Detection and quantification of soil-transmitted helminths in environmental samples: A review of current state-of-the-art and future perspectives

ASCARIS SUUM EGG RECOVERY FROM SLUDGE SAMPLES AFTER PHASE EXTRACTION

Some helminth test methods for sanitation samples include a phase extraction step to reduce lipid content and final pellet size before microscopy. Hydrophilic and lipophilic solutions are used to create 2 phases, with a plug of organic material or debris in between, whilst eggs are supposedly compacted at the bottom of the test tube. We tested 10% formalin, acetoacetic buffer, and acid alcohol as the hydrophilic solutions, and ethyl acetate and diethyl ether as the lipophilic solvents for egg recoverability from water, primary sludge, and fatty sludge. Normally, the supernatant and debris plug are discarded and the sedimented pellet of eggs is microscopically examined. We, however, also collected the entire supernatant plus debris plug to determine where eggs were possibly lost. We found that eggs were lost when samples were extracted with 10% formalin + ethyl acetate, 10% formalin + diethyl ether, acetoacetic buffer + ethyl acetate, and acetoacetic buffer + diethyl ether combinations (<50% egg recovery). Acid alcohol + ethyl acetate resulted in 93.2, 89.8, and 57.3% egg recovery in the pellet of water, primary sludge, and fatty sludge, respectively; however, the size of the final pellet was not reduced, defeating the purpose of the extraction step. We thus recommend that this step be excluded.

Contribution of wastewater irrigated vegetables to the prevalence of soil-transmitted helminth infection among female farmers in Addis Ababa, Ethiopia

BACKGROUND

Untreated or inadequately treated wastewater carrying human feces can host helminth eggs and larvae, contaminating the soil and plants that are irrigated with it. In Addis Ababa, farmers use untreated wastewater to grow vegetables; however, there are little data currently available published on vegetables' contribution to the prevalence of helminth among female farmers along the Akaki River, in Addis Ababa, Ethiopia.

METHODS

A cross-sectional study was conducted in Addis Ababa City in February 2022. A stratified random sampling method was used to sample farming households. The sample size for each district was determined by a proportional allocation to the total number of households in the area. Two hundred and fifty-two composite vegetable samples and 101 farmers' stool samples were collected and analyzed for helminth prevalence. Data on socio-demographics were collected by trained data collators using a structured questionnaire. Kato-Katz concentration was used to detect STH from a stool sample. Stata version 14.0 was used to process the data. Poisson regression was used to identify the association between STH prevalence in the vegetable and the farm's stool.

RESULTS

Helminths were found in 67.5% of vegetables sampled and 20.8% of female farmers' stools. Ascaris lumbricoides eggs (vegetable 48.4% and stool 9.9%) were identified in all analyzed samples. Hookworm eggs (vegetable 13.1% and stool 8.9%) and Trichuris trichiura eggs (vegetable 5.9% and stool 2%) were also isolated. The total number of helminth eggs present in wastewater-irrigated vegetables and female farmers' stool had a positive association (p < 0.05) with a regression coefficient of 1.92 (95% CI = 1.56-2.28).

CONCLUSIONS

The study found a significant prevalence of helminth infections, particularly Ascaris lumbricoides, in stool and vegetable samples irrigated with wastewater. A clear association was found between vegetable production and a higher prevalence of helminth infections among female farmers. Therefore, it is important to ensure that farmers are educated in the importance of food washing and sanitation/hygiene practices when using wastewater irrigation for vegetable crops.

Distribution of helminth eggs in environmental and stool samples of farming households along Akaki River in Addis Ababa, Ethiopia

BACKGROUND

Helminth infections are a public health issue in countries with poor sanitation facilities. However, there little information on the epidemiological association between helminths in wastewater and soil samples and rates of helminth infection among farming households along the Akaki River in Addis Ababa, Ethiopia.

METHODS

A cross-sectional study was conducted between November 2021 and February 2022. A stratified random sampling technique was used to select farming households. The sample size for each district was determined by a proportionate allocation to the number of households. From wastewater-irrigated farms, 70 wastewater samples, 28 soil samples, and 86 farmers' stool samples were collected and analyzed for helminths. A questionnaire was used to gather ethnographic data, about farming households, whereas wastewater and soil sample analysis was used to generate quantitative data on helminth loads. The data were systematically analysed by developing themes, and bias evaluated using triangulation validation methodologies. Potential pathways to helminth infection were evaluated by measuring. Total number of helminth eggs in wastewater, soil samples and farmer's stools was investigated using Poisson regression.

RESULTS

In this study, 82.9% of wastewater samples, 57.1% of soil samples, and 18.6% of farmers' stool samples contained helminth eggs. The most prevalent helminth was Ascaris lumbricoides in all samples (wastewater 67%, soil 25%, and stool 10.5%), followed by hookworm (wastewater 10%, soil 21.4%, and stool 6.9%) and Trichuris trichiura eggs (wastewater 5.7%, soil 10.7%, and stool 1.2%). There was a positive association between the total number of helminth eggs in wastewater and soil samples with counts in farmers' stool. The Poisson regression coefficients for wastewater and soil were, 1.63 (95% CI = 1.34-1.92) and 1.70 (95% CI = 1.39-2.01), (p < 0.05).

CONCLUSIONS

This research has shown a clear association between the total helminth eggs in wastewater and soil samples and farmer stools along the Akaki River. Therefore, an integrated approach is essential to address the issue in this area and prevent the spread of further helminth infections.

Investigating the Occurrence of Soil-Transmitted Parasites Contaminating Soil, Vegetables, and Green Fodder in the East of Nile Delta, Egypt

Background

Food-borne parasites are major sources of human and animal illness, posing severe health risks in places with contaminated soil, poor water quality, cleanliness, and poor sanitation. The usage of untreated organic fertilizers arising from the excreta of the parasites' definitive hosts either man or animal pollutes the agricultural soil and is reflected in its products of vegetables and green fodders causing serious health problems. Therefore, to the best of our knowledge, this will be the first study that investigated the combination of parasitic contamination of the agricultural soil and its products of raw eaten vegetables and green fodder in East Nile Delta, Egypt.

Aim

The purpose of this study was to investigate the type and degree of contamination caused by parasites in regularly used raw vegetables, green fodder, and soil samples collected from open fields in Egypt's East Nile Delta. Study Procedures. A cross-sectional study comprised a simple random collection of 400 soil samples, 180 green fodder samples, and as well as 400 vegetable samples, including lettuce, radish, coriander, parsley, dill, watercress, tomatoes, green pepper, cucumber, and carrot, that were gathered throughout one year period from January to December 2021 to represent all seasons (winter, spring, summer, and autumn). The research locations were chosen from various open green fields and farming regions in Egypt's East Nile Delta producing ready-to-eat vegetables for human consumptions and planting green fodder for animal feeding. Concentrations, including sedimentation, and flotation, and staining techniques were used to recover the greatest number of parasitic life forms. The parasitic structures discovered were identified using biometric and imaging data and compared with known parasite morphology. Statistical analysis was performed with the SPSS software version 22 (IBM, Chicago, IL, USA). Data were presented in numbers and percentages. P-values equal to or less than 0.05 were considered to be statistically significant. The difference in parasitic contamination among the different categories was compared using the chi-square test.

Results

In this investigation, 243 out of 400 soil samples (60.7%) confirmed positive for parasitic contamination (P < 0.05). Various parasitic life forms were significantly found in 249 out of 400 (62.25%) of the vegetable samples, with (65.1%) of them harboring one parasite species, whereas 9.2% significantly contained up to three parasites. Ascaris eggs, Trichuris eggs, and Giardia cysts were the most prevalent parasites, which were predominantly isolated from vegetables with uneven surfaces. 109 of 180 (60.0%) green fodder samples confirmed insignificantly positive for parasitic pollution. The proportion of parasite contamination in vegetable samples was insignificant although the highest was in spring (29.3%), followed by summer (27.7%), whereas it is significant in autumn (24.5%). The prevalence rate was the lowest in winter (20.1%). Conclusion and Recommendations. Our findings demonstrated a significant load of parasites notably the soil-transmitted parasitic infection in raw vegetables and green fodder cultivated in open fields as well as in their mother soil in the east of the Nile Delta, Egypt. These results confirm the urgent need to deploy strict control measures to the soil, especially during the pre-harvest period of raw eaten vegetables and green fodder, a critical step in reducing food-borne transmission of soil-transmitted parasites to man and animals.

