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

The research contribution of the Schistosomiasis Collection at the Natural History Museum (SCAN): highlights, challenges and future directions

BACKGROUND

The Schistosomiasis Collection at the Natural History Museum (SCAN) is a repository of schistosomiasis-related specimens, the development of which was funded by the Wellcome Trust between 2011 and 2021. With a view to facilitating research by improving access to genetically diverse material, SCAN was built from legacy research collections of schistosomiasis-related specimens amassed over decades, with more recent collections made through partnership with large field-based projects.

METHODS

We identified the literature associated with SCAN from 2012 until 2024, using both database searches (search terms: SCAN, the schistosomiasis collection at the NHM and schistosomiasis) and citations of the publication which originally laid out the scope of the SCAN Collection. Studies were included if the SCAN publication was cited, and/or if the SCAN Collection was utilised in the work. Data extracted included year of publication, authors, whether and how SCAN was used in the work, and type of specimens used.

RESULTS

The literature includes 88 published works, demonstrating the utility of large field-based collections in supporting research. The collection comprises around half a million larval schistosomes originating from the field, with approximately 3000 specimen lots of lab-passaged adult parasites stored in liquid nitrogen. The Collection includes 11 schistosome species, the majority being the human pathogens Schistosoma haematobium and S. mansoni, while also including many livestock-associated species. Genome analysis of S. haematobium and S. guineensis samples indicate historical introgression or ongoing hybridisation. In order of representation, the collection includes S. haematobium (> 19,000 larval forms and eggs, and 550 specimen lots of laboratory passaged adult worms), S. mansoni, S. japonicum, S. bovis, S. curassoni, S. mattheei, S. rodhaini and S. guineensis, with S. intercalatum, S. margrebowiei and S. spindale represented only by laboratory-passaged isolates in liquid nitrogen. SCAN also includes around 210,000 snails, with the collection as a whole encompassing 27 countries.

CONCLUSIONS

Improvements in DNA sequencing techniques have allowed genome-level data to be accessed from archived larval schistosomes and allowed retrospective analysis of samples collected decades ago. SCAN has been of use in exploring schistosome diversity, particularly with reference to hybridisation and drug resistance. Multiple author nationalities demonstrate the collaborative nature of research using the Collection, although more may need to be done in future, both to promote work led by developing countries and to ensure effective collaboration and sample sharing.

Genomic data reveal a north-south split and introgression history of blood fluke populations across Africa

The human parasitic fluke, Schistosoma haematobium hybridizes with the livestock parasite S. bovis in the laboratory, but the frequency of hybridization in nature is unclear. Here, we analyze 34.6 million single nucleotide variants in 162 samples from 18 African countries, revealing a sharp genetic discontinuity between northern and southern S. haematobium. We find no evidence for recent hybridization. Instead the data reveal admixture events that occurred 257-879 generations ago in northern S. haematobium populations. Fifteen introgressed S. bovis genes are approaching fixation in northern S. haematobium with four genes potentially driving adaptation. Further, we identify 19 regions that are resistant to introgression; these are enriched on the sex chromosomes. These results (i) suggest strong barriers to gene flow between these species, (ii) indicate that hybridization may be less common than currently envisaged, but (iii) reveal profound genomic consequences of rare interspecific hybridization between schistosomes of medical and veterinary importance.

A pilot investigation of bovine schistosomiasis on Unguja Island, Zanzibar, raises a new concern for elimination of urogenital schistosomiasis

