigated - to morphologically indistinguishable parasites from human hosts, were described as having zoonotic potential. More discriminatory molecular tools have now sub-divided some protozoa again. Meanwhile, some infection events indicate that, circumstances permitting, some "host-specific" protozoa, can actually infect various hosts. These repeated changes in our understanding are linked intrinsically to the investigative tools available. Here we review how molecular tools have assisted, or sometimes confused, our understanding of the public health threat from nine enteric protozoa and example wildlife hosts (Balantoides coli - wild boar; Blastocystis sp. - wild rodents; Cryptosporidium spp. - wild fish; Encephalitozoon spp. - wild birds; Entamoeba spp. - non-human primates; Enterocytozoon bieneusi - wild cervids; Giardia duodenalis - red foxes; Sarcocystis nesbitti - snakes; Toxoplasma gondii - bobcats). Molecular tools have provided evidence that some enteric protozoa in wildlife may infect humans, but due to limited discriminatory power, often only the zoonotic potential of the parasite is indicated. Molecular analyses, which should be as discriminatory as possible, are one, but not the only, component of the toolbox for investigating potential public health impacts from pathogenic enteric protozoa in wildlife.

Molecular Characterization of Entamoeba spp. in Wild Taihangshan Macaques (Macaca mulatta tcheliensis) in China

BACKGROUND

Entamoeba spp. is one of the most common enteric parasites of humans and animals.

PURPOSE

However, little information is available regarding prevalence and genotypes of Entamoeba spp. in wild Taihangshan macaques (Macaca mulatta tcheliensis).

METHODS

In the present study, a total of 458 fecal samples from wild rhesus macaque in Taihangshan mountains area between September 2015 and November 2016, were collected and examined for the presence of six Entamoeba species by PCR amplification of the SSU rRNA gene.

RESULTS

The overall prevalence of Entamoeba spp. infection was 89.96% (412/458). Four species of Entamoeba detected in our survey were E. chattoni (88.43%), E. hartmanni (79.91%), E. coil (69.87%) and E. dispar (58.30%), and among these, 398 (84.93%) were mixed infections. Phylogenetic analysis revealed that isolates were clustered into four known genotypes.

CONCLUSION

The present study firstly provides important information about the prevalence and diversity of Entamoeba species infecting wild Taihangshan macaques in China. Enough attention should be paid to monitor the potential interspecies transmission in the region.

Discrimination Experiments in Entamoeba and Evidence from Other Protists Suggest Pathogenic Amebas Cooperate with Kin to Colonize Hosts and Deter Rivals

Entamoeba histolytica is one of the least understood protists in terms of taxa, clone, and kin discrimination/recognition ability. However, the capacity to tell apart same or self (clone/kin) from different or nonself (nonclone/nonkin) has long been demonstrated in pathogenic eukaryotes like Trypanosoma and Plasmodium, free-living social amebas (Dictyostelium, Polysphondylium), budding yeast (Saccharomyces), and in numerous bacteria and archaea (prokaryotes). Kin discrimination/recognition is explained under inclusive fitness theory; that is, the reproductive advantage that genetically closely related organisms (kin) can gain by cooperating preferably with one another (rather than with distantly related or unrelated individuals), minimizing antagonism and competition with kin, and excluding genetic strangers (or cheaters = noncooperators that benefit from others' investments in altruistic cooperation). In this review, we rely on the outcomes of in vitro pairwise discrimination/recognition encounters between seven Entamoeba lineages to discuss the biological significance of taxa, clone, and kin discrimination/recognition in a range of generalist and specialist species (close or distantly related phylogenetically). We then focus our discussion on the importance of these laboratory observations for E. histolytica's life cycle, host infestation, and implications of these features of the amebas' natural history for human health (including mitigation of amebiasis).

