Development and Application of a Blastocystis Subtype-Specific PCR Assay Reveals that Mixed-Subtype Infections Are Common in a Healthy Human Population

Unveiling Blastocystis epidemiology in Morocco: subtype diversity among clinical patients with and without gastrointestinal manifestations in the Meknes region

Blastocystis is an intestinal protist frequently identified in humans and other animals, though its clinical significance remains controversial. This study aimed to determine the prevalence and genetic diversity of Blastocystis in faecal samples from symptomatic (n = 55) and asymptomatic (n = 50) individuals seeking medical care in Meknes, Morocco. Detection of the protist was accomplished through coproparasitological examination and culture in Jones medium. Culture-positive samples were subjected to molecular analyses (PCR and Sanger sequencing) based on sequences of the small subunit ribosomal RNA gene. Epidemiological questionnaires on demographics and potential risk factors were collected from participating patients. The overall Blastocystis infection rate was 51.4% (54/105), with no differences between symptomatic (52.7%, 29/55) and asymptomatic (50.0%, 25/50) individuals. Sequence analyses identified three Blastocystis subtypes, with ST3 being the most prevalent (42.0%), followed by ST1 (34.0%), and ST2 (12.0%). Regarding intra-subtype diversity, allele 4 was found within ST1; alleles 11/12 and alleles 34/36 (alone or in combination) were identified within ST2 and ST3 respectively. Allele 34 in ST3 (40.8%) and allele 4 in ST1 (34.7%) were the most common genetic variants circulating in the surveyed clinical population. A statistically significant association between ST2 and the presence of flatulence was observed. This is the first study assessing the epidemiology and genetic diversity of Blastocystis sp. in the Meknes region, Morocco.

Subtype Distribution of Blastocystis spp. in Patients with Gastrointestinal Symptoms in Northern Spain

Limited molecular data exist on the prevalence and subtype distribution of Blastocystis spp., the most prevalent parasite in human and animal feces worldwide. A total of 44 different subtypes (STs) of Blastocystis are currently recognized based on the sequence of the small subunit ribosomal RNA (SSU-rRNA) gene. This is a molecular study of Blastocystis spp. in hospitalized patients with gastrointestinal symptoms in northern Spain. We analyzed 173 Blastocystis-positive patients with gastrointestinal symptoms by using nested PCR for molecular detection, subtype identification, phylogenetic analyses, and genetic diversity assessment. ST2 (34.1%) and ST3 (34.7%) predominated, followed by ST1 (15.6%) and ST4 (15.6%). Mixed infections with different subtypes were observed in some patients. Sequence analysis revealed for the first time in European humans the allele 88 (a variant of ST1). In other cases, alleles commonly found in animal samples were detected (allele 9 in ST2, allele 34 in ST3, and allele 42 in ST4). Phylogenetic analysis showed high variability in ST1 and ST2, suggesting a polyphyletic origin, while both ST3 and ST4 exhibited higher genetic homogeneity, indicating a possible monophyletic origin and recent transmission to humans. These data confirm Blastocystis spp. subtype diversity and may help in understanding the evolutionary processes and potential zoonotic transmission of this parasite.

Metataxomics reveals Blastocystis subtypes mixed infections in Colombian children

Blastocystis sp., is an intestinal protist with a broad host range and a high prevalence in human populations worldwide, even in developed Western countries. The publication of conflicting evidence has divided the scientific community about the pathogenic role of this parasite. Even though, genetic studies on Blastocystis sp. revealed associations between genotypes and different pathogenic profiles. Conventionally, the detection of this parasite is based on microscopic or PCR methods, which offer meager or null performance in detecting mixed infections. In this work, we applied a metataxonomic NGS approach targeting the V4 region of the eukaryotic SSU-rRNA gene and classical phylogenetic methods. This approach allowed us to detect Blastocystis sp. in stool samples from infected children living in an urban setting in the city of Medellin attending the same daycare center. Phylogenetic analysis identified the subtypes present in the children as ST1, ST2, and ST3. Besides, mixed infections of subtypes ST1 + ST3 were spotted in 16% of the analyzed stool samples.

Epidemiology of Blastocystis Infection: A Review of Data from Poland in Relation to Other Reports

Blastocystis is a common gut protist of humans and various animals worldwide, with a high level of genetic diversity. Neither its zoonotic potential and transmission routes nor its pathogenicity are fully known. This fact, and the fact that Blastocystis is the most abundant eukaryote in human faeces, raises the question of its relevance to public health. Here, we summarise (in relation to other reports) the results of studies on the prevalence and genotypic variation of Blastocystis, which were carried out in animals, humans, and in water environments in Poland. In humans, the prevalence ranged between 0.14 and 23.6%, in some animals reached 58.97%, and in water environments was 5.1%. Seven subtypes were identified in humans (ST1-ST4, ST6, ST7, and ST9), of which ST3 was the most common. Among animals (wild, livestock, and pet animals), eleven STs were identified, with differential host specificity. Humans and animals shared ST1, ST2, ST3, ST6, and ST7, while ST1 and ST3 were present in humans, animals, and water sources. These observations indicate the possibility of Blastocystis transmission between animals and humans. Further studies should be continued in search of the sources and transmission routes of Blastocystis in order to prevent the spread of infections among humans and animals.

Systematic Review and Meta-Analysis: Epidemiology of Human Blastocystis spp. Infection in Malaysia

Blastocystis spp. is a unicellular enteric protozoan parasite in humans with a controversial role in disease etiology. It is common in developing countries among immunocompromised patients and people who have close contact with animals. In this study, we have systematically reviewed previous studies on the distribution and genotypes of human Blastocystis infection in Peninsular Malaysia. Studies examining the prevalence of Blastocystis in diverse demographics, including rural, urban, comorbid conditions, and high-risk populations, were taken into consideration. The infection has been reported in nine states; the total percentage of infection was 17.8% (1671/9397), with the most cases in Pahang (27.3%) and the least in Johor (3.4%). Molecular studies revealed the presence of six subtypes: ST1, ST2, ST3, ST4, ST5, and ST6. ST3 was reported as the predominant subtype in all the states, with a prevalence of 54.7% (338/618). The findings provide greater clarity on the epidemiology of Blastocystis in Malaysia, which will help in policy making towards planning and strategizing control measures against the parasite.

Draft genomes of Blastocystis subtypes from human samples of Colombia

BACKGROUND

Blastocystis is one of the most common eukaryotic microorganisms colonizing the intestines of both humans and animals, but the conditions under which it may be a pathogen are unclear.

METHODS

To study the genomic characteristics of circulating subtypes (ST) in Colombia, we established nine xenic cultures from Blastocystis isolated from human fecal samples, we identified 10 different subtypes, since one sample had a mixed infection. Thus, the genomes of the subtypes ST1 (n = 3), ST2 (n = 1), ST3 (n = 2), ST6 (n = 1), ST7 (n = 1), and ST8 (n = 2) were sequenced using Illumina and Oxford Nanopore Technologies (ONT).

RESULTS

Analyses of these draft nuclear genomes indicated remarkable diversity in terms of genome size and guanine-cytosine (GC) content among the compared STs. Illumina sequencing-only draft genomes contained 824 to 2077 scaffolds, with total genome size ranging from 12 to 13.2 Mb and N₅₀ values ranging from 10,585 to 29,404 base pairs (bp). The genome of one ST1 isolate was sequenced using ONT. This assembly was more contiguous, with a size of 20 million base pairs (Mb) spread over 116 scaffolds, and an N₅₀ of 248,997 bp.

CONCLUSION

This work represents one of the few large-scale comparative genomic analyses of Blastocystis isolates, providing an additional glimpse into its genomic diversity.

