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.

Prevalence of non-pathogenic types of gastrointestinal protozoa in population in Slovakia and their potential importance in the aspect of public health

The aim of the research was to determine the prevalence of non-pathogenic protozoa circulating in the human population of Slovakia. We particularly focused on the socially deprived areas with poor sanitation conditions, as they are one of the factors affecting the transmission of these infections. Within this study, 2760 people were coprologically screened for the presence of protozoan cysts. The analyzed group comprised 1173 men and 1587 women from different regions of Slovakia. The total prevalence (2.03%) of non-pathogenic protozoa species was determined. The prevalence of Entamoeba coli was 0.80%, the prevalence of Endolimax nana 0.58%, and the prevalence of Blastocystis hominis was 0.65%. The presence of non-pathogenic protozoa was more frequent in women than that in men, in all age groups. The highest incidence of Entamoeba coli was found in children aged one month - seven years (0.79%), the lowest in the age group of 19-88 years (0.66%). Endolimax nana was most frequent in 8-18 year-olds (0.95%), where the statistical significance was found (p<0.05). The prevalence of Blastocystis hominis by the age group ranged from 0.39 to 0.95%. We did not find any statistical significance (p>0.05) for Entamoeba coli, and similarly for Blastocystis hominis associated with the sex and age. Although the circulation of non-pathogenic protozoa in the human population is far from being limited to the developing countries, their occurrence is also frequent in the population of developed countries. Despite their controversial pathogenicity, they should not be neglected, particularly in the patients with gastrointestinal symptoms.

Clinical and microscopic predictors of Entamoeba histolytica intestinal infection in travelers and migrants diagnosed with Entamoeba histolytica/dispar infection

Background

Amebiasis is a protozoal infection caused by Entamoeba histolytica, while the morphologically indistinguishable E. dispar is considered as non-pathogenic. Polymerase chain reaction (PCR) assays are necessary to differentiate both species. The most common clinical presentations of E. histolytica disease are amebic colitis and amebic liver abscess, but asymptomatic infection is also possible. We assessed the frequency and pattern of clinical symptoms and microscopic features in travelers/migrants associated with E. histolytica intestinal infection and compared them to those found in individuals with E. dispar infection.

Methods

We conducted a retrospective study at the travel clinic of the Institute of Tropical Medicine, Antwerp, Belgium on travelers/migrants found from 2006 to 2016 positive for Entamoeba histolytica/dispar through antigen detection and/or through microscopy confirmed by PCR. All files of individuals with a positive PCR for E. histolytica (= cases) and a random selection of an equal number of Entamoeba dispar carriers (= controls) were reviewed. We calculated the sensitivity, specificity and likelihood ratios (LRs) of clinical symptoms (blood in stool, mucus in stool, watery diarrhea, abdominal cramps, fever or any of these 5 symptoms) and of microscopic features (presence of trophozoites in direct and in sodium acetate-acetic acid-formalin (SAF)-fixed stool smears) to discriminate between E. histolytica and E. dispar infection.

Results

Of all stool samples positive for Entamoeba histolytica/dispar for which PCR was performed (n = 810), 30 (3.7%) were true E. histolytica infections, of which 39% were asymptomatic. Sensitivity, specificity and positive LRs were 30%, 100% and 300 (p 0.007) for presence of blood in stool; 22%, 100% and 222 (p 0.03) for mucus in stool; 44%, 90% and 4.7 (p 0.009) for cramps and 14%, 97% and 4.8 (p = 0.02) for trophozoites in direct smears. For watery diarrhea, fever and for trophozoites in SAF fixated smears results were non-significant.

Conclusions

E. histolytica infection was demonstrated in a small proportion of travelers/migrants with evidence of Entamoeba histolytica/dispar infection. In this group, history of blood and mucus in stool and cramps had good to strong confirming power (LR+) for actual E. histolytica infection. Trophozoites were also predictive for true E. histolytica infection but in direct smears only.