Our pilot parasitological investigation of cattle, supplemented with molecular DNA characterisation of encountered schistosomes, sheds first light upon bovine schistosomiasis on Unguja Island, Zanzibar. During February 2024, a total of 99 cattle were examined. Of these, 47 were exported animals from the Tanzanian mainland, designated for slaughter at two governmental abattoirs (Kisakasaka and Muwanda), and 52 were free-grazing animals sampled from four grazing locations within the island's North and West-B regions. Upon visual inspection of 31 cattle carcasses at Kisakasaka for adult worms, the prevalence of bovine schistosomiasis was 51.6%; however, upon faecal miracidia hatching test (MHT) it was 80.6%. At Muwanda, only faecal MHT was used, finding a much lower prevalence of 12.5%. In free-grazing animals, the prevalence of bovine schistosomiasis by MHT was 0.0%. At Muwanda, the animal quarantine paddock was in disrepair, inclusive of a large pond now acting as a watering point. Here, numerous Bulinus forskalii sp. were found. Whilst no snails were observed to shed schistosome cercariae, molecular xenomonitoring did detect a pre-patent infection prevalence of 10.8%, with Schistosoma bovis firmly incriminated. Molecular DNA characterisation of adult schistosomes (n = 19) by real-time polymerase chain reaction (PCR) and high-resolution melt profiling, alongside DNA sequencing, also identified S. bovis, although two worms were putative S. bovis-S. mattheei hybrids. Atypical intrauterine eggs of S. bovis were noted upon microscopy of a worm pair. A broader screen of 92 miracidia confirmed S. bovis and three miracidia as S. bovis-S. mattheei hybrids. Contrasting with Pemba Island, Zanzibar, where autochthonous transmission of S. bovis can occur, bovine schistosomiasis on Unguja Island currently appears restricted to imported animals alone. However, the seminal detection of putative S. bovis-mattheei hybrids, alongside the current inadequate quarantine facilities at Muwanda, raises a new concern that such hybrid schistosomes may escape and enter the island's hinterland. Should this happen, surveillance and control of urogenital schistosomiasis on Unguja would be compromised and further complicated. We therefore strongly recommend immediate repair and improved maintenance of governmental animal quarantine facilities. Future epidemiological surveys of imported cattle are now well justified, not only to better understand the full repertoire of hybrid schistosomes present but also to develop appropriate mitigating interventions.

Schistosoma mansoni x S. haematobium hybrids frequently infecting sub-Saharan migrants in southeastern Europe: Egg DNA genotyping assessed by RD-PCR, sequencing and cloning

BACKGROUND

Globalization and neglected tropical diseases (NTDs) are increasingly closely linked. In recent years, Spain and Southern Europe are experiencing a considerable increase in the influx of migrants infected by NTDs, mainly from West African countries. This study focuses on imported schistosomiasis and the entry into Europe of hetero-specific hybrids between two human species, Schistosoma mansoni and S. haematobium, causing intestinal and urogenital schistosomiasis respectively.

METHODOLOGY/PRINCIPAL FINDINGS

Individualized genetic identification by molecular analysis using RD-PCR, sequencing and cloning of nuclear rDNA and mtDNA of 134 Schistosoma eggs was performed, including 41 lateral-spined and 84 terminal-spined eggs from urine, and nine lateral-spined eggs from stools. These eggs were recovered from six migrant males from Senegal, Guinea-Bissau, Côte d'Ivoire and Mali, who shared ectopic shedding of S. mansoni-like eggs in their urine. A high hybridization complexity was detected in the eggs of these patients, involving three Schistosoma species. The six patients were infected by S. mansoni x S. haematobium hybrids shedding S. mansoni-like eggs, and also S. haematobium x S. curassoni hybrids shedding S. haematobium-like eggs. SmxSh hybrids were mostly detected in S. mansoni-like eggs from urine (94.59%), whereas in feces the detection of those hybrids was less frequent (5.41%).

CONCLUSIONS/SIGNIFICANCE

This study contributes to: (i) a better understanding of the heterospecific hybrids between S. mansoni and S. haematobium from the genetic point of view; (ii) it shows the frequency with which they are entering non-endemic countries, such as Spain and consequently in Europe; (iii) it determines the diversity of hybrid eggs and haplotypes that can occur within a single patient, e.g., up to two types of hybrids involving three Schistosoma species and up to six different haplotypes; (iv) it provides information to be considered in clinical presentations, diagnosis, responses to treatment and epidemiological impact in relation to possible transmission and establishment in non-endemic areas.

