Prevalence and genotypic diversity of Entamoeba species in inhabitants in Kathmandu, Nepal

'A comparative study of traditional and molecular diagnostic methods for detection of gastrointestinal parasites in Nepalese migrants to the UK'

BACKGROUND

We evaluated the results of examining a single faecal sample for gastrointestinal parasites (GIP) using a combination of traditional methods with multiplex qPCR for helminths and protozoa, compared to a reference standard of examining three faecal samples from each person using traditional diagnostic methods alone.

METHODS

Three faecal samples were collected at weekly intervals from 596 healthy Nepalese men. Each sample underwent formalin-ethyl acetate (FEA) concentration and light microscopy, and charcoal culture. The combined results of these investigations for all three stool samples were designated the reference standard. The first sample was also analysed using a multiplex TaqManTM qPCR assay, screening for five helminths and three protozoa. We compared sensitivity and specificity of analysing the first faecal sample with qPCR alone, or a hybrid approach combining qPCR with traditional methods, to the reference standard. Additionally, a serum sample was taken from each participant for Strongyloides stercoralis IgG ELISA.

RESULTS

The reference standard identified 139 GIP infections in 133 (22.3%) participants. Use of qPCR alone in one stool identified 176 infections in 147 (24.8%) participants, rising to 187 infections in 156 (26.3%) when combined with FEA microscopy and charcoal culture. The sensitivity of this latter hybrid approach was 100% for Strongyloides spp., 90.9% for Trichuris trichiura, 86.8% for hookworm species and 75% for Giardia duodenalis compared to the reference standard. The hybrid approach increased the detected cases of G. duodenalis by 4.5% (46 cases) overall, T. trichiura by 2.9% (18 cases), Strongyloides spp. by 1% (6 cases), and hookworm by 0.5% (8 cases), compared to the reference standard.

CONCLUSION

Examination of a single faecal sample using qPCR alone showed superior or equivalent sensitivity to traditional methods for most GIP infections when both were compared to the reference standard. Combining molecular and traditional methods to analyse a single stool improved the detection rate for most studied parasites. This approach has value in settings where repeated sampling and/or faecal culture for helminths is impractical, but molecular diagnostics are available.

Survey of Entamoeba infections in schoolchildren and macaques in Kathmandu, Nepal, and analysis of genetic polymorphisms of Entamoeba nuttalli and Entamoeba dispar isolates

Entamoeba species infect humans and non-human primates, raising concerns associated with potential zoonotic transmission. Therefore, the prevalence of human Entamoeba infections is crucial for its management in areas, where macaques exhibit high infection rates. Previously, we demonstrated prevalent E. nuttalli infections in rhesus macaques in Kathmandu, Nepal. In this study, we surveyed Entamoeba infection among 185 schoolchildren from two schools visited by wild rhesus macaques to assess the risk of transmission. PCR-based screening for Entamoeba species identified E. coli in 13 % and E. dispar in 0.5 % of the human stool samples. However, E. nuttalli and E. chattoni infections, prevalent in macaques, were not detected in human samples. This suggests that Entamoeba spp. are not transmitted through macaques in the school environment. We surveyed the rhesus macaques living in the temple near schools as well as the rhesus and Assam macaques inhabiting Shivapri Nagarjun National Park, Kathmandu. Among the 49 macaque stool samples, E. chattoni, E. coli, E. nuttalli, and E. dispar were detected in 92 %, 86 %, 41 %, and 18 % of the samples, respectively. Notably, E. dispar infections in macaques were mostly prevalent in the temple. A sample isolated from Nagarujun showed an identical genotype at two tRNA-linked short tandem repeat loci to that of E. dispar isolated from humans, suggesting potential transmission from humans to macaques. Genotypic analysis of cultured E. nuttalli strains obtained from the macaques colonizing three locations demonstrated that the geographical distance rather than differences in macaque species played a crucial role in the genetic diversity of the parasites. The phylogenetic tree of E. nuttalli strains, including the previously isolated strains, reflected the geographical distribution of the isolation sites. This study sheds light on the intricate dynamics of Entamoeba transmission and genetic diversity in macaques and humans.