Correlation between genotypes and geographic distribution of Entamoeba nuttalli isolates from wild long-tailed macaques in Central Thailand

Entamoeba nuttalli found in non-human primates is the phylogenetically closest species to Entamoeba histolytica and is potentially pathogenic. However, infection of wild long-tailed macaques (Macaca fascicularis) with E. nuttalli has not been found. In this study, the prevalence of Entamoeba infections in wild long-tailed macaques was examined in seven locations in six provinces of Thailand. The positive rate for E. nuttalli in 214 fecal samples was 43.9% using PCR, but no infection with E. histolytica or Entamoeba dispar was found, demonstrating that long-tailed macaque is one of the natural hosts for E. nuttalli. Twenty-four E. nuttalli isolates were successfully cultured and four of them were axenized. The sequences of the 18S ribosomal RNA genes of E. nuttalli from long-tailed macaques differed from those of E. nuttalli isolates from other species of wild macaques. Eleven types of sequences in serine-rich protein genes were identified in the 24 isolates and these were specific for each location in Thailand. By analysis of six tRNA-linked short tandem repeat loci, these isolates were divided into 14 types, and each type was also location-specific. Phylogenetic analysis revealed correlation between genotypes of the parasite and the geographic distribution of the host macaques. Genetic distance and geographic distance correlated significantly in a Mantel test, with r values of 0.888 based on the tRNA-linked short tandem repeat loci and 0.815 based on the serine-rich protein genes. These results suggest that genetic divergence and co-evolution of the parasite occurred during dispersion and colonization of the host macaque, and that genotypic analysis of the parasite may enable identification of the geographic localization of the host.

Correlation of genetic diversity between hosts and parasites in Entamoeba nuttalli isolates from Tibetan and rhesus macaques in China

Entamoeba nuttalli infection is prevalent in captive and wild macaques. Recent studies have suggested that genotypes of E. nuttalli isolates are correlated with the geographical distribution of host macaques. Correlation of amoebic genotypes with genetic diversity of host macaques was analyzed in present study. Sixty fresh stool samples were obtained from wild Tibetan macaques living in Mount Huang (HS) of the An-hui Province in China. PCR analysis revealed that the most prevalent Entamoeba species was E. chattoni (E. polecki ST2) (86.7%) followed by E. nuttalli (58.3%) and E. coli (25%). Six E. nuttalli HS isolates were successfully cultured. The tRNA-linked short tandem repeat (STR) loci and serine-rich protein gene of E. nuttalli isolates from four different regions of China (Mount Long-hu, Gui-yang, Mount E-mei, and HS, the former three isolates were obtained in previous studies) were studied and high numbers of polymorphisms were detected. When genetic diversity of different populations of E. nuttalli isolates was compared with geographical distance, an r² value of 0.919 was assigned by a Mantel test based on the tRNA-STR loci. In host macaques, the mtDNA HVS-I gene was also highly polymorphic in each of the genomes. Multiple regression analysis using E. nuttalli tRNA-STR loci genetic, macaque mtDNA HVS-I gene, and geographic distances showed an r² value of 0.943, indicating that a higher relevance was demonstrated when geographic and host gene factors were considered. Analysis of genetic factor of host would benefit for better understanding of the evolution of E. nuttalli.

Diversity of Entamoeba spp. in African great apes and humans: an insight from Illumina MiSeq high-throughput sequencing

Understanding the complex Entamoeba communities in the mammalian intestine has been, to date, complicated by the lack of a suitable approach for molecular detection of multiple variants co-occurring in mixed infections. Here, we report on the application of a high throughput sequencing approach based on partial 18S rDNA using the Illumina MiSeq platform. We describe, to our knowledge, for the first time, the Entamoeba communities in humans, free-ranging western lowland gorillas and central chimpanzees living in the Dja Faunal Reserve in Cameroon. We detected 36 Entamoeba haplotypes belonging to six haplotype clusters, containing haplotypes possessing high and low host specificity. Most of the detected haplotypes belonged to commensal Entamoeba, however, the pathogenic species (Entamoeba histolytica and Entamoeba nuttalli) were also detected. We observed that some Entamoeba haplotypes are shared between humans and other hosts, indicating their zoonotic potential. The findings are important not only for understanding the epidemiology of amoebiasis in humans in rural African localities, but also in the context of wild great ape conservation.

Characteristics of inflammatory reactions during development of liver abscess in hamsters inoculated with Entamoeba nuttalli

Background

Entamoeba nuttalli is an intestinal protozoan with pathogenic potential that can cause amebic liver abscess. It is highly prevalent in wild and captive macaques. Recently, cysts were detected in a caretaker of nonhuman primates in a zoo, indicating that E. nuttalli may be a zoonotic pathogen. Therefore, it is important to evaluate the pathogenicity of E. nuttalli in detail and in comparison with that of E. histolytica.

