Schistosomiasis collection at NHM (SCAN)

Refining the Schistosoma haematobium recombinase polymerase amplification (Sh-RPA) assay: moving towards point-of-care use in endemic settings

BACKGROUND

Urogenital schistosomiasis is caused by the parasitic trematode Schistosoma haematobium. Sensitive and specific point-of-care diagnostics are needed for elimination of this disease. Recombinase polymerase amplification (RPA) assays meet these criteria, and an assay to diagnose S. haematobium has been developed (Sh-RPA). However, false-positive results can occur, and optimisation of reaction conditions to mitigate these is needed. Ease of use and compatibility of DNA extraction methods must also be considered.

METHODS

Using synthetic DNA, S. haematobium genomic DNA (gDNA), and urine samples from clinical cases, Sh-RPA reactions incorporating different betaine concentrations (0 M, 1 M, 2.5 M, 12.5 M) and the sample-to-water ratios were tested to determine effects on assay specificity and sensitivity. In addition, five commercial DNA extraction kits suitable for use in resource-limited settings were used to obtain gDNA from single S. haematobium eggs and evaluated in terms of DNA quality, quantity, and compatibility with the Sh-RPA assay. All samples were also evaluated by quantitative polymerase chain reaction (qPCR) to confirm DNA acquisition.

RESULTS

The analytical sensitivity of the Sh-RPA with all betaine concentrations was ≥ 10 copies of the synthetic Dra1 standard and 0.1 pg of S. haematobium gDNA. The addition of betaine improved Sh-RPA assay specificity in all reaction conditions, and the addition of 2.5 M of betaine together with the maximal possible sample volume of 12.7 µl proved to be the optimum reaction conditions. DNA was successfully isolated from a single S. haematobium egg using all five commercial DNA extraction kits, but the Sh-RPA performance of these kits varied, with one proving to be incompatible with RPA reactions.

CONCLUSIONS

The addition of 2.5 M of betaine to Sh-RPA reactions improved reaction specificity whilst having no detrimental effect on sensitivity. This increases the robustness of the assay, advancing the feasibility of using the Sh-RPA assay in resource-limited settings. The testing of commercial extraction kits proved that crude, rapid, and simple methods are sufficient for obtaining DNA from single S. haematobium eggs, and that these extracts can be used with Sh-RPA in most cases. However, the observed incompatibility of specific kits with Sh-RPA highlights the need for each stage of a molecular diagnostic platform to be robustly tested prior to implementation.

Extant interspecific hybridization among trematodes within the Schistosoma haematobium species complex in Nigeria

BACKGROUND

Natural interspecific hybridization between the human parasite (Schistosoma haematobium [Sh]) and bovine parasites (Schistosoma bovis [Sb], Schistosoma curassoni [Sc]) is increasingly reported in Africa. We developed a multi-locus PCR DNA-Seq strategy that amplifies two unlinked nuclear (transITS, BF) and two linked organellar genome markers (CO1, ND5) to genotype S. haematobium eggs collected from infected people in Ile Oluji/Oke Igbo, Ondo State (an agrarian community) and Kachi, Jigawa State (a pastoral community) in Southwestern and Northern Nigeria, respectively.

PRINCIPAL FINDINGS

Out of a total of 219 urine samples collected, 57 were positive for schistosomes. All patients from Jigawa state possessed an Sh mitochondrial genome and were infected with a genetic profile consistent with an Sh x Sb hybrid based on sequences obtained at CO1, ND5, transITS and BF nuclear markers. Whereas samples collected from Ondo state were more varied. Mitonuclear discordance was observed in all 17 patients, worms possessed an Sb mitochondrial genome but one of four different genetic profiles at the nuclear markers, either admixed (heterozygous between Sh x Sc or Sh x Sb) at both markers (n = 10), Sh at BF and admixed at transITS (Sh x Sc) (n = 5), admixed (Sh x Sc) at BF and homozygous Sc at transITS (n = 1) or homozygous Sh at BF and homozygous Sc at transITS (n = 1).

SIGNIFICANCE

Previous work suggested that zoonotic transmission of S. bovis in pastoral communities, where humans and animals share a common water source, is a driving factor facilitating interspecific hybridization. However, our data showed that all samples were hybrids, with greater diversity identified in Southwestern Nigeria, a non-pastoral site. Further, one patient possessed an S. bovis mitochondrial genome but was homozygous for S. haematobium at BF and homozygous for S. curassoni at transITS supporting at least two separate backcrosses in its origin, suggesting that interspecific hybridization may be an ongoing process.

Development, validation, and pilot application of a high throughput molecular xenomonitoring assay to detect Schistosoma mansoni and other trematode species within Biomphalaria freshwater snail hosts

Schistosomiasis is a neglected tropical disease (NTD) caused by infection with parasitic trematodes of the genus Schistosoma that can lead to debilitating morbidity and mortality. The World Health Organization recommend molecular xenomonitoring of Biomphalaria spp. freshwater snail intermediate hosts of Schistosoma mansoni to identify highly focal intestinal schistosomiasis transmission sites and monitor disease transmission, particularly in low-endemicity areas. A standardised protocol to do this, however, is needed. Here, two previously published primer sets were selected to develop and validate a multiplex molecular xenomonitoring end-point PCR assay capable of detecting S. mansoni infections within individual Biomphalaria spp. missed by cercarial shedding. The assay proved highly sensitive and highly specific in detecting and amplifying S. mansoni DNA and also proved highly sensitive in detecting and amplifying non-S. mansoni trematode DNA. The optimised assay was then used to screen Biomphalaria spp. collected from a S. mansoni-endemic area for infection and successfully detected S. mansoni infections missed by cercarial shedding as well as infections with non-S. mansoni trematodes. The continued development and use of molecular xenomonitoring assays such as this will aid in improving disease control efforts, significantly reducing disease-related morbidities experienced by those in schistosomiasis-endemic areas.

The long road to schistosomiasis elimination in Zanzibar: A systematic review covering 100 years of research, interventions and control milestones

Zanzibar is among the few places in sub-Saharan Africa where interruption of Schistosoma transmission seems an achievable goal. Our systematic review identifies and discusses milestones in schistosomiasis research, control and elimination efforts in Zanzibar over the past 100 years. The search in online databases, libraries, and the World Health Organization Archives revealed 153 records published between May 1928 and August 2022. The content of records was summarised to highlight the pivotal work leading towards urogenital schistosomiasis elimination and remaining research gaps. The greatest achievement following 100 years of schistosomiasis interventions and research is undoubtedly the improved health of Zanzibaris, exemplified by the reduction in Schistosoma haematobium prevalence from>50% historically down to<5% in 2020, and the absence of severe morbidities. Experiences from Zanzibar have contributed to global schistosomiasis guidelines, whilst also revealing challenges that impede progression towards elimination. Challenges include: transmission heterogeneity requiring micro-targeting of interventions, post-treatment recrudescence of infections in transmission hotspots, biological complexity of intermediate host snails, emergence of livestock Schistosoma species complicating surveillance whilst creating the risk for interspecies hybridisation, insufficient diagnostics performance for light intensity infections and female genital schistosomiasis, and a lack of acceptable sanitary alternatives to freshwater bodies. Our analysis of the past revealed that much can be achieved in the future with practical implementation of integrated interventions, alongside operational research. With continuing national and international commitments, interruption of S. haematobium transmission across both islands is within reach by 2030, signposting the future demise of urogenital schistosomiasis across other parts of sub-Saharan Africa.

CRISPR-assisted test for Schistosoma haematobium

Schistosomiasis is a major neglected tropical disease targeted for elimination as a public health issue by 2030, however there is an urgent need for more sensitive and specific diagnostic tests suitable to resource-limited settings. Here we developed CATSH, a CRISPR-assisted diagnostic test for Schistosoma haematobium, utilising recombinase polymerase amplification, Cas12a-targeted cleavage and portable real-time fluorescence detection. CATSH showed high analytical sensitivity, consistent detection of a single parasitic egg and specificity for urogenital Schistosoma species. Thanks to a novel CRISPR-compatible sample preparation developed using simulated urine samples containing parasitic eggs, CATSH had a sample-to-result within 2 h. The components of CATSH can be lyophilised, reducing cold chain dependence and widening access to lower and middle-income countries. This work presents a new application of CRISPR diagnostics for highly sensitive and specific detection of parasitic pathogens in remote areas and could have a significant impact on the elimination of neglected tropical diseases.

Advantages and Limitations of Microscopy and Molecular Detections for Diagnosis of Soil-transmitted Helminths: An Overview

World Health Organization (WHO) reported that over 1.5 billion people are infected by soil-transmitted helminths (STH) worldwide in sub-Saharan Africa, the United States of America, China, and East Asia. Heavy infections and polyparasitism are associated with higher morbidity rates, and the patients are exposed to increased vulnerability to other diseases. Therefore, accurate diagnosis followed by mass treatment for morbidity control is necessary.STH diagnosis commonly involves the microscopic observation of the presence of the STH eggs and larvae in the faecal samples. Furthermore, molecular approaches are increasingly utilised in monitoring and surveillance as they show higher sensitivity. Their capability to differentiate hookworm species is an advantage over the Kato-Katz technique. This review discusses the advantages and limitations of microscopy and various molecular tools used for STH detection.

Development of real-time and lateral flow recombinase polymerase amplification assays for rapid detection of Schistosoma mansoni

Background

Accurate diagnosis followed by timely treatment is an effective strategy for the prevention of complications together with reducing schistosomiasis transmission. Recombinase Polymerase Amplification (RPA) is a simple, rapid, sensitive, and specific isothermal method with low resource needs. This research aimed at the development and optimisation of a real-time (RT) and a lateral flow (LF) RPA assay for the detection of Schistosoma mansoni.

Methodology

Recombinase Polymerase Amplification reactions were performed at full- (as recommended) and half-volumes (to reduce costs), with RT or LF detection systems targeting the S. mansoni mitochondrial minisatellite region. The specificity was assessed using gDNA from other Schistosoma species, helminths co-endemic with S. mansoni, human stool, and urine, and Biomphalaria snail hosts. The analytical sensitivity was evaluated using serial dilutions of gDNA, synthetic copies of the target, and single eggs. The ability of both assays to detect the S. mansoni DNA in human urine and stool samples was also tested. The long-term stability of the RT-RPA reagents was evaluated by storing the reaction components in different temperature conditions for up to 3  weeks.