Gastrointestinal parasite infections in Nepalese Gurkha recruits arriving in the United Kingdom from 2012-2020

BACKGROUND

Gastrointestinal parasite (GIP) infections are a major cause of global morbidity, infecting hundreds of millions of people each year and potentially leading to lifelong infection and serious complications. Few data exist on screening for GIP infections in migrants entering the UK or on the current performance of different traditional diagnostic approaches. This study aimed to describe the prevalence of GIP infections in Nepalese Gurkha recruits screened on arrival in the UK.

METHODOLOGY/PRINCIPAL FINDINGS

We present a retrospective analysis of data from screening male adults (18-21 years) who arrived in the UK from Nepal between 2012 and 2020. Three separate faecal samples were obtained from participants at weekly intervals and processed for formalin-ethyl acetate (FEA) concentration/light microscopy and charcoal culture. Serum samples were analysed for IgG antibodies to Strongyloides stercoralis by ELISA. Results were available from 2,263 participants, of whom 463 (20.5%, 95% CI 18.8%-22.2%) had a positive diagnostic test for at least one GIP infection. A total of 525 potential infections were identified. Giardia duodenalis was most common (231/2263, 10.2%), followed by S. stercoralis (102/2263, 4.5%), and hookworm species (86/2263, 3.8%). Analysis (microscopy and culture) of the initial stool sample diagnosed only 244/427 (57.1%) faecally identified pathogens, including 41/86 (47.7%) hookworm infections. The proportion of participants infected with any GIP showed a downward trend over the study period. Log-binomial regression showed risk of infection decreasing by 6.1% year-on-year (95% CI 3.2% - 9.0%). This was driven predominantly by a fall in hookworm, S. stercoralis and Trichuris trichiura prevalence.

CONCLUSIONS/SIGNIFICANCE

The level of potentially pathogenic GIP infection in young Nepalese men migrating to the UK is high (20.5%) and requires a combined diagnostic approach including serology and analysis of multiple stool samples incorporating specialised parasitological methods. Advances in molecular approaches may optimise and simplify the intensive screening strategy required.

Global burden and trends of the Entamoeba infection-associated diseases from 1990 to 2019: An observational trend study

BACKGROUND

Entamoeba infection-associated diseases (EIADs) in humans are a worldwide public health problem, but there is a lack of a global picture of EIADs, which is vital to prevention and control.

METHODS

We applied 2019 Global Burden of Disease (GBD) data collected from multiple sources at global, national and regional levels. The disability-adjusted life years (DALYs) with corresponding 95% uncertainty intervals (95% UIs) were extracted as the main measure of the burden of EIADs. The Joinpoint regression model was used to estimate the trends of age-standardised DALY rates by age, sex, geographical region, and sociodemographic index (SDI). Besides, a generalized linear model was conducted to analyze the influence of sociodemographic factors on the DALY rate of EIADs.

RESULTS

In 2019, there were 2,539,799 (95% UI 850,865-6,186,972) DALY cases attributable to Entamoeba infection, and the global age-standardised DALY rate of EIADs was 36.77/100,000 (95% UI: 12.03-90.49). Although over the past 30 years, the age-standardised DALY rate of EIADs presented significantly declining trends [average annual percent change (AAPC) = -3.79%, 95% CI: -4.05% - -3.53%], it has remained a heavy burden among the age group of <5 years (257.43/100,000, 95% UI: 67.73-676.78) and the low SDI regions (100.47/100,000, 95% UI: 32.27-249.09). The age-standardized DALY rate in high-income North America and Australia had an increasing trend (AAPC = 0.38%, 95% CI: 0.47% - 0.28% and 0.38%, 95% CI: 0.46% - 0.29%, respectively). Furthermore, the DALY rates in high SDI regions showed statistically significant increasing trends among the age groups of 14-49, 50-69 years and 70+ years, with AAPCs of 1.01% (95% CI: 0.87% - 1.15%), 1.58% (95% CI: 1.43% - 1.73%), and 2.93% (95% CI: 2.58% - 3.29%), respectively.