Blastocystis occurrence in water sources worldwide from 2005 to 2022: a review

There has been increasing interest in the study of Blastocystis in the last two decades. Many studies have been carried out in human and animal hosts including environmental sources, but there is little or no information on the occurrence of Blastocystis in water sources worldwide. Therefore, this study aimed at assessing the occurrence of Blastocystis in water sources across the world from 2005 to 2022, noting the method of detection and the distribution of the subtypes from various water sources. A literature search was performed on internet-based databases including Google search, PubMed, Scopus, and Web of Science. Upon application of the criteria for inclusion, 25 articles revealing the occurrence of Blastocystis in water sources in 15 countries were included in the review. Blastocystis occurrence varies across water sources ranging from 0% in a drinking water source in Venezuela to 100% in rivers; well water, stored water, and fishpond in Nepal and Malaysia; and fountain water, irrigation water, and rainwater in Italy, Spain, and Thailand. The occurrence of the parasite was significantly associated with the coliform count, temperature, conductivity, dissolved oxygen, turbidity, total dissolved solids, and chemical oxygen demand. A total of 11 Blastocystis subtypes were identified in water sources worldwide, namely, ST1-ST8, ST10, ST23, and ST26 in which ST1 and ST3 were the most prevalent subtypes. Considering the importance of Blastocystis as a waterborne parasite, the subtype distribution and morphological distinction in water sources need to be carried out using molecular and electron microscopic techniques. Existing studies have covered only about 10% of the world's countries.

Resistance of Blastocystis to chlorine and hydrogen peroxide

Blastocystis is a ubiquitous, widely distributed protist inhabiting the gastrointestinal tract of humans and other animals. The organism is genetically diverse, and so far, at least 28 subtypes (STs) have been identified with ST1-ST9 being the most common in humans. The pathogenicity of Blastocystis is controversial. Several routes of transmission have been proposed including fecal-oral (e.g., zoonotic, anthroponotic) and waterborne. Research on the latter has gained traction in the last few years with the organism having been identified in various bodies of water, tap water, and rainwater collection containers including water that has been previously filtered and/or chlorinated. Herein, we assessed the resistance of 11 strains maintained in culture, spanning ST1-ST9 to various chlorine and hydrogen peroxide concentrations for 24 h, and performed recovery assays along with re-exposure. Following the treatment with both compounds, all subtypes showed increased resistance, and viability could be visualized at the cellular level. These results are hinting at the presence of mechanism of resistance to both chlorine and hydrogen peroxide. As such, this pilot study can be the platform for developing guidelines for water treatment processes.

Exosomes secreted by Blastocystis subtypes affect the expression of proinflammatory and anti-inflammatory cytokines (TNFα, IL-6, IL-10, IL-4)

Background

Blastocystis sp. is a common intestinal parasite, possibly responsible for diarrhea, vomiting and nausea, abdominal pain, and irritable bowel syndrome. However, many studies focused on this issue due to the uncertainty of its pathogenic potential. The extracellular vesicles (EVs) are significant mediators for cellular communication, carrying biological molecules such as proteins, lipids, and nucleic acids. Compared with other parasites, little is known about the Blastocystis EVs. Hence the present investigation was done.

Methods

The Blastocystis parasites were cultured in the DMEM medium, and a 550–585 bp fragment was amplified using PCR, and sequencing was done. A commercial kit was used for exosome extraction and dynamic light scattering (DLS), flow cytometry (CD63, CD81 markers), and electron microscopy tests to determine their morphology. The human leukemia monocytic cell line (THP-1) was exposed to Blastocystis EVs. Next, the expression of proinflammatory and anti-inflammatory cytokines, including IL-4, IL-6, IL-10, and tumor necrosis factor-alpha (TNF-α), were measured using quantitative PCR.

Results

Exosomes were extracted from ST1-3 Blastocystis sp. According to the DLS assay, the size of the exosomes was in the range of 30–100 nm. Electron microscopy images and CD63 and CD81 markers also confirmed the exosome's size, structure, and morphology. According to real-time PCR results, ST1-derived exosomes caused IL-6 and TNF-α upregulation and IL-10 and IL-4 downregulation, ST2- and ST3-derived exosomes downregulated IL-10, and ST3-derived exosomes caused IL-6 upregulation. There is a statistically significant difference (P ≤ 0.05).

Conclusion

To our knowledge, this is the first report of the release of exosome-like vesicles by the human parasite, Blastocystis, and the provided information demonstrates the role of this parasite, particularly ST1 on proinflammatory and anti-inflammatory cytokines and navigating the host response.

Comparison of molecular diagnostic approaches for the detection and differentiation of the intestinal protist Blastocystis sp. in humans

Blastocystis is the most commonly found intestinal protist in the world. Accurate detection and differentiation of Blastocystis including its subtypes (arguably species) are essential to understand its epidemiology and role in human health. We compared (i) the sensitivity of conventional PCR (cPCR) and qPCR in a set of 288 DNA samples obtained from stool samples of gut-healthy individuals, and (ii) subtype diversity as detected by next-generation sequencing (NGS) versus Sanger sequencing. Real-time PCR resulted in more positive samples than cPCR, revealing high fecal load of Blastocystis based on the quantification curve in most samples. In subtype detection, NGS was largely in agreement with Sanger sequencing but showed higher sensitivity for mixed subtype colonization within one host. This fact together with use of the combination of qPCR and NGS and obtaining information on the fecal protist load will be beneficial for epidemiological and surveillance studies.

Collateral Damage in the Human Gut Microbiome - Blastocystis Is Significantly Less Prevalent in an Antibiotic-Treated Adult Population Compared to Non-Antibiotic Treated Controls

Antibiotics can drive the rapid loss of non-target, phylogenetically diverse microorganisms that inhabit the human gut. This so-called “collateral damage” has myriad consequences for host health and antibiotic mediated changes to the gut microbiota have been implicated in the aetiology of many chronic diseases. To date, studies have largely focused on how antibiotics affect the bacterial fraction of the gut microbiome and their impact on non-bacterial members, including prevalent eukaryal species, such as Blastocystis, remains largely unknown. Here we assessed the prevalence and diversity of Blastocystis in an elderly adult group that were in receipt of antibiotics (n = 86) and an equivalent non-antibiotic treated group (n = 88) using a PCR-based approach. This analysis revealed that although similar subtypes were present in both groups, Blastocystis was significantly less prevalent in the antibiotic-treated group (16%) compared to non-antibiotic treated controls (55%); Fisher’s Exact test, p < 0.0001). Given that antibiotics target structures and molecules of prokaryotic cells to kill or inhibit bacterial populations, the most likely explanation for differences in prevalence between both groups is due to secondary extinctions owing to the potential dependence of Blastocystis on bacteria present in the gut microbiome that were negatively affected by antibiotic treatment. Although further work is required to explore this hypothesis in greater detail, these data clearly show that Blastocystis prevalence in human populations is negatively associated with antibiotic treatment. This finding may be relevant to explaining patterns of variation for this microorganism in different human populations and cohorts of interest.

Amplicon-based next-generation sequencing of eukaryotic nuclear ribosomal genes (metabarcoding) for the detection of single-celled parasites in human faecal samples

Comprehensive detection and differentiation of intestinal protists mostly rely on DNA-based methods. Here, we evaluated next-generation sequencing of eukaryotic nuclear ribosomal genes (metabarcoding) for the detection and differentiation of intestinal eukaryotic protists in the stool of healthy Tunisian individuals.

Thirty-six faecal DNA samples previously evaluated by microscopy and ameboid species-specific PCRs were tested. The hypervariable regions V3-V4 and V3-V5 of the 18S rRNA gene were amplified using three universal eukaryotic primer sets and sequenced using Illumina®MiSeq sequencing. In addition, real-time PCR assays were used to detect Dientamoeba fragilis, Giardia duodenalis, and Cryptosporidium spp.