Prevalence of helminths in fresh vegetables: a narrative literature review

The consumption of fresh vegetables is related to healthy lifestyle habits present in culinary preparations in different regions. The presence of pathogenic parasites in these foods can cause gastrointestinal disorders. Thus, the objective of the present study was to carry out a narrative review of the literature on the prevalence of helminths in fresh vegetable samples. The analysis of the studies published from 2016 to 2022 showed that hookworms and Ascaris lumbricoides are the most common pathogenic helminths in fresh vegetable samples, with a prevalence of up to 73.8% and 55.1%, respectively. In addition, studies have shown associations between the presence of helminths and pathogenic protozoa. The results obtained in this review indicate the urgent need to implement actions at all stages of the vegetable production chain, from the water used in planting irrigation to cleaning before sale to the final consumer. © 2022 Society of Chemical Industry.

Bioaccessibility and oral immunization efficacy of a chimeric protein vaccine against Ascaris suum

Human ascariasis has been characterized as the most prevalent neglected tropical disease worldwide. There is an urgent need for search to alternative prevention and control methods for ascariasis. Here we aimed to establish a protocol of oral immunization with a previously described chimera protein capable of resist through digestion and induce mucous protection against Ascaris suum infection. Mice were oral immunized with seven doses with one day interval and challenged with A. suum ten days after the last dose. In vitro digestion showed that 64% of chimeric protein was bioaccessible for absorption after digestion. Immunized mice display 66,2% reduction of larval burden in lungs compared to control group. In conclusion we demonstrated that oral immunization with chimera protein protects the host against A. suum larval migration leading to less pronounced histopathological lesions.

Characteristics of Solidified Carbon Dioxide and Perspectives for Its Sustainable Application in Sewage Sludge Management

Appropriate management is necessary to mitigate the environmental impacts of wastewater sludge. One lesser-known technology concerns the use of solidified CO₂ for dewatering, sanitization, and digestion improvement. Solidified CO₂ is a normal byproduct of natural gas treatment processes and can also be produced by dedicated biogas upgrading technologies. The way solidified CO₂ is sourced is fully in line with the principles of the circular economy and carbon dioxide mitigation. The aim of this review is to summarize the current state of knowledge on the production and application of solid CO₂ in the pretreatment and management of sewage sludge. Using solidified CO₂ for sludge conditioning causes effective lysis of microbial cells, which destroys activated sludge flocs, promotes biomass fragmentation, facilitates efficient dispersion of molecular associations, modifies cell morphology, and denatures macromolecules. Solidified CO₂ can be used as an attractive tool to sanitize and dewater sludge and as a pretreatment technology to improve methane digestion and fermentative hydrogen production. Furthermore, it can also be incorporated into a closed CO₂ cycle of biogas production-biogas upgrading-solidified CO₂ production-sludge disintegration-digestion-biogas production. This feature not only bolsters the technology's capacity to improve the performance and cost-effectiveness of digestion processes, but can also help reduce atmospheric CO₂ emissions, a crucial advantage in terms of environment protection. This new approach to solidified CO₂ generation and application largely counteracts previous limitations, which are mainly related to the low cost-effectiveness of the production process.

Environmental challenges of COVID-19 pandemic: resilience and sustainability - A review

The emergence of novel respiratory disease (COVID-19) caused by SARS-CoV-2 has become a public health emergency worldwide and perturbed the global economy and ecosystem services. Many studies have reported the presence of SARS-CoV-2 in different environmental compartments, its transmission via environmental routes, and potential environmental challenges posed by the COVID-19 pandemic. None of these studies have comprehensively reviewed the bidirectional relationship between the COVID-19 pandemic and the environment. For the first time, we explored the relationship between the environment and the SARS-CoV-2 virus/COVID-19 and how they affect each other. Supporting evidence presented here clearly demonstrates the presence of SARS-CoV-2 in soil and water, denoting the role of the environment in the COVID-19 transmission process. However, most studies fail to determine if the viral genomes they have discovered are infectious, which could be affected by the environmental factors in which they are found.The potential environmental impact of the pandemic, including water pollution, chemical contamination, increased generation of non-biodegradable waste, and single-use plastics have received the most attention. For the most part, efficient measures have been used to address the current environmental challenges from COVID-19, including using environmentally friendly disinfection technologies and employing measures to reduce the production of plastic wastes, such as the reuse and recycling of plastics. Developing sustainable solutions to counter the environmental challenges posed by the COVID-19 pandemic should be included in national preparedness strategies. In conclusion, combating the pandemic and accomplishing public health goals should be balanced with environmentally sustainable measures, as the two are closely intertwined.

What on earth? The impact of digestates and composts from farm effluent management on fluxes of foodborne pathogens in agricultural lands

The recycling of biomass is the cornerstone of sustainable development in the bioeconomy. In this context, digestates and composts from processed agricultural residues and biomasses are returned to the soil. Whether or not the presence of pathogenic microorganisms in these processed biomasses is a threat to the sustainability of the current on-farm practices is still the subject of debate. In this review, we describe the microbial pathogens that may be present in digestates and composts. We then provide an overview of the current European regulation designed to mitigate health hazards linked to the use of organic fertilisers and soil improvers produced from farm biomasses and residues. Finally, we discuss the many factors that underlie the fate of microbial pathogens in the field. We argue that incorporating land characteristics in the management of safety issues connected with the spreading of organic fertilisers and soil improvers can improve the sustainability of biomass recycling.

Potentials and challenges in the isolation and detection of ascarid eggs in complex environmental matrices

Ascarid infections constitute a major concern for both human and animal health risk assessment. Although being effectively transmitted by soil, water and contaminated food, reliable detection of ascarid eggs in environmental media often remains challenging. However, contamination of the environment with ascarid ova has gained more attention as a decisive part of proper risk assessment in recent years. Due to various factors, such as sample matrices, dissociation detergents and flotation solutions, defined and standardised protocols for the isolation of eggs from complex environmental matrices are difficult to establish and therefore limited. Thus, this study reviews common techniques used for the recovery of ascarid eggs from environmental media with special emphasis on sampling strategies, purification procedures and microscopic as well as molecular detection of egg contamination. Despite various advancements, mainly in the field of molecular methods leading to more reliable and sensitive detection, it can be concluded that there is still a need for unified guidelines for sampling and recovery of ascarid eggs derived from complex environmental matrices.

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Standardised methods to assess environmental ascarid egg contamination are needed.

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The environmental sampling strategy has to be adapted to the study hypothesis.

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Egg detection mostly relies on matrix homogenisation, filtration, sedimentation and flotation.

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Microscopic detection is still frequently applied.

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Molecular methods enable more reliable and sensitive detection.

Environmental detection of Fasciola hepatica by loop-mediated isothermal amplification

Fasciola hepatica, commonly referred to as liver flukes, is a substantial zoonotic parasitic disease of humans and livestock globally. While infection is readily controlled by anthelmintics, namely triclabendazole, the heavy reliance on triclabendazole has resulted in drug resistance appearing worldwide. Due to drug resistance, it is imperative to adopt an integrated parasite management program to preserve the efficacy of currently available anthelmintics. A integrated liver fluke management plan would benefit from a simple rapid, field-deployable diagnostic for detection of F. hepatica in environment and the host. Therefore, a rapid DNA test using loop-mediated isothermal amplification was developed and optimised for the detection of F. hepatica from faecal and water samples to enable the detection of parasites both within the host and from the environment. The assay presented here is fast, with amplification in ≤20 min, and highly sensitive, with a detection limit of 5 × 10^-4 ng/µL. The workflow presented here provides a time to result of ≤60 min without requiring a commercial kit for the extraction of DNA from faecal and water samples, and pending further validation from field-samples, could potentially be used to enable real-time decision making to mitigate parasite prevalence on a farming property and with no requirement for sample transportation.