Genomic data reveal a north-south split and introgression history of blood fluke (Schistosoma haematobium) populations from across Africa

The human parasitic fluke, Schistosoma haematobium hybridizes with the livestock parasite S. bovis in the laboratory, but the frequency of hybridization in nature is unclear. We analyzed 34.6 million single nucleotide variants in 162 samples from 18 African countries, revealing a sharp genetic discontinuity between northern and southern S. haematobium. We found no evidence for recent hybridization. Instead the data reveal admixture events that occurred 257-879 generations ago in northern S. haematobium populations. Fifteen introgressed S. bovis genes are approaching fixation in northern S. haematobium with four genes potentially driving adaptation. We identified 19 regions that were resistant to introgression; these were enriched on the sex chromosomes. These results (i) suggest strong barriers to gene flow between these species, (ii) indicate that hybridization may be less common than currently envisaged, but (iii) reveal profound genomic consequences of rare interspecific hybridization between schistosomes of medical and veterinary importance.

Schistosomiasis transmission: A machine learning analysis reveals the importance of agrochemicals on snail abundance in Rwanda

BACKGROUND

Schistosomiasis is an important snail-borne parasitic disease whose transmission is exacerbated by water resource management activities. In Rwanda, meeting the growing population's demand for food has led to wetlands reclamation for cultivation and increased agrochemical enrichment for crop production. However, the ecological consequences of agrochemical enrichment on schistosomiasis transmission remain unexplored.

METHODS

A malacological survey was conducted in 71 villages selected from 15 schistosomiasis endemic districts. Snail sampling was done in wetlands used for agriculture, along lake Kivu and at constructed multipurpose water dams. Water physico-chemical parameters were collected at all snail sampling sites. Analysis of collected data was performed using Xgboost (gain) and Random Forest (mean decrease in accuracy), machine learning techniques, to construct models that evaluate and categorize the importance of all physico-chemical properties on the presence and abundance of intermediate host snails (IHS).

RESULTS

Different sets of parameters were relevant for the presence and abundance of Biomphalaria spp. and/or Bulinus spp. snails. Electrical conductivity, elevation, magnesium and lead content were deemed to shape the presence and abundance of Bulinus spp. snails. The impact of phosphate ion concentration, ammonia ions, total nitrogen and total organic carbon levels mirrored their importance towards the presence and abundance of Biomphalaria spp. Factors such as pH, electric conductivity, total nitrogen content and total organic carbon influenced the coexistence of both species. Our study highlights the value of integrating a wide range of predictor variables, enabling effective variable selection to uncover important predictors of snail distribution.

CONCLUSION

The results suggest that agrochemical compounds can enhance the abundance of IHS leading to an increased risk of Schistosoma transmission. Snail surveillance could therefore be integrated into agricultural expansion projects in our match towards schistosomiasis elimination. Recognizing the impact of agrochemicals on IHS is crucial for minimizing schistosomiasis transmission among those working in wetlands while meeting the growing need for food.

Schistosoma haematobium and Schistosoma bovis first generation hybrids undergo gene expressions changes consistent with species compatibility and heterosis

When two species hybridize, the two parental genomes are brought together and some alleles might interact for the first time. To date, the extent of the transcriptomic changes in first hybrid generations, along with their functional outcome constitute an important knowledge gap, especially in parasite species. Here we explored the molecular and functional outcomes of hybridization in first-generation hybrids between the blood fluke parasites Schistosoma haematobium and S. bovis. Through a transcriptomic approach, we measured gene expression in both parental species and hybrids. We described and quantified expression profiles encountered in hybrids along with the main biological processes impacted. Up to 7,100 genes fell into a particular hybrid expression profile (intermediate between the parental expression levels, over-expressed, under-expressed, or expressed like one of the parental lines). Most of these genes were different depending on the direction of the parental cross (S. bovis mother and S. haematobium father or the reverse) and depending on the sex. For a given sex and cross direction, the vast majority of genes were hence unassigned to a hybrid expression profile: either they were differentially expressed genes but not typical of any hybrid expression profiles or they were not differentially expressed neither between hybrids and parental lines nor between parental lines. The most prevalent profile of gene expression in hybrids was the intermediate one (24% of investigated genes). These results suggest that transcriptomic compatibility between S. haematobium and S. bovis remains quite high. We also found support for an over-dominance model (over- and under-expressed genes in hybrids compared to parental lines) potentially associated with heterosis. In females in particular, processes such as reproductive processes, metabolism and cell interactions as well as signaling pathways were indeed affected. Our study hence provides new insight on the biology of Schistosoma hybrids with evidences supporting compatibility and heterosis.