In the present work, we found that E. histolytica intestinal infections are rarely diagnosed among travelers and migrants presenting in a national reference travel clinic in Europe. Microscopic finding of cysts or trophozoites and antigen testing cannot discriminate between Entamoeba histolytica/dispar infection, which leads to overdiagnosis of E. histolytica infections in low resource settings where PCR is not available. We found visualization of trophozoites under the microscope helpful in discriminating between E. histolytica and E. dispar infection in direct smears. Hematophagy is a very rare finding but in our experience was always associated with E. histolytica infection. In a context where only microscopy is available, a patient presenting with blood or mucus in stool or cramps should anyhow be treated as amoebiasis if Entamoeba histolytica/dispar cysts/trophozoites are found. Nevertheless it is worth noting that a sizeable proportion of E. histolytica cases were asymptomatic. Last, our study suggests that E. dispar might be pathogenic but symptoms in E. histolytica infected patients were clearly more often suggestive of intestinal tissue invasion.

Bacterial and parasitic contaminants of salad vegetables sold in markets in Fako Division, Cameroon and evaluation of hygiene and handling practices of vendors

OBJECTIVE

Increase in awareness of the health benefits of vegetables has resulted in an increase in consumption. Many vegetables are consumed raw to retain the natural taste and heat labile nutrients. The safety of raw vegetables is a great concern. We investigated the bacteriological and parasitological quality of salad vegetables sold in three major markets in Fako Division Cameroon, the hygiene and preservation practices of vendors and determined the antimicrobial sensitivity of bacterial isolates, to provide data that could be used to improve food safety and safeguard public health.

RESULTS

Bacterial contamination was high. Mean aerobic bacteria counts ranged from 2.5 × 106 to 15 × 106 cfu/g, total coliform counts from 4 to >  2400/g and fecal coliforms < 3 to 1100/g. Six bacterial species were isolated among which Staphylococcus aureus (35.4%) predominated while Serratia marcescens (8.5%) was the least. Bacteria showed high resistance to erythromycin (87.6%). Ten parasitic organisms were detected. Balantidium coli (25.6%) and Entamoeba spp. (21.7%) predominated. Contamination was highest in lettuce and lowest in green pepper. Hygiene and vegetable preservation practices of vendors were poor and could aggravate contamination. Contamination of fresh salad vegetables with pathogenic bacteria and parasites could be a food safety concern in study area.

Occurrence and removal efficiency of parasitic protozoa in Swedish wastewater treatment plants

Giardia intestinalis, Cryptosporidium spp., Entamoeba histolytica and Dientamoeba fragilis are parasitic protozoa and causative agents of gastroenteritis in humans. G. intestinalis and Cryptosporidium spp. in particular are the most common protozoa associated with waterborne outbreaks in high-income countries. Surveillance of protozoan prevalence in wastewater and evaluation of wastewater treatment removal efficiencies of protozoan pathogens is therefore imperative for assessment of human health risk. In this study, influent and effluent wastewater samples from three wastewater treatment plants in Sweden were collected over nearly one year and assessed for prevalence of parasitic protozoa. Quantitative real-time PCR using primers specific for the selected protozoa Cryptosporidium spp., G. intestinalis, E. histolytica, Entamoeba dispar and D. fragilis was used for protozoan DNA detection and assessment of wastewater treatment removal efficiencies. Occurrence of G. intestinalis, E. dispar and D. fragilis DNA was assessed in both influent (44, 30 and 39 out of 51 samples respectively) and effluent wastewater (14, 9 and 33 out of 51 samples respectively) in all three wastewater treatment plants. Mean removal efficiencies of G. intestinalis, E. dispar and D. fragilis DNA quantities, based on all three wastewater treatment plants studied varied between 67 and 87%, 37-75% and 20-34% respectively. Neither E. histolytica nor Cryptosporidium spp. were detected in any samples. Overall, higher quantities of protozoan DNA were observed from February to June 2012. The high prevalence of protozoa in influent wastewater indicates the need for continued monitoring of these pathogens in wastewater-associated aquatic environments to minimise the potential risk for human infection.

Morphological and molecular characterization of an uninucleated cyst-producing Entamoeba spp. in captured Rangeland goats in Western Australia

Uninucleated Entamoeba cysts measuring 7.3×7.7μm were detected in faecal samples collected from wild Rangeland goats (Capra hircus) after arrival at a commercial goat depot near Geraldton, Western Australia at a prevalence of 6.4% (8/125). Sequences were obtained at the 18S rRNA (n=8) and actin (n=5) loci following PCR amplification. At the 18S locus, phylogenetic analysis grouped the isolates closest with an E. bovis isolate (FN666250) from a sheep from Sweden with 99% similarity. At the actin locus, no E. bovis sequences were available, and the isolates shared 94.0% genetic similarity with E. suis from a pig in Western Japan. This is the first report to describe the morphology and molecular characterisation of Entamoeba from Rangeland goats in Western Australia and the first study to produce actin sequences from E. bovis-like Entamoeba sp.