Comparative Evaluation of an Easy Laboratory Method for the Concentration of Oocysts and Commercial DNA Isolation Kits for the Molecular Detection of Cyclospora cayetanensis in Silt Loam Soil Samples

Cyclospora cayetanensis is a protozoan parasite that causes foodborne outbreaks of diarrheal illness (cyclosporiasis) worldwide. Contact with soil may be an important mode of transmission for C. cayetanensis and could play a role in the contamination of foods. However, there is a scarcity of detection methods and studies for C. cayetanensis in soil. Traditional parasitology concentration methods can be useful for the detection of C. cayetanensis, as found for other protozoa parasites of similar size. The present study evaluated a concentration method using flotation in saturated sucrose solution, subsequent DNA template preparation and qPCR following the Bacteriological Analytical Manual (BAM) Chapter 19b method. The proposed flotation method was compared to three commercial DNA isolation kits (Fast DNATM 50 mL SPIN kit for soil (MP Biomedicals, Irvine, CA, USA), Quick-DNATM Fecal/Soil Microbe Midiprep kit (Zymo Research, Irvine, CA, USA) and DNeasy® PowerMax® Soil Kit (Qiagen, Hilden, Germany)) for the isolation and detection of DNA from experimentally seeded C. cayetanensis soil samples (5−10 g with 100 oocysts). Control unseeded samples were all negative in all methods. Significantly lower cycle threshold values (CT) were observed in the 100 oocyst C. cayetanensis samples processed via the flotation method than those processed with each of the commercial DNA isolation kits evaluated (p < 0.05), indicating higher recovery of the target DNA with flotation. All samples seeded with 100 oocysts (n = 5) were positive to the presence of the parasite by the flotation method, and no inhibition was observed in any of the processed samples. Linearity of detection of the flotation method was observed in samples seeded with different levels of oocysts, and the method was able to detect as few as 10 oocysts in 10 g of soil samples (limit of detection 1 oocyst/g). This comparative study showed that the concentration of oocysts in soil samples by flotation in high-density sucrose solutions is an easy, low-cost, and sensitive method that could be implemented for the detection of C. cayetanensis in environmental soil samples. The flotation method would be useful to identify environmental sources of C. cayetanensis contamination, persistence of the parasite in the soil and the role of soil in the transmission of C. cayetanensis.

Highly Sensitive Detection of Human Pluripotent Stem Cells by Loop-Mediated Isothermal Amplification

For safe regenerative medicines, contaminated or remaining tumorigenic undifferentiated cells in cell-derived products must be rigorously assessed through sensitive assays. Although in vitro nucleic acid tests offer particularly sensitive tumorigenicity-associated assays, the human pluripotent stem cell (hPSC) detectability is partly constrained by the small input amount of RNA per test. To overcome this limitation, we developed reverse transcription loop-mediated isothermal amplification (RT-LAMP) assays that are highly gene specific and robust against interfering materials. LAMP could readily assay microgram order of input sample per test and detected an equivalent model of 0.00002% hiPSC contamination in a simple one-pot reaction. For the evaluation of cell-derived total RNA, RT-LAMP detected spiked-in hPSCs among hPSC-derived trilineage cells utilizing multiple pluripotency RNAs. We also developed multiplex RT-LAMP assays and further applied for in situ cell imaging, achieving specific co-staining of pluripotency proteins and RNAs. Our attempts uncovered the utility of RT-LAMP approaches for tumorigenicity-associated assays, supporting practical applications of regenerative medicine.

Development of molecular detection methods of Bovicola ovis from sheep fleece

The sheep body louse (Bovicola ovis) commonly referred to as sheep lice are small chewing ectoparasites of sheep. Infection results in significant economic costs to the Australian sheep industry due to reduced wool quality caused by chronic itching from sheep rubbing and biting fleece. Treatment relies on use of insecticides; however, resistance has developed against pyrethroid and other insect growth regulator lousicides. There is urgent need to develop cost-effective lice management to reduce the use of insecticides, with the application of insecticidal treatments only applied when an infestation is detected. However, the current detection method relies on fleece parting for detection of B. ovis which is highly dependent on the skill of the inspector, the number of sheep examined, and the prevalence and severity of the infestation. To improve B. ovis detection, a highly sensitive (5 × 10-8 ng/μL) and specific multiplex quantitative PCR which simultaneously detects sheep lice and sheep DNA was developed. In addition, a B. ovis loop-mediated isothermal amplification (LAMP) assay was developed for field use. The B. ovis LAMP (Bov-LAMP) assay was optimized to reliably detect B. ovis from wool samples down to 5 × 10-6 ng/μL, with time to positive (Tp) < 10 min. Both assays demonstrate high sensitivity and specificity, enabling rapid identification of B. ovis DNA from sheep fleece samples and have the capacity to be used for ongoing management and surveillance of B. ovis in Australian sheep flocks.

Extended-spectrum-beta-lactamases and carbapenemase-producing Klebsiella pneumoniae isolated from fresh produce farms in different governorates of Egypt

Background and Aim: Fresh produce farms represents a major source of concern since they are becoming increasingly antibiotic resistant. This study aimed to investigate t he occurrence of carbapenemase and extended-spectrum-beta-lactamases (ESBL) - producing genes in Klebsiella pneumoniae isolated from fresh produce farms in Egypt, irrigation water, and people working in these fields. Materials and Methods: One hundred tomatoes from typical farms were collected in plastic bags. The study also included 20 surface-water samples from different irrigation watersheds in fresh produce farms, as well as 50 feces samples from farmworkers. Suspected K. pneumoniae was grown on Eosin Methylene Blue agar for 24 h before being biochemically identified using the RapID ONE test. PCR was used to detect carbapenemase (blaKPC, blaOXA-48, and blaNDM) and ESBL (blaSHV, blaTEM, and blaCTX) expressing genes on isolates. Results: K. pneumoniae was identified in 30% of water and 10% of worker samples, while only one isolate was found in tomato samples. One of the six irrigation water isolates tested positive for carbapenem-resistant NDM. In contrast, two isolates tested positive for ESBL determinants, one of which was blaSHV and the other having both blaSHV and blaTEM genes. Two of the five K. pneumoniae isolates from farmworkers were positive for blaNDM, with one isolate also testing positive for blaSHV and blaTEM. The blaOXA-48 gene was also discovered in the carbapenem-resistant K. pneumoniae tomato isolate used in this study. Conclusion: Carbapenemase- and ESBL-producing K. pneumoniae were found in fresh produce farms, implying that these resistance genes were being passed down to Egyptian consumers.

Back to basics: Could simple experiments resolve important parasitology enigmas? The rarity of Ascaris eggs compared with Trichuris eggs in archeology and other contexts

Most parasitologists face a conundrum throughout their careers: 'which parasite eggs are more resistant to environmental stress, Ascaris spp. or Trichuris spp.?' In this analysis, our experimental and statistical analyses demonstrated that Trichuris sp. is more resistant than Ascaris sp. We highlight that desiccation exerts a major effect on the conservation of Ascaris eggs, and this may result in an underestimation of Ascaris eggs in paleoparasitological records. This observation can be extrapolated to more modern scenarios, for example, parasitological research in animal feces from semiarid environments, where whipworms are more common than roundworms. Similarly, this could be a plausible explanation for the higher frequency and abundance of whipworms than roundworms, when other hypotheses are unsupported.

Treatment processes to eliminate potential environmental hazards and restore agronomic value of sewage sludge: A review

Land application of sewage sludge is increasingly used as an alternative to landfilling and incineration owing to a considerable content of carbon and essential plant nutrients in sewage sludge. However, the presence of chemical and biological contaminants in sewage sludge poses potential dangers; therefore, sewage sludge must be suitably treated before being applied to soils. The most common methods include anaerobic digestion, aerobic composting, lime stabilization, incineration, and pyrolysis. These methods aim at stabilizing sewage sludge, to eliminate its potential environmental pollution and restore its agronomic value. To achieve best results on land, a comprehensive understanding of the transformation of organic matter, nutrients, and contaminants during these sewage-sludge treatments is essential; however, this information is still lacking. This review aims to fill this knowledge gap by presenting various approaches to treat sewage sludge, transformation processes of some major nutrients and pollutants during treatment, and potential impacts on soils. Despite these treatments, overtime there are still some potential risks of land application of treated sewage sludge. Potentially toxic substances remain the main concern regarding the reuse of treated sewage sludge on land. Therefore, further treatment may be applied, and long-term field studies are warranted, to prevent possible adverse effects of treated sewage sludge on the ecosystem and human health and enable its land application.