Methodology/Principal findings

Trophozoites of E. nuttalli GY4 and E. histolytica SAW755 strains were inoculated into liver of hamsters. Expression levels of proinflammatory factors of hamsters and virulence factors from E. histolytica and E. nuttalli were compared between the two parasites. Inoculations with trophozoites of E. nuttalli resulted in an average necrotic area of 24% in liver tissue in 7 days, whereas this area produced by E. histolytica was nearly 50%. Along with the mild liver tissue damage induced by E. nuttalli, expression levels of proinflammatory factors (TNF-α, IL-6 and IL-1β) and amebic virulence protein genes (lectins, cysteine proteases and amoeba pores) in local tissues were lower with E. nuttalli in comparison with E. histolytica. In addition, M2 type macrophages were increased in E. nuttalli-induced amebic liver abscesses in the late stage of disease progression and lysate of E. nuttalli trophozoites induced higher arginase expression than E. histolytica in vitro.

Conclusions/Significance

The results show that differential secretion of amebic virulence proteins during E. nuttalli infection triggered lower levels of secretion of various cytokines and had an impact on polarization of macrophages towards a M1/M2 balance. However, regardless of the degree of macrophage polarization, there is unambiguous evidence of an intense acute inflammatory reaction in liver of hamsters after infection by both Entamoeba species.

Entamoeba nuttalli is the phylogenetically closest protozoan to Entamoeba histolytica and is highly prevalent in macaques. Previous studies have indicated that E. nuttalli is virulent in a hamster model. In this study, we compared the immunopathological basis of formation of liver abscess in hamsters between E. nuttalli and E. histolytica. Mild liver tissue damage developed after intrahepatic injection of trophozoites of E. nuttalli, and lower expression levels of genes for host proinflammatory factors and amebic virulence proteins were detected at the edges of liver abscesses induced by E. nuttalli. In addition, alternatively activated macrophages were increased in E. nuttalli-induced liver abscesses in the late stage of disease progression. The lysate of E. nuttalli trophozoites also induced higher arginase expression than E. histolytica in vitro. Polarization of macrophages is likely to affect the degree of acute inflammatory reactions in liver in an animal model during E. nuttalli infection. Our data reveal new characteristics of abscess formation by E. nuttalli.

Novel Entamoeba Findings in Nonhuman Primates

In addition to well-known human-infecting species, Entamoeba species not found in humans have been identified recently in nonhuman primates (NHPs). Importantly, it has become clear that the organism identified as Entamoeba histolytica in NHPs is usually a distinct species, Entamoeba nuttalli. Many DNA-based stool surveys use species-specific detection methods and so may miss the full range of Entamoeba species present. In addition, authors may be using the same species name to describe distinct organisms. These various shortcomings may not be obvious to readers. In this review, we clarify the relationships between Entamoeba species' names based on morphological and molecular data, and highlight gaps in recently published data on Entamoeba species in wild NHPs resulting from the use of variable methodology.

Prevalence, molecular epidemiology, and zoonotic potential of Entamoeba spp. in nonhuman primates in China

Amebiasis is a major public-health concern. It has a global distribution, and is listed as the third leading parasitic cause of human mortality. To survey the prevalence and assess the potential zoonotic transmission of Entamoeba spp. in nonhuman primates (NHPs) in China, 2688 fresh fecal specimens were collected from NHPs reared in farms or zoos/parks or free ranging in 13 districts. The overall prevalence of Entamoeba spp. infection determined with microscopy analysis was 39.4% (1059/2688). Higher infection rates were detected in the free ranging group (41.1%, 169/411) and in animals <1year old (58.7%, 556/947). Gene fragments were successfully amplified 463 (87.2%) out of the 531 selected specimens (approximately half of the total microscopy-positive specimens). Polymerase chain reaction (PCR) amplification identified 386 (83.4%) Entamoeba dispar and 287 (62.0%) E. coli infections, and among these, 210 (45.4%) were mixed infections. And that the E. dispar and E. coli had also been detected in humans. In phylogenetic analysis, the E. dispar and E. coli sequences clustered with reference E. dispar and E. coli, respectively. In conclusion, nonhuman primates infected with Entamoeba species, with high prevalence and zoonotic potential, should be considered when evaluating the maintenance of Entamoeba spp. and its transmission between animal reservoirs and humans.