CONCLUSIONS

Over the past 30 years, the burden of EIADs has declined significantly. However, it has still caused a high burden in the low SDI regions and the age group of <5 years. At the same time, in adults and the elderly of the high SDI regions, the increasing trends of Entamoeba infection-associated burden should also be given more attention.

First report on the molecular detection of Entamoeba bovis from the endangered wild water buffalo (Bubalus arnee) in Nepal

Background

The Asiatic wild water buffalo (Bubalus arnee) is an endangered species that is conserved in the Koshi Tappu Wildlife Reserve (KTWR), Nepal, and was recently translocated to the Chitwan National Park (CNP). Gastrointestinal (GI) parasites are the cause of significant negative health and production impacts on animals worldwide.

Methods

A coprological survey of GI parasites of wild water buffalo was carried out in the CNP in 2020. Fresh dung samples (n = 25) were collected from wild water buffaloes and analysed using sedimentation and flotation techniques for morphological identification of parasite cysts, oocysts and eggs.

Results

Nine different GI parasites were recorded of which Entamoeba spp. (20 samples, 80%) were the most common. The presence of Entamoeba spp. was further validated using polymerase chain reaction (PCR) analysis and DNA sequencing. The PCR results were positive for all of the microscopically positive samples, and the species was identified as Entamoeba bovis. Three samples were sequenced and formed a cluster of E. bovis, which was separated from other Entamoeba spp. in phylogenetic analysis.

Conclusion

This is the first report for molecular detection of E. bovis from wild water buffaloes in Nepal. Future work should focus on the prevalence of such infections in water buffaloes in forest environments.

Diversity, geographical distribution, and prevalence of Entamoeba spp. in Brazil: a systematic review and meta-analysis

The genus Entamoeba includes a variety of widely distributed species adapted to live in the digestive tracts of humans and a large variety of animals of different classes. The objective of this study was to investigate the prevalence, distribution, and molecular epidemiology of Entamoeba spp. in different classes of hosts in Brazil. Studies that analyzed hosts from several classes, including humans and domestic, wild, or captive animals, were considered. The pooled prevalence of Entamoeba spp. was calculated using the random-effects model. A total of 166 studies on humans and 16 on animals were included. The prevalence of Entamoeba spp. in the Brazilian population was 22% (95% CI: 21–24). The state with the highest prevalence was Paraiba with 72%, followed by Federal District with 53%, and Rondonia with 50%. In immunocompromized patients, the prevalence was 18%, and cancer (36%) was the most prevalent cause of immunosuppression. The prevalence of Entamoeba spp. in animal hosts was 12% (95% CI: 7–17). Captive wild animals and domestic farm animals showed the highest prevalence, with 16% and 15%, respectively. The species found more often were E. coli (86.5%), E. dispar (7.9%), and E. histolytica (3.1%). In conclusion, a high prevalence (22%) of Entamoeba spp. was found in the Brazilian population, with a prevalence of up to 50% mainly in the northern, northeastern, and central-western regions. The pathogenic species E. histolytica is distributed in most Brazilian regions, with significant prevalence percentages. Among animals, unidentified Entamoeba species were most prevalent in mammals.

Epidemiology, species composition and genetic diversity of tetra- and octonucleated Entamoeba spp. in different Brazilian biomes

Background

Entamoeba species harbored by humans have different degrees of pathogenicity. The present study explores the intra- and interspecific diversity, phylogenetic relationships, prevalence and distribution of tetra- and octonucleated cyst-producing Entamoeba in different Brazilian regions.

Methods

Cross-sectional studies were performed to collect fecal samples (n = 1728) and sociodemographic data in communities located in four Brazilian biomes: Atlantic Forest, Caatinga, Cerrado, and Amazon. Fecal samples were subjected to molecular analysis by partial small subunit ribosomal DNA sequencing (SSU rDNA) and phylogenetic analysis.