The metabarcoding assay detected Blastocystis (subtypes 1, 2, and 3) and archamoebid species and subtypes (Entamoeba dispar, Entamoeba hartmanni, Entamoeba coli RL1 and RL2, Endolimax nana, Iodamoeba bütschlii RL1) in 27 (75%) and 22 (61%) of the 36 stool samples, respectively. Meanwhile, the assay had limited sensitivity for flagellates as evidenced by the fact that no Giardia-specific reads were found in any of the five Giardia-positive samples included, and Dientamoeba-specific reads were observed only in 3/13 D. fragilis-positive samples. None of the samples were positive for Cryptosporidium by any of the methods. In conclusion, a large variety of intestinal eukaryotic protists were detected and differentiated at species and subtype level; however, limited sensitivity for common flagellates was observed.

Clinical Parasitology and Parasitome Maps as Old and New Tools to Improve Clinical Microbiomics

A growing body of evidence shows that dysbiotic gut microbiota may correlate with a wide range of disorders; hence, the clinical use of microbiota maps and fecal microbiota transplantation (FMT) can be exploited in the clinic of some infectious diseases. Through direct or indirect ecological and functional competition, FMT may stimulate decolonization of pathogens or opportunistic pathogens, modulating immune response and colonic inflammation, and restoring intestinal homeostasis, which reduces host damage. Herein, we discuss how diagnostic parasitology may contribute to designing clinical metagenomic pipelines and FMT programs, especially in pediatric subjects. The consequences of more specialized diagnostics in the context of gut microbiota communities may improve the clinical parasitology and extend its applications to the prevention and treatment of several communicable and even noncommunicable disorders.

Subtype analysis and prevalence of mixed subtype infection of Blastocystis in farmed pigs from Chiba Prefecture, Japan

Blastocystis is an intestinal eukaryotes found in a wide range of animals and in the human population globally. Blastocystis is reported in domestic pigs, with subtype (ST) 5 being the dominant ST, followed by ST1 and ST3. The common method used for ST identification in pigs is PCR-sequencing, which often results in underestimation of the prevalence of mixed infections. Here, we aimed to investigate the ST distribution and the prevalence of mixed ST infection of Blastocystis in pigs from Chiba Prefecture in eastern Japan. A total of 82 fecal samples positive for Blastocystis were collected from two different farms, A and B. PCR was performed with subtype-specific primers, ST1, ST2, ST3, and ST5. The prevalence of single ST5 infection was 37.8% (31/82), whereas mixed infection with ST5 and other STs was 57.3% (47/82). A high percentage of single ST5 infection was observed in sows, piglets, and weaners from farm A (13/15, 86.7%), whereas mixed infection of ST5 and other STs, ST1 and ST3, was observed in 3-5-month-old grower pigs (15/18, 83.3%). Similarly, in farm B, the majority of sows and piglets under 1 month of age showed a single ST5 infection (12/17, 70.6%), whereas weaner, grower, and finisher pigs showed mixed infections with ST5 and other STs, ST1, ST2 and ST3 (27/28, 96.4%). In domestic pigs, diet and rearing environment changes dramatically over the course of animal's lifetime, which may have caused this difference in the prevalence of mixed ST infection among different age groups.

Prevalence, subtypes and risk factors of Blastocystis spp. infection among pre- and perimenopausal women

Background

Blastocystis spp. are considered pathogenic or commensal organisms, although the majority of researchers suggest that these are neglected pathogens. The main aim of this study was to determine the prevalence and subtype distribution of Blastocystis spp. in pre- and perimenopausal women, with respect to socio-demographic (age and place of residence), and epidemiological factors, as well as drinking tap water, contact with domestic animals, traveling abroad, health status, and presence of gastrointestinal symptoms. Additionally, the objective was to compare hematological and biochemical parameters of Blastocystis spp. infected and uninfected women.

Methods

The study included 425 women aged 45–60. Their stool samples were examined microscopically and analyzed by a conventional polymerase chain reaction (cPCR).

Results

Blastocystis spp. were detected in 6.1% of pre- and perimenopausal women. Molecular analysis of the stool samples identified seven Blastocystis subtypes (ST1–ST4, ST6, ST7, and ST9). Blastocystis subtypes 2 and 3 were the most prevalent. The presence of Blastocystis spp. was not significantly related to socio-demographic and epidemiological factors. There were also no significant associations between Blastocystis spp. and blood parameters, or gastrointestinal symptoms.

Conclusion

This study complements the limited available data on the prevalence of Blastocystis spp. in pre- and perimenopausal women. It is also the first report showing the presence of Blastocystis subtype 9 in Poland.

Investigation of neglected protists Blastocystis sp. and Dientamoeba fragilis in immunocompetent and immunodeficient diarrheal patients using both conventional and molecular methods

Introduction

The clinical significance of Blastocystis sp. and Dientamoeba fragilis in patients with gastrointestinal symptoms is a controversial issue. Since the pathogenicity of these protists has not been fully elucidated, testing for these organisms is not routinely pursued by most laboratories and clinicians. Thus, the prevalence of these organisms and the subtypes of Blastocystis sp. in human patients in Turkey are not well characterized. This study aimed to determine the prevalence of Blastocystis sp. and D. fragilis in the diarrheic stool samples of immunodeficient and immunocompetent patients using conventional and molecular methods and to identify Blastocystis sp. subtypes using next generation sequencing.

Material and methods

Individual stool specimens were collected from 245 immunodeficient and 193 immunocompetent diarrheic patients between March 2017 and December 2019 at the Gazi University Training and Research Hospital in Ankara, Turkey. Samples were screened for Blastocystis sp. and D. fragilis by conventional and molecular methods. Molecular detection of both protists was achieved by separate qPCRs targeting a partial fragment of the SSU rRNA gene. Next generation sequencing was used to identify Blastocystis sp. subtypes.

Results

The prevalence of Blastocystis sp. and D. fragilis was 16.7% and 11.9%, respectively as measured by qPCR. The prevalence of Blastocystis sp. and D. fragilis was lower in immunodeficient patients (12.7% and 10.6%, respectively) compared to immunocompetent patients (21.8% and 13.5%, respectively). Five Blastocystis sp. subtypes were identified and the following subtype distribution was observed: ST3 54.4% (n = 37), ST2 16.2% (n = 11), ST1 4.4% (n = 3), ST6 2.9% (n = 2), ST4 1.5% (n = 1), ST2/ST3 11.8% (n = 8) and ST1/ST3 8.8% (n = 6). There was no statistically significant difference in the distribution of Blastocystis sp. subtypes between immunocompetent and immunodeficient patients.

Conclusion and recommendation

Our findings demonstrated that Blastocystis sp. and D. fragilis are commonly present in immunocompetent and immunodeficient patients with diarrhea. This study is the first to use next generation sequencing to address the presence of Blastocystis sp. mixed subtypes and intra-subtype variability in clinical samples in Turkey.

Blastocystis sp. and Dientamoeba fragilis are single-cell parasites of the human intestine which are common worldwide and reported in cases with gastrointestinal symptoms. However, the role of Blastocystis sp. and D. fragilis in patients with gastrointestinal symptoms is still controversial because their presence is not always associated with symptoms. As some intestinal parasitic infections can cause severe illness in immunocompromised individuals careful consideration of intestinal protist infection is warranted. However, testing for Blastocystis sp. and D. fragilis is not routinely carried out by most laboratories and clinicians. Therefore, this study aimed to determine the prevalence of Blastocystis sp. and D. fragilis in immunocompetent and immunosuppressed patients with diarrhea by conventional and molecular methods. Both Blastocystis sp. and D. fragilis were detected more frequently by quantitative polymerase chain reaction than by conventional methods. Next generation sequencing was used to characterize the diversity and frequency of Blastocystis sp. subtypes and mixed subtypes in patients in Turkey. Five Blastocystis sp. subtypes (ST1, ST2, ST3, ST4 and ST6) were detected. ST3 was the most frequent subtype in both immunocompetent and immunosuppressed patients. Mono-infections were more common than mixed subtype infections. Our findings showed that Blastocystis sp. and D. fragilis are commonly present in immunocompetent and immunodeficient patients with diarrhea.