Results

The RT- and the LF-RPA (SmMIT- and SmMIT-LF-RPA, respectively) presented similar results when used full- and half-volumes, thus the latter was followed in all experiments. The SmMIT-RPA was 100% specific to S. mansoni, able to detect a single egg, with a limit of detection (LOD) of down to 1  fg of gDNA and one synthetic copy of the target. The assay was able to detect S. mansoni DNA from stool containing 1 egg/g and in spiked urine at a concentration of 10  fg/μl. SmMIT-RPA reagents were stable for up to 3  weeks when kept at 19°C, and 2  weeks when stored at 27°C. The SmMIT-LF-RPA cross-reacted with Clinostomidae, presented the LOD of 10  fg and one synthetic copy of the target, being able to detect a single egg and 1 egg/g in a stool sample. The LOD in spiked urine samples was 10  pg/μl.

Conclusion

The half-volume SmMIT-RPA is a promising method to be used in the field. It is specific, sensitive, robust, and tolerant to inhibitors, with a long-term stability of the reaction components and the real-time visualisation of results.

Genomic evidence of contemporary hybridization between Schistosoma species

Hybridization between different species of parasites is increasingly being recognised as a major public and veterinary health concern at the interface of infectious diseases biology, evolution, epidemiology and ultimately control. Recent research has revealed that viable hybrids and introgressed lineages between Schistosoma spp. are prevalent across Africa and beyond, including those with zoonotic potential. However, it remains unclear whether these hybrid lineages represent recent hybridization events, suggesting hybridization is ongoing, and/or whether they represent introgressed lineages derived from ancient hybridization events. In human schistosomiasis, investigation is hampered by the inaccessibility of adult-stage worms due to their intravascular location, an issue which can be circumvented by post-mortem of livestock at abattoirs for Schistosoma spp. of known zoonotic potential. To characterise the composition of naturally-occurring schistosome hybrids, we performed whole-genome sequencing of 21 natural livestock infective schistosome isolates. To facilitate this, we also assembled a de novo chromosomal-scale draft assembly of Schistosoma curassoni. Genomic analyses identified isolates of S. bovis, S. curassoni and hybrids between the two species, all of which were early generation hybrids with multiple generations found within the same host. These results show that hybridization is an ongoing process within natural populations with the potential to further challenge elimination efforts against schistosomiasis.

Schistosomiasis is a chronic and debilitating major neglected tropical disease affecting both humans and livestock. Increasingly, zoonotic spillover of livestock infections, facilitated by hybridization between different Schistosoma species, is increasingly being recognised as a risk to human health. Multiple surveys conducted within endemic regions have found a high prevalence of these hybrid lineages. However, it is often unclear whether these lineages are derived from recent hybridization events, suggesting hybridization is ongoing and may be linked to anthropogenic environmental change, or simply indicators of introgression from ancient hybridization events. To understand the origin and evolution of these hybrid lineages, we produced a chromosomal-scale assembly of Schistosoma curassoni and performed whole-genome sequencing of 21 natural livestock-infective S. curassoni, S. bovis and hybridized schistosome isolates, including multi-stage sampling from the same hosts. Our analyses exclusively identified early generation hybrid lineages, including multiple unrelated generations within the same hosts, suggesting that these hybrids are viable and derived from multiple independent hybridization events.

Transmission and diversity of Schistosoma haematobium and S. bovis and their freshwater intermediate snail hosts Bulinus globosus and B. nasutus in the Zanzibar Archipelago, United Republic of Tanzania

Background

The Zanzibar Archipelago (Pemba and Unguja islands) is targeted for the elimination of human urogenital schistosomiasis caused by infection with Schistosoma haematobium where the intermediate snail host is Bulinus globosus. Following multiple studies, it has remained unclear if B. nasutus (a snail species that occupies geographically distinct regions on the Archipelago) is involved in S. haematobium transmission on Zanzibar. Additionally, S. haematobium was thought to be the only Schistosoma species present on the Zanzibar Archipelago until the sympatric transmission of S. bovis, a parasite of ruminants, was recently identified. Here we re-assess the epidemiology of schistosomiasis on Pemba and Unguja together with the role and genetic diversity of the Bulinus spp. involved in transmission.

Methodology/Principal findings

Malacological and parasitological surveys were conducted between 2016 and 2019. In total, 11,116 Bulinus spp. snails were collected from 65 of 112 freshwater bodies surveyed. Bulinus species identification were determined using mitochondrial cox1 sequences for a representative subset of collected Bulinus (n = 504) and together with archived museum specimens (n = 6), 433 B. globosus and 77 B. nasutus were identified. Phylogenetic analysis of cox1 haplotypes revealed three distinct populations of B. globosus, two with an overlapping distribution on Pemba and one on Unguja. For B. nasutus, only a single clade with matching haplotypes was observed across the islands and included reference sequences from Kenya. Schistosoma haematobium cercariae (n = 158) were identified from 12 infected B. globosus and one B. nasutus collected between 2016 and 2019 in Pemba, and cercariae originating from 69 Bulinus spp. archived in museum collections. Schistosoma bovis cercariae (n = 21) were identified from seven additional B. globosus collected between 2016 and 2019 in Pemba. By analysing a partial mitochondrial cox1 region and the nuclear ITS (1–5.8S-2) rDNA region of Schistosoma cercariae, we identified 18 S. haematobium and three S. bovis haplotypes representing populations associated with mainland Africa and the Indian Ocean Islands (Zanzibar, Madagascar, Mauritius and Mafia).

Conclusions/Significance

The individual B. nasutus on Pemba infected with S. haematobium demonstrates that B. nasutus could also play a role in the local transmission of S. haematobium. We provide preliminary evidence that intraspecific variability of S. haematobium on Pemba may increase the transmission potential of S. haematobium locally due to the expanded intermediate host range, and that the presence of S. bovis complicates the environmental surveillance of schistosome infections.

Schistosomiasis is a snail-borne neglected tropical disease caused by parasitic blood flukes of the genus Schistosoma. Human urogenital schistosomiasis is targeted for elimination on the Zanzibar Archipelago, United Republic of Tanzania, with multiple interventions being implemented to curtail transmission of the parasite to humans on the islands since 2012. Environmental surveillance for schistosomiasis transmission by collecting intermediate host snails, checking snails for Schistosoma infection, and preserving collected snails and Schistosoma parasites offers the possibility for molecular analyses to investigate the evolutionary/genetic relationships of both snails and parasites. Schistosome transmission on Zanzibar was believed to involve a single schistosome species (Schistosoma haematobium) transmitted via a single intermediate host species (Bulinus globosus). However, our findings demonstrate the locally established presence of S. bovis, responsible for bovine intestinal schistosomiasis, and an extended intermediate host compatibility of S. haematobium with the snail B. nasutus on Pemba. Increased parasite diversity and intermediate host species compatibility may increase the transmission of Schistosoma species on Zanzibar and stretch resources for public health interventions with the need for Schistosoma species specific surveillance.

Chromosome-level genome of Schistosoma haematobium underpins genome-wide explorations of molecular variation

Urogenital schistosomiasis is caused by the blood fluke Schistosoma haematobium and is one of the most neglected tropical diseases worldwide, afflicting > 100 million people. It is characterised by granulomata, fibrosis and calcification in urogenital tissues, and can lead to increased susceptibility to HIV/AIDS and squamous cell carcinoma of the bladder. To complement available treatment programs and break the transmission of disease, sound knowledge and understanding of the biology and ecology of S. haematobium is required. Hybridisation/introgression events and molecular variation among members of the S. haematobium-group might effect important biological and/or disease traits as well as the morbidity of disease and the effectiveness of control programs including mass drug administration. Here we report the first chromosome-contiguous genome for a well-defined laboratory line of this blood fluke. An exploration of this genome using transcriptomic data for all key developmental stages allowed us to refine gene models (including non-coding elements) and annotations, discover ‘new’ genes and transcription profiles for these stages, likely linked to development and/or pathogenesis. Molecular variation within S. haematobium among some geographical locations in Africa revealed unique genomic ‘signatures’ that matched species other than S. haematobium, indicating the occurrence of introgression events. The present reference genome (designated Shae.V3) and the findings from this study solidly underpin future functional genomic and molecular investigations of S. haematobium and accelerate systematic, large-scale population genomics investigations, with a focus on improved and sustained control of urogenital schistosomiasis.

More than 100 million people are infected with the carcinogenic blood fluke Schistosoma haematobium, the aetiological agent of urogenital schistosomiasis—a neglected tropical disease (NTD). In spite of its major significance, little is known about this fluke, its interactions with the human and snail intermediate hosts and the pathogenesis of the urogenital form of schistosomiasis at the molecular and biochemical levels. To enable research in these areas, we report the first chromosome-level genome and markedly enhanced gene models for S. haematobium. Comparative genomic analyses also reveal evidence of past introgression events between or among closely related schistosome species. This present reference genome for S. haematobium and the findings from this study should underpin future functional genomic and molecular investigations of S. haematobium and accelerate systematic, large-scale population genomics investigations, with a focus on improved control of urogenital schistosomiasis.

High prevalence of urinary schistosomiasis in a desert population: results from an exploratory study around the Ounianga lakes in Chad

BACKGROUND

Researching a water-borne disease in the middle of the Sahara desert might not seem the most relevant concern. However, nomadic Sahelian pastoralists health concerns regarding their livestock and anecdotal reports about trematode infections of Fasciola spp. and Schistosoma spp. in desert-raised animals justified an exploratory study focusing on the lakes of Ounianga in Northern Chad. The aim was to test whether trematode parasites such as Schistosoma spp. occur in human populations living around the Sahara desert lakes of Ounianga Kebir and Ounianga Serir in northern Chad.

METHODS

The study was carried out in January 2019 and comprised of three components. First, a cross sectional survey based on a random sample drawn from the population to detect infections with S. haematobium and S. mansoni; second, focus group discussions exploring disease priorities, access to health and health seeking behaviour; and third, surveying water contact sites for intermediate host snails. Samples of trematode parasites and snails were confirmed on species level by molecular genetic methods. For parasitological and malacological surveys descriptive statistics were performed. Qualitative data analysis included the full review of all transcripts, followed by a descriptive and explorative thematic analysis.

