Multiplex PCR detection of Cryptosporidium sp, Giardia lamblia and Entamoeba histolytica directly from dried stool samples from Guinea-Bissauan children with diarrhoea

Development of a new multiplex PCR to detect fecal coccidian parasite

BACKGROUND

Cryptosporidium spp., Cystoisospora belli and Cyclospora cayetanensis are common intestinal coccidian parasites causing gastroenteritis. The clinical presentation caused by each parasite is indistinguishable from each other. Uniplex polymerase chain reaction (PCR) for these three groups of intestinal coccidian parasites was developed by us in our laboratory. Thereafter, we planned to develop a single-run multiplex polymerase chain reaction (mPCR) assay to detect Cryptosporidium spp., C. belli and C. cayetanensis simultaneously from a stool sample and described it here as coccidian mPCR.

METHODS

New primers for C. belli and C. cayetanensis were designed and uniplex PCRs were standardized. The coccidian mPCR was standardized with known positive DNA control isolates. It was validated with 58 known positive and 58 known negative stool samples, which were previously identified by uniplex PCR.

RESULTS

The coccidian mPCR was standardized with earlier primers designed by us for Cryptosporidium spp. and C. cayetanensis, and a newly designed primer for the internal transcribed spacer-1 (ITS-1) gene for C. belli. The coccidian mPCR was 92.1% sensitive for Cryptosporidium spp., and 100% sensitive for C. belli and C. cayetanensis each, when tested on 116 known samples. It was 100% specific for all intestinal coccidian parasites. Two representative PCR products of the newly designed ITS-1 primer for C. belli were sequenced and submitted to the GenBank, which best match with the sequences of C. belli.

CONCLUSION

A highly sensitive, specific, cost-effective, indigenous, single-run coccidian mPCR has been developed, which can simultaneously detect Cryptosporidium spp., C. belli and C. cayetanensis.

Gastrointestinal parasites in Africa: A review

Data on human gastrointestinal parasites (GIP) infections in the african sub-regions and countries are mainly lacking in terms of prevalence and population stratification by afflicted age group, symptomatology, multi-parasitism, and diagnostic methods. This study aims to describe the GIP reported in african countries and discuss the extent of the burden in the african context. Only 68.42% (39/57) of african countries reported human cases of GIP with helminths (45%, CI: 40-50%, I²: 99.79%) as the predominant parasitic group infecting the african population. On a regional scale, Central Africa had the highest pooled prevalence for GIP (43%, CI: 32-54%, I²: 99.74%), while the Central African Republic led all countries with a pooled prevalence of 90% (CI: 89-92%, I²: 99.96%). The vulnerable population (patients who are minorities, children, old, poor, underfunded, or have particular medical conditions) was the most affected (50%, CI: 37-62%, I²: 99.33%), with the predominance of GIP in the 6 to <20 years age group (48%, CI: 43-54%, I²: 99.68%). Reports on multi-parasitism (44%, CI: 40-48%, I²: 99.73%) were almost double the reports of single infections (43%, CI: 27-59%, I²: 99.77%) with combined molecular and non-molecular techniques demonstrating the best performance for GIP identification. The current review spans more than 40 years of GIP reports from the african continent. Geographical characteristics, environmental factors, habits of its inhabitants, and their health status play a crucial role in GIP modulation and behaviour in its captive hosts. Strategies for regular and enhanced surveillance, policy formation, and high-level community awareness are necessary to identify the true incidence in Africa and the transmission of the pathogens via water and food.