Epidemiology and subtype distribution of Blastocystis in humans: A review

Blastocystis is a commonly encountered gastrointestinal protozoan in humans and animals with uncertain pathogenicity. Despite its potential public health impact, epidemiological data regarding the prevalence and molecular subtype (ST) distribution of Blastocystis have been rarely reported. Among Blastocystis STs, ST1-ST4 are common in humans, including healthy and immunodeficient populations. According to the Chi-squared (χ²) association based on the data compiled for this cross-sectional study, the presence of ST1 is associated with asymptomatic infection, whereas the presence of ST4 is associated with symptomatic infection. However, cross-sectional studies cannot clarify the potential pathogenicity of Blastocystis, unlike in vivo and in vitro studies. Poor hygiene, poor sanitation and zoonotic transmission are possible factors associated with high Blastocystis prevalence, although this protozoan may be part of the normal healthy human gastrointestinal microbiota. This review covers the prevalence, STs and distribution of Blastocystis infection in humans. Thus, future epidemiological and subtyping studies could reveal new STs in humans as well as possible associations of STs with disease, drug resistance and related mechanisms such as protease activity. These associations with proper ST identification may facilitate the control of potential threats to host health, including the direct pathogenic effects of Blastocystis or alterations of the gastrointestinal microbiome.

Identification of Multiple Blastocystis Subtypes in Domestic Animals From Colombia Using Amplicon-Based Next Generation Sequencing

Blastocystis is frequently reported in fecal samples from animals and humans worldwide, and a variety of subtypes (STs) have been observed in wild and domestic animals. In Colombia, few studies have focused on the transmission dynamics and epidemiological importance of Blastocystis in animals. In this study, we characterized the frequency and subtypes of Blastocystis in fecal samples of domestic animals including pigs, minipigs, cows, dogs, horses, goats, sheep, and llama from three departments of Colombia. Of the 118 fecal samples included in this study 81.4% (n = 96) were positive for Blastocystis using a PCR that amplifies a fragment of the small subunit ribosomal RNA (SSU rRNA) gene. PCR positive samples were sequenced by next generation amplicon sequencing (NGS) to determine subtypes. Eleven subtypes were detected, ten previously reported, ST5 (50.7%), ST10 (47.8%), ST25 (34.3%), ST26 (29.8%), ST21 (22.4%), ST23 (22.4%), ST1 (17.9%), ST14 (16.4%), ST24 (14.9%), ST3 (7.5%), and a novel subtype, named ST32 (3.0%). Mixed infection and/or intra -subtype variations were identified in most of the samples. Novel ST32 was observed in two samples from a goat and a cow. To support novel subtype designation, a MinION based sequencing strategy was used to generate the full-length of the SSU rRNA gene. Comparison of full-length nucleotide sequences with those from current valid subtypes supported the designation of ST32. This is the first study in Colombia using NGS to molecularly characterize subtypes of Blastocystis in farm animals. A great diversity of subtypes was observed in domestic animals including subtypes previously identified in humans. Additionally, subtype overlap between the different hosts examined in this study were observed. These findings highlight the presence of Blastocystis subtypes with zoonotic potential in farm animals indicating that farm animals could play a role in transmission to humans.

Evolution in a Community Context: towards Understanding the Causes and Consequences of Adaptive Evolution in the Human Gut Microbiota over Short Time Scales

How important is adaptive evolution to the unique diversity that we can observe for each individual human gut microbiome? How do gut microbes evolve in response to changes in their environment, and how does evolution in real time impact microbial functionality in the context of host health? My interdisciplinary research uses in vitro microcosm models to test how different abiotic and biotic factors impact microbial evolution in a community context. We complement this approach by tracking focal species as they evolve in real time and in their natural environment of the human gut. Our aim is to provide a better understanding of how the dynamics and outcomes of microbial evolution differ between individual gut environments, and in response to different selection pressures, so that we can move closer to rational gut microbiome treatments that promote host health and prevent and treat human disease.

Blastocystis sp. Prevalence and Subtypes Distribution amongst Syrian Refugee Communities Living in North Lebanon

Molecular data concerning the prevalence and subtype (ST) distribution of the intestinal parasite Blastocystis sp. remain scarce in the Middle East. Accordingly, we performed the first molecular epidemiological survey ever conducted in the Syrian population. A total of 306 stool samples were collected from Syrian refugees living in 26 informal tented settlements (ITS) subjected or not to water, sanitation, and hygiene (WASH) interventions in North Lebanon, then screened for the presence of Blastocystis sp. by real-time polymerase chain reaction followed by subtyping. The overall prevalence of the parasite was shown to reach 63.7%. Blastocystis sp. colonization was not significantly associated with gender, age, symptomatic status, abdominal pain or diarrhea. In contrast, WASH intervention status of ITS was identified as a risk factor for infection. Among a total of 164 subtyped isolates, ST3 was predominant, followed by ST1, ST2, and ST10. No particular ST was reported to be associated with age, gender, symptomatic status, digestive disorders, or WASH intervention status of ITS. Intra-ST diversity of ST1 to ST3 was low suggesting large-scale anthroponotic transmission. Moreover, comparative analysis of ST1 to ST3 genotypes revealed that the circulation of the parasite between Syrian refugees and the host population was likely limited.

First Report on the Occurrence and Subtypes of Blastocystis in Pigs in Poland Using Sequence-Tagged-Site PCR and Barcode Region Sequencing

Blastocystis is an enteric microorganism commonly found in humans and animals worldwide. Its pathogenic role in humans and transmission patterns has not been fully explained. However, nine subtypes (ST1-8, ST12) are considered as potentially zoonotic. Studies from various regions of the world show that pigs are mainly infected with ST5. Although pigs are important farmed animals in Poland, the question of Blastocystis infection in these animals has not yet been investigated. Herein, 149 pig stool samples from 10 Polish pig farms were analyzed using sequence-tagged-site PCR and barcode region sequencing. The percentage of samples in which Blastocystis was identified using each method separately was similar: 38.25% and 37.58%, respectively. However, the percentage of positive results obtained by combining both methods was 46.97%, which means that, depending on the method used, the number of undetected samples varied between 8.72% and 9.39%. This shows the methodological limitations of up-to-date molecular approaches commonly used in Blastocystis research. A moderate infection rate (44.4-50%) observed in different pig age groups with a vital predominance of ST5 (94.28%) in every age group shows that pigs are a likely natural host of ST5. A small percentage of mixed infections, namely ST5/ST1 (5.26%), ST5/ST3 (1.75%), and ST3/ST1 (1.75%), was observed only in animals of older age, suggesting that ST3 and ST1 can be acquired by pigs during contact with humans. This study provides the first data on the prevalence and Blastocystis subtypes (STs) distribution in pigs in Poland. The results also highlight the need for the development of new methods capable of detecting highly genetically diverse Blastocystis isolates and mixed infections.