RESULTS

Among 258 participants, the overall S. haematobium prevalence using urine filtration was 39.2% [95% confidence interval (CI): 33.5-45.1%], with 51.5% of the infected suffering from heavy infection. The intermediate host snail of S. haematobium (Bulinus truncatus) occurred at water contact sites near both study villages, revealing the potential for local transmission. Although a positive S. mansoni point-of-care circulating cathodic antigen (POC-CCA) test result was obtained from 8.6% (95% CI 5.7-12.8%) of the samples, no intermediate host snails of S. mansoni were found, and the relevance of S. mansoni remains uncertain. Qualitative findings underline the importance of morbidity caused by urinary schistosomiasis, and the lack of access to diagnostics and treatment as a major health concern.

CONCLUSIONS

This research revealed a high prevalence of urinary schistosomiasis in the population living around the lakes of Ounianga in the Sahara, a United Nations Educational, Scientific and Cultural Organization (UNESCO) world heritage site in Chad. Despite the high public health importance of the associated morbidity expressed by the population, there is no access to diagnostics and treatment. Further work is needed to develop and test a context-adapted intervention.

Integrating genomic and epidemiologic data to accelerate progress toward schistosomiasis elimination

The global community has adopted ambitious goals to eliminate schistosomiasis as a public health problem, and new tools are needed to achieve them. Mass drug administration programs, for example, have reduced the burden of schistosomiasis, but the identification of hotspots of persistent and reemergent transmission threaten progress toward elimination and underscore the need to couple treatment with interventions that reduce transmission. Recent advances in DNA sequencing technologies make whole-genome sequencing a valuable and increasingly feasible option for population-based studies of complex parasites such as schistosomes. Here, we focus on leveraging genomic data to tailor interventions to distinct social and ecological circumstances. We consider two priority questions that can be addressed by integrating epidemiological, ecological, and genomic information: (1) how often do non-human host species contribute to human schistosome infection? and (2) what is the importance of locally acquired versus imported infections in driving transmission at different stages of elimination? These questions address processes that can undermine control programs, especially those that rely heavily on treatment with praziquantel. Until recently, these questions were difficult to answer with sufficient precision to inform public health decision-making. We review the literature related to these questions and discuss how whole-genome approaches can identify the geographic and taxonomic sources of infection, and how such information can inform context-specific efforts that advance schistosomiasis control efforts and minimize the risk of reemergence.

Genetic analysis of praziquantel response in schistosome parasites implicates a transient receptor potential channel

[Figure: see text].

Development of a novel real-time polymerase chain reaction assay for the sensitive detection of Schistosoma japonicum in human stool

BACKGROUND

Elimination and control of Schistosoma japonicum, the most virulent of the schistosomiasis-causing blood flukes, requires the development of sensitive and specific diagnostic tools capable of providing an accurate measurement of the infection prevalence in endemic areas. Typically, detection of S. japonicum has occurred using the Kato-Katz technique, but this methodology, which requires skilled microscopists, has been shown to radically underestimate levels of infection. With the ever-improving capabilities of next-generation sequencing and bioinformatic analysis tools, identification of satellite sequences and other highly repetitive genomic elements for use as real-time PCR diagnostic targets is becoming increasingly common. Assays developed using these targets have the ability to improve the sensitivity and specificity of results for epidemiological studies that can in turn be used to inform mass drug administration and programmatic decision making.

METHODOLOGY/PRINCIPAL FINDINGS

Utilizing Tandem Repeat Analyzer (TAREAN) and RepeatExplorer2, a cluster-based analysis of the S. japonicum genome was performed and a tandemly arranged genomic repeat, which we named SjTR1 (Schistosoma japonicum Tandem Repeat 1), was selected as the target for a real-time PCR diagnostic assay. Based on these analyses, a primer/probe set was designed and the assay was optimized. The resulting real-time PCR test was shown to reliably detect as little as 200 ag of S. japonicum genomic DNA and as little as 1 egg per gram of human stool. Based on these results, the index assay reported in this manuscript is more sensitive than previously published real-time PCR assays for the detection of S. japonicum.

CONCLUSIONS/SIGNIFICANCE

The extremely sensitive and specific diagnostic assay described in this manuscript will facilitate the accurate detection of S. japonicum, particularly in regions with low levels of endemicity. This assay will be useful in providing data to inform programmatic decision makers, aiding disease control and elimination efforts.

Whole-genome sequencing of Schistosoma mansoni reveals extensive diversity with limited selection despite mass drug administration

Control and elimination of the parasitic disease schistosomiasis relies on mass administration of praziquantel. Whilst these programmes reduce infection prevalence and intensity, their impact on parasite transmission and evolution is poorly understood. Here we examine the genomic impact of repeated mass drug administration on Schistosoma mansoni populations with documented reduced praziquantel efficacy. We sequenced whole-genomes of 198 S. mansoni larvae from 34 Ugandan children from regions with contrasting praziquantel exposure. Parasites infecting children from Lake Victoria, a transmission hotspot, form a diverse panmictic population. A single round of treatment did not reduce this diversity with no apparent population contraction caused by long-term praziquantel use. We find evidence of positive selection acting on members of gene families previously implicated in praziquantel action, but detect no high frequency functionally impactful variants. As efforts to eliminate schistosomiasis intensify, our study provides a foundation for genomic surveillance of this major human parasite.

Identification of Snails and Schistosoma of Medical Importance via Convolutional Neural Networks: A Proof-of-Concept Application for Human Schistosomiasis

In recent decades, computer vision has proven remarkably effective in addressing diverse issues in public health, from determining the diagnosis, prognosis, and treatment of diseases in humans to predicting infectious disease outbreaks. Here, we investigate whether convolutional neural networks (CNNs) can also demonstrate effectiveness in classifying the environmental stages of parasites of public health importance and their invertebrate hosts. We used schistosomiasis as a reference model. Schistosomiasis is a debilitating parasitic disease transmitted to humans via snail intermediate hosts. The parasite affects more than 200 million people in tropical and subtropical regions. We trained our CNN, a feed-forward neural network, on a limited dataset of 5,500 images of snails and 5,100 images of cercariae obtained from schistosomiasis transmission sites in the Senegal River Basin, a region in western Africa that is hyper-endemic for the disease. The image set included both images of two snail genera that are relevant to schistosomiasis transmission – that is, Bulinus spp. and Biomphalaria pfeifferi – as well as snail images that are non-component hosts for human schistosomiasis. Cercariae shed from Bi. pfeifferi and Bulinus spp. snails were classified into 11 categories, of which only two, S. haematobium and S. mansoni, are major etiological agents of human schistosomiasis. The algorithms, trained on 80% of the snail and parasite dataset, achieved 99% and 91% accuracy for snail and parasite classification, respectively, when used on the hold-out validation dataset – a performance comparable to that of experienced parasitologists. The promising results of this proof-of-concept study suggests that this CNN model, and potentially similar replicable models, have the potential to support the classification of snails and parasite of medical importance. In remote field settings where machine learning algorithms can be deployed on cost-effective and widely used mobile devices, such as smartphones, these models can be a valuable complement to laboratory identification by trained technicians. Future efforts must be dedicated to increasing dataset sizes for model training and validation, as well as testing these algorithms in diverse transmission settings and geographies.

Multihost Transmission of Schistosoma mansoni in Senegal, 2015-2018

In West Africa, Schistosoma spp. are capable of infecting multiple definitive hosts, a lifecycle feature that may complicate schistosomiasis control. We characterized the evolutionary relationships among multiple Schistosoma mansoni isolates collected from snails (intermediate hosts), humans (definitive hosts), and rodents (definitive hosts) in Senegal. On a local scale, diagnosis of S. mansoni infection ranged 3.8%-44.8% in school-aged children, 1.7%-52.6% in Mastomys huberti mice, and 1.8%-7.1% in Biomphalaria pfeifferi snails. Our phylogenetic framework confirmed the presence of multiple S. mansoni lineages that could infect both humans and rodents; divergence times of these lineages varied (0.13-0.02 million years ago). We propose that extensive movement of persons across West Africa might have contributed to the establishment of these various multihost S. mansoni clades. High S. mansoni prevalence in rodents at transmission sites frequented by humans further highlights the implications that alternative hosts could have on future public health interventions.

Diverging patterns of introgression from Schistosoma bovis across S. haematobium African lineages

Hybridization is a fascinating evolutionary phenomenon that raises the question of how species maintain their integrity. Inter-species hybridization occurs between certain Schistosoma species that can cause important public health and veterinary issues. In particular hybrids between Schistosoma haematobium and S. bovis associated with humans and animals respectively are frequently identified in Africa. Recent genomic evidence indicates that some S. haematobium populations show signatures of genomic introgression from S. bovis. Here, we conducted a genomic comparative study and investigated the genomic relationships between S. haematobium, S. bovis and their hybrids using 19 isolates originating from a wide geographical range over Africa, including samples initially classified as S. haematobium (n = 11), S. bovis (n = 6) and S. haematobium x S. bovis hybrids (n = 2). Based on a whole genomic sequencing approach, we developed 56,181 SNPs that allowed a clear differentiation of S. bovis isolates from a genomic cluster including all S. haematobium isolates and a natural S. haematobium-bovis hybrid. All the isolates from the S. haematobium cluster except the isolate from Madagascar harbored signatures of genomic introgression from S. bovis. Isolates from Corsica, Mali and Egypt harbored the S. bovis-like Invadolysin gene, an introgressed tract that has been previously detected in some introgressed S. haematobium populations from Niger. Together our results highlight the fact that introgression from S. bovis is widespread across S. haematobium and that the observed introgression is unidirectional.

Hybridization is a fascinating evolutionary phenomenon that raises the question of how species maintain their integrity. Inter-species hybridization occurs between certain Schistosoma species that can cause important public health and veterinary issues. In particular hybrids between Schistosoma haematobium and S. bovis associated with humans and animals respectively are frequently identified in Africa. Recent genomic evidence indicates that some S. haematobium populations show signatures of genomic introgression from S. bovis. Here we conducted a comparative genomic study to assess the genomic diversity within S. haematobium and S. bovis species and genetic differentation at the genome scale between these two sister species over the African continent. We also investigated traces of possible ancient introgression from one species to another. We found that S. haematobium display low genetic diversity compared to S. bovis. We also found that most S. haematobium samples harbor signature of past introgression with S. bovis at some genomic positions. Our results strongly suggest that introgression occurred long time ago and that such introgression is unidirectional from S. bovis within S. haematobium. Such introgresssion event(s) result in diverging patterns of genomic introgression across S. haematobium lineages.