Cyst detection and viability assessment of Balantioides coli in environmental samples: Current status and future needs

The ciliate Balantioides coli is a human enteric parasite that can cause life-threatening infections. It is a food- and waterborne parasite, with cysts being the infective stage. Despite its importance as a potential pathogen, few reports have investigated its presence in environmental samples, and some issues need attention including i) The accuracy of B. coli identification. In most cases, the protozoa is identified only by its morphological traits, which can be identical to those from other parasitic ciliates of animals. Genetic analysis of cysts recovered from environmental samples is necessary for species confirmation. In addition, genetic methods used with faecal samples need to be adequately validated with environmental matrices. ii) The methodology for searching this parasite in environmental samples. The protocols include an initial phase to isolate the cysts from the matrix followed by a second phase in which concentration procedures are usually applied. The methods may be valid but are not standardised and differences between studies could affect the results obtained. iii) The areas that needs further research. The development of genetic identification methods and standardised analytical protocols in environmental samples are required, as well as the assessment of viability and infectivity of B. coli cysts. The development of axenic culture systems will boost research on this parasite.

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Balantioides coli is mainly considered a foodborne parasite for humans.

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Detection methods in environmental samples are not standardised.

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Correct identification should be made by genetic analysis.

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Methods for B. coli cyst viability and infectivity assessment are to be developed.

Development of a loop-mediated isothermal amplification assay for detection of Austropeplea tomentosa from environmental water samples

Lymnaeid snails are key intermediate hosts for the development and survival of Fasciola spp., the causative agent of Fascioliasis which are economically important parasites infecting humans and livestock globally. The current control method for treating Fascioliasis is heavily reliant on anthelmintic drugs, particularly Triclabendazole (TCBZ) which has resulted in drug-resistant parasites and poses significant risk as there are no long-term efficacious alternatives available. Sustainable control measures at the farm level could include both parasite and snail control will play an important role in Fasciola spp. control and reduce the reliance on anthelmintic drugs. Implementation of such sustainable control measures requires effective identification of snails on the property however Lymnaeid snails are small and difficult to physically locate. Snail identification using an environmental DNA approach is a recent approach in which physically locating snails are not required. Austropeplea tomentosa, is the primary intermediate snail host for F. hepatica transmission in South-East Australia and we present an in-field loop-mediated isothermal amplification and water filtering method for the detection of A. tomentosa eDNA from water samples to improve current surveillance methods. This methodology is highly sensitive with a detection limit of 5 × 10^− 6 ng/μL, detected in < 20 minutes, with cumulative sample preparation and amplification time under 1 hour. This proposed workflow could assist in monitoring areas to determine the risk of Fascioliasis infection and implement strategies to manage snail populations to ultimately reduce the risk of infection for humans and livestock.

Soil contamination by Echinococcus multilocularis in rural and urban vegetable gardens in relation to fox, cat and dog faecal deposits

Echinococcus multilocularis eggs are deposited on the ground with the faeces of the carnivore definitive hosts. A reliable assessment of the spatial distribution of E. multilocularis eggs in environments used by humans is crucial for the prevention of alveolar echinococcosis (AE). This study was conducted in 192 rural and 71 urban vegetable gardens in AE endemic areas of north-eastern France. Its objective was to explore the relationship between the spatial distribution of E. multilocularis estimated from the collection and molecular analysis of two types of samples: faeces and soil. A total of 1024 carnivore faeces and 463 soil samples were collected and analysed by real-time PCR. No fox droppings and no positive soil samples were collected from the urban gardens. Positive soil samples, positive carnivore faeces, or both, were found in 42%, 24% and 6% of the sampled rural gardens, respectively. No significant association was found between the detection of E. multilocularis in soil samples collected from 50 gardens during a single sampling session and the extent and frequency of deposits of fox and cat faeces collected during repeated sampling sessions conducted in the previous months. In 19/50 gardens, E. multilocularis was detected in the soil while no positive faeces had been collected in the previous 12 months. Conversely, in 8/50 gardens, no soil samples were positive although positive faeces had been collected in the previous months. Collecting and analysing faeces provide information on soil contamination at a given time, while analysing soil samples provides an overview of long-term contamination.

Evaluation of the efficiency of some disinfectants on the viability of Hymenolepis nana eggs isolated from wastewater and faecal sludge in Yaounde (Cameroon): importance of some abiotic variables

Hymenolepis nana is responsible for many parasitic infections in tropical areas, with its persistence in aquatic environments as major contributory factor. A study aimed at demonstrating the effectiveness of some disinfectants on the viability of Hymenolepis nana eggs was conducted in microcosm. Sampling consisted of taking wastewater and sewage sludge samples in sterilized containers and then transporting to the laboratory of Hydrobiology and Environmental Sciences for the determination of Hymenolepis nana eggs using standard protocols. The experimental set-up consisted of five replicates, four tests and a control. The test samples were successively treated with four disinfectants (calcium chlorite, hydrogen peroxide, gypsum and sodium hypochlorite). The physico-chemical parameters were measured before and after disinfection. The samples were then observed under an optical microscope after concentration of the sample through sedimentation and McMaster technique. The viability of the eggs was determined using incubation and staining techniques. The analysis revealed that the selected disinfectants significantly reduced the physico-chemical parameters (with an average yield ranging from 79.24 ± 19.43% to 99.24 ± 1.47%). These physico-chemical parameters can significantly influence the treatment of Hymenolepis nana eggs either by absorbing the disinfectant or by constituting a protective barrier for the eggs, and the physico-chemical nature of the disinfectant strongly influences the formation of disinfection by-products. Calcium chlorite showed a greater effectiveness in reducing egg viability with efficiency rates of 93.12 ± 9.12% followed by hydrogen peroxide (89.57 ± 14.55%), sodium hypochlorite (82.51 ± 14.39%) and gypsum (80.85 ± 12.88%). The results obtained with gypsum are almost similar to those obtained with other disinfectants (calcium chlorite, hydrogen peroxide and sodium hypochlorite) and clearly show that this disinfectant can be used in water treatment because, unlike other chemical disinfectants, it has no known toxic effects.

Application of molecular tools in detecting zoonotic pathogens in organic fertilizers and liquid supplements

The use of organic fertilizers and liquid supplements for crop production is rapidly growing as an alternative system to conventional agriculture. However, very little is known about the public health issues related to pathogens. This study endeavors to identify the important zoonotic pathogens with the current molecular diagnostic tools, Loop-mediated isothermal amplification (LAMP) and Recombinase polymerase amplification (RPA), against the conventional pathogen detection. These cost-effective molecular techniques have proven to be confirmatory tests of the target pathogens present in organic fertilizers and liquid supplements, which recommends an advancement for the comprehensive field surveillance-response approach in many developing countries with resource-limited settings quality assurance and safety implementation of organic biosolids for sustainable agricultural farming.

Soil-Transmitted Helminthic Infections and Geophagia among Pregnant Women in Jimma Town Health Institutions, Southwest Ethiopia

Background

Pregnancy is a key step for human's reproduction and continuity of generation. Pregnant women are among at risk groups for the infection of soil-transmitted helminths (STHs). STHs are highly prevalent in low- and middle-income countries due to the deprived environmental sanitation and personal hygiene. Eating soil (geophagia) is also commonly practiced by pregnant women, particularly in developing countries. The aim of this study was to determine the prevalence of STHs and geophagia, and to assess associated factors among pregnant women in Jimma, Southwest Ethiopia.

Methods

A cross sectional study was conducted among 407 pregnant women attending antenatal care (ANC) at different health facilities located in Jimma Town. Data related to sociodemographic and geophagia practice was collected using a structured questionnaire and STH infections status was determined by using McMaster technique.

Results

A total of 407 pregnant women were included in this study. The overall prevalence of any STHs was 19.7% (80/407). Ascaris lumbricoides was the most prevalent 45(56.2%), followed by Trichuris trichiura 19(23.8%) and hookworms 12(15%). There were 4(5%) of double infection with A. lumbricoides and T. trichiura. Overall, 71 (17.4%) of the pregnant women responded to practice geophagia. STHs infection was significantly higher among geophagic pregnant women (p<0.01) and pregnant women who practiced geophagia were 3 times more likely (OR 2.9, 95% CI 1.3–4.2) to have the STHs compared to non-geophagic. Out of those who claimed soil eating habits, 59.1% preferred reddish soil type. Geophagia practice was significantly higher during the third trimester as compared to first and second (p<0.05).

Conclusion

Geophagia is a risky behavior and this study showed a significant association of geophagia practice with STH infections, although the causal relation could not be established.