Prevalence and subtype distribution of Blastocystis sp. infecting children from a rural community in Panama

Blastocystis sp. is a commonly reported intestinal parasite with a worldwide distribution. Phylogenetic analyses describe at least 17 subtypes for this parasite, and nine of them have been found in humans. However, the prevalence and some epidemiological characteristics of this parasitic infection in rural communities are not well known. The objective of this cross-sectional study was to evaluate the prevalence, subtypes, and epidemiological factors related to Blastocystis sp. Infection in children from of a small rural community in the central area of Panama. For this, 66 fecal samples from children (1 to 12 years old), were initially analyzed for the presence of parasites by a formalin-ethyl acetate/concentration method. Molecular detection and identification of Blastocystis sp. subtypes were carried out by amplification and sequencing of a partial fragment of the small-subunit ribosomal RNA gene. Using data from a questionnaire, analyses of epidemiological conditions potentially associated with Blastocystis sp. transmission were also conducted. Microscopic diagnostics showed that 33.3% (22/66) of the analyzed samples presented entero-parasites. Among them, Blastocystis sp. was the most prevalent, with 21.2% (14/66), followed by the E. histolytica/dispar/moshkovskii complex 4.5% (3/66), Giardia lamblia 1.5% (1/66) and Strongyloides stercoralis 1.5% (1/66). PCR-based analyses detected a prevalence of Blastocystis sp. infection of 74.2% (49/66) in apparently healthy children. Phylogenetic analysis revealed two different subtypes of this parasite: ST1 with 42.2% (28/66) infected, and ST3 with 31.8% (21/66) infected. In addition, recent diarrhea was significantly associated with Blastocystis sp. infection. None of the other risk factors evaluated was statistically associated with infection. These results highlight the need to further investigate clinical, epidemiological, and genetic characteristics of Blastocystis sp. infections in this community.

Use of next-generation amplicon sequencing to study Blastocystis genetic diversity in a rural human population from Mexico

BACKGROUND

The intestinal parasite Blastocystis is found in humans and animals around the world. It is spread through the consumption of contaminated food and water and has been associated with a variety of intestinal symptoms. Blastocystis is one of the most common intestinal parasites in humans, yet its prevalence and distribution in humans in North America is not well characterized.

METHODS

Next-generation amplicon sequencing of a region of the Blastocystis SSU rRNA gene was applied to DNA extracted from fecal specimens obtained from 182 inhabitants of a rural population in Mexico to characterize Blastocystis prevalence, subtype distribution, and intra-host subtype diversity in humans.

RESULTS

Of the 182 samples tested in this study, 68.1% (124) contained one or more Blastocystis subtypes. Subtype 3 was the most common subtype observed and was found in 81.5% of the positive samples. Subtype 1, 16.9% of the positive samples, and subtype 2, 17.7% of the positive samples, were also found in this population. Mixed infections were observed in 13.7% of the positive samples. In this population, the odds of having Blastocystis increased in adulthood (> 15 years; OR: 1.72, P < 0.0001), and the odds of having subtype 1 increased in the presence of farm animals (OR: 1.51, P = 0.03). The odds of having subtype 1, subtype 2, or a mixed infection decreased in the presence of cement flooring (OR: - 1.61, P = 0.005; OR: - 1.14, P = 0.03; OR: - 1.48, P = 0.02) possibly indicating socioeconomic factors are involved in the risk of acquiring one of these subtypes.

CONCLUSIONS

These data contribute to our understanding of the epidemiology of Blastocystis infection in humans and can be used to shape future studies which aim to better characterize the transmission pathways and health outcomes of Blastocystis infections.

Molecular epidemiology of Blastocystis spp. in children referred to Qods hospital in northwest of Iran

Blastocystis sp. is a polymorphic intestinal parasite in humans and animals. The parasite has a worldwide distribution, especially in developing countries with poor sanitation, exposure to animals, and improper disposal systems. The aim of this study was to identify the subtypes of Blastocystis sp. among children of Qazvin, northwest Iran. Totally, 864 stool samples were collected from the children referred to Qods hospital in Qazvin, Iran. Fecal specimens were investigated by formalin-ethyl acetate concentration method and trichrome staining as well as cultivation of all samples in clotted fetal bovine medium. DNA extraction of culture-positive specimens and PCR amplification of 18S ribosomal RNA gene region was performed. The sequences detected were compared with reference genes in the GenBank, and the sequences further deposited in the GenBank database. Data analysis was performed by Chi square test while a p value of < 0.05 was considered as significant. Of 864 isolates, 4.1% (36/864) were positive for Blastocystis sp. with infection rate insignificantly higher among the females than males. The highest infection rate was estimated at 6.8% in 6-9 years old age group with abdominal pain as the most common (33%) gastrointestinal sign. No statistically significant difference was found between the variables and Blastocystis infection. Molecular analysis clarified the presence of three subtypes of Blastocystis including ST1 (56%), ST2 (28%), and ST3 (16%) of among specimens with ST1 as the predominant subtype. A significant association between intestinal signs and the subtypes was not found. Considering ST1 as the predominant subtype, it seems that zoonotic transmission is a main route of human infections with Blastocystis sp. in the area studied.

Characterization of subtypes of Blastocystis sp. isolated from patients with urticaria, São Paulo, Brazil

Blastocystis sp. is described as an enteric protist prevalent in fecal samples from humans and animals; its pathogenicity and epidemiology are still controversial. Currently, it has been associated with intestinal diseases such as irritable bowel syndrome and clinical manifestations of allergic skin, such as chronic urticaria. In the context of urticaria, it is still uncertain whether this organism is directly related to the allergic manifestation or just a common component of the intestinal microbiota. This study aimed to evaluate the occurrence and molecular diversity of Blastocystis sp. in individuals with urticaria from a dermatology outpatient clinic, São Paulo, Brazil. Fecal samples of 58 patients with urticaria were examined using parasitological methods; and subsequently tested by polymerase chain reaction using Blastocystis-specific primers. The subtypes (STs) and alleles (a) were determined using BLASTn and MLST tools. ST1, ST2, ST3, ST4, ST6 and mixed infection (ST1 + ST3) were identified in the patients with urticaria; ST1 (a4), ST3 (a34 and a36) and ST4 (a42) were the most prevalent. Our molecular analyses allowed an initial description of Blastocystis subtypes in patients with urticaria from São Paulo city, Brazil.

Microbiota-Immune Interaction in the Pathogenesis of Gut-Derived Infection

Gut-derived infection is among the most common complications in patients who underwent severe trauma, serious burn, major surgery, hemorrhagic shock or severe acute pancreatitis (SAP). It could cause sepsis and multiple organ dysfunction syndrome (MODS), which are regarded as a leading cause of mortality in these cases. Gut-derived infection is commonly caused by pathological translocation of intestinal bacteria or endotoxins, resulting from the dysfunction of the gut barrier. In the last decades, the studies regarding to the pathogenesis of gut-derived infection mainly focused on the breakdown of intestinal epithelial tight junction and increased permeability. Limited information is available on the roles of intestinal microbial barrier in the development of gut-derived infection. Recently, advances of next-generation DNA sequencing techniques and its utilization has revolutionized the gut microecology, leading to novel views into the composition of the intestinal microbiota and its connections with multiple diseases. Here, we reviewed the recent progress in the research field of intestinal barrier disruption and gut-derived infection, mainly through the perspectives of the dysbiosis of intestinal microbiota and its interaction with intestinal mucosal immune cells. This review presents novel insights into how the gut microbiota collaborates with mucosal immune cells to involve the development of pathological bacterial translocation. The data might have important implication to better understand the mechanism underlying pathological bacterial translocation, contributing us to develop new strategies for prevention and treatment of gut-derived sepsis.