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.

Ultrafast learning of four-node hybridization cycles in phylogenetic networks using algebraic invariants

Motivation

The abundance of gene flow in the Tree of Life challenges the notion that evolution can be represented with a fully bifurcating process which cannot capture important biological realities like hybridization, introgression, or horizontal gene transfer. Coalescent-based network methods are increasingly popular, yet not scalable for big data, because they need to perform a heuristic search in the space of networks as well as numerical optimization that can be NP-hard. Here, we introduce a novel method to reconstruct phylogenetic networks based on algebraic invariants. While there is a long tradition of using algebraic invariants in phylogenetics, our work is the first to define phylogenetic invariants on concordance factors (frequencies of four-taxon splits in the input gene trees) to identify level-1 phylogenetic networks under the multispecies coalescent model.

Results

Our novel hybrid detection methodology is optimization-free as it only requires the evaluation of polynomial equations, and as such, it bypasses the traversal of network space, yielding a computational speed at least 10 times faster than the fastest-to-date network methods. We illustrate our method's performance on simulated and real data from the genus Canis.

Availability and implementation

We present an open-source publicly available Julia package PhyloDiamond.jl available at https://github.com/solislemuslab/PhyloDiamond.jl with broad applicability within the evolutionary community.

Reaching the World Health Organization elimination targets for schistosomiasis: the importance of a One Health perspective

The past three years has seen the launch of a new World Health Organization (WHO) neglected tropical diseases (NTDs) roadmap, together with revised control and elimination guidelines. Across all, there is now a clear emphasis on the need to incorporate a One Health approach, recognizing the critical links between human and animal health and the environment. Schistosomiasis, caused by Schistosoma spp. trematodes, is a NTD of global medical and veterinary importance, with over 220 million people and untold millions of livestock currently infected. Its burden remains extremely high in certain regions, particularly within sub-Saharan Africa, despite over two decades of mass preventive chemotherapy (mass drug administration), predominantly to school-aged children. In Africa, in contrast to Asia, any zoonotic component of schistosomiasis transmission and its implications for disease control has, until recently, been largely ignored. Here, we review recent epidemiological, clinical, molecular, and modelling work across both Asia and Africa. We outline the evolutionary history and transmission dynamics of Schistosoma species, and emphasize the emerging risk raised by both wildlife reservoirs and viable hybridization between human and animal schistosomes. To achieve the 2030 WHO roadmap elimination targets, a truly multi-disciplinary One Health perspective must be implemented. This article is part of the theme issue 'Challenges and opportunities in the fight against neglected tropical diseases: a decade from the London Declaration on NTDs'.

A duplex tetra-primer ARMS-PCR assay to discriminate three species of the Schistosoma haematobium group: Schistosoma curassoni, S. bovis, S. haematobium and their hybrids

BACKGROUND

The use of applications involving single nucleotide polymorphisms (SNPs) has greatly increased since the beginning of the 2000s, with the number of associated techniques expanding rapidly in the field of molecular research. Tetra-primer amplification refractory mutation system-PCR (T-ARMS-PCR) is one such technique involving SNP genotyping. It has the advantage of amplifying multiple alleles in a single reaction with the inclusion of an internal molecular control. We report here the development of a rapid, reliable and cost-effective duplex T-ARMS-PCR assay to distinguish between three Schistosoma species, namely Schistosoma haematobium (human parasite), Schistosoma bovis and Schistosoma curassoni (animal parasites), and their hybrids. This technique will facilitate studies of population genetics and the evolution of introgression events.