Optimized DNA-based identification of Toxocara spp. eggs in soil and sand samples

Background

Toxocara canis and Toxocara cati are globally distributed roundworms and causative agents of human toxocariasis, via ingestion of Toxocara eggs. Control of Toxocara infections is constrained by a lack of sensitive methods for screening of animal faeces and environmental samples potentially contaminated by Toxocara eggs. In this work, a pre-analytical method for efficient extraction of DNA from Toxocara eggs in environmental samples was set up using our previously validated T. canis- and T. cati-specific quantitative real-time polymerase chain reaction (qPCR). For this purpose, the influence of different methods for egg lysis, DNA extraction and purification for removal of PCR inhibitors were assessed on environmental samples.

Methods

To select the best egg disruption method, six protocols were compared on pure T. canis egg suspensions, including enzymatic lysis and thermal or mechanical disruption. Based on the selected best method, an analytical workflow was set up to compare two DNA extraction methods (FastDNA™ SPIN Kit for Soil versus DNeasy^® PowerMax^® Soil Kit) with an optional dilution and/or clean-up (Agencourt^® AMPure^®) step. This workflow was evaluated on 10-g soil and 10-g sand samples spiked with egg suspensions of T. canis (tenfold dilutions of 10⁴ eggs in triplicate). The capacity of the different methods, used alone or in combination, to increase the ratio of positive tests was assessed. The resulting optimal workflow for processing spiked soil samples was then tested on environmental soil samples and compared with the conventional flotation-centrifugation and microscopic examination of Toxocara eggs.

Results

The most effective DNA extraction method for Toxocara eggs in soil samples consisted in the combination of mechanical lysis of eggs using beads, followed by DNA extraction with the DNeasy^® PowerMax^® Soil Kit, and completed with an additional DNA clean-up step with AMPure^® beads and a sample DNA dilution (1:10). This workflow exhibited a limit of detection of 4 and 46 T.canis eggs in 10-g sand and 10-g soil samples, respectively.

Conclusions

The pre-analytical flow process developed here combined with qPCR represents an improved, potentially automatable, and cost-effective method for the surveillance of Toxocara contamination in the environment.

Graphical Abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s13071-021-04904-1.

Insights into geohelminth contamination in Bangladesh: feasibility of a modified diagnostic method and prevalence study

INTRODUCTION

The objectives of this study were to evaluate a modified method for isolating geohelminth eggs and to assess the geohelminth contamination in Bangladesh.

METHODS

The efficacy of the modified method was evaluated using naturally contaminated and experimentally seeded soil samples. In total, 240 samples were assessed from four different sites in three geographic contexts. A questionnaire survey with 50 professionals was conducted.

RESULTS

The modified method showed considerable efficacy in isolating parasitic eggs from naturally contaminated soil (54.0%) and experimentally seeded soils (63.0% for Toxocara eggs and 52.0% for Ascaris eggs). The modified method was described as convenient by the majority of participants. Overall prevalence was 52.5%, with several species of helminth observed, including Toxocara sp., Ascaridia galli/Heterakis gallinarum, Ascaris sp., hookworms/strongyles, Capillaria sp., Trichuris sp., and taeniids). The contamination rate was found to be higher around livestock farms (76.7%), followed by latrines (63.3%), households (41.6%), and schools (28.3%).

CONCLUSIONS

The modified method was shown to be feasible in terms of field applicability and egg recovery rate, and could be adopted in low-resource settings. A substantial prevalence of geohelminths was observed, with some of the species associated with zoonoses. These findings highlight the urgent need for widespread mapping of geohelminths to avoid spillovers to animals and humans.

Diagnostic Techniques for Soil-Transmitted Helminths - Recent Advances

Soil-transmitted helminth (STH) infections (hookworms, Trichuris, Ascaris) and Strongyloides spp. are associated with a substantial global burden and high morbidity. Sensitive and specific methods for diagnosis of these infections are essential for mapping the burden in communities, accurate assessment of infection levels, to guide interventions and monitoring the success of STH control programs. Despite considerable progress to control STH over several decades, we are still far from identifying a fully adequate diagnostic test. Conventional microscopy-based methods such as direct Kato–Katz smear or mounts after stool centrifugation/flotation-based concentration techniques have been the mainstay of diagnosis, especially in resource-poor countries where these infections abound. However, recently, these are being adapted to closed, easy to perform, digital formats, thereby improving the sensitivity as well as applicability in a remote, resource-limited setting. The use of image analysis systems to identify and quantify helminth eggs, with potential adaptation to smartphones, is also promising. Antibody detection tests have a limited role mostly in the case of Strongyloides hyperinfection. Coproantigen detection tests have been developed and used in veterinary practice for detection of STH, but these have not been evaluated for use in humans. More sensitive molecular diagnostics, including assays developed with new bioinformatic tools and techniques such as polymerase chain reaction (PCR), quantitative PCR (qPCR) and loop-mediated amplification assay, can help in the clear and precise assessment of STH burden during elimination phase and are of immense value for diagnosis in areas with low endemicity and in travelers to endemic regions. Moreover, the molecular techniques will help detect new species that may emerge. Sample preservation and efficient DNA extraction are critical and significantly affect the efficiency of molecular diagnostic tests. In addition to the diagnosis of clinical or asymptomatic infection in humans, detection of STH eggs in environmental samples is imperative to boost STH control efforts. Overall the diagnostic performance, cost-effectiveness, ease of performance, rapidity and in-field applicability of any test should be considered when choosing from the various diagnostic assays in areas with different endemicity, in addition to striving towards the development of novel technologies and optimization of existing methods.

Mining Public Metagenomes for Environmental Surveillance of Parasites: A Proof of Principle

Parasites often have complex developmental cycles that account for their presence in a variety of difficult-to-analyze matrices, including feces, water, soil, and food. Detection of parasites in these matrices still involves laborious methods. Untargeted sequencing of nucleic acids extracted from those matrices in metagenomic projects may represent an attractive alternative method for unbiased detection of these pathogens. Here, we show how publicly available metagenomic datasets can be mined to detect parasite specific sequences, and generate data useful for environmental surveillance. We use the protozoan parasite Cryptosporidium parvum as a test organism, and show that detection is influenced by the reference sequence chosen. Indeed, the use of the whole genome yields high sensitivity but low specificity, whereas specificity is improved through the use of signature sequences. In conclusion, querying metagenomic datasets for parasites is feasible and relevant, but requires optimization and validation. Nevertheless, this approach provides access to the large, and rapidly increasing, number of datasets from metagenomic and meta-transcriptomic studies, allowing unlocking hitherto idle signals of parasites in our environments.

Development of a Droplet Digital PCR for Detection of Trichuriasis in Sheep

Trichuriasis is a serious threat to the economic development of animal husbandry. This research aimed to establish a droplet digital PCR (ddPCR) method to detect Trichuris spp. for the early diagnosis and prevention of trichuriasis in sheep. The real-time quantitative PCR (qPCR) and ddPCR methods were used for the detection of nematodes by targeted amplification of the ITS gene. Each means was evaluated to optimize the limit of detection and reproducibility. For a recombinant plasmid, the qPCR results showed that the detection limit was 31.7 copies per reaction. In contrast to qPCR, ddPCR was able to detect concentrations below 3.17 copies per reaction. Both assays exhibited good reproducibility. However, the ddPCR method was more stable for low-copy-number detection. This new assay was specific for Trichuris spp. and did not cross-react with other relevant gastrointestinal nematodes. A total of 98 clinical samples were tested with both assays. The results showed that the positive rate of ddPCR (80.6%) was higher than that of qPCR (72.4%). This method could be used as an efficient molecular biology tool to test for Trichuris spp. and could be a new valuable tool for the clinical diagnosis and prevention of trichuriasis.