Intestinal parasites in stool samples and perianal swabs examined by The Voivodeship Sanitary-Epidemiological Station in Bydgoszcz between 2000-2014

INTRODUCTION

Epidemiological conditions are changing due to the modifications in human behavior and environment. Parasitic diseases are most often caused by intestinal parasites. The frequency of Echinococcus multilocularis and tropical diseases increases in Poland.

AIM OF STUDY

Analysis of intestinal parasites’ occurrence in stool samples and perianal swabs tested in Medical Diagnostics Department of The Voivodeship Sanitary-Epidemiological Station in Bydgoszcz between 2000-2014.

MATERIAL AND METHODS

24 609 fecal samples and perianal swabs were tested using microscopic method for intestinal parasites’ presence and immunoenzymatic method (ELISA) for Giardia intestinalis presence. The study population was sorted into four groups according to age.

RESULTS

Prevalence of intestinal parasites in persons tested over 2000-2014 period ranged between 2.15% - 7.04%. The most common invasive parasite was Enterobius vermicularis, especially among children between 3-7 years (64.58%). In the same time period the most prevalent pathogenic intestinal parasite in adults (>16 years) was Giardia intestinalis (65.81%).

CONCLUSIONS

1. The prevalence of intestinal parasites infection changes depending on the number of tests carried out. The number of infections may be underestimated given that the testing encompassed only a part of population. A need for more thorough examination exists. 2. Enterobius vermicularis infection was most often found in children between 3-7 years, mainly from specific communities (kindergartens, orphanages).

Diagnostics of intestinal parasites in light microscopy among the population of children in eastern Afghanistan

OBJECTIVES

The Afghans, living in poor socioeconomic conditions, are estimated to be a community with a high rate of intestinal parasitic infections. The aim of the study was to estimate the prevalence and species of intestinal parasites among children's population in eastern Afghanistan and to present the methods of optimizing the techniques for identification of pathogens in light microscopy. The research was carried out as a part of humanitarian project Capacity building of health care system in Ghazni Province.

MATERIALS AND METHOD

The study involved 500 children aged 7-18 attending the Share Kona and the Khuija Ali High Schools in Ghazni, eastern Afghanistan in the period November 2013-April 2014. Three stool samples were collected from each patient at 2-day intervals, the samples were fixed in 10% formalin, transported to the Military Institute of Medicine in Poland, where they were pooled and examined using five different diagnostic methods in light microscopy (direct smear in Lugol's solution, Fülleborne's flotation, decantation in distilled water, Kato-Miura thick smear, and DiaSys/PARASYS sedimentation system).

RESULTS

Pathogenic intestinal parasites were detected in 217 patients (43.4%), with the most common Ascaris lumbricoides (35.3%), Giardia intestinalis (31.1%), and Hymenolepis nana (15.7%). The use of direct smear method allowed for the detection of intestinal parasites in 161 individuals. The application of four following testing methods has improved the detection rates of infected patients by 11.2%.

CONCLUSIONS

The variety of detected intestinal pathogens in examined children's population has required the use of combination of multiple diagnostic methods in light microscopy, and finally improved the detection rates of intestinal parasites and helped eliminate infections with nematodes, cestodes, trematodes, and protozoa using appropriate treatment in the study population.

First report of mixed Entamoeba polecki (ST 1) and E. suis infection in piglets shedding abnormalfeces by histopathological and molecular surveys

Of the three species of Entamoeba found in swine, namely E. histolytica, E. polecki and E. suis, E. histolytica can also infect humans, producing colitis or abscesses of liver and leading to death. However, the pathogenicity of other species of Entamoeba has not been fully characterized. Here, we conducted histopathology and molecular surveys on a pig farm where piglets had blackish feces or muddy diarrhea. Histopathological examination of two piglets showed necrosis of the mucous surface at the ileum, cecum, or colon, infiltration of neutrophils, and formation of ulcers. Based on morphological characteristics, E. polecki and E. suis trophozoites were mainly detected at lamina propria and surface of the lesion, respectively, and Lawsonia intracellularis, a bacterial pathogen, was also detected. Molecular analysis using the small subunit ribosomal RNA gene on other piglets and a sow revealed infection with both E. polecki and E. suis. These findings corroborate our previous reports that the two Entamoeba spp. are pathogenic in pigs as aggravations of symptoms with L. intracellularis. This is the first report about mixed infection with E. polecki and E. suis.