Preserve a Voucher Specimen! The Critical Need for Integrating Natural History Collections in Infectious Disease Studies

Despite being nearly 10 months into the COVID-19 (coronavirus disease 2019) pandemic, the definitive animal host for SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), the causal agent of COVID-19, remains unknown. Unfortunately, similar problems exist for other betacoronaviruses, and no vouchered specimens exist to corroborate host species identification for most of these pathogens. This most basic information is critical to the full understanding and mitigation of emerging zoonotic diseases. To overcome this hurdle, we recommend that host-pathogen researchers adopt vouchering practices and collaborate with natural history collections to permanently archive microbiological samples and host specimens. Vouchered specimens and associated samples provide both repeatability and extension to host-pathogen studies, and using them mobilizes a large workforce (i.e., biodiversity scientists) to assist in pandemic preparedness. We review several well-known examples that successfully integrate host-pathogen research with natural history collections (e.g., yellow fever, hantaviruses, helminths). However, vouchering remains an underutilized practice in such studies. Using an online survey, we assessed vouchering practices used by microbiologists (e.g., bacteriologists, parasitologists, virologists) in host-pathogen research. A much greater number of respondents permanently archive microbiological samples than archive host specimens, and less than half of respondents voucher host specimens from which microbiological samples were lethally collected. To foster collaborations between microbiologists and natural history collections, we provide recommendations for integrating vouchering techniques and archiving of microbiological samples into host-pathogen studies. This integrative approach exemplifies the premise underlying One Health initiatives, providing critical infrastructure for addressing related issues ranging from public health to global climate change and the biodiversity crisis.

Schistosomiasis Consortium for Operational Research and Evaluation (SCORE): Its Foundations, Development, and Evolution

The Schistosomiasis Consortium for Operational Research and Evaluation (SCORE) was established in late 2008 to conduct operational research that would inform practices related to the control and elimination of schistosomiasis. This article traces SCORE’s beginnings and underpinnings. These include an emphasis on openness and contributing to the development of a cohesive schistosomiasis control community, building linkages between researchers and national programs, and focusing on answering questions that will help Neglected Tropical Disease program managers to better control and eliminate schistosomiasis. It describes the development and implementation of SCORE’s multiple projects. SCORE began by drawing on advice from a broad range of experts by holding wide-ranging meetings that informed the priorities and protocols for SCORE research. SCORE’s major efforts included large, multicountry field studies comparing multiple strategies for mass drug administration with praziquantel, assessment of approaches to elimination, evaluation of a point-of-care assay for field mapping Schistosoma mansoni, and increasing the sensitivity of a laboratory-based diagnostic. SCORE also supported studies on morbidity due to schistosomiasis, quantification of vector snails and the detection of schistosome infections in snails, and changes in schistosome population genetics under praziquantel drug pressure. SCORE data and specimens are archived and will remain available for future research. Although much remains to be carried out, our hope is that through the already published articles and SCORE results described in this supplement, we will have provided a body of evidence to assist policy makers in the development of judicious guidelines for the control and elimination of schistosomiasis.

Parasite Population Genetic Contributions to the Schistosomiasis Consortium for Operational Research and Evaluation within Sub-Saharan Africa

Analyses of the population genetic structure of schistosomes under the "Schistosomiasis Consortium for Operational Research and Evaluation" (SCORE) contrasting treatment pressure scenarios in Tanzania, Niger, and Zanzibar were performed to provide supplementary critical information with which to evaluate the impact of these large-scale control activities and guide how activities could be adjusted. We predicted that population genetic analyses would reveal information on a range of important parameters including, but not exclusive to, recruitment and transmission of genotypes, occurrence of hybridization events, differences in reproductive mode, and degrees of inbreeding, and hence, the evolutionary potential, and responses of parasite populations under contrasting treatment pressures. Key findings revealed that naturally high levels of gene flow and mixing of the parasite populations between neighboring sites were likely to dilute any effects imposed by the SCORE treatment arms. Furthermore, significant inherent differences in parasite fecundity were observed, independent of current treatment arm, but potentially of major impact in terms of maintaining high levels of ongoing transmission in persistent "biological hotspot" sites. Within Niger, naturally occurring Schistosoma haematobium/Schistosoma bovis viable hybrids were found to be abundant, often occurring in significantly higher proportions than that of single-species S. haematobium infections. By examining parasite population genetic structures across hosts, treatment regimens, and the spatial landscape, our results to date illustrate key transmission processes over and above that which could be achieved through standard parasitological monitoring of prevalence and intensity alone, as well as adding to our understanding of Schistosoma spp. life history strategies in general.

Contributions of the Schistosomiasis Consortium for Operational Research and Evaluation (SCORE) to Schistosomiasis Control and Elimination: Key Findings and Messages for Future Goals, Thresholds, and Operational Research

Herein, we summarize what we consider are major contributions resulting from the Schistosomiasis Consortium for Operational Research and Evaluation (SCORE) program, including its key findings and key messages from those findings. Briefly, SCORE's key findings are as follows: i) biennial mass drug administration (MDA) with praziquantel can control schistosomiasis to moderate levels of prevalence; ii) MDA alone will not achieve elimination; iii) to attain and sustain control throughout endemic areas, persistent hotspots need to be identified following a minimal number of years of annual MDA and controlled through adaptive strategies; iv) annual MDA is more effective than biennial MDA in high-prevalence areas; v) the current World Health Organization thresholds for decision-making based on the prevalence of heavy infections should be redefined; and vi) point-of-care circulating cathodic antigen urine assays are useful for Schistosoma mansoni mapping in low-to-moderate prevalence areas. The data and specimens collected and curated through SCORE efforts will continue to be critical resource for future research. Besides providing useful information for program managers and revision of guidelines for schistosomiasis control and elimination, SCORE research and outcomes have identified additional questions that need to be answered as the schistosomiasis community continues to implement effective, evidence-based programs. An overarching contribution of SCORE has been increased cohesiveness within the schistosomiasis field-oriented community, thereby fostering new and productive collaborations. Based on SCORE's findings and experiences, we propose new approaches, thresholds, targets, and goals for control and elimination of schistosomiasis, and recommend research and evaluation activities to achieve these targets and goals.

Analytical and Clinical Assessment of a Portable, Isothermal Recombinase Polymerase Amplification (RPA) Assay for the Molecular Diagnosis of Urogenital Schistosomiasis

Accurate diagnosis of urogenital schistosomiasis is crucial for disease surveillance and control. Routine diagnostic methods, however, lack sensitivity when assessing patients with low levels of infection still able to maintain pathogen transmission. Therefore, there is a need for highly sensitive diagnostic tools that can be used at the point-of-care in endemic areas. Recombinase polymerase amplification (RPA) is a rapid and sensitive diagnostic tool that has been used to diagnose several pathogens at the point-of-care. Here, the analytical performance of a previously developed RPA assay (RT-ShDra1-RPA) targeting the Schistosoma haematobium Dra1 genomic region was assessed using commercially synthesised S. haematobium Dra1 copies and laboratory-prepared samples spiked with S. haematobium eggs. Clinical performance was also assessed by comparing diagnostic outcomes with that of a reference diagnostic standard, urine-egg microscopy. The RT-ShDra1-RPA was able to detect 1 × 10¹ copies of commercially synthesised Dra1 DNA as well as one S. haematobium egg within laboratory-spiked ddH₂O samples. When compared with urine-egg microscopy, the overall sensitivity and specificity of the RT-ShDra1-RPA assay was 93.7% (±88.7–96.9) and 100% (±69.1–100), respectively. Positive and negative predictive values were 100% (±97.5–100) and 50% (±27.2–72.8), respectively. The RT-ShDra1-RPA therefore shows promise as a rapid and highly sensitive diagnostic tool able to diagnose urogenital schistosomiasis at the point-of-care.

Development of a Molecular Snail Xenomonitoring Assay to Detect Schistosoma haematobium and Schistosoma bovis Infections in their Bulinus Snail Hosts

Schistosomiasis, a neglected tropical disease of medical and veterinary importance, transmitted through specific freshwater snail intermediate hosts, is targeted for elimination in several endemic regions in sub-Saharan Africa. Multi-disciplinary methods are required for both human and environmental diagnostics to certify schistosomiasis elimination when eventually reached. Molecular xenomonitoring protocols, a DNA-based detection method for screening disease vectors, have been developed and trialed for parasites transmitted by hematophagous insects, such as filarial worms and trypanosomes, yet few have been extensively trialed or proven reliable for the intermediate host snails transmitting schistosomes. Here, previously published universal and Schistosoma-specific internal transcribed spacer (ITS) rDNA primers were adapted into a triplex PCR primer assay that allowed for simple, robust, and rapid detection of Schistosoma haematobium and Schistosoma bovis in Bulinus snails. We showed this two-step protocol could sensitively detect DNA of a single larval schistosome from experimentally infected snails and demonstrate its functionality for detecting S. haematobium infections in wild-caught snails from Zanzibar. Such surveillance tools are a necessity for succeeding in and certifying the 2030 control and elimination goals set by the World Health Organization.

Snail-Related Contributions from the Schistosomiasis Consortium for Operational Research and Evaluation Program Including Xenomonitoring, Focal Mollusciciding, Biological Control, and Modeling

The Schistosomiasis Consortium for Operational Research and Evaluation (SCORE) was created in 2008 to answer questions of importance to program managers working to reduce the burden of schistosomiasis in Africa. In the past, intermediate host snail monitoring and control was an important part of integrated schistosomiasis control. However, in Africa, efforts to control snails have declined dramatically over the last 30 years. A resurgence of interest in the control of snails has been prompted by the realization, backed by a World Health Assembly resolution (WHA65.21), that mass drug administration alone may be insufficient to achieve schistosomiasis elimination. SCORE has supported work on snail identification and mapping and investigated how xenomonitoring techniques can aid in the identification of infected snails and thereby identify potential transmission areas. Focal mollusciciding with niclosamide was undertaken in Zanzibar and Côte d'Ivoire as a part of elimination studies. Two studies involving biological control of snails were conducted: one explored the association of freshwater riverine prawns and snail hosts in Côte d'Ivoire and the other assessed the current distribution of Procambarus clarkii, the invasive Louisiana red swamp crayfish, in Kenya and its association with snail hosts and schistosomiasis transmission. SCORE also supported modeling studies on the importance of snail control in achieving elimination and a meta-analysis of the impact of molluscicide-based snail control programs on human schistosomiasis prevalence and incidence. SCORE's snail control studies contributed to increased investment in building capacity, and specimens collected during SCORE research deposited in the Schistosomiasis Collections at the Natural History Museum (SCAN) will provide a valuable resource for the years to come.