First report of Giardia duodenalis assemblage F in humans and dogs in southern Brazil

The present study aimed to molecularly characterize Giardia duodenalis from stool samples of humans, dogs, and cats. Molecular analyses were performed on 59 samples that tested positive for G. duodenalis on coproparasitological examinations. After extraction, the samples were first tested by nested polymerase chain reaction (n-PCR) analysis of the SSU-rRNA gene, and for the samples that were positive, the β-giardin, TPI, and GDH genes were analyzed. The amplicons obtained in the n-PCR of the β-giardin gene were subjected to PCR-restriction length polymorphism (RFLP) analysis and subsequent digestion with the enzyme HaeIII to differentiate the assemblages. Seven (11.8 %), 34 (57.7 %), and 18 (30.5 %) out of 59 samples were from humans, dogs, and cats, respectively. Nested-PCR results showed that 49.2 % (29/59) of samples were positive for the SSU-rRNA gene, with 42.9 % (3/7) of humans, 55.9 % (19/34) of dogs, and 38.9 % (7/18) of catsve. Of the other genes analyzed, β-giardin was amplified most frequently, in 34.5 % (10/29) of samples, followed by GDH in 27.6 % (8/29) of samples, and TPI in 10.3 % (3/29) of samples. Only one sample from a dog showed the amplification of all genes. PCR-RFLP analysis showed assemblage F in a human, dog, and cat samples; and assemblage C and D in dog samples. This is the first description of assemblage F in humans from Brazil and the first description of assemblage F in dogs. Further studies are needed to verify the frequency with which these infections occur, and provide information that will contribute to the molecular epidemiological understanding of giardiasis.

Acute Infectious Gastroenteritis: The Causative Agents, Omics-Based Detection of Antigens and Novel Biomarkers

Acute infectious gastroenteritis (AGE) is among the leading causes of mortality in children less than 5 years of age worldwide. There are many causative agents that lead to this infection, with rotavirus being the commonest pathogen in the past decade. However, this trend is now being progressively replaced by another agent, which is the norovirus. Apart from the viruses, bacteria such as Salmonella and Escherichia coli and parasites such as Entamoeba histolytica also contribute to AGE. These agents can be recognised by their respective biological markers, which are mainly the specific antigens or genes to determine the causative pathogen. In conjunction to that, omics technologies are currently providing crucial insights into the diagnosis of acute infectious gastroenteritis at the molecular level. Recent advancement in omics technologies could be an important tool to further elucidate the potential causative agents for AGE. This review will explore the current available biomarkers and antigens available for the diagnosis and management of the different causative agents of AGE. Despite the high-priced multi-omics approaches, the idea for utilization of these technologies is to allow more robust discovery of novel antigens and biomarkers related to management AGE, which eventually can be developed using easier and cheaper detection methods for future clinical setting. Thus, prediction of prognosis, virulence and drug susceptibility for active infections can be obtained. Case management, risk prediction for hospital-acquired infections, outbreak detection, and antimicrobial accountability are aimed for further improvement by integrating these capabilities into a new clinical workflow.

Prevalence of diarrhoeal pathogens among children under five years of age with and without diarrhoea in Guinea-Bissau

BACKGROUND

Childhood diarrhoea, a major cause of morbidity and mortality in low-income regions, remains scarcely studied in many countries, such as Guinea-Bissau. Stool sample drying enables later qPCR analyses of pathogens without concern about electricity shortages.

METHODS

Dried stool samples of children under five years treated at the Bandim Health Centre in Bissau, Guinea-Bissau were screened by qPCR for nine enteric bacteria, five viruses, and four parasites. The findings of children having and not having diarrhoea were compared in age groups 0-11 and 12-59 months.

RESULTS

Of the 429 children- 228 with and 201 without diarrhoea- 96.9% and 93.5% had bacterial, 62.7% and 44.3% viral, and 52.6% and 48.3% parasitic pathogen findings, respectively. Enteroaggregarive Escherichia coli (EAEC; 60.5% versus 66.7%), enteropathogenic E. coli (EPEC; 61.4% versus 62.7%), Campylobacter (53.2% versus 51.8%), and enterotoxigenic E. coli (ETEC; 54.4% versus 44.3%) were the most common bacterial pathogens. Diarrhoea was associated with enteroinvasive E. coli (EIEC)/Shigella (63.3%), ETEC (54.4%), astrovirus (75.0%), norovirus GII (72.6%) and Cryptosporidium (71.2%). The only pathogen associated with severe diarrhoea was EIEC/Shigella (p<0.001). EAEC was found more frequent among the infants, and EIEC/Shigella, Giardia duodenalis and Dientamoeba fragilis among the older children.