METHODS

During the development of the technique we focused on one of the five inter-species internal transcribed spacer (ITS) SNPs and one of the inter-species 18S SNPs which, when combined, discriminate between all three Schistosoma species and their hybrid forms. We designed T-ARMS-PCR primers to amplify amplicons of specific lengths for each species, which in turn can then be visualized on an electrophoresis gel. This was further tested using laboratory and field-collected adult worms and field-collected larval stages (miracidia) from Spain, Egypt, Mali, Senegal and Ivory Coast. The combined duplex T-ARMS-PCR and ITS + 18S primer set was then used to differentiate the three species in a single reaction.

RESULTS

The T-ARMS-PCR assay was able to detect DNA from both species being analysed at the maximum and minimum levels in the DNA ratios (95/5) tested. The duplex T-ARMS-PCR assay was also able to detect all hybrids tested and was validated by sequencing the ITS and the 18S amplicons of 148 of the field samples included in the study.

CONCLUSIONS

The duplex tetra-primer ARMS-PCR assay described here can be applied to differentiate between Schistosoma species and their hybrid forms that infect humans and animals, thereby providing a method to investigate the epidemiology of these species in endemic areas. The addition of several markers in a single reaction saves considerable time and is of long-standing interest for investigating genetic populations.

MALDI-TOF: A new tool for the identification of Schistosoma cercariae and detection of hybrids

Schistosomiasis is a neglected water-born parasitic disease caused by Schistosoma affecting more than 200 million people. Introgressive hybridization is common among these parasites and raises issues concerning their zoonotic transmission. Morphological identification of Schistosoma cercariae is difficult and does not permit hybrids detection. Our objective was to assess the performance of MALDI-TOF (Matrix Assistated Laser Desorption-Ionization–Time Of Flight) mass spectrometry for the specific identification of cercariae in human and non-human Schistosoma and for the detection of hybridization between S. bovis and S. haematobium. Spectra were collected from laboratory reared molluscs infested with strains of S. haematobium, S. mansoni, S. bovis, S. rodhaini and S. bovis x S. haematobium natural (Corsican hybrid) and artificial hybrids. Cluster analysis showed a clear separation between S. haematobium, S. bovis, S. mansoni and S. rodhaini. Corsican hybrids are classified with those of the parental strain of S. haematobium whereas other hybrids formed a distinct cluster. In blind test analysis the developed MALDI-TOF spectral database permits identification of Schistosoma cercariae with high accuracy (94%) and good specificity (S. bovis: 99.59%, S. haematobium 99.56%, S. mansoni and S. rodhaini: 100%). Most misidentifications were between S. haematobium and the Corsican hybrids. The use of machine learning permits to improve the discrimination between these last two taxa, with accuracy, F1 score and Sensitivity/Specificity > 97%. In multivariate analysis the factors associated with obtaining a valid identification score (> 1.7) were absence of ethanol preservation (p < 0.001) and a number of 2–3 cercariae deposited per well (p < 0.001). Also, spectra acquired from S. mansoni cercariae are more likely to obtain a valid identification score than those acquired from S. haematobium (p<0.001). MALDI-TOF is a reliable technique for high-throughput identification of Schistosoma cercariae of medical and veterinary importance and could be useful for field survey in endemic areas.

Population genomics of helminth parasites

Next generation sequencing technologies have facilitated a shift from a few targeted loci in population genetic studies to whole genome approaches. Here, we review the types of questions and inferences regarding the population biology and evolution of parasitic helminths being addressed within the field of population genomics. Topics include parabiome, hybridization, population structure, loci under selection and linkage mapping. We highlight various advances, and note the current trends in the field, particularly a focus on human-related parasites despite the inherent biodiversity of helminth species. We conclude by advocating for a broader application of population genomics to reflect the taxonomic and life history breadth displayed by helminth parasites. As such, our basic knowledge about helminth population biology and evolution would be enhanced while the diversity of helminths in itself would facilitate population genomic comparative studies to address broader ecological and evolutionary concepts.