Results

Light microscopy analysis revealed that tetranucleated cysts were found in all the studied biomes. The highest positivity rates were observed in the age group 6–10 years (23.21%). For octonucleated cysts, positivity rates ranged from 1 to 55.1%. Sixty SSU rDNA Entamoeba sequences were obtained, and four different species were identified: the octonucleated E. coli, and the tetranucleated E. histolytica, E. dispar, and E. hartmanni. Novel haplotypes (n = 32) were characterized; however, new ribosomal lineages were not identified. The Entamoeba coli ST1 subtype predominated in Atlantic Forest and Caatinga, and the ST2 subtype was predominant in the Amazon biome. E. histolytica was detected only in the Amazon biome. In phylogenetic trees, sequences were grouped in two groups, the first containing uni- and tetranucleated and the second containing uni- and octonucleated cyst-producing Entamoeba species. Molecular diversity indexes revealed a high interspecific diversity for tetra- and octonucleated Entamoeba spp. (H ± SD = 0.9625 ± 0.0126). The intraspecific diversity varied according to species or subtype: E. dispar and E. histolytica showed lower diversity than E. coli subtypes ST1 and ST2 and E. hartmanni.

Conclusions

Tetra- and octonucleated cyst-producing Entamoeba are endemic in the studied communities; E. histolytica was found in a low proportion and only in the Amazon biome. With regard to E. coli, subtype ST2 was predominant in the Amazon biome. The molecular epidemiology of Entamoeba spp. is a field to be further explored and provides information with important implications for public health.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13071-021-04672-y.

Analysis of D-A locus of tRNA-linked short tandem repeats reveals transmission of Entamoeba histolytica and E. dispar among students in the Thai-Myanmar border region of northwest Thailand

Intestinal parasitic infections, including those caused by Entamoeba species, are a persistent problem in rural areas of Thailand. The aims of this study were to identify pathogenic Entamoeba species and to analyze their genotypic diversity. Stool samples were collected from 1,233 students of three schools located in the Thai-Myanmar border region of Tak Province, Thailand. The prevalence of Entamoeba infection was measured by polymerase chain reaction (PCR) using species-specific primers. Thirty-one (2.5%) positive cases were detected for E. histolytica, 55 (4.5%) for E. dispar, and 271 (22.0%) for E. coli. Positive samples for E. histolytica and E. dispar were exclusively obtained from a few school classes, whereas E. coli was detected in all grades. No infections caused by E. moshkovskii, E. nuttalli, E. chattoni, and E. polecki were detected in the students studied. The D-A locus of tRNA-linked short tandem repeats was analyzed in samples of E. histolytica (n = 13) and E. dispar (n = 47) to investigate their diversity and potential modes of transmission. Five genotypes of E. histolytica and 13 genotypes of E. dispar were identified. Sequences of the D-A were divergent, but several unique genotypes were significantly prevalent in limited classes, indicating that intra-classroom transmission has occurred. As it was unlikely that infection would have been limited within school classes if the mode of transmission of E. histolytica and E. dispar had been through the intake of contaminated drinking water or food, these results suggest a direct or indirect person-to-person transmission mode within school classes. Positive rates for three Entamoeba species were 2-fold higher in students who had siblings in the schools than in those without siblings, suggesting that transmission occurred even at home due to heavy contacts among siblings.

Transmissions in endemic areas of the pathogen Entamoeba histolytica and other non-pathogenic Entamoeba species such as E. dispar and E. coli are caused by ingestion of drinking water and foods contaminated with cysts of the parasites. Cases of Entamoeba infections among school-aged children have been reported in several countries. However, it has not been demonstrated that transmission of protozoa of the Entamoeba genus occurs within school facilities. In addition, genetic information on E. histolytica and other morphologically indistinguishable species, including E. dispar and E. moshkovskii, in Thailand remains scarce. In the present study, we demonstrated that E. histolytica and/or E. dispar are prevalent among school-aged children, but limited to few classes in three rural schools in the Thai-Myanmar border region of northwest Thailand. Although various genotypes of these Entamoeba species were identified, identical genotypes were significantly more prevalent in certain school classes and also among siblings, suggesting that transmission occurred within the classrooms and at home. The possibility of person-to-person transmission among these students via direct or indirect contact during daily activities in classrooms and home is proposed.

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.

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.