CONCLUSIONS

Stool pathogens proved common among all the children regardless of them having diarrhoea or not.

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.

Comparative Performance of Eight PCR Methods to Detect Cryptosporidium Species

Diagnostic approaches based on PCR methods are increasingly used in the field of parasitology, particularly to detect Cryptosporidium. Consequently, many different PCR methods are available, both “in-house” and commercial methods. The aim of this study was to compare the performance of eight PCR methods, four “in-house” and four commercial methods, to detect Cryptosporidium species. On the same DNA extracts, performance was evaluated regarding the limit of detection for both C. parvum and C. hominis specificity and the ability to detect rare species implicated in human infection. Results showed variations in terms of performance. The best performance was observed with the FTD^® Stool parasites method, which detected C. parvum and C. hominis with a limit of detection of 1 and 10 oocysts/gram of stool respectively; all rare species tested were detected (C. cuniculus, C. meleagridis, C. felis, C. chipmunk, and C. ubiquitum), and no cross-reaction was observed. In addition, no cross-reactivity was observed with other enteric pathogens. However, commercial methods were unable to differentiate Cryptosporidium species, and generally, we recommend testing each DNA extract in at least triplicate to optimize the limit of detection.

Bacterial, viral and parasitic pathogens analysed by qPCR: Findings from a prospective study of travellers' diarrhoea

BACKGROUND

The diagnostics of travellers' diarrhoea (TD) has been revolutionised by multiplex qPCR assays. While mostly of bacterial aetiology, viruses and parasites account for the disease among 10-20% of travellers. Despite this, prospective studies applying qPCR assays remain scarce that cover not only bacteria, such as the various diarrhoeagenic Escherichia coli (DEC), but also viral and parasitic pathogens.

METHOD

We analysed by qPCR pre- and post-travel stool samples of 146 Finnish travellers for bacterial, viral and parasitic pathogens: enteropathogenic (EPEC), enteroaggregative (EAEC), enterotoxigenic (ETEC), enterohaemorrhagic (EHEC), and enteroinvasive (EIEC) E. coli; Shigella, Campylobacter, Salmonella, Yersinia and Vibrio cholerae; norovirus G1 and G2, rotavirus, enteroviruses, and sapovirus; and Giardia lamblia, Entamoeba histolytica, and Cryptosporidium. Symptoms and medication data during travel were collected by questionnaires.

RESULTS

We detected bacterial pathogens in 102/146 samples (69.9%; EAEC, EPEC, ETEC most common), viral ones in 13 (8.9%; norovirus most common), and parasitic ones in one (0.7%; Giardia). Noroviruses were associated with severe symptoms (23.5% versus non-severe 4.9%). In the TD group, 41.7% (5/12) of those with viral pathogens (vs. 13.3%; 11/83 without) took antibiotics.

CONCLUSION

Viral pathogens, particularly noroviruses, prevail in severe TD. The symptoms of viral disease are often severe and lead to unwarranted use of antibiotics.

A Real-Time PCR Assay for Simultaneous Detection and Differentiation of Four Common Entamoeba Species That Infect Humans