Prevalence and Intensity of Intestinal Helminth Infections in Preschool Pupils in Lugari Subcounty, Kakamega County, Kenya

Intestinal helminths cause anaemia, malnutrition, indigestion disorders, retarded growth, and low mental abilities in pupils. About 1.5 billion are infected globally. Intestinal helminth infections are caused by Ascaris lumbricoides, Trichuris trichiura, Strongyloides stercoralis, Enterobius vermicularis, Ancylostoma duodenale, and Necator americanus. Lugari Subcounty has poor sanitation and inadequate clean water. This study determined the prevalence of intestinal helminth infections in preschool pupils in Lugari Subcounty. A stratified multistage cluster experimental design was used. Sampling was carried out in four wards: Lumakanda, Lugari, Luandeti, and Chekalini. Preschool pupils of either gender were selected randomly. Written consents and verbal assent were obtained from parents or guardians and preschool pupils, respectively. Questionnaires were administered in order to collect sociodemographic data. Stool samples were collected and tested for the presence of eggs using the standard Kato-Katz technique. Prevalence rate and prevalence ratio were calculated as the percentage of infected preschool pupils among the total number of preschool pupils examined. Preschool pupils positive with helminths were treated freely, and a follow-up screening was conducted three months after treatment. Approval of the study was sought from the Masinde Muliro University of Science and Technology Institutional Ethical Review Board (MMUST IRB). The overall prevalence of intestinal helminths was 12.3%. Only one species, Ascaris lumbricoides, was identified. Statistical tests were carried out at a 5% significance level (p < 0.05, confidence interval (CI) 95%). There was a statistically significant association for prevalence and intensity of intestinal helminths versus factors like school location, knowledge of washing hands before eating, and awareness of washing hands after visiting a toilet. Although this study revealed a low prevalence and light intensity, some factors had significant effects on intestinal helminth infections among the preschool children. Therefore, there is a need to intensify efforts for their intestinal helminth control.

Preliminary data on Ascaridia galli infections in Gallus gallus domesticus and the development of a specific primer based on the NADH dehydrogenase subunit 4

One major problem of chicken (Gallus gallus domesticus) farming was various parasitic infections, especially Ascaridia galli that can cause the Ascaridiosis and is commonly found worldwide. The purpose of this study was to investigate the epidemiological situation of gastrointestinal tract parasitic infections and to develop species-specific primer for A. galli detection. A total of 247 chicken gastrointestinal tract specimens from 5 fresh markets in Bangkok. The species-specific primers of A. galli were manually designed using the mitochondrial genome at the NADH dehydrogenase subunit 4 (MT-ND 4) gene. As a result, PCR assays were optimized for the specific PCR product approximately 198 bp with the optimal temperature of 51 °C. In addition, sensitivity tests provided the detection of adult and egg stages at the minimum concentrations of 156.3 ng and 2.8 ng (70 eggs), respectively. This research can be used as preliminary information regarding the epidemic situation of gastrointestinal tract infections in chickens and detection of A. galli infection in definitive hosts, which plans programs for the effective control and prevention of parasitic infections.

Loop-Mediated Isothermal Amplification as Point-of-Care Diagnosis for Neglected Parasitic Infections

The World Health Organisation (WHO) has placed twenty diseases into a group known as neglected tropical diseases (NTDs), twelve of them being parasitic diseases: Chagas’ disease, cysticercosis/taeniasis, echinococcosis, food-borne trematodiasis, human African trypanosomiasis (sleeping sickness), leishmaniasis, lymphatic filariasis, onchocerciasis (river blindness), schistosomiasis, soil-transmitted helminthiasis (ascariasis, hookworm, trichuriasis), guinea-worm and scabies. Such diseases affect millions of people in developing countries where one of the main problems concerning the control of these diseases is diagnosis-based due to the most affected areas usually being far from laboratories having suitable infrastructure and/or being equipped with sophisticated equipment. Advances have been made during the last two decades regarding standardising and introducing techniques enabling diagnoses to be made in remote places, i.e., the loop-mediated isothermal amplification (LAMP) technique. This technique’s advantages include being able to perform it using simple equipment, diagnosis made directly in the field, low cost of each test and the technique’s high specificity. Using this technique could thus contribute toward neglected parasite infection (NPI) control and eradication programmes. This review describes the advances made to date regarding LAMP tests, as it has been found that even though several studies have been conducted concerning most NPI, information is scarce for others.

Measuring Environmental Exposure to Enteric Pathogens in Low-Income Settings: Review and Recommendations of an Interdisciplinary Working Group

Infections with enteric pathogens impose a heavy disease burden, especially among young children in low-income countries. Recent findings from randomized controlled trials of water, sanitation, and hygiene interventions have raised questions about current methods for assessing environmental exposure to enteric pathogens. Approaches for estimating sources and doses of exposure suffer from a number of shortcomings, including reliance on imperfect indicators of fecal contamination instead of actual pathogens and estimating exposure indirectly from imprecise measurements of pathogens in the environment and human interaction therewith. These shortcomings limit the potential for effective surveillance of exposures, identification of important sources and modes of transmission, and evaluation of the effectiveness of interventions. In this review, we summarize current and emerging approaches used to characterize enteric pathogen hazards in different environmental media as well as human interaction with those media (external measures of exposure), and review methods that measure human infection with enteric pathogens as a proxy for past exposure (internal measures of exposure). We draw from lessons learned in other areas of environmental health to highlight how external and internal measures of exposure can be used to more comprehensively assess exposure. We conclude by recommending strategies for advancing enteric pathogen exposure assessments.

Epidemiology of intestinal helminthiases in a rural community of Ethiopia: Is it time to expand control programs to include Strongyloides stercoralis and the entire community?

BACKGROUND

Soil transmitted helminths are highly prevalent worldwide. Globally, approximately 1.5 billion people are infected with Ascaris lumbricoides, Trichuris trichiura or hookworm. Endemic countries carry out periodic mass treatment of at-risk populations with albendazole or mebendazole as a control measure. Most prevalence studies have focused on school aged children and therefore control programs are implemented at school level, not at community level. In this study, the prevalence of intestinal helminths, including Strongyloides stercoralis, was examined using a comprehensive laboratory approach in a community in north-western Ethiopia.

METHODS

A cross-sectional survey was conducted on 792 individuals ≥5 years old in randomly selected houses in a rural district. Stools were examined using three techniques: a formol-ether concentration, the Baermann technique and a real time polymerase chain reaction test (these last two specific for S. stercoralis). Statistical analyses were performed between two large age groups, children (≤14 years old) and adults (≥15 years old).

RESULTS

The prevalence of helminths was 91.3%; (95% CI: 89.3-93.3%). Hookworm was the most prevalent, 78.7% (95% CI 75.6-81.4%), followed by S. stercoralis 55.7% (95% CI 52.2-59.1%). Co-infection with both was detected in 45.4% (95% CI 42.0-49.0%) of the participants. The mean age of hookworm-infected individuals was significantly higher than non-infected ones (p = 0.003). Also, S. stercoralis infection was significantly associated with age, being more prevalent in adults (p = 0.002).

CONCLUSIONS

This is the highest prevalence of S. stercoralis detected in Ethiopia so far. Our results highlight the need of searching specifically for infection by this parasite since it usually goes unnoticed if helminth studies rely only on conventional diagnostic techniques, i.e. Kato-Katz. Moreover, the focus of these programs on children undermines the actual prevalence of hookworm. The adult population acts as a reservoir for both hookworm and S. stercoralis and this fact may negatively impact the current control programs in Ethiopia which only target treatment of school aged children. This reservoir, together with a lack of adequate water, sanitation and hygiene, increases the probability of re-infection in children. Finally, the high prevalence of S. stercoralis found calls for a comprehensive diagnostic approach in endemic areas in addition to a revision of control measures that is, adding ivermectin to current albendazole/mebendazole, since it is the drug of choice for S. stercoralis.

A historical review of the techniques of recovery of parasites for their detection in human stools

Since the early 20th century, the detection of intestinal parasites has improved with the development of several techniques for parasitic structures recovery and identification, which differ in sensitivity, specificity, practicality, cost, and infrastructure demand. This study aims to review, in chronological order, the stool examination techniques and discuss their advantages, limitations, and perspectives, and to provide professionals and specialists in this field with data that lays a foundation for critical analysis on the use of such procedures. The concentration procedures that constitute the main techniques applied in routine research and in parasitological kits are a) spontaneous sedimentation; b) centrifugation-sedimentation with formalin-ethyl acetate; and c) flotation with zinc sulfate solution. While selecting a technique, one should consider the purpose of its application and the technical-operational, biological, and physicochemical factors inherent in the procedures used in stool processing, which may restrict its use. These intrinsic limitations may have undergone procedural changes driven by scientific and technological development and by development of alternative methods, which now contribute to the improvement of diagnostic accuracy.

