Molecular testing for clinical diagnosis and epidemiological investigations of intestinal parasitic infections

Trichuriasis in Human Patients from Côte d'Ivoire Caused by Novel Trichuris incognita Species with Low Sensitivity to Albendazole/Ivermectin Combination Treatment

Albendazole/ivermectin combination therapy is a promising alternative to benzimidazole monotherapy alone for Trichuris trichiura control. We used fecal DNA metabarcoding to genetically characterize Trichuris spp. populations in patient samples from Côte d'Ivoire showing lower (egg reduction rate <70%) albendazole/ivermectin sensitivity than those from Laos and Tanzania (egg reduction rates >98%). Internal transcribed spacer (ITS) 1 and ITS2 metabarcoding revealed the entire detected Côte d'Ivoire Trichuris population was phylogenetically distinct from T. trichiura found in Laos and Tanzania and was more closely related to T. suis. Mitochondrial genome sequencing of 8 adult Trichuris worms from Côte d'Ivoire confirmed their species-level differentiation. Sequences from human patients in Cameroon and Uganda and 3 captive nonhuman primates suggest this novel species, T. incognita, is distributed beyond Côte d'Ivoire and has zoonotic potential. Continued surveillance by using fecal DNA metabarcoding will be needed to determine Trichuris spp. geographic distribution and control strategies.

Prevalence and molecular identification of protozoan intestinal parasitic infections in cancer patients and a control group

BACKGROUND

Parasitic infections, especially opportunistic infections, are important issues for immunocompromised patients, including cancer patients. In this study, the prevalence of intestinal protozoan infections was investigated in Iranian cancer patients and a control group using microscopic and molecular methods.

METHODS

This cross-sectional study was conducted on a group of 158 individuals with gastrointestinal and non-gastrointestinal cancers from hospitals affiliated with the Iran University of Medical Sciences, alongside 158 healthy individuals included in the control group. Stool samples were collected and examined using direct and concentration methods. The modified acid-fast staining method was used to detect coccidian parasite infections. DNA was extracted from the patients' samples, and PCR and sequencing were performed.

RESULTS

The overall prevalence of protozoan infections was higher in the cancer patients (31.6%) than in the control group (12.0%), with the difference between the two groups being statistically significant (P = 0.0001). The study identified Blastocystis hominis as the most common protozoan, with a prevalence of 22.8%, followed by Giardia lamblia, Entamoeba coli, Dientamoeba fragilis, and Chilomastix mesnili, with rates of 2.5%, 1.3%, 1.3%, and 0.6%, respectively, in the cancer patients. Cystoisospora belli and Cryptosporidium sp. were found as opportunistic infections in 2.5% and 0.6% of the cancer patients, respectively. Blastocystis hominis, with a prevalence of 9.5%, followed by Giardia lamblia at 1.3%, were the most common parasitic infections in the control group. A statistical difference was found for Cystoisospora belli (P = 0.044) and Blastocystis hominis (P = 0.0013) between the cancer patients and the control group. Cryptosporidium sp. was confirmed as Cryptosporidium parvum, and Cystoisospora belli was confirmed by PCR sequencing.

CONCLUSION

Chemotherapy, aside from corticosteroids, increases susceptibility to intestinal Protozoan infections in patients with hematological malignancies, particularly those with lymphoma and leukemia. The results indicated a higher risk of intestinal Protozoan infections, including opportunistic infections, in the cancer patients than in the control group. Cystoisospora belli and Cryptosporidium parvum were found to cause diarrhea in hematological malignancy patients undergoing chemotherapy.

Crucial role of biosensors in the detection of helminth biomarkers in public health programmes

Helminthiases are highly prevalent but neglected infections that affect more than 1·5 billion people worldwide. Considering the worldwide prevalence of helminthiases, WHO has declared them a public health concern since 2001, necessitating rigorous control and elimination efforts. However, only a few reliable point-of-care diagnostic tests are available for assessing the effectiveness of public health interventions targeting helminthiases, thus increasing the risk of suboptimal outcomes, misallocation of resources, and emergence of drug-resistant helminths. This Review provides an introduction on helminthiases and strategies to achieve control, elimination, interruption in transmission, and eradication of these infections. The Review then comprehensively details the existent biosensors that can be used to detect these infections in human samples, focusing on their target biomarkers, the bioreceptors used, and the sensing readouts. The Review concludes with an in-depth discussion on the persistent challenges related to helminthiases, aiming to encourage the development of much-needed diagnostics specific to these neglected infections.

Detection of soil-transmitted helminths and Schistosoma spp. by nucleic acid amplification test: Results of the first 5 years of the only international external quality assessment scheme

BACKGROUND

Infections with soil-transmitted helminths (STH) and schistosomiasis (SCH) result in a significant global health burden, particularly in rural communities in low and middle-income countries. While microscopy remains the primary diagnostic method for STH and SCH in resource-limited settings, nucleic acid amplification tests (NAATs) are gaining prominence as tools for evaluation of public health control programs in endemic countries, and individual diagnosis in high-income countries. Despite the high sensitivity and specificity of NAATs, previous research has highlighted inter-laboratory variations, both in technical and clinical performance, justifying the need for continuous proficiency testing.

METHODOLOGY

Results from 5 rounds over a 5-year period of the so far only longitudinal international Helminth External Molecular Quality Assessment Scheme (HEMQAS), coordinated by the Dutch Foundation for Quality Assessment in Medical Laboratories (SKML), were examined in order to (i) assess the diagnostic proficiency of laboratories in detecting helminths in stool and (ii) identify potential factors contributing to variations in performance.

OUTCOME AND CONCLUSIONS

Thirty-six laboratories, from 18 countries and 5 continents, participated in HEMQAS. The overall diagnostic performances were satisfying, with remarkably low numbers (<2%) of false-positive results. False-negative results were more often reported for stool (15%) than for DNA (5%) samples. False-negative results varied largely between targets (the highest number (29%) for Trichuris trichiura). Twenty-five laboratories provided a sufficient number of results for a robust comparison between participating laboratories, which confirmed substantial inter-laboratory variability in quantitative NAAT results (Cq-values). This variability likely arises from differences in pre-treatment, DNA isolation and DNA-target amplification procedures. This study emphasizes the complexity of molecular diagnosis for STH and SCH, highlighting the critical role of proper stool preparation and DNA isolation methods. The results underscore the necessity for laboratory professionals and public health decision-makers to recognize these complexities and continuously undertake external quality assessment schemes to ensure accurate and reliable performance in molecular diagnosis.

The epidemiology of intestinal protozoa in the Israeli population based on molecular stool test: a nationwide study

Stool examination using microscopy was the traditional method for the diagnosis of intestinal parasites. Recently, the use of molecular tests to identify stool protozoa has become the main tool used in most clinical laboratories in Israel. This study aimed to evaluate the prevalence of intestinal parasites in Israel and to compare this prevalence in laboratories that use molecular tests vs a laboratory that uses microscopy. Samples collected from January to October 2021 at seven laboratories were analyzed by real-time PCR (RT-PCR) or by microscopy. The multiplex panel included the following pathogens: Giardia lamblia, Entamoeba histolytica, Cryptosporidium spp., Cyclospora, Dientamoeba fragilis, and Blastocystis spp. Overall, 138,415 stool samples were tested by RT-PCR and 6,444 by microscopy. At least one protozoa species was identified in 28.4% of the PCR-tested samples compared to 4.6% of the microscopy-tested samples. D. fragilis was the most common PCR-identified species (29%). D. fragilis, G. lamblia, and Cryptosporidium spp. were mainly found in pediatric population, while Blastocystis spp. was most prevalent among adults (P < 0.001). In a sub-cohort of 21,480 samples, co-infection was found in 4,113 (19.15%) samples, with Blastocystis spp. and D. fragilis being the most common (14.9%) pair. Molecular stool testing proved more sensitive compared to microscopy. D. fragilis was the most commonly detected pathogen. The above profile was identified during the COVID pandemic when traveling was highly restricted and most likely represents the locally circulating protozoa.

IMPORTANCE

This study sheds light on the prevalence of stool parasites in Israel. Additionally, this study indicates that the shift from microscope analysis to molecular tests improved protozoa diagnosis.

