Environmental DNA-based xenomonitoring for determining Schistosoma presence in tropical freshwaters

Methodological assessment for efficient collection of Schistosoma mansoni environmental DNA and improved schistosomiasis surveillance in tropical wetlands

Schistosomiasis, caused by trematodes of genus Schistosoma, is among the most seriously neglected tropical diseases. Although rapid surveillance of risk areas for Schistosoma transmission is vital to control schistosomiasis, the habitat and infection status of this parasite are difficult to assess. Environmental DNA (eDNA) analysis, involving the detection of extra-organismal DNA in water samples, facilitates cost-efficient and sensitive biomonitoring of aquatic environments and is a promising tool to identify Schistosoma habitat and infection risk areas. However, in tropical wetlands, highly turbid water causes filter clogging, thereby decreasing the filtration volume and increasing the risk of false negatives. Therefore, in this study, we aimed to conduct laboratory experiments and field surveys in Lake Victoria, Mbita, to determine the appropriate filter pore size for S. mansoni eDNA collection in terms of particle size and filtration volume. In the laboratory experiment, aquarium water was sequentially filtered using different pore size filters. Targeting >3 µm size fraction was found to be sufficient to capture S. mansoni eDNA particles, regardless of their life cycle stage (egg, miracidia, and cercaria). In the field surveys, GF/D (2.7 µm nominal pore size) filter yielded 2.5-times the filtration volume obtained with a smaller pore size filter and pre-filtration methods under the same time constraints. Moreover, a site-occupancy model was applied to the field detection results to estimate S. mansoni eDNA occurrence and detection probabilities and assess the number of water samples and PCR replicates necessary for efficient eDNA detection. Overall, this study reveals an effective method for S. mansoni eDNA detection in turbid water, facilitating the rapid and sensitive monitoring of its distribution and cost-effective identification of schistosomiasis transmission risk areas.

DNA Barcoding of Trichobilharzia (Trematoda: Schistosomatidae) Species and Their Detection in eDNA Water Samples

We designed and tested species-specific PCR primers to detect Trichobilharzia species via environmental DNA (eDNA) barcoding in selected Austrian water bodies. Tests were performed with eDNA samples from the field as well as with artificial samples from the lab, where snails releasing cercariae were kept in aquariums. From two localities, Trichobilharzia was documented based on the release of cercariae from snails, enabling morphological species identification. In both cases, the corresponding species were detected via eDNA: Trichobilharzia szidati and Trichobilharzia physellae. Nonetheless, the stochasticity was high in the replicates. PCR tests with aquarium water into which the cercariae had been released allowed eDNA detection even after 44 days. As in the PCRs with eDNA samples from the field, positive results of these experiments were not obtained for all samples and replicates. PCR sensitivity tests with dilution series of T. szidati genomic DNA as well as of PCR amplification products yielded successful amplification down to concentrations of 0.83 pg/µL and 0.008 pg/µL, respectively. Our results indicate that the presumed species specificity of PCR primers may not be guaranteed, even if primers were designed for specific species. This entails misidentification risks, particularly in areas with incomplete species inventories.

Assessment of schistosomiasis transmission in the River Nile at Greater Cairo using malacological surveys and cercariometry

Continuous field studies on the abundance and distribution of freshwater snails and cercarial populations are important for schistosomiasis control programs. In the present work, snail surveys and cercariometry were conducted for four successive seasons at 12 sites on the Nile River banks in the area of Greater Cairo to identify potential transmission foci for schistosomiasis. In addition, water physicochemical parameters were recorded. The results showed that the electrical conductivity, total dissolved solids, dissolved oxygen, and pH were within the permissible levels, except that the water temperature increased, especially in the spring season. Malacological surveys identified 10 native snail species at the studied sites of the Nile River, namely Bulinus truncatus, Biomphalaria alexandrina, Lymnaea natalensis, Lanistes carinatus, Cleopatra bulimoides, Melanoides tuberculata, Helisoma duryi, Bellamya unicolor, Physa acuta, Thedoxus niloticus, and one invasive snail species, Thiara scabra. The calculated diversity index indicated that the structure of snails' habitats was poor, while Evenness index indicated that the individuals were not distributed equally. Natural infection results identified no schistosome cercariae in B. truncatus and B. alexandrina. However, the cercariometry recovered Schistosoma cercariae in all the surveyed sites during all seasons with variable distribution. The preceding data suggest that there are still some active transmission foci for schistosomiasis infection in the Nile River. Moreover, the present finding highlights the importance of cercariomety as a complementary approach to snail samplings for identifying the transmission foci for schistosomiasis.