Real-time detection and identification of nematode eggs genus and species through optical imaging

Nematode eggs are pervasive pathogens that infect billions of people and livestock every year. Adult parasitic nematode worms can be distinguished based on their size and morphology. However, their eggs, particularly their species Ascaris lumbricoides and Ascaris suum cannot be identified from each other. Identifying eggs of helminths from wastewater and sludge is important from a public health perspective to minimize the spread of Ascaris infections. Numerous methods exist for nematode identification, from a morphological-based approach to high throughput sequencing technology. However, these techniques are not consistent and often laborious and time-consuming. In this study, we demonstrate that non-invasive real-time identification of eggs is possible based on their intrinsic fluorescence. Using confocal microscopy, we investigate the autofluorescence properties of five species of nematode eggs and observe clear differences between genus and for the first time their species in sludge samples. This non-invasive imaging technique could lead to better understanding of these species and may assist in early control of diseases.

Development and evaluation of a loop-mediated isothermal amplification (LAMP) diagnostic test for detection of whipworm, Trichuris trichiura, in faecal samples

Whipworm infection or trichuriasis caused by Trichuris trichiura is of major public health concern in sub-Saharan Africa, particularly among pre-school and school-going children. It is among the neglected tropical diseases targeted for elimination through mass drug administration (MDA). One of the outcomes of MDA is a rapid decline in levels of infection intensity, making it difficult to monitor effectiveness of control measures using the conventional Kato-Katz procedure, which relies on the microscopic detection of parasite ova in faecal samples. In the present study, a loop-mediated isothermal amplification (LAMP) test was developed for the detection of T. trichiura infection in faecal samples. LAMP technology offers greater sensitivity and specificity than the microscopy-based tests. A set of four specific primers targeting the internal transcribed spacer 2 region of the ribosomal DNA were designed using Primer Explorer software. DNA was extracted from faecal samples using the alkaline lysis method (HotSHOT) and the LAMP reaction performed at 63°C for 1 h. The amplicons were visualized by both gel electrophoresis and with the naked eye following staining with SYBR green dye. Sensitivity and specificity tests were determined using the standard Kato-Katz diagnostic procedure as a reference test. The developed LAMP assay reliably detected T. trichiura DNA in faecal samples, with a specificity and sensitivity of 88% and 77%, respectively. No cross-reactivity was observed with several common helminth parasites. The developed LAMP assay is an appropriate diagnostic method for the detection of T. trichiura DNA in human faecal samples due to its simplicity, low cost, high sensitivity and specificity.

Drug discovery technologies: Caenorhabditis elegans as a model for anthelmintic therapeutics

Helminthiasis is one of the gravest problems worldwide. There is a growing concern on less available anthelmintics and the emergence of resistance creating a major threat to human and livestock health resources. Novel and broad-spectrum anthelmintics are urgently needed. The free-living nematode Caenorhabditis elegans could address this issue through automated high-throughput technologies for the screening of large chemical libraries. This review discusses the strong advantages and limitations for using C elegans as a screening method for anthelmintic drug discovery. C elegans is the best model available for the validation of novel effective drugs in treating most, if not all, helminth infections, and for the elucidation the mode of action of anthelmintic candidates. This review also focuses on available technologies in the discovery of anthelmintics published over the last 15 years with particular attention to high-throughput technologies over conventional screens. On the other hand, this review highlights how combinatorial and nanomedicine strategies could prolong the use of anthelmintics and control resistance problems.

Detection of Helminth Ova in Wastewater Using Recombinase Polymerase Amplification Coupled to Lateral Flow Strips

Ascaris lumbricoides is a major soil-transmitted helminth that is highly infective to humans. The ova of A. lumbricoides are able to survive wastewater treatment, thus making it an indicator organism for effective water treatment and sanitation. Hence, Ascaris ova must be removed from wastewater matrices for the safe use of recycled water. Current microscopic techniques for identification and enumeration of Ascaris ova are laborious and cumbersome. Polymerase chain reaction (PCR)-based techniques are sensitive and specific, however, major constraints lie in having to transport samples to a centralised laboratory, the requirement for sophisticated instrumentation and skilled personnel. To address this issue, a rapid, highly specific, sensitive, and affordable method for the detection of helminth ova was developed utilising recombinase polymerase amplification (RPA) coupled with lateral flow (LF) strips. In this study, Ascaris suum ova were used to demonstrate the potential use of the RPA-LF assay. The method was faster (< 30 min) with optimal temperature at 37 °C and greater sensitivity than PCR-based approaches with detection as low as 2 femtograms of DNA. Furthermore, ova from two different helminth genera were able to be detected as a multiplex assay using a single lateral flow strip, which could significantly reduce the time and the cost of helminth identification. The RPA-LF system represents an accurate, rapid, and cost-effective technology that could replace the existing detection methods, which are technically challenged and not ideal for on-site detection in wastewater treatment plants.

Sources of environmental contamination with Toxocara spp.: An omnipresent parasite

Embryonated Toxocara eggs in the environment are considered to be the most important source of human toxocariasis. These eggs, however, are also a source of infection for the definitive and paratenic hosts. Most available literature focuses on Toxocara canis in dogs, or other canids. There are, however, other Toxocara species with their accompanying definitive hosts. Results from studies that modelled patent infections in dogs, cats and foxes show that although dogs are a very important source for environmental contamination with Toxocara eggs, other sources cannot be ignored. For a good understanding of the relative contributions of different definitive hosts to environmental contamination with Toxocara eggs, computational models should be built and fed with data from different fields of expertise as is discussed in this paper.

Dry Taps? A Synthesis of Alternative "Wash" Methods in the Absence of Water and Sanitizers in the Prevention of Coronavirus in Low-Resource Settings

Objective: Social distancing and hand washing with soap and water have been advocated as the main proactive measures against the spread of coronavirus. We sought to find out what other alternative materials and methods would be used among populations without running water and who may not afford alcohol-based sanitizers. Results: We reviewed studies that reported use of sand, soil, ash, soda ash, seawater, alkaline materials, and sunlight as possible alternatives to handwashing with soap and water. We identified the documented mechanism of actions of these alternative wash methods on both inanimate surfaces and at cellular levels. The consideration of use of these alternative locally available in situations of unavailability of soap and water and alcohol-based sanitizers is timely in the face of coronavirus pandemic. Further randomized studies need to be carried out to evaluate the effectiveness of these alternatives in management of SARS-Cov-2.

Recent advances in nucleic acid-based methods for detection of helminth infections and the perspective of biosensors for future development

Pathogenic helminth infections are responsible for severe health problems and economic losses worldwide. Timely and accurate diagnosis of helminth infections is critical for adopting suitable strategies for pathogen control. Here, we review recent advances in nucleic acid-based diagnostic methods, including polymerase chain reaction, quantitative qPCR, loop-mediated isothermal amplification and recombinase polymerase amplification, and discuss their advantages and disadvantages for diagnosing helminth infections. In addition, we highlight recent advances in biosensors for the detection of nucleic acid biomarkers that can potentially be used for the diagnosis of helminth infection.

Viability determination of Ascaris ova in raw wastewater: a comparative evaluation of culture-based, BacLight Live/Dead staining and PMA-qPCR methods

Accurate evaluation of viable Ascaris ova in wastewater is the key to mitigating Ascaris reinfections in endemic regions. In this study, the viability of Ascaris ova in raw wastewater was determined using three different detection methods: culture-based, BacLight Live/Dead staining and propidium monoazide-quantitative polymerase chain reaction (PMA-qPCR). Furthermore, comparative assessment of viability utilising the aforementioned detection methods was performed using seeded experiments in wastewater. The percentage of viability was: culture-based (82%), BacLight Live/Dead staining (87%) and PMA-qPCR (85%) respectively. Despite the fact that no statistical difference was shown in the viability determination among the three methods, PMA-qPCR-based viability determination would be preferable over the other two methods for evaluating potential public health risks with A. suum ova due to its accuracy, being least subjective and its rapid reaction time.

Comparative assessment of DNA extraction procedures for Ascaris spp. eggs

A central and critical step in the molecular detection of soil-transmitted helminths from environmental sources is the extraction of DNA from the eggs. In this study, we investigated the yield of DNA extracted from known quantities (500, 100, 50, 20, 10 and 5) of Ascaris suum eggs, as well as directly from wastewater and sludge samples containing Ascaris spp. eggs, using six commercial DNA extraction kits. The amount of DNA extracted was quantified with NanoDrop, Qubit and Ct values from quantitative polymerase chain reaction (qPCR) assay using CFX96 Touch™ real-time PCR equipment. The PowerLyzer Ultraclean Microbial DNA isolation kit and PowerSoil DNA isolation kit gave the highest yield of DNA based on the NanoDrop, Qubit and Ct values. However, the qPCR results indicate that in some of the kits, PCR inhibitors may have been carried over to the PCR reaction. DNA extraction kits that incorporate a bead-beating step as well as other mechanical eggshell disruption steps were superior in extracting DNA from Ascaris spp. eggs. Additionally, for the accurate quantification of extracted DNA, the use of Ct values from qPCR and Qubit readings gives better results compared to the NanoDrop readings. For efficient downstream applications, the use of DNA extraction kits with superior inhibitor removal technology is essential, in addition to a high yield of DNA.