Evaluation of the Use of Singleplex and Duplex CerTest VIASURE Real-Time PCR Assays to Detect Common Intestinal Protist Parasites

Cryptosporidium spp., Giardia duodenalis and Entamoeba histolytica are species of protozoa- causing diarrhoea that are common worldwide, while Entamoeba dispar, Dientamoeba fragilis and Blastocystis sp. appear to be commensal parasites whose role in pathogenicity remains controversial. We conducted the clinical evaluation of five singleplex and one duplex CerTest VIASURE Real-Time PCR Assays against a large panel of positive DNA samples (n = 358), and specifically to Cryptosporidium spp. (n = 96), G. duodenalis (n = 115), E. histolytica (n = 25) E. dispar (n = 11), Blastocystis sp. (n = 42), D. fragilis (n = 37), and related parasitic phylum species such as Apicomplexa, Euglenozoa, Microsporidia and Nematoda. DNA samples were obtained from clinical stool specimens or cultured isolates in a national reference centre. Estimated diagnostic sensitivity and specificity values were 0.94-1 for Cryptosporidium spp., 0.96-0.99 for G. duodenalis, 0.96-1 for E. histolytica, 1-1 for E. dispar, and 1-0.99 for D. fragilis in the evaluated singleplex assays. In the duplex assay for the simultaneous detection of Blastocystis sp. and D. fragilis these values were 1-0.98 and 1-0.99, respectively. Measures of diagnostic precision for repeatability and reproducibility were found to be under acceptable ranges. The assays identified six Cryptosporidium species (C. hominis, C. parvum, C. canis, C. felis, C. scrofarum, and C. ryanae), four G. duodenalis assemblages (A, B, C, and F), and six Blastocystis subtypes (ST1-ST5, and ST8). The evaluated singleplex and duplex VIASURE Real-Time PCR assays provide sensitive, practical, and cost-effective choices to the molecular diagnosis of the main diarrhoea-causing intestinal protists in clinical microbiology and research laboratories.

Prevalence and virulence potential of Aeromonas spp. isolated from human diarrheal samples in North East Italy

IMPORTANCE

In this work, we demonstrate the epidemiologic relevance of the Aeromonas genus as the cause of infective diarrhea in North East Italy, both in children and adult subjects, with the significative presence of highly pathogenic strains. Aeromonas strains possess a heterogeneous armamentarium of pathogenicity factors that allows the microbe to affect a wide range of human intestinal epithelial cell processes that justify the ability to induce diarrhea through different mechanisms and cause diseases of variable severity, as observed for other gastrointestinal pathogens. However, it remains to be determined whether specific genotype(s) are associated with clinical pictures of different severity to implement the diagnostic and therapeutic approaches for this relevant enteric pathogen.

Droplet digital PCR as a tool to detect resistant isolates of Dirofilaria immitis

Prevention of canine heartworm disease, caused by Dirofilaria immitis, relies on macrocyclic lactones for which drug resistance is now a concern. Although genetic polymorphisms have been associated with resistance in D. immitis populations, the mechanism is still not well understood. The lack of reliable in vitro assays to detect resistance is a limitation for confirming resistance. Ten single nucleotide polymorphisms (SNPs) were previously clinically validated in D. immitis resistant isolates, using the MiSeq platform. This technique although useful for research studies is expensive and does not facilitate rapid detection of these markers in small numbers of clinical samples. We developed a droplet digital PCR protocol for detecting SNPs correlating with ML resistance. Specific primers and hydrolysis probes encompassing the wildtype and mutant alleles were designed to amplify the SNP targets from genomic DNA of different D. immitis isolates. Allele frequencies were determined and the suitability of the ddPCR assay was assessed and compared with MiSeq data. The ddPCR assay accurately detected and quantified alternate nucleotides in two isolates of reference, the ML-susceptible Missouri (MO) and ML-resistant JYD-34, at the previously identified SNP positions. The presence of the SNPs was also determined in additional isolates with known or putative susceptible or resistant phenotypes. We observed SNP1 and SNP2 are more predictive markers and appear suitable for rapid detection and monitoring of drug resistance. Our results suggested that ddPCR could be employed to distinguish infection due to actual genetic resistance from infection with susceptible parasites and also for rapid detection of isolates not only with ML susceptible and resistant genotypes but also mixed genotypes that correspond to heterogeneous isolates containing a mixed population of ML susceptible and resistant parasites. DdPCR may be a useful tool for conducting surveys, or assessments of individual isolates, for genetic evidence of resistance or developing resistance.

Evaluation of Kato-Katz and multiplex quantitative polymerase chain reaction performance for clinical helminth infections in Thailand using a latent class analysis

Using an appropriate diagnostic tool is essential to soil-transmitted helminth control and elimination efforts. Kato-Katz (KK) is the most commonly used diagnostic, but recently other tools, such as real-time quantitative polymerase chain reaction (multiplex qPCR), are starting to be employed more. Here, we evaluated the performance of these two diagnostic tools for five helminth species in Thailand. In the absence of a gold standard, diagnostic performance can be evaluated using latent class analysis. Our results suggest that in moderate to high prevalence settings above 2% multiplex qPCR could be more sensitive than KK, this was particularly apparent for Opisthorchis viverrini in the northeastern provinces. However, for low prevalence, both diagnostics suffered from low sensitivity. Specificity of both diagnostics was estimated to be high (above 70%) across all settings. For some specific helminth infection such as O. viverrini, multiplex qPCR is still a preferable choice of diagnostic test. KK performed equally well in detecting Ascaris lumbricoides and Taenia solium when the prevalence is moderate to high (above 2%). Neither test performed well when the prevalence of infection is low (below 2%), and certainly in the case for hookworm and Trichuris trichiura. Combination of two or more diagnostic tests can improve the performance although the cost would be high. Development of new methods for helminth surveillance at the pre-elimination phase is therefore very important. This article is part of the theme issue 'Challenges and opportunities in the fight against neglected tropical diseases: a decade from the London Declaration on NTDs'.

A high-resolution melting approach for the simultaneous differentiation of five human babesiosis-causing Babesia species

BACKGROUND

Six species of apicomplexan parasites of the genus Babesia, namely B. microti, B. divergens, B. duncani, B. motasi, B. crassa-like and B. venatorum, are considered to be the primary causal agents of human babesiosis in endemic areas. These six species possess variable degrees of virulence for their primary hosts. Therefore, the accurate identification of these species is critical for the adoption of appropriate therapeutic strategies.

METHODS

We developed a real-time PCR-high-resolution melting (qPCR-HRM) approach targeting 18S ribosomal RNA gene of five Babesia spp. based on melting temperature (Tm) and genotype confidence percentage values. This approach was then evaluated using 429 blood samples collected from patients with a history of tick bites, 120 DNA samples mixed with plasmids and 80 laboratory-infected animal samples.

RESULTS

The sensitivity and specificity of the proposed qPCR-HRM method were 95% and 100%, respectively, and the detection limit was 1-100 copies of the plasmid with the cloned target gene. The detection level depended on the species of Babesia analyzed. The primers designed in this study ensured not only the high interspecific specificity of our proposed method but also a high versatility for different isolates from the same species worldwide. Additionally, the Tm obtained from the prepared plasmid standard is theoretically suitable for identifying isolates of all known sequences of the five Babesia species.

CONCLUSIONS

The developed detection method provides a useful tool for the epidemiological investigation of human babesiosis and pre-transfusion screening.

Design of a Protocol for Soil-Transmitted Helminths (in Light of the Nematode Toxocara canis) DNA Extraction from Feces by Combining Commercially Available Solutions

One of the main challenges for the mass introduction of the molecular diagnostics of soil-transmitted helminths (STHs) into clinical practice is the lack of a generally recognized effective method for isolating parasitic DNA from fecal samples. In the present study, we assessed the effects of various pretreatment procedures on the efficiency of removing PCR inhibitors and extracting Toxocara canis DNA from feces. We evaluated the effectiveness of four destructive methods (bead beating, the action of temperature-dependent enzymes, freeze-heat cycles, and incubation in a lysis buffer) on the integrity of T. canis eggs and the efficiency of DNA extraction. Also, we evaluated the effects of prewashes and the use of commercial concentrators on DNA extraction from fecal samples contaminated with T. canis eggs. A bead beating procedure was sufficient to destroy the T. canis eggs, while the effects of enzymes and freeze-heat cycles did not lead to a significant destruction of the eggs or the release of Toxocara DNA. Helminth DNA isolation protocols that do not include a bead beating step are not preferred. The preconcentration of STH eggs from feces using a commercial concentrator and subsequent washing can significantly increase the yield of DNA from STHs and reduce PCR inhibition.

Rapid Single-Step Immunochromatographic Assay for Angiostrongylus cantonensis Specific Antigen Detection

Angiostrongylus cantonensis is the major etiological nematode parasite causing eosinophilic meningitis and/or eosinophilic meningoencephalitis in humans. The rapid global spread of Angiostrongylus cantonensis and the emerging occurrence of the infection have exposed the shortcomings of traditional/conventional diagnostics. This has spurred efforts to develop faster, simpler and more scalable platforms that can be decentralized for point-of-need laboratory testing. By far, the point-of-care immunoassays such as the lateral flow assay (LFA) are the best-placed. In this work, a LFA in the form of an immunochromatographic test device (designated AcAgQuick^Dx), based on the detection of a circulating Angiostrongylus cantonensis-derived antigen, was established using anti-31 kDa Angiostrongylus cantonensis antibody as the capture reagent and anti-Angiostrongylus cantonensis polyclonal antibody as the indicator reagent. The AcAgQuick^Dx was evaluated for its diagnostic potential with a total of 20 cerebrospinal fluids (CSF) and 105 serum samples from patients with angiostrongyliasis and other clinically related parasitic diseases, as well as serum samples from normal healthy subjects. Three of the ten CSF samples from serologically confirmed angiostrongyliasis cases and two of the five suspected cases with negative anti-Angiostrongylus cantonensis antibodies showed a positive AcAgQuick^Dx reaction. Likewise, the AcAgQuick^Dx was able to detect Angiostrongylus cantonensis specific antigens in four serum samples of the 27 serologically confirmed angiostrongyliasis cases. No positive reaction by AcAgQuick^Dx was observed in any of the CSF (n = 5) and serum (n = 43) samples with other parasitic infections, or the normal healthy controls (n = 35). The AcAgQuick^Dx enabled the rapid detection of active/acute Angiostrongylus cantonensis infection. It is easy to use, can be transported at room temperature and does not require refrigeration for long-term stability over a wide range of climate. It can supplement existing diagnostic tests for neuroangiostrongyliasis under clinical or field environments, particularly in remote and resource-poor areas.