There are over 40 species within the genus Entamoeba, eight of which infect humans. Of these, four species (Entamoeba histolytica, E. dispar, E. moshkovskii, and E. bangladeshi) are morphologically indistinguishable from each other, and yet differentiation is important for appropriate treatment decisions. Here, we developed a hydrolysis probe-based tetraplex real-time PCR assay that can simultaneously detect and differentiate these four species in clinical samples. In this assay, multicopy small-subunit (SSU) ribosomal DNA (rDNA) sequences were used as targets. We determined that the tetraplex real-time PCR can detect amebic DNA corresponding to as little as a 0.1 trophozoite equivalent of any of these species. We also determined that this assay can detect E. histolytica DNA in the presence of 10-fold more DNA from another Entamoeba species in mixed-infection scenarios. With a panel of more than 100 well-characterized clinical samples diagnosed and confirmed using a previously published duplex real-time PCR (capable of detecting E. histolytica and E. dispar), our tetraplex real-time PCR assay demonstrated levels of sensitivity and specificity comparable with those demonstrated by the duplex real-time PCR assay. The advantage of our assay over the duplex assay is that it can specifically detect two additional Entamoeba species and can be used in conventional PCR format. This newly developed assay will allow further characterization of the epidemiology and pathogenicity of the four morphologically identical Entamoeba species, especially in low-resource settings.

One-Step Surface Modification to Graft DNA Codes on Paper: The Method, Mechanism, and Its Application

Glass slides have been widely used for DNA immobilization in DNA microarray and numerous bioassays for decades, whereas they are faced with limitations of low probe density, time-consuming modification steps, and expensive instruments. In this work, a simple one-step surface modification method using 3-aminopropyl trimethoxysilane (APTMS) has been developed and applied to graft DNA codes on paper. Higher DNA immobilization efficiency was obtained in comparison with that in a conventional method using glass slides. Fluorescence detection, X-ray photoelectron spectroscopy (XPS), infrared spectra (FT-IR), and pH influence studies were employed to characterize the surface modification and subsequent DNA immobilization, which further reveals a mechanism in which this method lies in ionic interactions between the positively charged APTMS-modified paper surface and negatively charged DNA probes. Furthermore, an APTMS-modified paper-based device has been developed to demonstrate application in low-cost detection of a foodborne pathogen, Giardia lamblia, with high sensitivity (the detection limit of 22 nM) and high specificity. Compared with conventional methods using redundant cross-linking reactions, our method is simpler, faster, versatile, and lower-cost, enabling broad applications of paper-based bioassays especially for point-of-care detection in resource-poor settings.

Update on the major imported protozoan infections in travelers and migrants

Globalization has contributed to the emergence of specific parasitic diseases in novel geographical areas, and in these regions, these infections in travelers and immigrants may cause a considerable burden of disease. Timely diagnosis and treatment of protozoan infections to decrease mortality and prevent associated complications are essential. In this respect, the increased availability of specific DNA-detection procedures has improved the diagnosis of many imported parasitic infections. Travelers and immigrants with associated comorbidities or immunosuppression may pose a special challenge regarding management. An updated review of the main protozoan infections in mobile populations (malaria, Chagas disease, leishmaniasis, enteric protozoan infections) is provided, focusing on the changing epidemiology of these diseases, recent developments in diagnosis and management and the possibility of local transmission of imported infections.

New Tools to Test Stool: Managing Travelers' Diarrhea in the Era of Molecular Diagnostics

Travelers' diarrhea affects up to 60% of visitors to tropical and subtropical regions. Although symptoms are generally self-limited, some infections are associated with significant morbidity and occasional mortality. Newer molecular diagnostic techniques allow for highly sensitive, specific, and expeditious testing of a wide range of potential pathogens. Identification of the causative pathogen of travelers' diarrhea allows for targeted therapy and management and a reduction in empiric broad-spectrum coverage.

Whatman Protein Saver Cards for Storage and Detection of Parasitic Enteropathogens