Interactions between Schistosoma haematobium group species and their Bulinus spp. intermediate hosts along the Niger River Valley

Background

Urogenital schistosomiasis, caused by infection with Schistosoma haematobium, is endemic in Niger but complicated by the presence of Schistosoma bovis, Schistosoma curassoni and S. haematobium group hybrids along with various Bulinus snail intermediate host species. Establishing the schistosomes and snails involved in transmission aids disease surveillance whilst providing insights into snail-schistosome interactions/compatibilities and biology.

Methods

Infected Bulinus spp. were collected from 16 villages north and south of the Niamey region, Niger, between 2011 and 2015. From each Bulinus spp., 20–52 cercariae shed were analysed using microsatellite markers and a subset identified using the mitochondrial (mt) cox1 and nuclear ITS1 + 2 and 18S DNA regions. Infected Bulinus spp. were identified using both morphological and molecular analysis (partial mt cox1 region).

Results

A total of 87 infected Bulinus from 24 sites were found, 29 were molecularly confirmed as B. truncatus, three as B. forskalii and four as B. globosus. The remaining samples were morphologically identified as B. truncatus (n = 49) and B. forskalii (n = 2). The microsatellite analysis of 1124 cercariae revealed 186 cercarial multilocus genotypes (MLGs). Identical cercarial genotypes were frequently (60%) identified from the same snail (clonal populations from a single miracidia); however, several (40%) of the snails had cercariae of different genotypes (2–10 MLG’s) indicating multiple miracidial infections. Fifty-seven of the B. truncatus and all of the B. forskalii and B. globosus were shedding the Bovid schistosome S. bovis. The other B. truncatus were shedding the human schistosomes, S. haematobium (n = 6) and the S. haematobium group hybrids (n = 13). Two B. truncatus had co-infections with S. haematobium and S. haematobium group hybrids whilst no co-infections with S. bovis were observed.

Conclusions

This study has advanced our understanding of human and bovid schistosomiasis transmission in the Niger River Valley region. Human Schistosoma species/forms (S. haematobium and S. haematobium hybrids) were found transmitted only in five villages whereas those causing veterinary schistosomiasis (S. bovis), were found in most villages. Bulinus truncatus was most abundant, transmitting all Schistosoma species, while the less abundant B. forskalii and B. globosus, only transmitted S. bovis. Our data suggest that species-specific biological traits may exist in relation to co-infections, snail-schistosome compatibility and intramolluscan schistosome development.

No barrier breakdown between human and cattle schistosome species in the Senegal River Basin in the face of hybridisation

Schistosomiasis is widely distributed along the Senegal River Basin (SRB), affecting both the human population and their livestock. Damming of the Senegal River for irrigation purposes in the 1980s induced ecological changes that resulted in a large outbreak of Schistosoma mansoni, followed a few years later by an increase and spread of Schistosoma haematobium infections. The presence of hybrid crosses between the human and cattle schistosomes, S. haematobium and Schistosoma bovis, respectively, is adding complexity to the disease epidemiology in this area, and questions the strength of the species boundary between these two species. This study aimed to investigate the epidemiology of S. haematobium, S. bovis and their hybrids along the Senegal River basin using both microsatellite genetic markers and analysis of mitochondrial and nuclear DNA markers. Human schistosome populations with a S. haematobium cox1 mtDNA profile and those with a S. bovis cox1 mtDNA profile (the so-called hybrids) appear to belong to a single randomly mating population, strongly differentiated from the pure S. bovis found in cattle. These results suggest that, in northern Senegal, a strong species boundary persists between human and cattle schistosome species and there is no prolific admixing of the populations. In addition, we found that in the SRB S. haematobium was spatially more differentiated in comparison to S. mansoni. This may be related either to the presence and susceptibility of the intermediate snail hosts, or to the colonisation history of the parasite.

Precision mapping of snail habitat provides a powerful indicator of human schistosomiasis transmission

Recently, the World Health Organization recognized that efforts to interrupt schistosomiasis transmission through mass drug administration have been ineffective in some regions; one of their new recommended strategies for global schistosomiasis control emphasizes targeting the freshwater snails that transmit schistosome parasites. We sought to identify robust indicators that would enable precision targeting of these snails. At the site of the world's largest recorded schistosomiasis epidemic-the Lower Senegal River Basin in Senegal-intensive sampling revealed positive relationships between intermediate host snails (abundance, density, and prevalence) and human urogenital schistosomiasis reinfection (prevalence and intensity in schoolchildren after drug administration). However, we also found that snail distributions were so patchy in space and time that obtaining useful data required effort that exceeds what is feasible in standard monitoring and control campaigns. Instead, we identified several environmental proxies that were more effective than snail variables for predicting human infection: the area covered by suitable snail habitat (i.e., floating, nonemergent vegetation), the percent cover by suitable snail habitat, and size of the water contact area. Unlike snail surveys, which require hundreds of person-hours per site to conduct, habitat coverage and site area can be quickly estimated with drone or satellite imagery. This, in turn, makes possible large-scale, high-resolution estimation of human urogenital schistosomiasis risk to support targeting of both mass drug administration and snail control efforts.

Development of a recombinase polymerase amplification (RPA) fluorescence assay for the detection of Schistosoma haematobium

Background

Accurate diagnosis of urogenital schistosomiasis is vital for surveillance and control programmes. While a number of diagnostic techniques are available there is a need for simple, rapid and highly sensitive point-of-need (PON) tests in areas where infection prevalence and intensity are low. Recombinase Polymerase Amplification (RPA) is a sensitive isothermal molecular diagnostic technology that is rapid, portable and has been used at the PON for several pathogens.

Results

A real time fluorescence RPA assay (RT-ShDra1-RPA) targeting the Schistosoma haematobium Dra1 genomic repeat region was developed and was able to detect 1 fg of S. haematobium gDNA. Results were obtained within 10 minutes using a small portable battery powered tube scanner device that incubated reactions at 40 °C, whilst detecting DNA amplification and fluorescence over time. The assay’s performance was evaluated using 20 urine samples, with varying S. haematobium egg counts, from school children from Pemba Island, Zanzibar Archipelago, Tanzania. Prior to RPA analysis, samples were prepared using a quick crude field DNA extraction method, the Speed Extract Kit (Qiagen, Manchester, UK). Positive assay results were obtained from urine samples with egg counts of 1–926 eggs/10 ml, except for two samples, which had inconclusive results. These two samples had egg counts of two and three eggs/10 ml of urine.

Conclusions

The RT-ShDra1-RPA assay proved robust for S. haematobium gDNA detection and was able to amplify and detect S. haematobium DNA in urine samples from infected patients. The assay’s speed and portability, together with the use of crude sample preparation methods, could advance the rapid molecular diagnosis of urogenital schistosomiasis at the PON within endemic countries.

Oxamniquine resistance alleles are widespread in Old World Schistosoma mansoni and predate drug deployment

Do mutations required for adaptation occur de novo, or are they segregating within populations as standing genetic variation? This question is key to understanding adaptive change in nature, and has important practical consequences for the evolution of drug resistance. We provide evidence that alleles conferring resistance to oxamniquine (OXA), an antischistosomal drug, are widespread in natural parasite populations under minimal drug pressure and predate OXA deployment. OXA has been used since the 1970s to treat Schistosoma mansoni infections in the New World where S. mansoni established during the slave trade. Recessive loss-of-function mutations within a parasite sulfotransferase (SmSULT-OR) underlie resistance, and several verified resistance mutations, including a deletion (p.E142del), have been identified in the New World. Here we investigate sequence variation in SmSULT-OR in S. mansoni from the Old World, where OXA has seen minimal usage. We sequenced exomes of 204 S. mansoni parasites from West Africa, East Africa and the Middle East, and scored variants in SmSULT-OR and flanking regions. We identified 39 non-synonymous SNPs, 4 deletions, 1 duplication and 1 premature stop codon in the SmSULT-OR coding sequence, including one confirmed resistance deletion (p.E142del). We expressed recombinant proteins and used an in vitro OXA activation assay to functionally validate the OXA-resistance phenotype for four predicted OXA-resistance mutations. Three aspects of the data are of particular interest: (i) segregating OXA-resistance alleles are widespread in Old World populations (4.29–14.91% frequency), despite minimal OXA usage, (ii) two OXA-resistance mutations (p.W120R, p.N171IfsX28) are particularly common (>5%) in East African and Middle-Eastern populations, (iii) the p.E142del allele has identical flanking SNPs in both West Africa and Puerto Rico, suggesting that parasites bearing this allele colonized the New World during the slave trade and therefore predate OXA deployment. We conclude that standing variation for OXA resistance is widespread in S. mansoni.

It has been argued that drug resistance is unlikely to spread rapidly in helminth parasites infecting humans. This is based, at least in part, on the premise that resistance mutations are rare or absent within populations prior to treatment, and take a long time to reach appreciable frequencies because helminth parasite generation time is long. This argument is critically dependent on the starting frequency of resistance alleles–if high levels of “standing variation” for resistance are present prior to deployment of treatment, resistance may spread rapidly. We examined frequencies of oxamniquine resistance alleles present in Schistosoma mansoni from Africa and the Middle East where oxamniquine has seen minimal use. We found that oxamniquine resistance alleles are widespread in the Old World, ranging from 4.29% in the Middle East to 14.91% in East African parasite populations. Furthermore, we show that resistance alleles from West African and the Caribbean schistosomes share a common origin, suggesting that these alleles travelled to the New World with S. mansoni during the transatlantic slave trade. Together, these results demonstrate extensive standing variation for oxamniquine resistance. Our results have important implications for both drug treatment policies and drug development efforts, and demonstrate the power of molecular surveillance approaches for guiding helminth control.

Freshwater snails of biomedical importance in the Niger River Valley: evidence of temporal and spatial patterns in abundance, distribution and infection with Schistosoma spp

BACKGROUND

Sound knowledge of the abundance and distribution of intermediate host snails is key to understanding schistosomiasis transmission and to inform effective interventions in endemic areas.