Molecular detection and characterization of Cryptosporidium spp., Giardia duodenalis, and Enterocytozoon bieneusi infections in dromedary camels (Camelus dromedaries) in Egypt

Introduction

Few studies have investigated the occurrence of microeukaryotic gut parasites in dromedary camels in Egypt, and the majority of these investigations are based on microscopic analysis of fecal material.

Methods

Herein, we assessed the occurrence, molecular diversity, and zoonotic potential of protozoan (Cryptosporidium spp. and Giardia duodenalis) and microsporidian (Enterocytozoon bieneusi) pathogens in individual fecal samples (n = 102) of dromedary camels with (n = 26) and without (n = 76) diarrhea from Aswan Governorate, Upper Egypt. Other factors possibly associated with an increased risk of infection (geographical origin, sex, age, and physical condition) were also analyzed. The SSU rRNA or ITS genes were targeted by molecular (PCR and Sanger sequencing) techniques for pathogen detection and species identification.

Results and discussion

The most abundant species detected was G. duodenalis (3.9%, 4/102; 95% CI: 1.1-9.7), followed by Cryptosporidium spp. (2.9%, 3/102; 95% CI: 0.6-8.4). All samples tested negative for the presence of E. bieneusi. Sequence analysis data confirmed the presence of zoonotic C. parvum (66.7%, 2/3) and cattle-adapted C. bovis (33.3%, 1/3). These Cryptosporidium isolates, as well as the four Giardia-positive isolates, were unable to be amplified at adequate genotyping markers (Cryptosporidium: gp60; Giardia: gdh, bg, and tpi). Camels younger than 2 years old were significantly more likely to harbor Cryptosporidium infections. This connection was not statistically significant, although two of the three cryptosporidiosis cases were detected in camels with diarrhea. The spread of G. duodenalis infections was unaffected by any risk variables studied. This is the first report of C. parvum and C. bovis in Egyptian camels. The finding of zoonotic C. parvum has public health implications since camels may function as sources of oocyst pollution in the environment and potentially infect livestock and humans. Although preliminary, this study provides useful baseline data on the epidemiology of diarrhea-causing microeukaryotic parasites in Egypt. Further research is required to confirm and expand our findings in other animal populations and geographical regions of the country.

Modular nanotheranostic agents for protistan parasitic diseases: Magic bullets with tracers

Protistan parasitic infections contribute significantly to morbidity and mortality, causing more than 2 billion human infections annually. However, current treatments are often limited; due to ineffective drugs and drug resistance, thus better options are urgently required. In the present context, theranostics agents are those that offer simultaneous detection, diagnosis and even treatment of protistan parasitic diseases. "Nanotheranostics" is the term used to describe such agents, that are around 100 nm or less in size. Anti-parasitic activity of nanoparticles (NPs) has been reported, and many have useful intrinsic imaging properties, but it is perhaps their multifunctional nature that offers the greatest potential. NPs may be used as adapters onto which various subunits with different functions may be attached. These subunits may facilitate targeting parasites, coupled with toxins to eradicate parasites, and probe subunits for detection of particles and/or parasites. The modular nature of nano-platforms promises a "mix and match" approach for the construction of tailored agents by using combinations of these subunits against different protistan parasites. Even though many of the subunits have shown promise alone, these have not yet been put together convincingly enough to form working theranostics against protistan parasites. Although the clinical application of nanotheranostics to protistan parasitic infections in humans requires more research, we conclude that they offer not just a realisation of Paul Ehrlich's long imagined "magic bullet" concept, but potentially are magic bullets combined with tracer bullets.

Effect of incorporation of bead-beating during DNA extraction for quantitative polymerase chain reaction-based detection of Trichuris trichiura in stool samples in community settings: a systematic review

This meta-analysis was designed to assess the effect of the addition of a bead-beating (BB) step during DNA extraction to effectively isolate Trichuris trichiura DNA from stool samples for quantitative polymerase chain reaction (qPCR)-based diagnosis. qPCR-based molecular studies comparing the inclusion of a bead-beating step during the DNA extraction from stool samples with extraction without the step were included in the analysis. Studies using real patient samples in community settings were included. The PubMed database and Google search engine were searched in December 2019. Risk of bias and applicability were assessed using the Quality Assessment of Diagnostic Accuracy Studies-2 checklist. Odds ratios (ORs) for individual studies were combined to estimate the random effects model OR. A total of six independent sub-studies were gathered from two published original articles. The division of the two major studies into six sub-studies was indispensable due to the nature of the study carried out. 128 of the total 192 samples (in all studies) were positive for T. trichiura when BB was used during DNA extraction compared to 108/192 when BB was excluded. The combined OR was 1.66 (95% confidence interval: 1.059 to 2.602). Though only two articles were included in the study, six exclusive individual sub-studies were analyzed. Inherent differences in the background prevalence of helminths in the study population could impact the sensitivity of qPCR. It was found that the inclusion of the BB step during DNA extraction significantly increased the sensitivity of the test. This study was not registered in any database.

Development of duplex real-time PCR for quick detection of cryptosporidiosis in goats

Cryptosporidium spp. is the most important foodborne and waterborne pathogens and a leading cause of mortality from foodborne and waterborne gastrointestinal diseases. In neonates of domestic animals, it is associated with consistent diarrhea and dehydration. Cryptosporidium infection begins with the ingestion of sporulated oocytes disseminated by carrier animals that consistently contaminate the environment. Many diagnostic tests are available including microscopy and antigen trap-ELISA, but none of the diagnostic tests available currently cannot differentiate between active and passive infection in the host. In the current study, to address this challenge an mRNA-based duplex TaqMan® probe PCR was developed to target the Cryptosporidium oocyst wall protein gene and 18SSU rRNA gene in a single tube that can detect metabolically active cryptosporidial oocysts. The mRNA transcripts are the direct indicator of any actively replicating cell and they will help decipher the active stages of its lifecycle in a host. This diagnostic assay was standardized by computing transcript copy number-based limit of detection (LOD). For COWP and 18SSU rRNA genes, the LOD was 7.08 × 10⁰⁴ and 5.95 × 10⁰⁵ , respectively. During active infections, the oocyst wall protein will be active and so its COWP gene transcripts will act as a marker for active infection. While transcripts for 18SSU rRNA are constitutively expressed in cryptosporidial life cycle. This current diagnostic assay will be a quantitative marker that will help assess the active stages of Cryptosporidium infection in neonates. The disease dynamics will help better understand to formulate the control strategies and contain infection among healthy animals.

An adaptive phase II/III safety and efficacy randomized controlled trial of single day or three-day fixed-dose albendazole-ivermectin co-formulation versus albendazole for the treatment of Trichuris trichiura and other STH infections. ALIVE trial protocol

Background: Soil-transmitted helminths (STH) are targeted for control through mass drug-administration campaigns to prevent morbidity affecting at-risk groups in endemic regions. Although broadly successful, the use of albendazole and mebendazole achieved variable progress, with deficiencies against Trichuris trichiura and a predictable low efficacy against Strongyloides stercoralis. Novel drug combinations offer a potential solution, providing they can be delivered safely and maintain efficacy against all STH species. Here we present the protocol of a clinical trial to evaluate a fixed-dose combination (FDC) tablet containing albendazole and ivermectin that will be compared against albendazole against STH . Methods: An adaptive phase II/III randomized controlled trial will be undertaken in STH endemic sites in Ethiopia, Kenya and Mozambique to evaluate an oral FDC of 400 mg albendazole and either 9- or 18 mg ivermectin. FDC will be administered as a single dose or single doses over three-consecutive days and assessed against a single dose of 400 mg albendazole. In the phase II trial, 126 T. trichiura-infected children weighting 15 to 45 kg will be treated in a dose-escalation manner to determine safety objectives. In the phase III trial, 1097 participants aged 5 to 18 years old infected with T. trichiura, hookworm and S. stercoralis will be recruited to determine safety and efficacy. The trial will be open-label with blinded outcome assessors. Cure rate measured 21-days after-treatment in duplicate Kato-Katz is the primary efficacy outcome. Secondary objectives include efficacy evaluation by quantitative polymerase chain reaction (PCR) as an outcome measurement, description of pharmacokinetic parameters, palatability and acceptability evaluations, and monitoring of anthelmintic resistance. Conclusions: This trial with registrational goals seeks to evaluate an innovative fixed-dose combination of albendazole and ivermectin co-formulated tablets, with the goal of providing an anthelmintic regimen with improved efficacy and spectrum of coverage against STH. ClinicalTrials.gov registration: NCT05124691 (18/11/2021).