Simultaneous detection and differentiation of Entamoeba histolytica, E. dispar, E. moshkovskii, Giardia lamblia and Cryptosporidium spp. in human fecal samples using multiplex PCR and qPCR-MCA

Entamoeba histolytica, Giardia lamblia and Cryptosporidium spp. are common causes of diarrheal and intestinal diseases all over the world. Microscopic methods are useful in the diagnosis of intestinal parasites (IPs), but their sensitivity was assessed approximately 60 percent. Recently, molecular techniques have been used increasingly for the identification and characterization of the parasites. Among those, in this study we have used multiplex PCR and Real-time PCR with melting curve analysis (qPCR-MCA) for simultaneous detection and differentiation of E. histolytica, E. dispar, E. moshkovskii, G. lamblia and Cryptosporidium spp. in human fecal samples. Twenty DNA samples from 12 E. histolytica and 8 E. dispar samples and twenty stool samples confirmed positive for G. lamblia and Cryptosporidium spp. were analyzed. After DNA extraction from the samples, multiplex PCR was done for detection and differentiation of above mentioned parasites. QPCR-MCA was also performed for the detection and differentiation of 11 isolates of above mentioned parasite in a cycle with a time and temperature. Multiplex PCR was able to simultaneous detect and differentiate of above mentioned parasite in a single reaction. QPCR-MCA was able to differentiate genus and species those five protozoa using melting temperature simultaneously at the same time and temperature programs. In total, qPCR-MCA diagnosed 7/11 isolation of E. histolytica, 6/8 isolation of E. dispar, 1/1 E. moshkovskii Laredo, 10/11 G. Lamblia and 6/11 Cryptosporidium spp. Application of multiplex PCR for detection of more than one species in a test in developing countries, at least in reference laboratories has accurate diagnosis and plays a critical role in differentiation of protozoan species. Multiplex PCR assay with a template and multi template had different results and it seems that using a set of primers with one template has higher diagnostic capability in compare with multi template. The results of this study showed that the use of the qPCR-MCA can be an effective method to simultaneous distinguish of the above mentioned parasites.

Entamoeba histolytica and Entamoeba dispar infection in Mexican school children: genotyping and phylogenetic relationship

BACKGROUND

This study aimed to determine the frequency of Entamoeba histolytica and Entamoeba dispar infection in school children in the community of Tlaltizapan, in order to understand the dynamics of infection within the school and family spheres of this population. Amoebiasis is an unsolved public health problem and an endemic disease in Mexico. The incidence rate varies depending on the state; the most affected states show the highest numbers of new cases of amoebiasis per year. Previously, we reported the molecular frequency of infection with E. histolytica and/or E. dispar in other rural communities of the state of Morelos.

METHODS

Children from 3 schools were studied to estimate the frequency of intestinal parasites through microscopic examination of fresh stool samples. The number of studied individuals were 309 school children. The molecular characterization of E. histolytica or E. dispar was carried out by Polymerase Chain Reaction (PCR) using species-specific primers to amplify short tandem repeats (STR) in non-coding sequences associated with the tRNA gene; the amplified fragments were sequenced and analyzed.

RESULTS

Eight different genotypes were obtained from E. dispar isolates with the molecular marker NKD3-D5. None of the cases in which the species E. histolytica was detected developed symptoms attributable to an invasive process of disease. Moreover, the parasitized condition appeared to have no significant impact on the development or nutritional status of affected children. Genotype 1, which corresponds to the reference strain E. dispar SAW760, considered a non-pathogenic amoeba, was the most prevalent.

CONCLUSIONS

The comparison of the genotypes of Entamoeba species did not show a correlation between children and their relatives. In this community, the species Entamoeba dispar genotype 1 was the most widespread. Based on the indicators of growth, development and nutrition status, the studied community seems to be reasonably adapted to constant exposure to intestinal parasites, since there were no evidences of a serious impact of the parasitized condition on the children's health.

Investigation of Entamoeba gingivalis and Trichomonas tenax in Periodontitis or Gingivitis Patients in Kayseri

OBJECTIVE

The aim of this study was to determine the prevalence of Entamoeba gingivalis and Trichomonas tenax in periodontitis and gingivitis patients.