METHODS

A longitudinal field survey of freshwater snails of biomedical importance was undertaken in the Niger River Valley (NRV) between July 2011 and January 2016, targeting Bulinus spp. and Biomphalaria pfeifferi (intermediate hosts of Schistosoma spp.), and Radix natalensis (intermediate host of Fasciola spp.). Monthly snail collections were carried out in 92 sites, near 20 localities endemic for S. haematobium. All bulinids and Bi. pfeifferi were inspected for infection with Schistosoma spp., and R. natalensis for infection with Fasciola spp.

RESULTS

Bulinus truncatus was the most abundant species found, followed by Bulinus forskalii, R. natalensis and Bi. pfeifferi. High abundance was associated with irrigation canals for all species with highest numbers of Bulinus spp. and R. natalensis. Seasonality in abundance was statistically significant in all species, with greater numbers associated with dry season months in the first half of the year. Both B. truncatus and R. natalensis showed a negative association with some wet season months, particularly August. Prevalences of Schistosoma spp. within snails across the entire study were as follows: Bi. pfeifferi: 3.45% (79/2290); B. truncatus: 0.8% (342/42,500); and B. forskalii: 0.2% (24/11,989). No R. natalensis (n = 2530) were infected. Seasonality of infection was evident for B. truncatus, with highest proportions shedding in the middle of the dry season and lowest in the rainy season, and month being a significant predictor of infection. Bulinus spp. and Bi. pfeifferi showed a significant correlation of snail abundance with the number of snails shedding. In B. truncatus, both prevalence of Schistosoma spp. infection, and abundance of shedding snails were significantly higher in pond habitats than in irrigation canals.

CONCLUSIONS

Evidence of seasonality in both overall snail abundance and infection with Schistosoma spp. in B. truncatus, the main intermediate host in the region, has significant implications for monitoring and interrupting transmission of Schistosoma spp. in the NRV. Monthly longitudinal surveys, representing intensive sampling effort have provided the resolution needed to ascertain both temporal and spatial trends in this study. These data can inform planning of interventions and treatment within the region.

Ancient Hybridization and Adaptive Introgression of an Invadolysin Gene in Schistosome Parasites

Introgression among parasite species has the potential to transfer traits of biomedical importance across species boundaries. The parasitic blood fluke Schistosoma haematobium causes urogenital schistosomiasis in humans across sub-Saharan Africa. Hybridization with other schistosome species is assumed to occur commonly, because genetic crosses between S. haematobium and livestock schistosomes, including S. bovis, can be staged in the laboratory, and sequencing of mtDNA and rDNA amplified from microscopic miracidia larvae frequently reveals markers from different species. However, the frequency, direction, age, and genomic consequences of hybridization are unknown. We hatched miracidia from eggs and sequenced the exomes from 96 individual S. haematobium miracidia from infected patients from Niger and the Zanzibar archipelago. These data revealed no evidence for contemporary hybridization between S. bovis and S. haematobium in our samples. However, all Nigerien S. haematobium genomes sampled show hybrid ancestry, with 3.3-8.2% of their nuclear genomes derived from S. bovis, providing evidence of an ancient introgression event that occurred at least 108-613 generations ago. Some S. bovis-derived alleles have spread to high frequency or reached fixation and show strong signatures of directional selection; the strongest signal spans a single gene in the invadolysin gene family (Chr. 4). Our results suggest that S. bovis/S. haematobium hybridization occurs rarely but demonstrate profound consequences of ancient introgression from a livestock parasite into the genome of S. haematobium, the most prevalent schistosome species infecting humans.

Mini-FLOTAC as an alternative, non-invasive diagnostic tool for Schistosoma mansoni and other trematode infections in wildlife reservoirs

BACKGROUND

Schistosomiasis and food-borne trematodiases are not only of major public health concern, but can also have profound implications for livestock production and wildlife conservation. The zoonotic, multi-host nature of many digenean trematodes is a significant challenge for disease control programmes in endemic areas. However, our understanding of the epidemiological role that animal reservoirs, particularly wild hosts, may play in the transmission of zoonotic trematodiases suffers a dearth of information, with few, if any, standardised, reliable diagnostic tests available. We combined qualitative and quantitative data derived from post-mortem examinations, coprological analyses using the Mini-FLOTAC technique, and molecular tools to assess parasite community composition and the validity of non-invasive methods to detect trematode infections in 89 wild Hubert's multimammate mice (Mastomys huberti) from northern Senegal.

RESULTS

Parasites isolated at post-mortem examination were identified as Plagiorchis sp., Anchitrema sp., Echinostoma caproni, Schistosoma mansoni, and a hybrid between Schistosoma haematobium and Schistosoma bovis. The reports of E. caproni and Anchitrema sp. represent the first molecularly confirmed identifications for these trematodes in definitive hosts of sub-Saharan Africa. Comparison of prevalence estimates derived from parasitological analysis at post-mortem examination and Mini-FLOTAC analysis showed non-significant differences indicating comparable results between the two techniques (P = 1.00 for S. mansoni; P = 0.85 for E. caproni; P = 0.83 for Plagiorchis sp.). A Bayesian model, applied to estimate the sensitivities of the two tests for the diagnosis of Schistosoma infections, indicated similar median posterior probabilities of 83.1% for Mini-FLOTAC technique and 82.9% for post-mortem examination (95% Bayesian credible intervals of 64.0-94.6% and 63.7-94.7%, respectively).

CONCLUSIONS

Our results showed that the Mini-FLOTAC could be applied as an alternative diagnostic technique for the detection of the zoonotic S. mansoni and other trematodes in rodent reservoirs. The implementation of non-invasive diagnostics in wildlife would offer numerous advantages over lethal sampling methodologies, with potential impact on control strategies of zoonotic helminthiases in endemic areas of sub-Saharan Africa and on fostering a framework of animal use reduction in scientific practice.

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.

Molecular characterization and distribution of Schistosoma cercariae collected from naturally infected bulinid snails in northern and central Côte d'Ivoire

Background

Accurate identification of schistosome species infecting intermediate host snails is important for understanding parasite transmission, schistosomiasis control and elimination. Cercariae emerging from infected snails cannot be precisely identified morphologically to the species level. We used molecular tools to clarify the distribution of the Schistosoma haematobium group species infecting bulinid snails in a large part of Côte d’Ivoire and confirmed the presence of interspecific hybrid schistosomes.

Methods

Between June 2016 and March 2017, Bulinus snails were sampled in 164 human-water contact sites from 22 villages of the northern and central parts of Côte d’Ivoire. Multi-locus genetic analysis (mitochondrial cox1 and nuclear ITS) was performed on individual schistosome cercariae shed from snails, in the morning and in the afternoon, for species and hybrid identification.

Results

Overall, 1923 Bulinus truncatus, 255 Bulinus globosus and 1424 Bulinus forskalii were obtained. Among 2417 Bulinus screened, 25 specimens (18 B. truncatus and seven B. globosus) shed schistosomes, with up to 14% infection prevalence per site and time point. Globally, infection rates per time point ranged between 0.6 and 4%. Schistosoma bovis, S. haematobium and S. bovis × S. haematobium hybrids infected 0.5%, 0.2% and 0.4% of the snails screened, respectively. Schistosoma bovis and hybrids were more prevalent in B. truncatus, whereas S. haematobium and hybrid infections were more prevalent in B. globosus. Schistosoma bovis-infected Bulinus were predominantly found in northern sites, while S. haematobium and hybrid infected snails were mainly found in central parts of Côte d’Ivoire.

Conclusions

The data highlight the necessity of using molecular tools to identify and understand which schistosome species are transmitted by specific intermediate host snails. The study deepens our understanding of the epidemiology and transmission dynamics of S. haematobium and S. bovis in Côte d’Ivoire and provides the first conclusive evidence for the transmission of S. haematobium × S. bovis hybrids in this West African country.

Trial registration ISRCTN, ISRCTN10926858. Registered 21 December 2016; retrospectively registered (see: http://www.isrctn.com/ISRCTN10926858)

Electronic supplementary material

The online version of this article (10.1186/s13071-019-3381-3) contains supplementary material, which is available to authorized users.

Whole-genome sequence of the bovine blood fluke Schistosoma bovis supports interspecific hybridization with S. haematobium

Mesenteric infection by the parasitic blood fluke Schistosoma bovis is a common veterinary problem in Africa and the Middle East and occasionally in the Mediterranean Region. The species also has the ability to form interspecific hybrids with the human parasite S. haematobium with natural hybridisation observed in West Africa, presenting possible zoonotic transmission. Additionally, this exchange of alleles between species may dramatically influence disease dynamics and parasite evolution. We have generated a 374 Mb assembly of the S. bovis genome using Illumina and PacBio-based technologies. Despite infecting different hosts and organs, the genome sequences of S. bovis and S. haematobium appeared strikingly similar with 97% sequence identity. The two species share 98% of protein-coding genes, with an average sequence identity of 97.3% at the amino acid level. Genome comparison identified large continuous parts of the genome (up to several 100 kb) showing almost 100% sequence identity between S. bovis and S. haematobium. It is unlikely that this is a result of genome conservation and provides further evidence of natural interspecific hybridization between S. bovis and S. haematobium. Our results suggest that foreign DNA obtained by interspecific hybridization was maintained in the population through multiple meiosis cycles and that hybrids were sexually reproductive, producing viable offspring. The S. bovis genome assembly forms a highly valuable resource for studying schistosome evolution and exploring genetic regions that are associated with species-specific phenotypic traits.

In this article we detail the assembly and functional annotation of the Schistosoma bovis genome. S. bovis is a parasitic flatworm that primarily infects bovines, with important economic consequences in affected countries. However, it is also a close relative of the human carcinogenic parasite Schistosoma haematobium which is a serious health issue in many endemic countries in Sub-Saharan Africa. The close relationship and overlapping geographical distribution of S. bovis and S. haematobium allows these to hybridise in the wild increasing their genetic diversity and presenting the risk of zoonotic transmission, i.e. the transmission from animals to humans. The hybridization between human and ruminant schistosomes is of particular interest as interspecific hybridization may have dramatic impacts on transmission rates, disease dynamics, control interventions and parasite evolution. By whole-genome sequencing and comparative genomics we present evidence that fertile hybrids are indeed present in the wild, presenting the potential risk of transmission from animal reservoirs to humans.