Next generation amplicon sequencing improves detection of Blastocystis mixed subtype infections

Blastocystis is a highly prevalent enteric protist parasite of humans and animals. Transmission occurs via the fecal-oral route through ingestion of contaminated food or water. Genetic diversity studies have identified numerous subtypes (STs) within the genus Blastocystis based on polymorphism at the SSU rRNA gene. Although there is evidence of frequent mixed subtype infections, the extent of within-host subtype diversity remains largely unexplored. Accurate assessment of Blastocystis ST diversity is crucial to understand epidemiology and sources of Blastocystis transmission to humans. Here, we report the application of next generation sequencing (NGS) for detection and characterization of Blastocystis subtypes to investigate intra-host Blastocystis diversity. A total of 75 specimens obtained from cattle feces, previously identified as Blastocystis positive, were examined using next generation amplicon sequencing. A fragment of the SSU rRNA gene was amplified using Blastocystis-specific primers and resulting amplicons were used for NGS. Comparison of Sanger and NGS results suggest greater sensitivity using the NGS approach. Using Sanger sequencing, mixed infections were suspected in 18 specimens but only confirmed through cloning in three, while NGS identified 49 mixed infections (16 times more). In addition, NGS revealed greater diversity of subtypes with 14 detected compared to 11 by Sanger. Nine more infections with potentially zoonotic STs were detected by NGS than Sanger. Indeed, subtype 3, the most common subtype found in humans, was found in 37% (28) of specimens tested by NGS but in only four specimens using Sanger. Our findings indicate that mixed Blastocystis infections may be far more common than previously thought due to the limitations of current detection methods. This next generation amplicon sequencing strategy improves detection of mixed subtype infections and low abundance subtypes and represents a valuable resource for future Blastocystis studies to improve our understanding of its epidemiology.

A Simple Genotyping Method for Rapid Differentiation of Blastocystis Subtypes and Subtype Distribution of Blastocystis spp. in Thailand

Blastocystis spp. is one of the most common protozoa of humans and animals worldwide. The genetic diversity of Blastocystis spp. might be associated with a wide range of symptoms. However, the prevalence of each subtype is different in each country. Until now, there is no standard method for subtyping of Blastocystis spp. We developed a sequential restriction fragment length polymorphism (RFLP) analysis for the rapid differentiation of human Blastocystis subtypes. A large-scale study was also conducted to determine the subtype distribution of Blastocystis spp. in Thailand. Stool samples were collected from 1025 school-age students in four regions of Thailand. Blastocystis infections were identified by direct smear, formalin ethyl-acetate concentration technique (FECT), Boeck and Drbohlav’s Locke-Egg-Serum (LES) medium culture, and polymerase chain reaction (PCR) of small-subunit ribosomal DNA (SSU rDNA). Subtypes of Blastocystis spp. were determined by RFLP. Phylogenetic tree of partial SSU rDNA sequences of Blastocystis spp. was constructed using the Maximum Likelihood (ML) method. Out of 1025 students, 416 (40.6%) were positive for Blastocystis spp. Using two steps of RFLP reactions, we could determine subtype one–three among these students. Subtype 3 was the most common subtype (58.72%) in Thai students, followed by subtype 1 (31.2%), and subtype 2 (10.1%). Blastocystis subtype 3 was the most prevalent in all regions of Thailand. The subtype distribution of Blastocystis spp. in Thailand was different from other countries.

Use of shotgun metagenomics for the identification of protozoa in the gut microbiota of healthy individuals from worldwide populations with various industrialization levels

Protozoa have long been considered undesirable residents of the human gut, but recent findings suggest that some of them may positively affect the gut ecosystem. To better understand the role and ecological dynamics of these commensal and potentially beneficial protozoan symbionts, we need efficient methods to detect them, as well as accurate estimates of their prevalence across human populations. Metagenomics provides such an opportunity, allowing simultaneous detection of multiple symbionts in a single analytical procedure. In this study, we collected fecal samples of 68 individuals from three Cameroonian populations with different subsistence modes and compared metagenomics-based and targeted methods of detection for two common protozoan genera: Blastocystis and Entamoeba. In addition, we analyzed our data along with publicly available fecal metagenomes from various worldwide populations to explore the prevalence and association patterns of ten protozoan genera. Regarding the detection method, microscopy was much less sensitive than metagenomics for Entamoeba, whereas qPCR was at least as sensitive as metagenomics for Blastocystis sp. However, metagenomics was more likely to detect co-colonizations by multiple subtypes. Out of the ten examined genera in 127 individuals from Cameroon, Tanzania, Peru, Italy or USA, only three (Blastocystis, Entamoeba and Enteromonas) had an overall prevalence exceeding 10%. All three genera were more common in less industrialized populations and their prevalence differed between continents and subsistence modes, albeit not in a straightforward manner. The majority (72.5%) of colonized individuals carried at least two protozoan species, indicating that mixed-species colonizations are common. In addition, we detected only positive and no negative association patterns between different protozoa. Despite the pitfalls of the metagenomic approach, ranging from the availability of good-quality sequencing data to the lack of standard analytical procedures, we demonstrated its utility in simultaneous detection of multiple protozoan genera, and especially its ability to efficiently detect mixed-species colonizations. Our study corroborates and expands prevalence results previously obtained for Blastocystis sp. and provides novel data for Entamoeba spp. and several other protozoan genera. Furthermore, it indicates that multiple protozoa are common residents of the healthy human gut worldwide.

Blastocystis prevalence and subtypes in autochthonous and immigrant patients in a referral centre for parasitic infections in Italy

In this study we characterized the presence and subtype (ST1-ST4) of Blastocystis in patients attended at a referral center for tropical diseases in Northern Italy. We also, evaluated the organism's association with other intestinal parasites. Parasite screening was performed on 756 patients, from different geographical origins (namely, Italians, Africans, South Americans, Asian and non-Italian Europeans) in which Italians represented the largest group. Blastocystis was seen to be the most prevalent parasite in the study. Subtype 3 and 1 were the most frequently found in the Italians and Africans. Our data confirmed previous studies performed in Italy, in which ST3 proved to be the most prevalent subtype, but we highlighted also a high frequency of mixed subtypes, which were probably underestimated in former analyses. Interestingly, the mixed subtypes group was the most prevalent in all the analysed geographical areas. About half of our cases showed other co-infecting parasites and the most frequent was Dientamoeba fragilis. Our study confirms that, in Blastocystis infection, multiple subtypes and co-infecting parasites are very frequently present, in particular Dientamoeba fragilis.

Design and application of a novel two-amplicon approach for defining eukaryotic microbiota

BACKGROUND

Due to a lack of systematic diagnostics, our understanding of the diversity and role of eukaryotic microbiota in human health is limited. While studies have shown fungal communities to be significant modulators of human health, information on the prevalence of taxa such as protozoa and helminths has been limited to a small number of species for which targeted molecular diagnostics are available. To probe the diversity of eukaryotic microbes and their relationships with other members of the microbiota, we applied in silico and experimental approaches to design a novel two-amplicon surveillance tool, based on sequencing regions of ribosomal RNA genes and their internal transcribed spacers. We subsequently demonstrated the utility of our approach by characterizing the eukaryotic microbiota of 46 hospitalized Malawian children suffering from Severe Acute Malnutrition (SAM).

RESULTS

Through in silico analysis and validation on a diverse panel of eukaryotes, we identified 18S rRNA variable genetic regions 4 and 5 (18S V4 V5), together with a region encoding 28S rRNA variable genetic region 2 and the internal transcribed spacers (transITS), as optimal for the systematic classification of eukaryotes. Sequencing of these regions revealed protozoa in all stool samples from children with SAM and helminths in most, including several eukaryotes previously implicated in malnutrition and diarrheal disease. Clinical comparisons revealed no association between protozoan parasites and diarrhea or HIV reactivity. However, the presence of Blastocystis correlated with bacterial alpha diversity and increased abundance of specific taxa, including Sporobacter, Cellulosibacter, Oscillibacter, and Roseburia.

CONCLUSION

We suggest this novel two-amplicon based strategy will prove an effective tool to deliver new insights into the role of eukaryotic microbiota in health and disease.