METHODS

The study consisted of 107 periodontitis patients and 68 gingivitis patients. Bacterial plaque samples were collected with a curette from the deepest pocket in each quadrant and placed into separate tubes containing sterile 0.9% saline solution. Samples were examined at a magnification of ×400 by light microscopy. Cultivation for T. tenax was performed using the same samples, and the cultures were examined after 48 hours.

RESULTS

E. gingivalis was present in the samples from 38 periodontitis patients, whereas T. tenax was present in samples from only 3 periodontitis patients. Both E. gingivalis and T. tenax were found together in the samples from 2 periodontitis patients. In total, 22 and 2 gingivitis patients were found to be infected with E. gingivalis and with T. tenax, respectively. Only 1 gingivitis patient was found to be infected with both E. gingivalis and T. tenax.

CONCLUSION

In our study, oral protozoa were found in a high percentage in periodontitis and gingivitis patients. We believe that the prevalence of E. gingivalis and T. tenax should be determined via new studies and, in particular, the protection principles should be complied with.

Identification of Entamoeba moshkovskii in Treated Waste Water Used for Agriculture

We conducted an observational study to determine the prevalence of Entamoeba spp., in samples collected in a waste water treatment plant that provides water for agricultural irrigation. Samples were collected weekly over a period of 10 weeks at representative contamination stages from within the treatment plant. Protozoan identification was performed via light microscopy and culture. PCR amplification of small subunit rRNA gene sequences of E. histolytica/dispar/moshkovskii was performed in culture positive samples. Light microscopy revealed the presence of Entamoeba spp., in 70% (14/20) of the raw waste water samples and in 80% (8/10) of the treated water samples. PCR amplification after culture at both 24 and 37°C revealed that 100% (29/29) of the raw waste water samples and 78.6% (11/14) of the treated waste water were positive for E. moshkovskii. We report the first isolation of E. moshkovskii in Colombia, confirmed by PCR. Recent reports of E. moshkovskii pathogenic potential suggest this finding could constitute a public health risk for people exposed to this water.

Variation in Rural African Gut Microbiota Is Strongly Correlated with Colonization by Entamoeba and Subsistence

The human gut microbiota is impacted by host nutrition and health status and therefore represents a potentially adaptive phenotype influenced by metabolic and immune constraints. Previous studies contrasting rural populations in developing countries to urban industrialized ones have shown that industrialization is strongly correlated with patterns in human gut microbiota; however, we know little about the relative contribution of factors such as climate, diet, medicine, hygiene practices, host genetics, and parasitism. Here, we focus on fine-scale comparisons of African rural populations in order to (i) contrast the gut microbiota of populations inhabiting similar environments but having different traditional subsistence modes and either shared or distinct genetic ancestry, and (ii) examine the relationship between gut parasites and bacterial communities. Characterizing the fecal microbiota of Pygmy hunter-gatherers as well as Bantu individuals from both farming and fishing populations in Southwest Cameroon, we found that the gut parasite Entamoeba is significantly correlated with microbiome composition and diversity. We show that across populations, colonization by this protozoa can be predicted with 79% accuracy based on the composition of an individual's gut microbiota, and that several of the taxa most important for distinguishing Entamoeba absence or presence are signature taxa for autoimmune disorders. We also found gut communities to vary significantly with subsistence mode, notably with some taxa previously shown to be enriched in other hunter-gatherers groups (in Tanzania and Peru) also discriminating hunter-gatherers from neighboring farming or fishing populations in Cameroon.