Current methods to identify the etiology of diarrhea require laboratory facilities for storage of pathogens, which is often challenging in low-resource settings. This study evaluated the efficacy of a low-cost method for preserving stool specimens for the detection of parasitic enteropathogens using Whatman 903 protein saver cards (Sigma-Aldrich, St. Louis, MO). Stool samples known to be positive by multiplex real-time polymerase chain reaction for Giardia lamblia, Cryptosporidium spp., and Entamoeba histolytica parasites were preserved on 232 Whatman cards. DNA was then extracted from cards using Chelex and Qiagen extraction protocols, and tested for these parasites using multiplex real-time PCR. We included stool samples known to have a higher parasite load (cycle threshold [ct]-value < 30) and those with a lower parasite load (ct values 30-35). Sensitivities and specificities were determined using DNA extracted directly from whole stool samples using Qiagen kits (QIAGEN, Hilden, Germany). For whole stool samples with ct values < 30, preserved directly on Whatman 903 protein saver cards for Giardia analysis, the sensitivity was 100% for both Qiagen and Chelex DNA extraction. For E. histolytica, this was 100% for sensitivity for Qiagen and 80% for Chelex DNA extractions, and for Cryptosporidium, this was 80% for Qiagen and 50% for Chelex DNA extraction. The specificity was 100% for all parasites for all extraction procedures. Given the high sensitivity for stool samples with higher parasite loads, we recommend the use of the Whatman 903 protein saver card for preserving fecal specimens for the analysis of Giardia and E. histolytica using Qiagen DNA extractions in low-resource settings.

Prevalence and potential risk factors for gastrointestinal parasitic infections in children in urban Bissau, Guinea-Bissau

BACKGROUND

Gastrointestinal (GI) parasitic infections cause significant morbidity and mortality in tropical and subtropical countries. We aimed to investigate the prevalence of GI parasitic infections in children from Bissau, Guinea-Bissau and to identify the possible risk factors for these infections.

METHODS

We performed an observational study on two comparable cohorts of children 2-15 y of age: one study covering health care-seeking children (n=748) and one study covering children from the background population (n=851). A total of 1274 faecal samples from the two cohorts were investigated for parasites by microscopy and the risk factors for infection were identified by logistic regression.

RESULTS

Intestinal parasitic infections were found in 54.8% of health care-seeking children and 55.5% of children from the background population. Helminth infections were more common among health care-seeking children and were mainly due to hookworms. Pathogenic protozoa included Entamoeba histolytica/dispar and Giardia lamblia. The risk factors for infections included increasing age, household crowding and poor sanitation and water supply.

CONCLUSIONS

We found a high prevalence of intestinal parasites among both health care-seeking children and children from the background population. Compared with previous studies, we found a decreasing prevalence of intestinal helminths. This study further identifies potential risk factors for infections, including inadequate sanitation and water supply.

Molecular epidemiology of Giardia and Cryptosporidium infections - What's new?

New information generated since 2016 from the application of molecular tools to infections with Giardia and Cryptosporidium is critically summarised. In the context of molecular epidemiology, nomenclature, taxonomy, in vitro culture, detection, zoonoses, population genetics and pathogenicity, are covered. Whole genome sequencing has had the greatest impact in the last three years. Future advances will provide a much better understanding of the zoonotic potential of both parasites, their diversity and how this is linked to pathogenesis in different hosts.

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

BACKGROUND

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

RESULTS

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

CONCLUSION

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

Cryptosporidiosis: A zoonotic disease concern

Cryptosporidiosis is considered to be a crucial zoonotic disease caused by worldwide distributing parasitic protozoa called Cryptosporidium spp. Cryptosporidiosis becomes a major public health and veterinary concern by affecting in human and various host range species of animals. Essentially, its importance of infection is increasing because of the high incidence in young children, immunocompromised persons, or immunodeficiency syndrome patients, especially in HIV/AIDS, and it is also one of the most causes of mortality in those patients who infected with Cryptosporidium spp. as well as young animals. All domestic animal, livestock, wildlife, and human can be potential reservoirs that contribute Cryptosporidium spp. to food and surface waters and transmitted to other hosts through fecal-oral route. The oocyst stage of Cryptosporidium spp. can remain infective and resistant to various environmental exposure and also resistant to many general disinfecting agents including chlorination which normally used in water treatment. Therefore, the understanding of these zoonotic pathogens is very essential in both animal and human health. This review focuses on the biology, life cycle, transmission, diagnosis, treatment, prevention, and control of this protozoan infection to emphasize and remind as the significant One Health problem.