Environmental DNA study on aquatic ecosystem monitoring and management: Recent advances and prospects

Environmental DNA (eDNA) is organismal DNA that can be detected in the environment and is derived from cellular material of organisms shed into aquatic or terrestrial environments. It can be sampled and monitored using molecular methods, which is important for the early detection of invasive and native species as well as the discovery of rare and cryptic species. While few reviews have summarized the latest findings on eDNA for most aquatic animal categories in the aquatic ecosystem, especially for aquatic eDNA processing and application. In the present review, we first performed a bibliometric network analysis of eDNA studies on aquatic animals. Subsequently, we summarized the abiotic and biotic factors affecting aquatic eDNA occurrence. We also systematically discussed the relevant experiments and analyses of aquatic eDNA from various aquatic organisms, including fish, molluscans, crustaceans, amphibians, and reptiles. Subsequently, we discussed the major achievements of eDNA application in studies on the aquatic ecosystem and environment. The application of eDNA will provide an entirely new paradigm for biodiversity conservation, environment monitoring, and aquatic species management at a global scale.

Simplifying Schistosome Surveillance: Using Molecular Cercariometry to Detect and Quantify Cercariae in Water

Avian schistosomes are considered a public health nuisance due to their ability to cause swimmer’s itch when accidentally encountering humans rather than their intended avian hosts. Researchers have been monitoring their presence and abundance through snail collections and cercariometry. Cercariometry methods have evolved over the last several decades to detect individual schistosome species from a single water sample, simplifying the monitoring of these parasites. This methodological evolution coincides with the development of the field of environmental DNA (eDNA) where genetic material is extracted from environmental samples, rather than individual organisms. While there are some limitations with using molecular cercariometry, notably the cost and its inability to differentiate between life cycle stages, it substantially reduces the labor required to study trematode populations. It also can be used in complement with snail collections to understand the composition of avian schistosomes in an environment.

The particle size distribution of environmental DNA varies with species and degradation

Environmental DNA (eDNA) analysis is frequently used as a non-invasive method to investigate species and biodiversity in ecosystems. However, such eDNA may represent both organisms currently present as well as species that released their DNA some point in the past, thereby representing a mix of current and historic biodiversity. This may lead to a false-positive detection of organisms' presence. As the eDNA particle size distribution (PSD) changes along with the decay process, it may facilitate solving the above problem. Here, we set up tank experiments with snails, zebrafish and daphnids, respectively, to monitor the change in eDNA PSD and eDNA degradation through time after removing organisms. We found that zebrafish eDNA decays more slowly for larger particle sizes. Across all species tested, the percentage of large size ranges tended to increase over time while the smaller sizes showed relatively fast decay rates. As a result, PSD changed consistently with eDNA decay, although initial PSD varied between species. In combination, we propose that eDNA PSD can be used to assess the current prevalence of organisms at an eDNA sampling location while avoiding false-positives on the presence of species. Our findings expand the applicability of eDNA for monitoring target species in freshwater ecosystems.

Simultaneous genotyping of snails and infecting trematode parasites using high-throughput amplicon sequencing

Several methodological issues currently hamper the study of entire trematode communities within populations of their intermediate snail hosts. Here we develop a new workflow using high-throughput amplicon sequencing to simultaneously genotype snail hosts and their infecting trematode parasites. We designed primers to amplify four snail and five trematode markers in a single multiplex PCR. While also applicable to other genera, we focused on medically and economically important snail genera within the superorder Hygrophila and targeted a broad taxonomic range of parasites within the class Trematoda. We tested the workflow using 417 Biomphalaria glabrata specimens experimentally infected with Schistosoma rodhaini, two strains of Schistosoma mansoni and combinations thereof. We evaluated the reliability of infection diagnostics, the robustness of the workflow, its specificity related to host and parasite identification, and the sensitivity to detect co-infections, immature infections and changes of parasite biomass during the infection process. Finally, we investigated its applicability in wild-caught snails of other genera naturally infected with a diverse range of trematodes. After stringent quality control the workflow allows the identification of snails to species level, and of trematodes to taxonomic levels ranging from family to strain. It is sensitive to detect immature infections and changes in parasite biomass described in previous experimental studies. Co-infections were successfully identified, opening the possibility to examine parasite-parasite interactions such as interspecific competition. Together, these results demonstrate that our workflow provides a powerful tool to analyse the processes shaping trematode communities within natural snail populations.