Genotyping of Giardia lamblia and Entamoeba spp from river waters in Iran

In this study, DNA from 55 surface and river water samples, which were collected from some water sources of Tehran and the Guilan Province, Iran, were extracted and examined for Entamoeba spp. and Giardia lamblia by PCR and genotyping. Twenty-seven samples, which were concentrated using the immunomagnetic separation technology (IMS) method, were examined for Giardia alone. Twenty-eight samples, which were concentrated using the sucrose flotation (SF) method, were examined for both Giardia and Entamoeba species. The results showed that 27/55 (17/27 and 10/28) (49 %), 4 /28 (14.28 %) and 3/28 (10.7 %) of the samples were positive for Giardia lamblia, Entamoeba spp and mixed infections (Entamoeba spp. and Giardia spp.), respectively. Sixteen out of 55 samples were negative. Entamoeba genus-specific PCR primers in single-round PCR were used to differentiate between the Entamoeba spp. (E. histolytica, E. dispar and E. moshkovskii). With respect to the 7 samples that were positive for Entamoeba, (14.28 %) 4 out of 28 were positive for E. moshkovskii, (7.14 %), 2 out of 28 were positive for E. histolytica and (3.57 %) 1 out of 28 was positive for E. dispar. Genus-specific PCR primers in a semi-nested PCR assay was performed to genotype Giardia species. Of the 27 samples that were positive for Giardia, 10 samples were sequences. All 10 successfully sequenced samples contained assemblage B of Giardia lamblia.This is first study to investigate the G. lamblia genotypes in the water supply of the Tehran and Guilan provinces, and it is the first study to investigate Entamoeba species in the water supplies of Iran. The investigated river water supplies, which are used for agriculture, camping and animal farming, were heavily contaminated by the human pathogenic Entamoeba and Giardia parasites. There is a potential risk of waterborne outbreaks in humans and animals.

Molecular Detection of the Carriage Rate of Four Intestinal Protozoa with Real-Time Polymerase Chain Reaction: Possible Overdiagnosis of Entamoeba histolytica in Nigeria

Diarrhea remains the second largest killer of children worldwide, and Nigeria ranks number two on the list of global deaths attributable to diarrhea. Meanwhile, prevalence studies on potentially diarrheagenic protozoa in asymptomatic carriers using molecular detection methods remain scarce in sub-Saharan countries. To overcome sensitivity issues related to microscopic detection and identification of cysts in stool concentrates, real-time polymerase chain reaction (PCR) was used to analyze genomic DNAs extracted from stool samples from 199 healthy school children for Entamoeba histolytica, E. dispar, Giardia intestinalis, and Cryptosporidium. Questionnaires were administered for epidemiological data collection. E. histolytica was not detected in any of the samples, whereas Giardia (37.2%), E. dispar (18.6%), and Cryptosporidium (1%) were found. Most of the children sourced their drinking water from community wells (91%), while the majority disposed of feces in the bush (81.9%). Our study is the first to use real-time PCR to evaluate the epidemiology of E. histolytica, Giardia, and Cryptosporidium in Nigeria where previous studies using traditional diagnostic techniques have suggested higher and lower carriage rates of E. histolytica and Giardia, respectively. It is also the first study to accurately identify the prevalence of common potentially diarrheagenic protozoa in asymptomatic carriers in sub-Saharan Africa.

Evaluation of factors affecting real-time PCR performance for diagnosis of Entamoeba histolytica and Entamoeba dispar in clinical stool samples

Although PCR offers the potential for sensitive detection of parasites there are several pitfalls for optimal performance, especially when DNA is extracted from a complex sample material such as stool. With the aid of a sensitive inhibitor control in a duplex real-time PCR (qPCR) for identification of Entamoeba histolytica and Entamoeba dispar we have evaluated factors that influenced the performance of the qPCR and have suggested a rationale to be used in the analysis of clinical samples. Pre-PCR processing was found to be of outmost importance for an optimal amplification since inhibitors caused false-negative results when higher amounts of sample were used. Stool sampling with a flocked swab (ESwab, Copan), yielding on average 173 mg, gave positive qPCR results in samples with cysts of E. dispar that were negative in serially diluted stool samples. The degree of inhibition found varied between samples and was not an on-off phenomenon. Even low-grade inhibition, shown as an increase of two cycles in the qPCR for the inhibitor control, could lead to false negativity in samples with low amounts of parasites. Lack of amplification in the qPCR due to inhibition could be overcome by dilution of the extracted DNA by 1/10-1/20. We also describe the use of guanidinium thiocyanate buffer for transport and storage of samples as well as a time-saving semi-automated DNA extraction method in an Arrow instrument (Nordiag) preceded by bead beating.

[Environmental conditions and prevalence of parasitic infection in Xukuru-Kariri indigenous people, Caldas, Brazil]

OBJECTIVE

To describe the environmental conditions and the parasitic infection status of Xukuru-Kariri individuals living in the municipality of Caldas, state of Minas Gerais, Brazil.

METHODS

A cross-sectional study was carried out in March 2009. Sociodemographic and environmental data were collected through interviews. Water and fecal samples were collected for determination of environmental contamination and parasitic infection status.