Development, Optimisation and Validation of a Novel Multiplex Real-Time PCR Method for the Simultaneous Detection of Cryptosporidium spp., Giardia duodenalis and Dientamoeba fragilis

The enteric protozoan parasites Cryptosporidium spp., Giardia duodenalis and Dientamoeba fragilis are-to various extents-contributors to the burden of gastrointestinal illness in high-income countries. Detection of these pathogens by microscopy examination is challenging because of the limited sensitivity and need for specific staining procedures. We developed and optimised a new multiplex real-time PCR assay for the simultaneous detection of Cryptosporidium spp., G. duodenalis and D. fragilis in clinical (stool) samples. The diagnostic performance of the assay was evaluated against a large panel of well-characterised DNA samples positive for Cryptosporidium spp. (n = 126), G. duodenalis (n = 132) and D. fragilis (n = 49). The specificity of the test was assessed against a DNA panel from other intestinal or phylogenetically related parasites (n = 105) and faecal DNA from individuals without clinical manifestations (n = 12). The assay exhibited a diagnostic sensitivity of 0.90-0.97 and a diagnostic specificity of 1. The limit of detection was estimated for Cryptosporidium (1 oocyst) and G. duodenalis (5 × 10-4 cysts). The method allowed the detection of four Cryptosporidium species (C. hominis, C. parvum, C. meleagridis and C. cuniculus) and five G. duodenalis assemblages (A-E) without cross-reacting with other parasites belonging to the phyla Amoebozoa, Apicomplexa, Euglenozoa, Microsporidia, Nematoda and Platyhelminthes. This newly developed multiplex real-time PCR assay represents a novel alternative for the rapid and accurate detection of Cryptosporidium, G. duodenalis and D. fragilis in clinical settings.

Diagnostic Methods of Common Intestinal Protozoa: Current and Future Immunological and Molecular Methods

Intestinal protozoan infection is a persisting public health problem affecting the populations of developing countries in the tropical and subtropical regions. The diagnosis of intestinal protozoa remains a challenge especially in developing countries due to a shortage of laboratory facilities, limited health funding, and the remoteness of communities. Despite still being widely used, conventional diagnoses using microscopy and staining methods pose important limitations, particularly due to their low sensitivities and specificities. The selection of diagnostic methods needs to be carefully considered based on the objective of examination, availability of resources, and the expected parasite to be found. In this review, we describe various immunodiagnosis and molecular diagnostic methods for intestinal protozoa infection, including their advantages, disadvantages, and suitability for different settings, with a focus on Entamoeba histolytica, Giardia duodenalis, and Cryptosporidium spp.

Comparative Evaluation of Real-Time Screening PCR Assays for Giardia duodenalis and of Assays Discriminating the Assemblages A and B

Due to superior sensitivity compared to traditional microscopy, real-time PCR has been well established for the diagnosis of Giardia duodenalis in human stool samples. In this study, screening real-time PCRs for different target genes of G. duodenalis, i.e., the 18S rRNA gene, the gdh (glutamate dehydrogenase) gene and the bg (beta-giardin) gene, were comparatively assessed next to various real-time PCR assays for the discrimination of the assemblages A and B of G. duodenalis targeting the bg gene with and without locked nucleic acid–containing probes as well as the tpi (triose phosphate isomerase) gene. The screening PCRs were assessed by including 872 non-preselected samples with a high pre-test probability for G. duodenalis in the statistical analysis, while 53 G. duodenalis-positive samples as indicated by at least two screening PCRs were finally included in the assessment of the assemblage-specific PCRs. For the screening PCRs, sensitivity estimated with latent class analysis (LCA) ranged from 17.5% to 100%, specificity from 92.3% to 100% with an accuracy-adjusted prevalence of 7.2% for G. duodenalis within the non-preselected sample collection. In detail, sensitivity and specificity were 100% and 100% for the 18S rRNA gene-specific assay, 17.5% and 92.3% for the gdh gene-specific assay, and 31.7% and 100% for the bg gene-specific assay, respectively. Agreement kappa was slight with only 15.5%. For the assemblage-specific PCRs, estimated sensitivity ranged from 82.1% to 100%, specificity from 84.0% to 100% with nearly perfect agreement kappa of 90.1% for assemblage A and yet substantial agreement of 74.8% for assemblage B. In detail for assemblage A, sensitivity and specificity were 100% and 100% for the bg gene-specific assay without locked nucleic acids (LNA) as well as 100% and 97.8% for both the bg gene-specific assay with LNA and the tri gene-specific assay, respectively. For assemblage B, sensitivity and specificity were 100% and 100% for the bg gene-specific assay without LNA, 96.4% and 84.0% for the bg gene-specific assay with LNA, and 82.1% and 100% for the tri gene-specific assay, respectively. Within the assessed sample collection, the observed proportion comprised 15.1% G. duodenalis assemblage A, 52.8% G. duodenalis assemblage B and 32.1% non-resolved assemblages. Only little differences were observed regarding the cycle threshold (Ct) values when comparing the assays. In conclusion, best diagnostic accuracy was shown for an 18S rRNA gene-specific screening assay for G. duodenalis and for a differentiation assay discriminating the G. duodenalis assemblages A and B by targeting the bg gene with probes not containing locked nucleic acids. By adding additional highly specific competitor assays for confirmation testing, diagnostic specificity can be further increased on the cost of sensitivity if optimized specificity is desired.

The Novodiag® Stool parasites assay, an innovative high-plex technique for fast detection of protozoa, helminths and microsporidia in stool samples: a retrospective and prospective study

OBJECTIVES

We provide the first evaluation of the CE-IVD marked Novodiag® stool parasites assay (NVD), allowing rapid and high-plex detection of 26 distinct targets, encompassing protozoans, helminths and microsporidia in stool samples.

METHODS

A total of 254 samples (n = 205 patients) were prospectively processed by the NVD and our routine procedure (RP). Performances of the NVD were compared with RP. Samples only positive by the NVD assay were investigated by external PCR assays. Sensitivity and specificity (Se/Sp) and time from sample receipt to results were determined for each method. The NVD was also evaluated against 77 additional samples positive for a wide range of parasites.

RESULTS

Overall positivity rate was 16.9% for RP compared with 34% using the NVD assay, and 164 samples (66%) were negative by both methods. Only 30 positive samples (12%) showed full concordance between RP and NVD. Fifty-three discordant samples were sent for external investigations. Except for Giardia intestinalis and Trichuris spp., higher Se was observed for the NVD assay for Blastocystis spp. (100% vs. 63%), Dientamoeba fragilis (100% vs. 0%), Schistosoma spp. (100% vs. 17%), and Enterobius vermicularis (100% vs. 67%) but roughly similar to RP for the remaining parasites tested. False-positive results were identified for Blastocystis spp., G. intestinalis, and Trichuris spp. using the NVD assay. The NVD mostly provides a diagnosis on the day of sample receipt compared with a mean of three days with RP.

CONCLUSIONS

Besides some limitations, the NVD is a new diagnostic strategy allowing rapid and high-plex detection of gastrointestinal parasites from unpreserved stools.

Worms and bugs of the gut: the search for diagnostic signatures using barcoding, and metagenomics-metabolomics

Gastrointestinal (GI) helminth infections cause significant morbidity in both humans and animals worldwide. Specific and sensitive diagnosis is central to the surveillance of such infections and to determine the effectiveness of treatment strategies used to control them. In this article, we: (i) assess the strengths and limitations of existing methods applied to the diagnosis of GI helminth infections of humans and livestock; (ii) examine high-throughput sequencing approaches, such as targeted molecular barcoding and shotgun sequencing, as tools to define the taxonomic composition of helminth infections; and (iii) discuss the current understanding of the interactions between helminths and microbiota in the host gut. Stool-based diagnostics are likely to serve as an important tool well into the future; improved diagnostics of helminths and their environment in the gut may assist the identification of biomarkers with the potential to define the health/disease status of individuals and populations, and to identify existing or emerging anthelmintic resistance.

