Commensal Intestinal Protozoa-Underestimated Members of the Gut Microbial Community

The human gastrointestinal microbiota contains a diverse consortium of microbes, including bacteria, protozoa, viruses, and fungi. Through millennia of co-evolution, the host-microbiota interactions have shaped the immune system to both tolerate and maintain the symbiotic relationship with commensal microbiota, while exerting protective responses against invading pathogens. Microbiome research is dominated by studies describing the impact of prokaryotic bacteria on gut immunity with a limited understanding of their relationship with other integral microbiota constituents. However, converging evidence shows that eukaryotic organisms, such as commensal protozoa, can play an important role in modulating intestinal immune responses as well as influencing the overall health of the host. The presence of several protozoa species has recently been shown to be a common occurrence in healthy populations worldwide, suggesting that many of these are commensals rather than invading pathogens. This review aims to discuss the most recent, conflicting findings regarding the role of intestinal protozoa in gut homeostasis, interactions between intestinal protozoa and the bacterial microbiota, as well as potential immunological consequences of protozoa colonization.

A novel 5-Plex qPCR-HRM assay detecting human diarrheal parasites

Background

Intestinal parasitic diseases occur worldwide, and their diagnosis poses considerable challenges. Cryptosporidium spp., Entamoeba histolytica, Giardia intestinalis, (and, arguably, Dientamoeba fragilis and Blastocystis spp.) are among the most important and common parasitic protozoans causing diarrhea. Several multiplex real-time PCR assays have been developed for the synchronous detection of these parasites. However, most assays include the use of hydrolysis probes, increasing the cost of stool examination. In this study, we designed and evaluated a real-time PCR protocol, based on high-resolution melting (HRM) curve analysis, to simultaneously detect and differentiate five gastrointestinal parasites.

Results

Using a blinded panel of 143 clinical samples with laboratory diagnostic data to evaluate the method, we obtained a 95.8% concordance with conventional methods. Moreover, 4.2% of the samples were positive for D. fragilis and 2.8% additional Cryptosporidium infections were found with our multiplex assay. Our method is sensitive and specific for the selected parasites with the additional possibility of being run in single-plex as a backup control for mixed infections.

Conclusions

The assay is a convenient and cost-effective method that could contribute to a quicker and accurate diagnosis as well as to more targeted therapies of parasite-derived diarrhea. Finally, this new multiplex PCR assay could also be instrumental in epidemiology studies on these parasites.

Comparison and Recommendations for Use of Dientamoeba fragilis Real-Time PCR Assays

Dientamoeba fragilis is a gastrointestinal trichomonad parasite whose pathogenicity is yet to be determined. The difficulty involved in microscopically diagnosing D. fragilis in feces led to the development of real-time PCR methodologies for the detection of D. fragilis in stool samples. Prevalence studies in Europe show much higher levels of infection where a laboratory-developed real-time assay is the predominant assay for the detection of Dientamoeba fragilis than in regions that use the EasyScreen assay for detection of gastrointestinal pathogens. The aim of this study was to compare a commercially available Dientamoeba fragilis assay (Genetic Signatures EasyScreen assay) to a widely used laboratory-developed real-time PCR method. Two hundred fifty fecal samples were screened using the laboratory-developed real-time assay on four real-time PCR platforms producing a number of discrepant results. Limit-of-detection studies were undertaken to attempt to resolve sensitivity for each platform tested. The presence or absence of Dientamoeba fragilis DNA in discrepant samples was shown using PCR amplicon next-generation sequencing. Eukaryotic 18S diversity profiling was conducted on discrepant samples to identify the presence or absence of additional protozoan species in samples that may be responsible for cross-reactivity seen in these samples. The results revealed the potential for multiple false-positive results when using the laboratory-developed real-time assay across multiple real-time platforms using manufacturer default settings. This report provides recommendations to resolve these issues where possible and suggestions for future prevalence studies, and it emphasizes the EasyScreen assay as the molecular method of choice as well as the need for standardization of detection assays across all nations screening for D. fragilis.

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.