RESULTS

The Xukuru-Kariri population living in Caldas included 86 people divided into 22 families. Of 22 heads of household, 81.8% had low schooling (not higher than elementary education). Of 26 water samples collected for microbiological analysis, 77.0% were positive for total coliforms and 4.0% for Escherichia coli. Residents of 27.3% of households defecated in the open. Trash was scattered in the yard of 54.5% of households. Fecal samples were collected from 60 individuals, with parasitic infection in 66.6%. The following prevalence rates were recorded: Entamoeba histolytica/dispar, 6.7%; Entamoeba coli, 60.0%; Endolimax nana, 1.8%; and Giardia duodenalis, 6.6%.

CONCLUSIONS

The people included in this study faced environmental characteristics that contributed to their health vulnerability. Health actions as well as the implementation of public policies to provide sanitation, with quality water and adequate collection and treatment of human and household waste, are essential to prevent environmental degradation and improve the quality of life of these individuals.

Outbreak of acute gastroenteritis caused by contamination of drinking water in a factory, the Basque Country

On 18 September 2013, the Gipuzkoa Epidemiology Unit was notified of an outbreak of acute gastroenteritis (AGE) among employees at a domestic appliance factory. The first signs of the outbreak had emerged at the end of June and at the time of the notification 30 workers were on sick leave for gastroenteritis. Some employees had had more than one episode and the main symptoms were diarrhoea and vomiting. An investigation began to identify the causative agent, assess exposure and determine the route of transmission. Data collected by a questionnaire identified 302 episodes of AGE among 238 people affected between June and September 2013. The source of water consumed was found to be a risk factor associated with the appearance of symptoms both in the crude and the adjusted analysis: odds ratio 1.8 (0.8-4.2) and 6.4 (4.2-9.8), respectively. Microbiological analysis of stool samples and of water confirmed the presence of norovirus and rotavirus. The environmental study detected a connection between an industrial use water system and drinking water at the factory. It was concluded that the outbreak was caused by mixed viral infections, due to contamination of drinking water.

Molecular detection of Entamoeba histolytica and Entamoeba dispar infection among wild rats in Kuala Lumpur, Malaysia

Entamoeba histolytica infection is the third-greatest parasitic disease responsible for death in the world. Wild rats harbouring E. histolytica can be the possible reservoir hosts for human amoebiasis. There were numerous studies on prevalence of intestinal parasites among wild rats in Malaysia but none has reported E. histolytica. Rats were captured from Sentul and Chow Kit areas, Kuala Lumpur, Malaysia. The preserved stool samples were used for microscopy examination and molecular analysis. Out of 137 samples collected, 12 were positive for E. histolytica / E. dispar / E. moshkovskii microscopically. Two E. histolytica (1.4%), 1 E. dispar (0.7%) and 6 mixed infections of E. histolytica and E. dispar (4.3%) were detected using PCR. This is the first report of molecular detection of E. histolytica/dispar infection among wild rats in Malaysia. This study provides useful information about the potential risks of zoonotic agents and the importance of developing control measures to prevent zoonotic transmission.

Differential diagnosis of Entamoeba spp. in clinical stool samples using SYBR green real-time polymerase chain reaction

Amoebiasis, a disease caused by Entamoeba histolytica, is usually diagnosed by microscopic examination, which does not differentiate the morphologically identical species of the E. histolytica/E. dispar complex. Furthermore, morphologically similar species such as Entamoeba hartmanni contribute to misidentification. Therefore, there is a need for more sensitive and specific methods. This study standardized a multiplex real-time PCR system for E. histolytica and E. dispar and a single real-time PCR for E. hartmanni. The multiplex protocol detected up to 0.0143 pg of E. histolytica DNA and 0.5156 pg of E. dispar DNA, and the average melting temperature (T(m)) was 73 °C and 70 °C, respectively. For E. hartmanni, the T(m) was 73 °C and the amplification was successful down to 0.03 fg of plasmid DNA. Negative controls and other intestinal parasites presented no amplification. Among the 48 samples tested, E. dispar DNA was detected in 37; none exhibited E. histolytica DNA and 11 were negative in the multiplex protocol. In 4 of these 11 samples, however, E. hartmanni DNA was amplified. SYBR Green is demonstrated to be an interesting option and these combined PCR reactions can improve laboratory diagnosis of amoebiasis in developing countries.