Phylogeography of Bulinus truncatus (Audouin, 1827) (Gastropoda: Planorbidae) in Selected African Countries

The transmission of some schistosome parasites is dependent on the planorbid snail hosts. Bulinus truncatus is important in urinary schistosomiasis epidemiology in Africa. Hence, there is a need to define the snails' phylogeography. This study assessed the population genetic structure of B. truncatus from Giza and Sharkia (Egypt), Barakat (Sudan) and Madziwa, Shamva District (Zimbabwe) using mitochondrial cytochrome oxidase subunit 1 gene (COI) and internal transcribed spacer 1 (ITS 1) markers. COI was sequenced from 94 B. truncatus samples including 38 (Egypt), 36 (Sudan) and 20 (Zimbabwe). However, only 51 ITS 1 sequences were identified from Egypt (28) and Sudan (23) (because of failure in either amplification or sequencing). The unique COI haplotypes of B. truncatus sequences observed were 6, 11, and 6 for Egypt, Sudan, and Zimbabwe, respectively. Also, 3 and 2 unique ITS 1 haplotypes were observed in sequences from Egypt and Sudan respectively. Mitochondrial DNA sequences from Sudan and Zimbabwe indicated high haplotype diversity with 0.768 and 0.784, respectively, while relatively low haplotype diversity was also observed for sequences from Egypt (0.334). The location of populations from Egypt and Sudan on the B. truncatus clade agrees with the location of both countries geographically. The clustering of the Zimbabwe sequences on different locations on the clade can be attributed to individuals with different genotypes within the population. No significant variation was observed within B. truncatus populations from Egypt and Sudan as indicated by the ITS 1 tree. This study investigated the genetic diversity of B. truncatus from Giza and Sharkia (Egypt), Barakat area (Sudan), and Madziwa (Zimbabwe), which is necessary for snail host surveillance in the study areas and also provided genomic data of this important snail species from the sampled countries.

Whole genome amplification and exome sequencing of archived schistosome miracidia

Adult schistosomes live in the blood vessels and cannot easily be sampled from humans, so archived miracidia larvae hatched from eggs expelled in feces or urine are commonly used for population genetic studies. Large collections of archived miracidia on FTA cards are now available through the Schistosomiasis Collection at the Natural History Museum (SCAN). Here we describe protocols for whole genome amplification of Schistosoma mansoni and Schistosome haematobium miracidia from these cards, as well as real time PCR quantification of amplified schistosome DNA. We used microgram quantities of DNA obtained for exome capture and sequencing of single miracidia, generating dense polymorphism data across the exome. These methods will facilitate the transition from population genetics, using limited numbers of markers to population genomics using genome-wide marker information, maximising the value of collections such as SCAN.

Urogenital schistosomiasis and hybridization between Schistosoma haematobium and Schistosoma bovis in adults living in Richard-Toll, Senegal

Since the construction of the Diama Dam (1985), the epidemiology of schistosomiasis along the Senegal River Basin (SRB) has been extremely dynamic with outbreaks of both intestinal and urogenital schistosomiasis. In the early 2000s, technicians reported cases of suspected urogenital schistosomiasis in adults from the local hospital in Richard-Toll, Lower SRB. The genetic analysis of schistosome miracidia isolated from 11 patients in 2012 from two neighbourhoods (Campement and Gaya) of Richard-Toll confirmed infection with Schistosoma haematobium but also S. haematobium/S. bovis hybrids. Thirty-seven per cent of the miracidia were S. bovis/S. haematobium hybrids and 63% were pure S. haematobium. The data are discussed in relation to the ongoing dynamic epidemiology of the schistosomes in Senegal and the need to treat non-target individuals.

Genetic Crosses and Linkage Mapping in Schistosome Parasites

Linkage mapping - utilizing experimental genetic crosses to examine cosegregation of phenotypic traits with genetic markers - is now 100 years old. Schistosome parasites are exquisitely well suited to linkage mapping approaches because genetic crosses can be conducted in the laboratory, thousands of progeny are produced, and elegant experimental work over the last 75 years has revealed heritable genetic variation in multiple biomedically important traits such as drug resistance, host specificity, and virulence. Application of this approach is timely because the improved genome assembly for Schistosoma mansoni and developing molecular toolkit for schistosomes increase our ability to link phenotype with genotype. We describe current progress and potential future directions of linkage mapping in schistosomes.

Barcoding hybrids: heterogeneous distribution of Schistosoma haematobium × Schistosoma bovis hybrids across the Senegal River Basin

Hybridization events between Schistosoma species (Digenea, Platyhelminthes) are reported with increasing frequency, largely due to improved access to molecular tools. Nevertheless, little is known about the distribution and frequency of hybrid schistosomes in nature. Screening for hybrids on a large scale is complicated by the need for nuclear and mitochondrial sequence information, precluding a 'simple' barcoding approach. Here we aimed to determine and understand the spatiotemporal distribution of Schistosoma haematobium × Schistosoma bovis hybrids in the Senegal River Basin. From ten villages, distributed over the four main water basins, we genotyped a total of 1236 schistosome larvae collected from human urine samples using a partial mitochondrial cox1 fragment; a subset of 268 parasites was also genotyped using ITS rDNA. Hybrid schistosomes were unevenly distributed, with substantially higher numbers in villages bordering Lac de Guiers than in villages from the Lampsar River and the Middle Valley of the Senegal River. The frequency of hybrids per village was not linked with the prevalence of urinary schistosomiasis in that village. However, we did find a significant positive association between the frequency of hybrids per village and the prevalence of Schistosoma mansoni. We discuss the potential consequences of adopting a barcoding approach when studying hybrids in nature.

Neglected Tropical Disease Control - The Case for Adaptive, Location-specific Solutions

The world is experiencing environmental and social change at an unprecedented rate, with the effects being felt at local, regional, and international scales. This phenomenon may disrupt interventions against neglected tropical diseases (NTDs) that operate on the basis of linear scaling and 'one-size-fits-all'. Here we argue that investment in field-based data collection and building modelling capacity is required; that it is important to consider unintended consequences of interventions; that inferences can be drawn from wildlife ecology; and that interventions should become more location-specific. Collectively, these ideas underpin the development of adaptive decision-support tools that are sufficiently flexible to address emerging issues within the Anthropocene.

Development of a lateral flow recombinase polymerase assay for the diagnosis of Schistosoma mansoni infections

Infection with Schistosoma mansoni causes intestinal schistosomiasis, a major health problem across Africa. The accurate diagnosis of intestinal schistosomiasis is vital to inform surveillance/control programs. Diagnosis mainly relies on microscopic detection of eggs in faecal samples but many factors affect sensitivity. Molecular diagnostics are sensitive and specific but application is limited as necessary infrastructure, financial resources and skilled personnel are often lacking in endemic settings. Recombinase Polymerase Amplification (RPA) is an isothermal DNA amplification/detection technology that is practical in nearly any setting. Here we developed a RPA lateral flow (LF) assay targeting the 28S rDNA region of S. mansoni. The 28S LF-RPA assay's lower limit of detection was 10pg DNA with the lower test parameters permitting sufficient amplification being 6 min and 25°C. Optimal assay parameters were 40-45°C and 10 min with an analytical sensitivity of 10² copies of DNA. Additionally the PCRD3 lateral flow detection cassettes proved more robust and sensitive compared to the Milenia HybriDetect strips. This 28S LF-RPA assay produces quick reproducible results that are easy to interpret, require little infrastructure and is a promising PON test for the field molecular diagnosis of intestinal schistosomiasis.

Interrupting seasonal transmission of Schistosoma haematobium and control of soil-transmitted helminthiasis in northern and central Côte d'Ivoire: a SCORE study protocol

Background

To achieve a world free of schistosomiasis, the objective is to scale up control and elimination efforts in all endemic countries. Where interruption of transmission is considered feasible, countries are encouraged to implement a comprehensive intervention package, including preventive chemotherapy, information, education and communication (IEC), water, sanitation and hygiene (WASH), and snail control. In northern and central Côte d’Ivoire, transmission of Schistosoma haematobium is seasonal and elimination might be achieved. In a cluster-randomised trial, we will assess different treatment schemes to interrupt S. haematobium transmission and control soil-transmitted helminthiasis over a 3-year period. We will compare the impact of (i) arm A: annual mass drug administration (MDA) with praziquantel and albendazole before the peak schistosomiasis transmission season; (ii) arm B: annual MDA after the peak schistosomiasis transmission season; (iii) arm C: two yearly treatments before and after peak schistosomiasis transmission; and (iv) arm D: annual MDA before peak schistosomiasis transmission, coupled with chemical snail control using niclosamide.

Methods/design

The prevalence and intensity of S. haematobium and soil-transmitted helminth infections will be assessed using urine filtration and Kato-Katz thick smears, respectively, in six administrative regions in northern and central parts of Côte d’Ivoire. Once a year, urine and stool samples will be collected and examined from 50 children aged 5–8 years, 100 children aged 9–12 years and 50 adults aged 20–55 years in each of 60 selected villages. Changes in S. haematobium and soil-transmitted helminth prevalence and intensity will be assessed between years and stratified by intervention arm. In the 15 villages randomly assigned to intervention arm D, intermediate host snails will be collected three times per year, before niclosamide is applied to the selected freshwater bodies. The snail abundance and infection rates over time will allow drawing inference on the force of transmission.

Discussion

This cluster-randomised intervention trial will elucidate whether in an area with seasonal transmission, the four different treatment schemes can interrupt S. haematobium transmission and control soil-transmitted helminthiasis. Lessons learned will help to guide schistosomiasis control and elimination programmes elsewhere in Africa.

Trial registration

ISRCTNISRCTN10926858. Registered 21 December 2016. Retrospectively registered.

Mapping freshwater snails in north-western Angola: distribution, identity and molecular diversity of medically important taxa

BACKGROUND

This study was designed to determine the distribution and identity of potential intermediate snail hosts of Schistosoma spp. in Bengo, Luanda, Kwanza Norte and Malanje Provinces in north-western Angola. This is an area where infection with Schistosoma haematobium, causing urogenital schistosomiasis, is common but little is yet known about transmission of the disease. Angola has had a varied past with regard to disease control and is revitalising efforts to combat neglected tropical diseases.