Challenges and Opportunities Presented by Current Techniques for Detecting Schistosome Infections in Intermediate Host Snails: A Scoping Review

Schistosomiasis, a neglected tropical disease (NTD), causes morbidity and mortality in over 250 million people globally. And 700 million people are at risk of contracting it. It is caused by a parasite of the genus Schistosoma. Freshwater snails of the family Planorbidae are of public health significance as they are intermediate hosts of these highly infective flukes. Accurate diagnostic techniques to detect schistosome infections in intermediate host snails (IHS) and environmental surveillance are needed to institute measures for the interruption of transmission and eventual elimination. We carried out a systematic review of the literature to assess advantages and limitations of different diagnostic techniques for detecting schistosome infections in snails. Literature from Scopus, Web of Science, and PubMed databases from 2008 to 2020 were searched using combinations of predefined search terms with Boolean operators. The studies revealed that conventional diagnostics are widely used, although they are labor-intensive, have low specificity and sensitivity levels, and cannot detect prepatent infections. Whereas more advanced techniques such as immunological, nucleic-acid amplification, and eDNA diagnostics have high sensitivity and specificity levels, they are costly, hence, not suitable for field applications and large-scale surveys. Our review highlights the importance of designing and developing innovative diagnostics that are high in specificity and sensitivity as well as affordable and technically feasible for use in field laboratories and for large-scale surveys.

Piloting an integrated approach for estimation of environmental risk of Schistosoma haematobium infections in pre-school-aged children and their mothers at Barombi Kotto, Cameroon

Within schistosomiasis control, assessing environmental risk of currently non-treated demographic groups e.g. pre-school-aged children (PSAC) and their mothers is important. We conducted a pilot micro-epidemiological assessment at the crater lake of Barombi Kotto, Cameroon with GPS tracking and infection data from 12 PSAC-mother pairs (n = 24) overlaid against environmental sampling inclusive of snail, parasite and water-use information. Several high-risk locations or 'hotspots' with elevated water contact, increased intermediate snail host densities and detectable schistosome environmental DNA (eDNA) were identified. Exposure between PSAC and mother pairs was temporally and spatially associated, suggesting interventions which can benefit both groups simultaneously might be feasible. When attempting to interrupt parasite transmission in future, overlaid maps of snail, parasite and water contact data can guide fine-scale spatial targeting of environmental interventions.

Intestinal Schistosomiasis and Giardiasis Co-Infection in Sub-Saharan Africa: Can a One Health Approach Improve Control of Each Waterborne Parasite Simultaneously?

Both intestinal schistosomiasis and giardiasis are co-endemic throughout many areas of sub-Saharan Africa, significantly impacting the health of millions of children in endemic areas. While giardiasis is not considered a neglected tropical disease (NTD), intestinal schistosomiasis is formally grouped under the NTD umbrella and receives significant advocacy and financial support for large-scale control. Although there are differences in the epidemiology between these two diseases, there are also key similarities that might be exploited within potential integrated control strategies permitting tandem interventions. In this review, we highlight these similarities and discuss opportunities for integrated control of giardiasis in low and middle-income countries where intestinal schistosomiasis is co-endemic. By applying new, advanced methods of disease surveillance, and by improving the provision of water, sanitation and hygiene (WASH) initiatives, (co)infection with intestinal schistosomiasis and/or giardiasis could not only be more effectively controlled but also better understood. In this light, we appraise the suitability of a One Health approach targeting both intestinal schistosomiasis and giardiasis, for if adopted more broadly, transmission of both diseases could be reduced to gain improvements in health and wellbeing.