Bulky Trichomonad Genomes: Encoding a Swiss Army Knife

The trichomonads are a remarkably successful lineage of ancient, predominantly parasitic protozoa. Recent molecular analyses have revealed extensive duplication of certain genetic loci in trichomonads. Consequently, their genomes are exceptionally large compared to other parasitic protozoa. Retention of these large gene expansions across different trichomonad families raises the question: do these duplications afford an advantage? Many duplicated genes are linked to the parasitic lifestyle and some are regulated differently to their paralogues, suggesting they have acquired new functions. It is proposed that these large genomes encode a Swiss army knife of sorts, packed with a multitude of tools for use in many different circumstances. This may have bestowed trichomonads with the extraordinary versatility that has undoubtedly contributed to their success.

Transmission of Dientamoeba fragilis: pinworm or cysts?

Recently, conflicting evidence has been published on the mode of transmission of the trichomonad Dientamoeba fragilis. Detection of D. fragilis DNA inside Enterobius vermicularis eggs agrees with the prediction of Dobell in 1940 that the eggs of a nematode act as a vector for transmission. However, the identification of a cyst stage of D. fragilis in the stool of rodents infected with a human isolate has also been reported, and this implies a life cycle similar to those of most other intestinal protistan parasites. Herein we discuss the recent data, identify gaps in the experimental evidence, and propose a method for determining which view of the life cycle of this organism is correct.

Evaluation of the EasyScreen™ enteric parasite detection kit for the detection of Blastocystis spp., Cryptosporidium spp., Dientamoeba fragilis, Entamoeba complex, and Giardia intestinalis from clinical stool samples

The aim of this study was to evaluate the EasyScreen™ Enteric Parasite Detection Kit (Genetic Signatures, Sydney, Australia) for the detection and identification of 5 common enteric parasites: Blastocystis spp., Cryptosporidium spp., Dientamoeba fragilis, Entamoeba complex, and Giardia intestinalis in human clinical samples. A total of 358 faecal samples were included in the study. When compared to real-time PCR and microscopy, the EasyScreen™ Enteric Parasite Detection Kit exhibited 92-100% sensitivity and 100% specificity and detected all commonly found genotypes and subtypes of clinically important human parasites. No cross reactivity was detected in stool samples containing various other bacterial, viral, and/or protozoan species. The EasyScreen™ PCR assay was able to provide rapid, sensitive, and specific simultaneous detection and identification of the 5 most important diarrhoea-causing enteric parasites that infect humans. It should be noted, however, that the EasyScreen™ Kit does not substitute for microscopy or for additional PCRs as it does not detect the pathogenic Coccidia spp. Cystoisospora belli or Cyclospora cayetanensis and it does not differentiate between pathogenic and nonpathogenic Entamoeba spp. This study also highlights the lack of sensitivity demonstrated by microscopy; as such, molecular methods should be considered the diagnostic method of choice for enteric parasites.

Cyst formation and faecal-oral transmission of Dientamoeba fragilis--the missing link in the life cycle of an emerging pathogen

Dientamoeba fragilis is a protozoan parasite emerging as a cause of diarrhoea and "irritable-bowel-like" gastrointestinal disease in humans with a propensity for establishing long-term, chronic infections in humans. Although Dientamoeba was discovered over a century ago its life cycle and mode of transmission is not known. No cyst stage has been described and no animal models are presently available for the study of this parasite. Here we describe the establishment of an animal model using laboratory rodents, the fulfilling of Koch's postulates, and the discovery of a new cyst stage in the life cycle of D. fragilis. Our demonstration of long-term parasite carriage by rodents and prolonged shedding of cysts, together with elevated levels of calprotectin in the stool, confirms the capacity of this organism to cause disease and indicates dientamoebiasis should be considered in the differential diagnosis of gastrointestinal diseases such as Inflammatory Bowel Syndrome (IBS). Finally, we suggest that the cyst stage described here is the vehicle that mediates faecal-oral transmission of D. fragilis between hosts.

Limited intra-genetic diversity in Dientamoeba fragilis housekeeping genes

Dientamoeba fragilis is a common intestinal parasite of unsettled clinical significance. Differences in clinical outcome of parasitic infections may reflect parasite genetic diversity, and so tools to study intra-genetic diversity that could potentially reflect differences in clinical phenotypes are warranted. Here, we show that genetic analysis of three D. fragilis housekeeping genes enables clear distinction between the two known genotypes, but that integration of housekeeping genes in multi-locus sequencing tools for D. fragilis may have limited epidemiological and clinical value due to no further added genetic resolution.