Selecting a multiplex PCR panel for accurate molecular diagnosis of intestinal protists: a comparative study of Allplex® (Seegene®), G-DiaParaTrio (Diagenode®), and RIDA®GENE (R-Biopharm®) assays and microscopic examination

Commercial multiplex PCR assay panels were developed to overcome the limitations of microscopic examination for parasitological diagnosis on stool samples. However, given the increased supply of this diagnostic approach, these assays must be evaluated to position them in a diagnostic algorithm. Analytical performances of the multiplex PCR assay G-DiaParaTrio, Allplex^® GI parasite and RIDA^®GENE parasitic stool panel for detecting Blastocystis sp., Entamoeba histolytica, Giardia duodenalis, Cryptosporidium spp., Dientamoeba fragilis, and Cyclospora cayetanensis, were assessed through a retrospective comparative study on 184 stool samples initially sent for parasitological investigation. The composite reference method for parasitological diagnosis was microscopic observation and Entamoeba histolytica-specific adhesion detection when necessary. Multiplex PCR assays were performed on extracted DNA from each stool, following the manufacturer's recommendations. Discrepant results with the composite reference method were investigated with species-specific PCR to approach a final parasitological diagnosis. Overall sensitivity/specificity for the multiplex PCR assays was 93.2%/100% for G-DiaParaTrio, 96.5%/98.3% for Allplex^® GI parasite and 89.6%/98.3% for RIDA^®GENE, whereas the composite reference method presented an overall sensitivity/specificity of 59.6%/99.8%. These results confirmed the added diagnostic value of the multiplex PCR approach for gastrointestinal protists. Nevertheless, the PCR procedure and the analytical performance for each protist of interest, variable depending on the multiplex PCR assay, must be considered when implementing a PCR-based diagnostic approach.

Assessment of three DNA extraction kits for the absolute quantification of strongyle nematode eggs in faecal samples

BACKGROUND

Haemonchus contortus is one of the most pathogenic gastrointestinal nematodes of small ruminants. The current diagnostic approach for the detection of this species relies on coproscopic methods, which both have low sensitivity and are time consuming. Methods employing detection through DNA amplification, such as droplet digital polymerase chain reaction (ddPCR), offer an advantageous approach to the diagnosis of H. contortus. However, DNA extraction protocols need to be constantly updated for the optimal retrieval of diagnostically usable template. Here, we describe the evaluation of three genomic DNA extraction kits for the detection and quantification of H. contortus ITS2 amplicon DNA from faecal samples, using droplet digital PCR.

RESULTS

DNA samples, extracted from faecal material with the Nucleospin DNA Stool kit, produced the highest amounts of ITS2 amplicon copies and had the lowest coefficient of variation across different dilutions and sample types (fresh or frozen) out of the tested kits (Nucleospin DNA Stool, E.Z.N.A.® Stool DNA Kit and QIAamp Fast DNA Stool Mini Kit). Furthermore, the protocol of this kit has the fewest number of steps and the price of DNA extraction per sample is reasonable (2.77 €).

CONCLUSIONS

The Nucleospin DNA Stool kit is an attractive option for the detection and quantification of H. contortus DNA in faecal samples of small ruminants in a diagnostic setting.

Prevalence of intestinal protozoan parasites among school children in africa: A systematic review and meta-analysis

Introduction

Parasitic infections, especially intestinal protozoan parasites (IPPs) remain a significant public health issue in Africa, where many conditions favour the transmission and children are the primary victims. This systematic review and meta-analysis was carried out with the objective of assessing the prevalence of IPPs among school children in Africa.

Methods

Relevant studies published between January 2000 and December 2020 were identified by systematic online search on PubMed, Web of Science, Embase and Scopus databases without language restriction. Pooled prevalence was estimated using a random-effects model. Heterogeneity of studies were assessed using Cochrane Q test and I² test, while publication bias was evaluated using Egger’s test.

Results

Of the 1,645 articles identified through our searches, 46 cross-sectional studies matched our inclusion criteria, reported data from 29,968 school children of Africa. The pooled prevalence of intestinal protozoan parasites amongst African school children was 25.8% (95% CI: 21.2%-30.3%) with E. histolytica/ dispar (13.3%; 95% CI: 10.9%-15.9%) and Giardia spp. (12%; 95% CI: 9.8%-14.3%) were the most predominant pathogenic parasites amongst the study participants. While E. coli was the most common non-pathogenic protozoa (17.1%; 95% CI: 10.9%-23.2%).

Conclusions

This study revealed a relatively high prevalence of IPPs in school children, especially in northern and western Africa. Thus, poverty reduction, improvement of sanitation and hygiene and attention to preventive control measures will be the key to reducing protozoan parasite transmission.

Pathogenic intestinal protozoan parasites (IPPs) remain a major public health concern. Studies have documented that, the prevalence rates of protozoan infections are quite high in developing regions, particularly Africa and children are the primary victims. Despite numerous studies have been conducted on IPPs in school children in African countries, data on the burden of these infections in African school children have not yet been synthesised. This systematic review and meta-analysis was conducted to provide continent-wide prevalence of IPPs amongst African school children. Our study found that about 25.8% of the children had one or more species of intestinal protozoan parasites in their faecal specimens. E. histolytica/ dispar and Giardia spp. were the most predominant parasites amongst the study participants. The relatively high prevalence estimate of IPPs amongst African children and the considerable variation in the disease prevalence over the years, between and within countries and regions clearly indicates the needs to improve sanitation and hygiene, paying more attention to preventive control measures as well as poverty reduction which are the key to reducing protozoan parasite transmission.

Comparison of Three Real-Time PCR Assays for the Detection of Cyclospora cayetanensis in Stool Samples Targeting the 18S rRNA Gene and the hsp70 Gene

Diagnostic real-time PCR for the detection of Cyclospora cayetanensis in human stool samples has been applied for two decades. However, recent comparative assessments between in-house and commercial assays suggested room for improvement regarding the agreement of positive signals of the applied real-time PCRs. In order to assess the effect of the choice of the target sequence, 3 inhouse real time PCR assays targeting the 18S rRNA gene (n = 2, one of them later referred to as SSU rRNA gene assay to avoid confusion) and the hsp70 gene of C. cayetanensis were compared in a head-to-head comparison with 905 samples with high pretest probability for C. cayetanensis infections from Ghanaian HIV patients in a test comparison without a reference standard. Only slight agreement kappa of 0.095 was observed. In the assays targeting the SSU rRNA gene, the 18S rRNA gene, and hsp70, positive signals were recorded in 63, 45, and 0 instances, respectively, with latent class analysis-based estimation of sensitivity of 32.2%, 23.3%, 0% as well as of specificity of 99.7%, 99.9% and 100%, respectively. High cycle threshold values with an average of about 35 indicated low quantities of target DNA in the samples with similar Ct values in concordantly and discordantly positive samples. In conclusion, the study suggested target-gene-specific differences in the diagnostic accuracy of real-time PCR-based diagnosis of C. cayetanensis as well as an ongoing need for further standardization of this diagnostic approach.

Comprehensive review of conventional and state-of-the-art detection methods of Cryptosporidium

Cryptosporidium is a critical waterborne protozoan pathogen found in water resources that have been a major cause of death and serious illnesses worldwide, costing millions of dollars annually for its detection and treatment. Over the past several decades, substantial efforts have been made towards developing techniques for the detection of Cryptosporidium. Early diagnostic techniques were established based on the existing tools in laboratories, such as microscopes. Advancements in fluorescence microscopy, immunological, and molecular techniques have led to the development of several kits for the detection of Cryptosporidium spp. However, these methods have several limitations, such as long processing times, large sample volumes, the requirement for bulky and expensive laboratory tools, and the high cost of reagents. There is an urgent need to improve these existing techniques and develop low-cost, portable and rapid detection tools for applications in the water quality industry. In this review, we compare recent advances in nanotechnology, biosensing and microfluidics that have facilitated the development of sophisticated tools for the detection of Cryptosporidium spp.Finally, we highlight the advantages and disadvantages, of these state-of-the-art detection methods compared to current analytical methodologies and discuss the need for future developments to improve such methods for detecting Cryptosporidium in the water supply chain to enable real-time and on-site monitoring in water resources and remote areas.

High occurrence of Blastocystis sp. subtype 3 in individuals referred to medical laboratories in Kermanshah, Iran

Aim

The current study investigated the prevalence and genotypes of Blastocystis sp. in individuals who referred to medical laboratories in Kermanshah, Iran.

Background

Blastocystis sp. is a common intestinal protozoan found in humans and a wide range of animals, and it is involved in the development of gastrointestinal disorders.

Methods

A total of 950 stool samples were examined using the standard formalin-ether concentration technique. All specimens were cultured in Robinson xenic medium. Subsequently, DNA extraction and PCR amplification of subtype specific sequence-tagged site (STS) were conducted.

Results

Microscopic examination showed that 86 out of 950 samples (9.05%) were infected with Blastocystis sp. Subsequently, 33 of 86 positive samples were cultured and molecularly confirmed by conventional PCR, indicating six subtypes (ST1-ST6). Of note, ST3 (45.0%) was the predominant subtype, followed by ST1 (15.15%) and ST5 (12%).

Conclusion

Based on the current findings, ST3 was the most frequent subtype among all positive samples. Having a better understanding of Blastocystis sp. subtype distribution and risk factors would lead to improved preventive measures.