METHODS

Snails were sampled from 60 water-contact points. Specimens of the genera Bulinus, Biomphalaria or Lymnaea were screened for trematode infections by inducing cercarial shedding. Snails were initially identified using shell morphology; subsequently a cytochrome c oxidase subunit 1 (cox1) gene fragment was amplified from a subset of snails from each site, for molecular identification. Cercariae were captured onto FTA cards for molecular analysis. Specimens of Bulinus angolensis collected from the original locality of the type specimen have been characterised and comparisons made with snails collected in 1957 held at the Natural History Museum, London, UK.

RESULTS

In total snails of nine genera were identified using morphological characteristics: Biomphalaria, Bulinus, Gyraulus, Lanistes, Lentorbis, Lymnaea, Melanoides, Physa and Succinea. Significant for schistosomiasis transmission, was the discovery of Bulinus globosus, B. canescens, B. angolensis, B. crystallinus and Biomphalaria salinarum in their type-localities and elsewhere. Bulinus globosus and B. angolensis occurred in two distinct geographical areas. The cox1 sequence for B. globosus differed markedly from those from specimens of this species collected from other countries. Bulinus angolensis is more closely related to B. globosus than originally documented and should be included in the B. africanus group. Schistosoma haematobium cercariae were recovered from B. globosus from two locations: Cabungo, Bengo (20 snails) and Calandula, Malanje (5 snails). Schistosoma haematobium cercariae were identified as group 1 cox1 corresponding to the type common throughout the African mainland.

CONCLUSIONS

Various freshwater bodies in north-western Angola harbour potential intermediate snail hosts for urogenital schistosomiasis, highlighting the need to map the rest of the country to identify areas where transmission can occur and where control efforts should be targeted. The molecular phylogeny generated from the samples confirmed that considerable variation exists in B. globosus, which is the primary snail host for S. haematobium in many regions of Africa.

The substructure of three repetitive DNA regions of Schistosoma haematobium group species as a potential marker for species recognition and interbreeding detection

Background

Schistosoma haematobium is the causative agent of human urogenital schistosomiasis affecting ~112 million people in Africa and the Middle East. The parasite is transmitted by snails of the genus Bulinus, which also transmit other closely related human and animal schistosomes. The accurate discrimination of S. haematobium from species infecting animals will aid effective control and elimination programs. Previously we have shown the utility of different repetitive nuclear DNA sequences (DraI, sh73bp, and sh77bp) for the identification of S. haematobium-group species and inter-repeat sequences for discriminating S. haematobium from S. bovis.

Results

In this current study we clarify the structural arrangement and association between the three repetitive sequences (DraI, sh73bp, and sh77bp) in both S. haematobium and S. bovis, with a unique repeat linker being found in S. haematobium (Sh64bp repeat linker) and in S. bovis (Sb30bp repeat linker). Sequence data showed that the 3′-end of the repeat linker was connected to the DraI repetitive sequence array, and at the 5′-end of the repeat linker sh73bp and sh77bp were arranged in an alternating manner. Species-specific oligonucleotides were designed targeting the species-specific repeat linkers and used in a reverse line blot (RLB) hybridization assay enabling differentiation between S. haematobium and S. bovis. The assay was used to discriminate natural infections in wild caught Bulinus globosus.

Conclusion

This research enabled the characterisation of species-specific DNA regions that enabled the design of species-specific oligonucleotides that can be used to rapidly differentiate between S. haematobium and S. bovis and also have the potential to aid the detection of natural hybridization between these two species.

Longitudinal survey on the distribution of Biomphalaria sudanica and B. choanomophala in Mwanza region, on the shores of Lake Victoria, Tanzania: implications for schistosomiasis transmission and control

BACKGROUND

Schistosomiasis is hyper-endemic in the Lake Victoria basin; with intestinal schistosomiasis plaguing communities adjacent to the lake, where the intermediate host snails live. The two intermediate host species of Schistosoma mansoni in the Mwanza region are Biomphalaria sudanica, found on the banks of the lakes, and B. choanomphala, found in the lake itself. There are few longitudinal surveys documenting changing abundance and differential transmission patterns of these Biomphalaria snails across seasons and years. We undertook 15 field surveys at 26 sites over four years to determine the parameters that influence Biomphalaria abundance, presence of S. mansoni-shedding snails and impact of schistosomiasis treatment interventions on transmission potential in the Mwanza region.

RESULTS

Statistical analysis revealed seasonal difference in the abundance of B. sudanica with the highest number of snails found in the dry season (Kruskal-Wallis χ ² = 37.231, df = 3, P < 0.0001). Water measurements were not associated with B. sudanica abundance; however, high levels of rainfall did have a negative effect on B. sudanica [coefficient effect -0.1405, 95% CI (-0.2666, -0.0144)] and B. choanomphala abundance [coefficient effect -0.4388, 95% CI (-0.8546, -0.0231)] potentially due to inundation of sites "diluting" the snails and influencing collection outcome. Biomphalaria sudanica snails were found at all sites whereas B. choanomphala were far more focal and only found in certain sites. Shedding Biomphalaria did not show any variation between dry and rainy seasons; however, a decrease in shedding snails was observed in year 4 of the study.

CONCLUSIONS

Biomphalaria sudanica is uniformly present in the Mwanza region whereas B. choanomphala is far more focal. Seasonality plays a role for B. sudanica abundance, likely due to its habitat preference on the banks of the lake, but not for B. choanomphala. The decrease in shedding Biomphalaria abundance in Year 4 could be linked to ongoing schistosomiasis treatment efforts in the neighbouring human populations. The highest number of shedding Biomphalaria was observed at sites with high levels of human movement. Prioritising snail control at such sites could greatly reduce transmission in these high-risk areas.

Urogenital schistosomiasis transmission on Unguja Island, Zanzibar: characterisation of persistent hot-spots

BACKGROUND

Elimination of urogenital schistosomiasis transmission is a priority for the Zanzibar Ministry of Health. Preventative chemotherapy together with additional control interventions have successfully alleviated much of the disease burden. However, a persistently high Schistosoma haematobium prevalence is found in certain areas. Our aim was to characterise and evaluate these persistent "hot-spots" of transmission and reinfection in comparison with low-prevalence areas, to support the intervention planning for schistosomiasis elimination in Zanzibar.

METHODS

Prevalences of S. haematobium were annually determined by a single urine filtration in schoolchildren from 45 administrative areas (shehias) in Unguja in 2012, 2013 and 2014. Coverage data for biannual treatment with praziquantel were available from ministerial databases and internal surveys. Among the 45 shehias, five hot-spot (≥ 15 % prevalence) and two low-prevalence (≤ 5 %) shehias were identified and surveyed in mid-2014. Human-water contact sites (HWCSs) and the presence of S. haematobium-infected and uninfected Bulinus globosus, as well as safe water sources (SWSs) and their reliability in terms of water availability were determined and mapped.

RESULTS

We found no major difference in the treatment coverage between persistent hot-spot and low-prevalence shehias. On average, there were considerably more HWCSs containing B. globosus in hot-spot than in low-prevalence shehias (n = 8 vs n = 2) and also more HWCSs containing infected B. globosus (n = 2 vs n = 0). There was no striking difference in the average abundance of SWSs in hot-spot and low-prevalence shehias (n = 45 vs n = 38) and also no difference when considering SWSs with a constant water supply (average: 62 % vs 62 %). The average number of taps with a constant water supply, however, was lower in hot-spot shehias (n = 7 vs n = 14). Average distances from schools to the nearest HWCS were considerably shorter in hot-spot shehias (n = 229 m vs n = 722 m).

CONCLUSION

The number of HWCSs, their infestation with B. globosus and their distance to schools seem to play a major role for a persistently high S. haematobium prevalence in children. In addition to treatment, increasing access to reliably working taps, targeted snail control at HWCSs near schools and enhanced behaviour change measures are needed to reduce prevalences in hot-spot areas and to finally reach elimination.

TRIAL REGISTRATION

ISRCTN48837681 .

Whole genome resequencing of the human parasite Schistosoma mansoni reveals population history and effects of selection

Schistosoma mansoni is a parasitic fluke that infects millions of people in the developing world. This study presents the first application of population genomics to S. mansoni based on high-coverage resequencing data from 10 global isolates and an isolate of the closely-related Schistosoma rodhaini, which infects rodents. Using population genetic tests, we document genes under directional and balancing selection in S. mansoni that may facilitate adaptation to the human host. Coalescence modeling reveals the speciation of S. mansoni and S. rodhaini as 107.5-147.6KYA, a period which overlaps with the earliest archaeological evidence for fishing in Africa. Our results indicate that S. mansoni originated in East Africa and experienced a decline in effective population size 20-90KYA, before dispersing across the continent during the Holocene. In addition, we find strong evidence that S. mansoni migrated to the New World with the 16-19th Century Atlantic Slave Trade.

"Life in Data"--Outcome of a Multi-Disciplinary, Interactive Biobanking Conference Session on Sample Data

INTRODUCTION

Clinical, biodiversity, and environmental biobanks share many data standards, but there is a lack of harmonization on how data are defined and used among biobank fields. This article reports the outcome of an interactive, multidisciplinary session at a meeting of the European, Middle Eastern, and African Society for Biopreservation and Biobanking (ESBB) designed to encourage a 'learning-from-each-other' approach to achieve consensus on data needs and data management across biobank communities.

MATERIALS, METHODS, AND RESULTS

The Enviro-Bio and ESBBperanto Working Groups of the ESBB co-organized an interactive session at the 2013 conference (Verona, Italy), presenting data associated with biobanking processes, using examples from across different fields. One-hundred-sixty (160) diverse biobank participants were provided electronic voting devices with real-time screen display of responses to questions posed during the session. The importance of data standards and robust data management was recognized across the conference cohort, along with the need to raise awareness about these issues within and across different biobank sectors.

DISCUSSION AND CONCLUSION

While interactive sessions require a commitment of time and resources, and must be carefully coordinated for consistency and continuity, they stimulate the audience to be pro-active and direct the course of the session. This effective method was used to gauge opinions about significant topics across different biobanking communities. The votes revealed the need to: (a) educate biobanks in the use of data management tools and standards, and (b) encourage a more cohesive approach for how data and samples are tracked, exchanged, and standardized across biobanking communities. Recommendations for future interactive sessions are presented based on lessons learned.