The intestinal protist Blastocystis is not a common member of the healthy infant gut microbiota in a Westernized country (Ireland)

Research into the gut microbiota of human infants is necessary in order to better understand how inter-species interactions and ecological succession shape the diversity of the gut microbiota, and in turn, how the specific composition of the gut microbiota impacts on host health both during infancy and in later years. Blastocystis is a ubiquitous intestinal protist that has been linked to a number of intestinal and extra-intestinal diseases. However, emerging data show that asymptomatic carriage is common and that Blastocystis is prevalent in the healthy adult gut microbiota. Nonetheless, little is known about the prevalence and diversity of this microorganism in the healthy infant gut, including when and how individuals become colonized by Blastocystis. Here, we surveyed the prevalence and diversity of Blastocystis in an infant population (n = 59) from an industrialized country (Ireland) using Blastocystis-specific primers at three or more time-points up to 24 months old. Only three infants were positive for Blastocystis (prevalence = 5%) and this was only noted for samples collected at month 24. This rate is comparatively low relative to previously reported prevalence rates in the contemporaneous adult population. These data suggest that infants in Westernized countries that are successfully colonized by Blastocystis most likely acquire this microorganism via horizontal transfer.

The relation between Blastocystis and the intestinal microbiota in Swedish travellers

Background

Blastocystis sp. is a unicellular eukaryote that is commonly found in the human intestine. Its ability to cause disease is debated and a subject for ongoing research. In this study, faecal samples from 35 Swedish university students were examined through shotgun metagenomics before and after travel to the Indian peninsula or Central Africa. We aimed at assessing the impact of travel on Blastocystis carriage and seek associations between Blastocystis and the bacterial microbiota.

Results

We found a prevalence of Blastocystis of 16/35 (46%) before travel and 15/35 (43%) after travel. The two most commonly Blastocystis subtypes (STs) found were ST3 and ST4, accounting for 20 of the 31 samples positive for Blastocystis. No mixed subtype carriage was detected. All ten individuals with a typable ST before and after travel maintained their initial ST. The composition of the gut bacterial community was not significantly different between Blastocystis-carriers and non-carriers. Interestingly, the presence of Blastocystis was accompanied with higher abundances of the bacterial genera Sporolactobacillus and Candidatus Carsonella. Blastocystis carriage was positively associated with high bacterial genus richness, and negatively correlated to the Bacteroides-driven enterotype. These associations were both largely dependent on ST4 – a subtype commonly described from Europe – while the globally prevalent ST3 did not show such significant relationships.

Conclusions

The high rate of Blastocystis subtype persistence found during travel indicates that long-term carriage of Blastocystis is common. The associations between Blastocystis and the bacterial microbiota found in this study could imply a link between Blastocystis and a healthy microbiota as well as with diets high in vegetables. Whether the associations between Blastocystis and the microbiota are resulting from the presence of Blastocystis, or are a prerequisite for colonization with Blastocystis, are interesting questions for further studies.

Electronic supplementary material

The online version of this article (10.1186/s12866-017-1139-7) contains supplementary material, which is available to authorized users.

Clarifying the Cryptic Host Specificity of Blastocystis spp. Isolates from Alouatta palliata and A. pigra Howler Monkeys

Although the presence of cryptic host specificity has been documented in Blastocystis, differences in infection rates and high genetic polymorphism within and between populations of some subtypes (ST) have impeded the clarification of the generalist or specialist specificity of this parasite. We assessed the genetic variability and host specificity of Blastocystis spp. in wild howler monkeys from two rainforest areas in the southeastern region of Mexico. Fecal samples of 225 Alouatta palliata (59) and A. pigra (166) monkeys, belonging to 16 sylvatic sites, were analyzed for infection with Blastocystis ST using a region of the small subunit rDNA (SSUrDNA) gene as a marker. Phylogenetic and genetic diversity analyses were performed according to the geographic areas where the monkeys were found. Blastocystis ST2 was the most abundant (91.9%), followed by ST1 and ST8 with 4.6% and 3.5%, respectively; no association between Blastocystis ST and Alouatta species was observed. SSUrDNA sequences in GenBank from human and non-human primates (NHP) were used as ST references and included in population analyses. The haplotype network trees exhibited different distributions: ST1 showed a generalist profile since several haplotypes from different animals were homogeneously distributed with few mutational changes. For ST2, a major dispersion center grouped the Mexican samples, and high mutational differences were observed between NHP. Furthermore, nucleotide and haplotype diversity values, as well as migration and genetic differentiation indexes, showed contrasting values for ST1 and ST2. These data suggest that ST1 populations are only minimally differentiated, while ST2 populations in humans are highly differentiated from those of NHP. The host generalist and specialist specificities exhibited by ST1 and ST2 Blastocystis populations indicate distinct adaptation processes. Because ST1 exhibits a generalist profile, this haplotype can be considered a metapopulation; in contrast, ST2 exists as a set of local populations with preferences for either humans or NHP.

Molecular Identification and Subtype Analysis of Blastocystis

Several typing methods have been used in studies aiming to unravel the molecular epidemiology of Blastocystis, which is one of the most common intestinal parasites in human and many non-human hosts. Such studies have the potential to add to knowledge on Blastocystis transmission, host specificity, phylogeography, and clinical and public health significance, but rely on robust, standardized methods by which data can be generated and compared directly between studies. One of the most used methods is "barcoding,", which involves single-round PCR amplification and sequencing of partial small subunit ribosomal RNA genes of the parasites. Recently, a publicly available online facility was developed for quick and standardized identification of subtypes (ribosomal lineages) and subtype alleles (variation within subtypes) based on sequence data obtained by barcoding PCR. Moreover, a modified barcoding approach is now available using nested PCR, which enables detection of mixed subtype infections. © 2016 by John Wiley & Sons, Inc.

Prevalence and genetic diversity of Blastocystis in family units living in the United States

The human gut is host to a diversity of microorganisms including the single-celled microbial eukaryote Blastocystis. Although Blastocystis has a global distribution, there is dearth of information relating to its prevalence and diversity in many human populations. The mode of Blastocystis transmission to humans is also insufficiently characterised, however, it is speculated to vary between different populations. Here we investigated the incidence and genetic diversity of Blastocystis in a US population and also the possibility of Blastocystis human-human transmission between healthy individuals using family units (N=50) living in Boulder, Colorado as our sample-set. Ten of the 139 (~7%) individuals in our dataset were positive for Blastocystis, nine of whom were adults and one individual belonging to the children/adolescents group. All positive cases were present in different family units. A number of different Blastocystis subtypes (species) were detected with no evidence of mixed infections. The prevalence of Blastocystis in this subset of the US population is comparatively low relative to other industrialised populations investigated to date; however, subtype diversity was largely consistent with that previously reported in studies of European populations. The distribution of Blastocystis within family units indicates that human-human transmission is unlikely to have occurred within families that participated in this study. It is not unexpected that given the world-wide variation in human living conditions and lifestyles between different populations, both the prevalence of Blastocystis and its mode of transmission to humans may vary considerably.

High occurrence of Blastocystis sp. subtypes 1-3 and Giardia intestinalis assemblage B among patients in Zanzibar, Tanzania

BACKGROUND

Blastocystis is a common intestinal parasite with worldwide distribution but the distribution of Blastocystis and its subtypes in East Africa is largely unknown. In this study, we investigate the distribution of Blastocystis subtypes in Zanzibar, Tanzania and report the prevalence of intestinal parasites using both molecular methods and microscopy.

METHODS

Stool samples were collected from both diarrhoeic and non-diarrhoeic outpatients in Zanzibar. In addition to microscopy, real-time PCR for Blastocystis, Entamoeba histolytica and E. dispar, Giardia intestinalis, Cryptosporidium spp., and Dientamoeba fragilis was used. Blastocystis subtypes were determined by a conventional PCR followed by partial sequencing of the SSU-rRNA gene. Genetic assemblages of Giardia were determined by PCR with assemblage specific primers.