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.

Gut Microbiome Profiles in Colonizations with the Enteric Protozoa Blastocystis in Korean Populations

The influence of unicellular eukaryotic microorganisms on human gut health and disease is largely unexplored. Blastocystis species commonly colonize the gut, but their clinical significance and ecological role are unclear. We evaluated the effect of Blastocystis colonization on the fecal microbiota of Koreans. In total, 39 Blastocystis-positive and -negative fecal samples were analyzed. The fecal microbiome was assessed by targeting the V3–V4 region of the bacterial 16S ribosomal gene. Bacterial diversity was greater in the Blastocystis-positive than in the Blastocystis-negative group. The bacterial community structure and phylogenetic diversity differed according to the presence of Blastocystis. The mean proportions of Faecalibacterium species and Ruminococcaceae were larger in the Blastocystis-positive group, and that of Enterococcus species was larger in the Blastocystis-negative group. Linear discriminant analysis showed that Faecalibacterium, Prevotella 9, Ruminococcaceae UCG-002, Muribaculaceae, Rikenellaceae, Acidaminococcaceae, Phascolarctobacterium, and Ruminococcaceae UCG-005 were highly enriched in the Blastocystis-positive group, whereas Enterococcus hirae, Enterococcus faecalis, Enterococcus durans, Enterococcaceae, Lactobacillales, and Bacilli were highly abundant in the Blastocystis-negative group. Overall, our results enlighten the notion that Blastocystis colonization is associated with a healthy gut microbiota.

Commercial Simplex and Multiplex PCR Assays for the Detection of Intestinal Parasites Giardia intestinalis, Entamoeba spp., and Cryptosporidium spp.: Comparative Evaluation of Seven Commercial PCR Kits with Routine In-House Simplex PCR Assays

Nowadays, many commercial kits allowing the detection of digestive parasites by DNA amplification methods have been developed, including simplex PCR assays (SimpPCRa) allowing the identification of a single parasite, and multiplex PCR assays (MultPCRa) allowing the identification of several parasites at once. Thus, aimed at improving the diagnosis of intestinal protozoal infections, it is essential to evaluate the performances of these new tools. A total of 174 DNA samples collected between 2007 and 2017 were retrospectively included in this study. Performances of four commercial SimpPCRa (i.e., CerTest-VIASURE^TM) and three MultPCRa (i.e., CerTest-VIASURE^TM, FAST-TRACK-Diagnostics-FTD-Stool-Parasite^TM and DIAGENODE-Gastroenteritis/Parasite-panel-I^TM) were evaluated for the detection of Cryptosporidium spp., Entamoeba spp., and Giardia intestinalis in stool samples compared to our routinely used in-house SimpPCRa. Globally, the SimpPCRa showed better sensitivity/specificity for the detection of G. intestinalis, E. histolytica, E. dispar, and Cryptosporidium spp. (i.e., 96.9/93.6%; 100/100%; 95.5/100%; and 100/99.3%, respectively), compared to the three commercial MultPCRa tested. All in all, we showed that MultPCRa offer an interesting alternative for the detection of protozoans in stool samples depending on the clinical context.

Foodborne Parasites Dominate Current Parasitic Infections in Hunan Province, China

Great progress has been made in the prevention and treatment of human parasitic diseases in China over the past six decades, but parasitic diseases are still one of the most serious public health problems in the world. The specific prevalence of parasitic diseases varies in different provinces due to their geographical environment and the dietary habits of people. In this study, a total of 4,428 patients suspected to have parasitic infection by clinicians or themselves from January 1, 2016, to December 31, 2020 were recommended to our laboratory for further testing. In total, 5,246 samples including fecal, blood, and other body fluids were detected by etiological and immunological methods. Approximately 15.20% (673/4,428) of all suspected patients were infected by at least one species of parasite, and the overall positive rate of suspected patients from Hunan Province was 15.10% (594/3,933). A total of 18 species of parasites, namely, nematodes (4 species), trematodes (5 species), cestodes (4 species), protozoa (2 species), and medical arthropods (3 species), and 3 of them were imported parasites outside of Hunan Province. There are 9 species of foodborne parasites, accounting for 89.92% (464/516) of patients infected by one species of parasite. Common parasites in Hunan Province include plerocercoid, Paragonimus westermani, Clonorchis sinensis, cysticercus, Toxoplasma gondii, and Schistosoma japonicum. In this study, we found that the incidence of soilborne nematode infections has decreased significantly. However, foodborne parasites gradually become the main parasitic infections as well as multiple infections are becoming more common. Therefore, we should not only continue the prevention and control of soil-derived nematodes but also focus on the prevention and control of foodborne parasites in the future.

Diagnosis of human strongyloidiasis: Application in clinical practice

This review considers the advantages and disadvantages of parasitological techniques, methods of detecting antibodies and antigens, as well as molecular biology techniques in the diagnosis of human strongyloidiasis. In addition, it elucidates the potential of different techniques for rapid and effective detection of clinical cases, thus enabling early treatment and preventing fatal consequences of this helminthiasis.

Chronic diarrhea and parasitic infections: Diagnostic challenges

BACKGROUND

Diarrhea is among the top ten global causes of death. Chronic diarrhea may have destructive impact on physical and mental health of patients and is also associated with high risk of mortality in children. Parasitic intestinal infections remain an important cause of chronic diarrhea especially in the developing part of the world.

OBJECTIVE

To study the parasitic causes of chronic diarrhea and highlight the challenges faced in the diagnosis of chronic diarrhea caused due to parasitic infections.

CONTENT

Due to non-specific symptoms, insensitive available diagnostic techniques, asymptomatic carriage and transmission, recurrent infections in endemic areas, pose a challenge for diagnosis of the parasitic infections and thus delay the treatment. Conventional techniques like microscopy, though cheaper are not very sensitive. Advanced techniques like molecular methods are more sensitive but expensive and are not readily available in resource limited settings. Newer cost-effective diagnostic techniques with higher sensitivity and specificity are required to detect the infectious agent and for appropriate management.

Detection of six soil-transmitted helminths in human stool by qPCR- a systematic workflow

Soil-transmitted helminths (STH) infect up to one-quarter of the global population, with a significant associated disease burden. The main human STH are: Ancylostoma spp. and Necator americanus (hookworms); Ascaris lumbricoides, Trichuris trichiura, and Strongyloides stercoralis. The aim of this study was to establish a scalable system for stool STH multiplex quantitative real-time polymerase chain reactions (qPCR). Stool samples collected in Fiji and preserved in potassium dichromate were transferred to Melbourne at ambient temperature. Samples were washed to remove potassium dichromate and DNA was extracted with the Mini-Beadbeater-24 and a column-based kit. A SYBR green qPCR to detect the vertebrate mitochondrial gene was used as a DNA extraction control. Samples were tested using a probe-based multiplex qPCR targeting A. lumbricoides, T. trichiura and S. stercoralis, and in a second multiplex reaction to detect hookworms to the species level (A. duodenale, A. ceylanicum, N. americanus). An internal amplification control in both multiplex assays was included to prevent false-negative results due to PCR inhibitors. Samples were homogenised for a single cycle of 40 seconds to release STH DNA and washed stool was stored for up to 15 weeks at -30°C without compromising DNA. Our multiplex qPCR detected multiple species of STH without reduced sensitivity compared to singleplex. qPCR data from 40 stools was validated against STH-positive stools determined by microscopy. We have developed and validated an efficient and staged system for detecting six clinically important STH affecting humans that could be easily implemented without advanced automation in any qPCR-capable laboratory.

Molecular detection of Cystoisospora belli by single-run polymerase chain reaction in stool samples

INTRODUCTION

Cystoisospora belli (C. belli) is the only pathogenic species of the Cystoisospora genus responsible for severe diarrhea in immunocompromised patients. Most common microscopic method of diagnosis is less sensitive due to intermittent shedding of oocysts. We developed a new single-run polymerase chain reaction (PCR)-based diagnostic assay for C. belli.

METHODS

A new single-run PCR-based diagnostic assay was standardized for the detection of C. belli. Diagnostic reproducibility and repeatability of the PCR assay were evaluated. A cross-sectional analytical study was done on a total of 354 stool samples collected from 331 immunocompromised patients with diarrhea. All the stool samples were tested for the presence of oocysts of C. belli and were also tested by our new PCR assay for C. belli. Three of the representative PCR products were confirmed by sequencing. Fisher's exact test was used to compare the two proportions.

RESULTS

Microscopy detected C. belli in 11/354 (3.1%) of stool samples, and the new PCR-based assay detected C. belli in 16/354 (4.5%). The new single-run PCR-based assay detected C. belli in all the stool samples which were tested positive by microscopy and additionally detected C. belli in five stool samples. The developed PCR assay detected statistically significant proportion of C. belli (p < 0.001) as compared to microscopy. The 795 base pair PCR product from one microscopy positive stool sample and two microscopy negative stool samples were confirmed by sequencing.