A Review on the Current Knowledge and Prospects for the Development of Improved Detection Methods for Soil-Transmitted Helminth Ova for the Safe Reuse of Wastewater and Mitigation of Public Health Risks

Climate change, increase in population and scarcity of freshwater have led to a global demand for wastewater reuse in irrigation. However, wastewater has to be treated in order to minimize the presence of pathogens, in particular, the ova of soil-transmitted helminthes (STHs). Limiting the transmission via removal of STH ova, accurate assessment of risks and minimizing the exposure to the public have been recommended by health regulators. The World Health Organization (WHO) guideline specifies a limit of ≤1 ova/L for safe wastewater reuse. Additionally, the Australian Guidelines for Water recycling (AGWR) recommend a hydraulic retention time of over 25 days in a lagoon or stabilization pond to ensure a 4 log reduction value of helminth ova and to mitigate soil-transmitted helminths associated risks to humans. However, the lack of fast and sensitive methods for assessing the concentration of STH ova in wastewater poses a considerable challenge for an accurate risk assessment. Consequently, it has been difficult to control soil-transmitted helminthiasis despite effective mass drug administration. This limitation can be overcome with the advent of novel techniques for the detection of helminth ova. Therefore, this review presents an assessment of the current methods to detect the viable ova of soil-transmitted helminths in wastewater. Furthermore, the review focuses on the perspectives for the emerging state-of-the-art research and developments that have the potential to replace currently available conventional and polymerase chain reaction based methods and achieve the guidelines of the WHO in order to allow the safe reuse of wastewater for non-potable applications, thereby minimizing public health risks.

Quantitative PCR-Based Diagnosis of Soil-Transmitted Helminth Infections: Faecal or Fickle?

Treatment and control programmes tackling soil-transmitted helminth (STH) infections require sensitive, reliable, and accurate diagnostic tools. There is a growing need for measures of infection intensity as programmes approach STH control. Quantitative real-time PCR (qPCR) is well suited to the detection of DNA targets present in stool, even in low-prevalence settings. Detecting low levels of infection becomes increasingly important when the breakpoint of transmission is approached, and is vital when monitoring for recrudescence once control, or possibly 'elimination', is achieved. We address key challenges and questions that remain as barriers to incorporating qPCR as a cornerstone diagnostic tool for STH infections.

Parasitological contamination with eggs Ascaris spp., Trichuris spp. and Toxocara spp. of dehydrated municipal sewage sludge in Poland

The objective of the present study was to evaluate the contamination of sewage sludge produced by municipal waste treatment plants in Poland by viable eggs of intestinal parasites of the genera Ascaris, Toxocara and Trichuris (ATT). Ninety-two municipal, mechanical-biological sewage treatment plants located within Poland were selected. These plants belonged to types of agglomerations: group 0 (large), group 1 (medium), group 2 (smaller) and group 3 (small). Samples were collected at the final stage of sewage treatment after the addition of flocculent to sludge, followed by dehydration. The samples were examined by a method adjusted to examine sewage sludge dehydrated using polyelectrolytes. The viability of the isolated eggs was evaluated based on incubation in a moist chamber. Live eggs of intestinal nematodes were found in 99% of samples. Most samples were contaminated by the eggs of Ascaris spp. (95%) and Toxocara spp. (96%). However, Trichuris spp. eggs were detected in 60% of samples. The mean number of eggs in 1 kg of dry mass (eggs/kg d.m.) was 5600 for Ascaris, 3700 for Toxocara and 1100 for Trichuris. The highest number of ATT eggs was detected in samples from sewage treatment plants located in south-eastern and central Poland. The highest number of ATT eggs was found in sewage sludge produced in large sewage treatment plants (agglomeration Groups 0 and 1), with mean values of 15,000 and 8900 eggs/kg d.m. The present study is the first parasitological investigation conducted on a large number of samples (92 samples) taken from various types of municipal sewage treatment plants located throughout Poland (16 regions) after the common introduction of polyelectrolytes during sewage sludge dehydration. The results of this study indicate that sludge produced in municipal sewage treatment plants is highly contaminated with parasite eggs.

Common workflow language (CWL)-based software pipeline for de novo genome assembly from long- and short-read data

BACKGROUND

Here, we created an automated pipeline for the de novoassembly of genomes from Pacific Biosciences long-read and Illumina short-read data using common workflow language (CWL). To evaluate the performance of this pipeline, we assembled the nuclear genomes of the eukaryotes Caenorhabditis elegans (∼100 Mb), Drosophila melanogaster (∼138 Mb), and Plasmodium falciparum (∼23 Mb) directly from publicly accessible nucleotide sequence datasets and assessed the quality of the assemblies against curated reference genomes.

FINDINGS

We showed a dependency of the accuracy of assembly on sequencing technology and GC content and repeatedly achieved assemblies that meet the high standards set by the National Human Genome Research Institute, being applicable to gene prediction and subsequent genomic analyses.

CONCLUSIONS

This CWL pipeline overcomes current challenges of achieving repeatability and reproducibility of assembly results and offers a platform for the re-use of the workflow and the integration of diverse datasets. This workflow is publicly available via GitHub (https://github.com/vetscience/Assemblosis) and is currently applicable to the assembly of haploid and diploid genomes of eukaryotes.

Shadow Puppets and Neglected Diseases: Evaluating a Health Promotion Performance in Rural Indonesia

'Rama and the Worm' is a shadow puppet production targeting neglected diseases in Central Java. It is an entertainment-based intervention study to promote health by reducing the impact of parasitic diseases such as soil-transmitted helminths (STH). The study uses traditional Javanese shadow puppetry (wayang kulit) as a vehicle in village communities to disseminate health messages and promote behaviour change to prevent diseases caused, primarily, by inadequate sanitation and poor hygiene. The health education messages contained in the play, although using traditional characters and themes, required the creation of a completely new narrative script, using characters and plot lines familiar to the wayang kulit repertoire, but placing them in new situations that relate specifically to health promotion objectives. The intervention was piloted in a village in Central Java, Indonesia using a pre/post design with both qualitative and quantitative analysis. A total of 96 male and female villagers, aged between 7 and 87 years, provided both baseline and follow up data. Participant knowledge and behaviours related to gastrointestinal and helminth-related disease were assessed before and after the intervention through a questionnaire administered by interview. Results revealed statistically significant improvements in both knowledge (48.6% pre-intervention score vs. 62.8% post-intervention score, p < 0.001) and behaviour (77.4% vs. 80.6%, p = 0.004) related to gastrointestinal and helminth disease. Findings of the study indicate the wayang kulit performance is an effective health education tool. The results provide proof of concept with scaling up the next step forward. The wayang kulit production provides a significant additional component for an integrated, comprehensive approach to reduction and elimination of STH infection.

Soil-Transmitted Helminths in Top Soils Used for Horticultural Purposes in Cape Coast, Ghana

This paper investigated the concentrations of eggs of three helminths (roundworm, hookworm, and whipworm) in the so-called black soils used for domestic and urban landscaping, home gardening and as growth medium for potted plants and pot experiments. The black soils are largely collected from active or abandoned waste dumpsites and fallowed or vegetated idle sites in the urban fringe or rural areas. Users buy black soils from dealers. Samples of black soils used for various purposes and at different places were collected for analysis of helminth eggs. The Modified EPA Method, which combines flotation and sedimentation, was used to isolate the eggs. The results show that these black soils have substantial loads of helminth eggs, with roundworm being dominant, followed by hookworm. Mean concentrations of helminth eggs were 2.45 (roundworm), 1.38 (hookworm), and 0.25 (whipworm) g^-1 soil, respectively. The helminth egg loads also declined with duration of use of the black soils. It is concluded that black soils used for horticultural purposes in Ghana can be a potential source of helminth infestation. Therefore, treatment of black soils, regulation of black soil market and use, and development of growth media industry should be important components of helminth control strategy.