First evidence of genetic intraspecific variability and occurrence of Entamoeba gingivalis in HIV(+)/AIDS

Entamoeba gingivalis is considered an oral commensal but demonstrates a pathogenic potential associated with periodontal disease in immunocompromised individuals. Therefore, this study evaluated the occurrence, opportunistic conditions, and intraspecific genetic variability of E. gingivalis in HIV(+)/AIDS patients. Entamoeba gingivalis was studied using fresh examination (FE), culture, and PCR from bacterial plaque samples collected from 82 HIV(+)/AIDS patients. Genetic characterization of the lower ribosomal subunit of region 18S (18S-SSU rRNA) was conducted in 9 positive samples using low-stringency single specific primer PCR (LSSP-PCR) and sequencing analysis. Entamoeba gingivalis was detected in 63.4% (52/82) of the samples. No association was detected between the presence of E. gingivalis and the CD4⁺ lymphocyte count (≤200 cells/mm³ (p = 0.912) or viral load (p = 0.429). The LSSP-PCR results helped group E. gingivalis populations into 2 polymorphic groups (68.3% similarity): group I, associated with 63.6% (7/11) of the samples, and group II, associated with 36.4% (4/11) of the samples, which shared 74% and 83.7% similarity and association with C and E isolates from HIV(−) individuals, respectively. Sequencing of 4 samples demonstrated 99% identity with the reference strain ATCC 30927 and also showed 2 divergent clusters, similar to those detected by LSSP-PCR. Opportunistic behavior of E. gingivalis was not detected, which may be related to the use of highly active antiretroviral therapy by all HIV(+)/AIDS patients. The high occurrence of E. gingivalis in these patients can be influenced by multifactorial components not directly related to the CD4⁺ lymphocyte counts, such as cholesterol and the oral microbiota host, which could mask the potential opportunistic ability of E. gingivalis. The identification of the 18S SSU-rRNA polymorphism by LSSP-PCR and sequencing analysis provides the first evidence of genetic variability in E. gingivalis isolated from HIV patients.

Molecular epidemiology and genetic diversity of Entamoeba species in a chelonian collection

Veterinary medicine has focused recently on reptiles, due to the existence of captive collections in zoos and an increase in the acquisition of reptiles as pets. The protozoan parasite, Entamoeba can cause amoebiasis in various animal species and humans. Although amoebiasis disease is remarkably rare in most species of chelonians and crocodiles, these species may serve as Entamoeba species carriers that transmit parasites to susceptible reptile species, such as snakes and lizards, which can become sick and die. In this study, we identified the Entamoeba species in a population of healthy (disease-free) chelonians, and evaluated their diversity through the amplification and sequencing of a small subunit rDNA region. Using this procedure, three Entamoeba species were identified: Entamoeba invadens in 4.76 % of chelonians, Entamoeba moshkovskii in 3.96 % and Entamoeba terrapinae in 50 %. We did not detect mixed Entamoeba infections. Comparative analysis of the amplified region allowed us to determine the intra-species variations. The E. invadens and E. moshkovskii strains isolated in this study did not exhibit marked differences with respect to the sequences reported in GenBank. The analysis of the E. terrapinae isolates revealed three different subgroups (A, B and C). Although subgroups A and C were very similar, subgroup B showed a relatively marked difference with respect to subgroups A and C (Fst = 0.984 and Fst = 1.000, respectively; 10-14 % nucleotide variation, as determined by blast) and with respect to the sequences reported in GenBank. These results suggested that E. terrapinae subgroup B may be either in a process of speciation or belong to a different lineage. However, additional research is necessary to support this statement conclusively.

Entamoeba dispar strains: analysis of polymorphism in Tunisian isolates

The ability to detect intra-species polymorphism in Entamoeba histolytica and Entamoeba dispar is an important tool for studying geographic distribution and transmission mechanisms. E. dispar and E. histolytica share the same mechanism for transmission among human hosts, and so after differentiation between these species. We studied the intra-species variation and distribution of E. dispar strains obtained from cyst passers, specifically from African students and Tunisian food handlers. We analyzed the polymorphic region of the chitinase protein gene in 13 individuals infected with E. dispar, of which 9 were from Tunisia and 4 from other African countries. We identified 7 different chitinase patterns in Tunisians while the 4 isolates from other countries each had a distinct pattern. Two of the patterns we found have been reported in studies from Mexico and India, possibly indicating worldwide spread of certain strains.