CONCLUSION

Our newly developed single-run PCR-based detection assay for C. belli is robust and reproducible. It may be used for molecular diagnosis of cystoisosporiasis especially in transplant, pediatrics, and human immunodeficiency virus (HIV) positive patients.

Comparison of Three Real-Time PCR Assays Targeting the SSU rRNA Gene, the COWP Gene and the DnaJ-Like Protein Gene for the Diagnosis of Cryptosporidium spp. in Stool Samples

As qualified microscopy of enteric parasitoses as defined by high diagnostic accuracy is difficult to maintain in non-endemic areas due to scarce opportunities for practicing with positive sample materials, molecular diagnostic options provide less investigator-dependent alternatives. Here, we compared three molecular targets for the real-time PCR-based detection of Cryptosporidium spp. From a population of 1000 individuals comprising both Ghanaian HIV (human immunodeficiency virus) patients and military returnees after deployment in the tropics, stool samples were assessed for Cryptosporidium spp. by real-time PCR targeting the small subunit ribosomal RNA (SSU rRNA) gene, the Cryptosporidium oocyst wall (COWP) gene, and the DnaJ-like protein gene (DnaJ), respectively. In declining order, sensitivity of 100% for the SSU rRNA gene PCR, 90.0% for the COWP PCR and 88.8% for the DnaJ PCR, respectively, as well as specificity of 99.6% for the COWP PCR and 96.9% for both the SSU rRNA gene PCR and the DnaJ PCR, respectively, were recorded. Substantial agreement (kappa value 0.663) between the three assays was observed. Further, an accuracy-adjusted Cryptosporidium spp. prevalence of 6.0% was calculated for the study population. In conclusion, none of the assessed real-time PCR assays were associated with perfect test accuracy. However, a combination of highly sensitive SSU rRNA gene PCR for screening purposes and more specific COWP PCR for confirmatory testing should allow reliable diagnosis of Cryptosporidium spp. in stool samples even in low prevalence settings.

Validation and maintaining laboratory developed molecular tests compliant with ISO15189 for diagnosis of intestinal parasitic infections

INTRODUCTION

Although, in the past few decades molecular diagnostics of parasitic infections have been accepted as first-line diagnostics, laboratories tend to be reluctant of introducing nucleic acid based tests as they dread the validation of laboratory developed tests (LDTs) compliant with ISO1589.

AREAS COVERED

This paper describes how to set tailor-made performance characteristics for the validation of laboratory developed tests (LDTs) for the molecular diagnosis of intestinal parasitic infections complying with the ISO 15189 guidelines. Then, just as important, maintaining these tests by daily monitoring, external quality assessment schemes, and reassessment of the test set-up.

EXPERT OPINION

Tailoring performance characteristics for the validation of LDTs defining criteria that make sense and actually leading to a process of continuous quality improvement in the day-to-day practice of a diagnostic laboratory. It is essential or even obligatory to modify these characteristics, skip, or to add additional characteristics based on personal or changing insights fitted for a specific setting.

Comparison of Two Real-Time PCR Assays Targeting Ribosomal Sequences for the Identification of Cystoisospora belli in Human Stool Samples

Cystoisospora (C.) belli is a coccidian parasite associated with acute or chronic gastroenteritis in immunocompromised patients. Dissatisfactory sensitivity of microscopy as the diagnostic standard approach has been described. Here, we comparatively evaluated two real-time PCRs targeting ribosomal RNA gene sequences of C. belli in stool in a test comparison without a reference standard applying latent class analysis. Therefore, 1000 stool samples from Ghanaian HIV (human immunodeficiency virus) patients (n = 905) as well as military returnees from the tropics (n = 95) were assessed by both assays in parallel. After the exclusion of 33 samples showing PCR inhibition, 29 and 33 positive results were recorded with the 5.8S rRNA gene/ITS-2 sequence PCR and the ITS-2 sequence PCR, respectively, resulting in an accuracy-adjusted prevalence of 3.2%. Nearly perfect agreement between both assays was indicated by Fleiss’ kappa of 0.933 with sensitivity and specificity of 92.8% and 100% as well as 100% and 99.8% for the 5.8S rRNA gene/ITS-2 sequence PCR and the ITS-2 sequence PCR, respectively. Both assays proved to be suitable for the diagnosis of C. belli in human stool samples with slightly better sensitivity of the ITS-2 sequence assay, while the 5.8S rRNA gene/ITS-2 sequence PCR may be considered for confirmatory testing.

Strongyloides stercoralis infestation in a pediatric patient

Strongyloidiasis is a parasitic disease, very rare in countries like Spain, caused by the Strongyloides stercoralis nematode. We present a case of a 5-year-old patient from Ecuador who came to the Emergency Department due to fever, colicky abdominal pain, watery diarrhea, and occasional vomiting of several days of evolution. In laboratory studies, a marked leukocytosis with eosinophilia stands out, for which reason a microscopic study of the stool was carried out where larval forms compatible with Strongyloides stercoralis were observed. The diagnostic strategy of parasitic infection in developed countries is highly influenced by the low prevalence and diversity of the parasitic species, causing the diagnosis, on many occasions, to be a challenge. In the presence of eosinophilia and abdominal symptoms, it is recommended to orient the diagnosis towards a possible infection of parasitic origin to make an early diagnosis of the infection and avoid possible serious complications.

Epidemiological and clinical study of microsporidiosis in French kidney transplant recipients from 2005 to 2019: TRANS-SPORE registry

INTRODUCTION

Microsporidiosis is an emerging opportunistic infection in renal transplantation (RT) recipients. We aimed to describe its clinical presentation and treatment.

MATERIALS AND METHODS

We collected microsporidiosis cases identified in RT recipients between 2005 and 2019 in six French centers from the Crystal, Divat and Astre prospective databases.

RESULTS

We report 68 RT recipients with intestinal microsporidiosis; the patients were predominantly male (61.8%), with a median age of 58 (46-69) years. Infection occurred at a median time of 3 (0.8-6.8) years posttransplant. Only Enterocytozoon bieneusi was found. Microsporidiosis manifested as diarrhea (98.5% of patients) with weight loss (72.1%) and acute renal injury (57.4%) without inflammatory biological parameters. The therapeutic approaches were no treatment (N = 9), reduction of the immunosuppressive regimen (∆IS) (N = 22), fumagillin alone (N = 9), fumagillin and ∆IS (N = 19), and albendazole or nitazoxanide and ∆IS (N = 9). Overall clinical remission was observed in 60 patients (88.2%). We observed no acute kidney rejection, renal transplant failure, or death within 6 months after microsporidiosis.

CONCLUSION

E. bieneusi is an underestimated opportunistic pathogen in RT recipients, and infection with E. bieneusi leads to diarrhea with important dehydration and acute renal injury. The treatment is based on the reduction of the immunosuppressive regimen and the administration of fumagillin if available.

Diagnóstico molecular de parasitosis intestinales

Infections causes by parasites of the gastrointestinal tract are a global public health problem. In industrialised countries, their particular epidemiological (low general prevalence of enteroparasites), economic (high labour costs) and clinical characteristics (constant increase in the number of samples and diagnostic determinations to be performed) have led molecular techniques to progressively replace conventional microscopy as the first-line diagnostic method of these pathogens in modern clinical laboratories. PCR-based techniques, particularly those developed for the simultaneous detection of the various agents that can cause the same infectious disease (syndromic diagnosis), already represent a cost-effective option that allow process automisation, workflow optimisation, and comparison of results among different laboratories, and facilitate accreditation of diagnostic procedures. This review clearly and concisely discusses the current situation of the molecular diagnosis of the main species of intestinal parasites in humans, particularly the enteric protozoans causing diarrhoea (Cryptosporidium spp., Giardia duodenalis, Entamoeba histolytica), the most important members the Microsporidia phyla (Enterocytozoon bieneusi) and Stramenopiles phyla (Blastocystis sp.), as well as the helminths transmitted by soil (Ancylostoma spp., Ascaris lumbricoides, Necator americanus, Strongyloides stercoralis and Trichuris trichiura) and food (Anisakis spp., Clonorchis sinensis, Fasciola spp., Taenia solium, and Trichinella spiralis). Special attention is paid to the description of available techniques and formats, to their diagnostic benefits and the most widely used genetic markers for their detection, both in clinical laboratories and genotyping in referral and research centres.