RESULTS

Intestinal parasites were detected in 85 % of the 174 participants, with two or more parasites present in 56 %. Blastocystis sp. and Giardia intestinalis were the most common parasites, identified by PCR in 61 and 53 % of the stool samples respectively, but no correlation between carriage of Blastocystis and Giardia was found. The Blastocystis subtype distribution was ST1 34.0 %, ST2 26.4 %, ST3 25.5 %, ST7 0.9 %, and 13.2 % were positive only by qPCR (non-typable). The Giardia genetic assemblages identified were A 6.5 %, B 85 %, A + B 4.3 %, and non-typable 4.3 %. The detection rate with microscopy was substantially lower than with PCR, 20 % for Blastocystis and 13.8 % for Giardia. The prevalence of Blastocystis increased significantly with age while Giardia was most prevalent in children two to five years old. No correlation between diarrhoea and the identification of Giardia, Blastocystis, or their respective genetic subtypes could be shown and, as a possible indication of parasite load, the mean cycle threshold values in the qPCR for Giardia were equal in diarrhoeic and non-diarrhoeic patients.

CONCLUSIONS

Carriage of intestinal parasites was very common in the studied population in Zanzibar. The most commonly detected parasites, Blastocystis and Giardia, had different age distributions, possibly indicating differences in transmission routes, immunity, and/or other host factors for these two species. In the Blastocystis subtype analysis ST1-3 were common, but ST4, a subtype quite common in Europe, was completely absent, corroborating the geographical differences in subtype distributions previously reported.

Epidemiological Aspects of Blastocystis Colonization in Children in Ilero, Nigeria

This study aimed to elucidate aspects of the epidemiology of Blastocystis in Nigerian school children, including the distribution of subtypes (STs) and ST alleles. A total of 199 genomic DNAs extracted from fecal samples from 199 Nigerian children aged 2-14 years were tested by real-time polymerase chain reaction for Blastocystis Positive DNAs were submitted to barcoding by PCR and sequencing to obtain information on STs and ST alleles. A total of 167 (84%) samples were positive for Blastocystis, with prevalence increasing by age. No association between Blastocystis colonization and gender (P = 0.51) or type/presence of toilet facilities (P = 0.21) was observed. Blastocystis carriers were more prone to using water collected from wells than from sachets (P = 0.0044). Moreover, Blastocystis positivity was associated with positivity for fecal-orally transmitted protozoa (P = 0.018) and helminths (P < 0.0001). A clear inverse association of Blastocystis colonization and malaria infection was observed (P < 0.0001); however, malaria-positive children being younger than malaria-negative children, this finding was attributed to the age effect of Blastocystis colonization. ST data were available for 127/167 (76%) samples. Fifty-one children were positive for ST1, while 42 and 33 children were colonized with ST2 and ST3, respectively; a single case of ST7 was observed. By and large, the ST alleles identified for ST1 and ST2 did not differ from those observed in humans in other regions of the world; meanwhile, the distribution of ST3 alleles was remarkably distinct and potentially specific to humans in sub-Saharan Africa.

Human Blastocystis subtyping with subtype-specific primers developed from unique sequences of the SSU rRNA gene

The genus Blastocystis is one of the most genetically diverse parasites. Blastocystis isolates from humans and animals have been classified into subtypes (STs) based on the phylogeny of the small subunit rRNA gene (SSU rDNA). Although human Blastocystis isolates are limited to STs 1-9, the identification of all 9 STs remains challenging due to the lack of specific primers for several STs. The sequencing of partial SSU rDNA is therefore essential for the identification of several STs. In this study, we developed 9 sets of PCR primers to detect each of the 9 kinds of ST in humans. When these ST-specific primer pairs were examined reference Blastocystis for the 9 STs, all 9 amplified only the target ST even in a DNA mixture of all 9 STs. The specificities of the 9 primer sets were tested against several intestinal parasites and fungi found in human stool samples. No amplification with these common human intestinal eukaryotes was observed using the primer pairs for 8 STs, while the ST5 primer set gave only faint bands with some parasites. Since genomic DNA levels of these parasites extracted from Blastocystis-positive cultures are expected to be markedly lower than the pure or highly concentrated DNA samples tested, the cross-amplifications with these organisms are unlikely to be detected when DNA samples are extracted from Blastocystis-positive cultures. The PCR conditions for all 9 primer sets were the same, hence a one-step analysis by PCR amplification, followed by electrophoresis has potential as a simple tool for the subtyping of human Blastocystis isolates.

Blastocystis in Health and Disease: Are We Moving from a Clinical to a Public Health Perspective?

Blastocystis is a genus of common single-celled intestinal parasitic protists with an unsettled role in human health and disease. Being a stable component of intestinal microbiota, once established, the Blastocystis parasite appears more common in healthy individuals than in patients with infectious, functional, or inflammatory bowel disease. Recent data suggest that the parasite is associated with certain gut microbiota profiles and health indices. Convincing data and tools differentiating asymptomatic colonization from infection are yet to be demonstrated. Although the parasite may elicit disease under certain circumstances, the focus on Blastocystis may be shifting from a clinical to a public health perspective.

Prevalence and subtype distribution of Blastocystis in healthy individuals in Sharjah, United Arab Emirates

Blastocystis is estimated to be one of the most common parasites of the intestinal tract of humans, comprising multiple subtypes (ST). Meanwhile, the distribution of Blastocystis ST in many communities and countries remains unknown. In the present work, we aimed to identify the prevalence of Blastocystis and the ST distribution in human stool samples collected from healthy expatriates from different geographical regions and residing in Sharjah, United Arabian Emirates (UAE). A total of 133 samples were screened and subtyped using partial small subunit ribosomal RNA gene sequencing. Fifty-nine (44.4%) samples were identified as positive. Among these, 39 were successfully sequenced and subtyped. The ST distribution was as follows: ST3, 58.9% (23/39); ST1, 28.2% (11/39); and ST2, 7.6% (3/39). No correlation between geographic origin and infection (χ(2)=11.006; P=0.528) nor gender and infection (χ(2)=1.264; P=0.261) was observed. The data were compared with those available for other Middle Eastern and North African neighboring countries. This study is the first to provide data concerning the prevalence of Blastocystis and the frequency of various STs in the UAE, confirming the absence of ST4 and the commonness of ST1, ST2, and ST3 in this geographical region.

Study of the gastrointestinal parasitic fauna of captive non-human primates (Macaca fascicularis)

The aim of this study was to examine helminths and protozoans in cynomolgus macaques (Macaca fascicularis) imported from registered breeding facilities in China and their relation to health risks for non-human primate handlers in biomedical research centers and in breeding facilities. Fresh fecal samples were collected from a total of 443 M. fascicularis and analyzed by copromicroscopical analysis, immunoenzymatic, or molecular assays. As to helminths, whose eggs were shed in 2.03% of the samples, Trichuris and Oesophagostomum were the only two taxa found, with low prevalence and low eggs per gram (EPG) values. Protozoans were more frequently detected (87.40%), with Entamoeba coli (85.19%) and Endolimax nana (79.26%) as the most prevalent species shed. Other parasites found by fecal smear examination were uninucleated-cyst-producing Entamoebas (78.52%), Iodamoeba bütschlii (42.96%), and Chilomastix mesnili (24.44%), while cysts of Balantidium coli (22.2%) were only observed by sedimentation. No coproantigens of Giardia duodenalis, Cryptosporidium spp., and Entamoeba histolytica complex were detected. Blastocystis sp. infection was noticed in 87.63% of macaques by PCR. These cynomolgus monkeys were infected with many subtypes (ST1, ST2, ST3, ST5, and ST7), where the predominant Blastocystis sp. subtypes were ST2 (77.5%), followed by ST1 (63.5%). Data collected confirmed the presence of potentially zoonotic parasites and a high parasite diversity, suggesting the need for appropriate and sensitive techniques to adequately control them and related health risks for handlers of non-human primates in biomedical research centers and in breeding facilities.