Serological assays for the diagnosis of Strongyloides stercoralis infection: a systematic review and meta-analysis of diagnostic test accuracy

The standard method for the diagnosis of Strongyloides stercoralis, stool examinations, is inconvenient and, therefore, serological methods have been proposed. This study aimed to evaluate the accuracy of serological assays for the diagnosis of strongyloidiasis using a systematic review and meta-analysis model. Four electronic databases were reviewed. We used a random effects model and 95% CIs to determine the overall sensitivity, specificity and diagnostic odds ratio (DOR). Heterogeneity was intended with Cochran Q χ2 test and I2 statistic. The accuracy of serological assays resulted in a sensitivity of 71.7% (95% CI: 56.07 to 83.4%), a specificity of 89.9% (95% CI: 80.8 to 94.9%) and a DOR of 22.5 (95% CI: 10.8 to 46.9). The forest plot showed high heterogeneity regarding sensitivity (I2=90.4%, 95% CI: 87.4 to 93.3%; Q=228.1, p=0.000) and specificity (I2=98.9%, 95% CI: 98.8 to 99.1%; Q=2066.4, p=0.000). Fagan's nomogram showed that the probability of someone having the infection and with a positive test result was 49%. Deeks' funnel plots showed no evidence of potential publication bias for the studies (p=0.26). The current review suggests that serological techniques have acceptable sensitivity and specificity and therefore can be recommended for the screening of S. stercoralis infection.

Evaluation of Artesunate-mefloquine as a Novel Alternative Treatment for Schistosomiasis in African Children (SchistoSAM): protocol of a proof-of-concept, open-label, two-arm, individually-randomised controlled trial

INTRODUCTION

Alternative drugs and diagnostics are needed for the treatment and control of schistosomiasis. The exclusive use of praziquantel (PZQ) in mass drug administration programmes may result in the emergence of drug resistance. PZQ has little activity against Schistosoma larvae, thus reinfection remains a problem in high-risk communities. Furthermore, the insufficient sensitivity of conventional microscopy hinders therapeutic response assessment. Evaluation of artesunate-mefloquine (AM) as a Novel Alternative Treatment for Schistosomiasis in African Children (SchistoSAM) aims to evaluate the safety and efficacy of the antimalarial combination artesunate-mefloquine, re-purposed for the treatment of schistosomiasis, and to assess the performance of highly sensitive novel antigen-based and DNA-based assays as tools for monitoring treatment response.

METHODS AND ANALYSIS

The SchistoSAM study is an open-label, two-arm, individually randomised controlled non-inferiority trial, with a follow-up of 48 weeks. Primary school-aged children from the Richard Toll district in northern Senegal, an area endemic for Schistosoma mansoni and Schistosoma haematobium, are allocated to the AM intervention arm (3-day courses at 6-week intervals) or the PZQ control arm (single dose of 40 mg/kg). The trial's primary endpoints are the efficacy (cure rate (CR), assessed by microscopy) and safety (frequency and pattern of drug-related adverse events) of one AM course versus PZQ at 4 weeks after treatment. Secondary endpoints include (1) cumulative CR, egg reduction rate and safety after each additional course of AM, and at weeks 24 and 48, (2) prevalence and severity of schistosomiasis-related morbidity and (3) malaria prevalence, incidence and morbidity, both after 24 and 48 weeks. CRs and intensity reduction rates are also assessed by antigen-based and DNA-based diagnostic assays, for which performance for treatment monitoring is evaluated.

ETHICS AND DISSEMINATION

Ethics approval was obtained both in Belgium and Senegal. Oral assent from the children and signed informed consent from their legal representatives was obtained, prior to enrolment. The results will be disseminated in peer-reviewed journals and at international conferences.

TRIAL REGISTRATION NUMBER

NCT03893097; pre-results.

Parasitic Intestinal Protists of Zoonotic Relevance Detected in Pigs by Metabarcoding and Real-Time PCR

Several parasite species are shared between humans and pigs. We explored the application of next-generation sequencing-based metabarcoding supplemented with real-time PCR to fecal DNAs from 259 samples from 116 pigs in Denmark to detect and differentiate single-celled intestinal parasites of zoonotic relevance. Enterocytozoon bieneusi, Balantioides coli, and Giardia duodenalis were observed in 34/37 (92%), 148/259 (57%), and 86/259 (33%) samples, respectively. Entamoeba polecki ST1, E. polecki ST3, and Entamoeba hartmanni were detected in 104/259 (40%), 161/259 (62%), and 8/259 (3%) samples, respectively. Metabarcoding and real-time PCR detected Cryptosporidium in 90/259 (35%) and 239/259 (92%) of the samples, respectively, with Cryptosporidium suis and Cryptosporidium scrofarum observed in nearly equal proportions. Blastocystis subtypes 1, 3, 5, and 15 were found in 72 (28%), 6 (2%), 176 (68%), and 36 (14%) of 259 samples, respectively. Iodamoeba was identified in 1/259 samples (<1%), while none of 37 tested samples was positive for Dientamoeba fragilis. Our results illustrate how metabarcoding exemplifies a 'one-fits-many' approach to detecting intestinal single-celled parasites in feces supplemented with real-time PCR for selected parasites. Using metabarcoding with pathogen-specific assays may help detect emerging and previously underdetected pathogens and further elucidate the role of micro-eukaryotic parasites in human and animal health and disease.

Full pathogen characterisation: species identification including the detection of virulence factors and antibiotic resistance genes via multiplex DNA-assays

Antibiotic resistances progressively cause treatment failures, and their spreading dynamics reached an alarming level. Some strains have already been classified as highly critical, e.g. the ones summarised by the acronym ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter spp.). To restrain this trend and enable effective medication, as much information as possible must be obtained in the least possible time. Here, we present a DNA microarray-based assay that screens for the most important sepsis-relevant 44 pathogenic species, 360 virulence factors (mediate pathogenicity in otherwise non-pathogenic strains), and 409 antibiotic resistance genes in parallel. The assay was evaluated with 14 multidrug resistant strains, including all ESKAPE pathogens, mainly obtained from clinical isolates. We used a cost-efficient ligation-based detection platform designed to emulate the highly specific multiplex detection of padlock probes. Results could be obtained within one day, requiring approximately 4 h for amplification, application to the microarray, and detection.

Intestinal protozoan infections shape fecal bacterial microbiota in children from Guinea-Bissau

Intestinal parasitic infections, caused by helminths and protozoa, are globally distributed and major causes of worldwide morbidity. The gut microbiota may modulate parasite virulence and host response upon infection. The complex interplay between parasites and the gut microbiota is poorly understood, partly due to sampling difficulties in remote areas with high parasite burden. In a large study of children in Guinea-Bissau, we found high prevalence of intestinal parasites. By sequencing of the 16S rRNA genes of fecal samples stored on filter paper from a total of 1,204 children, we demonstrate that the bacterial microbiota is not significantly altered by helminth infections, whereas it is shaped by the presence of both pathogenic and nonpathogenic protozoa, including Entamoeba (E.) spp. and Giardia (G.) lamblia. Within-sample diversity remains largely unaffected, whereas overall community composition is significantly affected by infection with both nonpathogenic E. coli (R2 = 0.0131, P = 0.0001) and Endolimax nana (R2 = 0.00902, P = 0.0001), and by pathogenic E. histolytica (R2 = 0.0164, P = 0.0001) and G. lamblia (R2 = 0.00676, P = 0.0001). Infections with multiple parasite species induces more pronounced shifts in microbiota community than mild ones. A total of 31 bacterial genera across all four major bacterial phyla were differentially abundant in protozoan infection as compared to noninfected individuals, including increased abundance of Prevotella, Campylobacter and two Clostridium clades, and decreased abundance of Collinsella, Lactobacillus, Ruminococcus, Veillonella and one Clostridium clade. In the present study, we demonstrate that the fecal bacterial microbiota is shaped by intestinal parasitic infection, with most pronounced associations for protozoan species. Our results provide insights into the interplay between the microbiota and intestinal parasites, which are valuable to understand infection biology and design further studies aimed at optimizing treatment strategies.

Sandwich dot-immunogold filtration assay (DIGFA) for specific immunodiagnosis of active neuroangiostrongyliasis

Serological tests may yield false-negative results for specific antibodies detection before or at the early seroconversion phase. Tests that detect circulating antigens of Angiostrongylus cantonensis would therefore be of value in diagnosis to distinguish current or past infection. Here, a quick, easy to perform, portable and inexpensive diagnostic device for detection of 31-kDa A. cantonensis specific antigens had been developed. This sandwich dot-immunogold filtration assay (AcDIGFAAg), for detecting active angiostrongyliasis was produced using anti-A. cantonensis polyclonal antibody dotted on the nitrocellulose membrane as a capture agent and colloidal gold-labelled anti-31 kDa A. cantonensis antibody as a detection agent. A well-defined pink dot, indicating positivity, was seen readily by naked eye within 10-15 min. The AcDIGFAAg detected A. cantonensis-specific antigens in cerebrospinal fluid samples from 4 out of 10 serologically confirmed angiostrongyliasis cases and 2 out of 5 suspected cases with negative anti-A. cantonensis antibodies. Among the 19 patient sera with A. cantonensis infection, 2 showed positive reaction by AcDIGFAAg. No positive AcDIGFAAg reaction was observed in all the serum samples with other parasitic diseases, and the healthy controls. The present 'AcDIGFAAg' enables rapid qualitative detection of the specific 31-kDa antigens of A. cantonensis in clinical samples with potential for application even under resource-limited settings.