Bulinus snails in the Lake Victoria Basin in Kenya: Systematics and their role as hosts for schistosomes

The planorbid gastropod genus Bulinus consists of 38 species that vary in their ability to vector Schistosoma haematobium (the causative agent of human urogenital schistosomiasis), other Schistosoma species, and non-schistosome trematodes. Relying on sequence-based identifications of bulinids (partial cox1 and 16S) and Schistosoma (cox1 and ITS), we examined Bulinus species in the Lake Victoria Basin in Kenya for naturally acquired infections with Schistosoma species. We collected 6,133 bulinids from 11 sites between 2014-2021, 226 (3.7%) of which harbored Schistosoma infections. We found 4 Bulinus taxa from Lake Victoria (B. truncatus, B. tropicus, B. ugandae, and B. cf. transversalis), and an additional 4 from other habitats (B. globosus, B. productus, B. forskalii, and B. scalaris). S. haematobium infections were found in B. globosus and B. productus (with infections in the former predominating) whereas S. bovis infections were identified in B. globosus, B. productus, B. forskalii, and B. ugandae. No nuclear/mitochondrial discordance potentially indicative of S. haematobium/S. bovis hybridization was detected. We highlight the presence of Bulinus ugandae as a distinct lake-dwelling taxon closely related to B. globosus yet, unlike all other members of the B. africanus species group, is likely not a vector for S. haematobium, though it does exhibit susceptibility to S. bovis. Other lake-dwelling bulinids also lacked S. haematobium infections, supporting the possibility that they all lack compatibility with local S. haematobium, thereby preventing widespread transmission of urogenital schistosomiasis in the lake's waters. We support B. productus as a distinct species from B. nasutus, B. scalaris as distinct from B. forskalii, and add further evidence for a B. globosus species complex with three lineages represented in Kenya alone. This study serves as an essential prelude for investigating why these patterns in compatibility exist and whether the underlying biological mechanisms may be exploited for the purpose of limiting schistosome transmission.

New challenges for the control of human schistosomiasis: The possible impact of wild rodents in Schistosoma mansoni transmission

Schistosomiasis is a neglected parasitic disease caused by digenean trematodes from the genus Schistosoma that affects millions of people worldwide. Despite efforts to control its transmission, this disease remains active within several endemic regions of Africa, Asia, and the Americas. In addition to the deficits in sanitation and educational structure, another major obstacle hindering the eradication of schistosomiasis is the ability of Schistosoma spp. to naturally infect multiple vertebrate hosts, particularly wild rodents. Due to climate change and other anthropogenic disturbances, contact between humans and wild animals has increased, and this has contributed to more frequent interactions between Schistosoma species that typically infect different hosts. This new transmission dynamic involving Schistosoma spp., humans, wild rodents, and livestock could potentially increase the frequency of Schistosoma hybridization and the establishment of new genotypes and strains. Although it is not currently possible to precisely measure how this biological phenomenon affects the epidemiology and morbidity of schistosomiasis, we speculate that these Schistosoma variants may negatively impact control strategies, treatment regimens, and disease burden in humans. In the present study, we discuss the natural infections of wild rodents with Schistosoma spp., the role of these animals as Schistosoma spp. reservoirs, and how they may select hybrids and strains of Schistosoma mansoni. We also discuss measures required to shed light on the actual role of the wild rodents Nectomys squamipes and Holochilus sciureus in the transmission and morbidity of schistosomiasis in Brazil.

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.

Mating Interactions between Schistosoma bovis and S. mansoni and Compatibility of Their F1 Progeny with Biomphalaria glabrata and Bulinus truncatus

Contrary to the majority of other Trematoda, Schistosoma species are gonochoric. Consequently, in endemic areas where several schistosome species overlap and can co-infect the same definitive host, there may be frequent opportunities for interspecific pairing. Our experimental study provides novel insight on the pairing behavior between Schistosoma bovis and S. mansoni in mixed infections in mice. We used six mate choice experiments to assess mating interactions between the two schistosome species. We show that mating between the two Schistosoma species is not random and that S. mansoni exhibits greater mate recognition compared to S. bovis. We also performed reciprocal crosses (male S. mansoni × female S. bovis) and (female S. mansoni × male S. bovis) that produce active swimming miracidia. These miracidia were genotyped by ITS2 sequencing and proposed for mollusc infection. Molecular analyses show that all the miracidia are parthenogenetically produced (i.e., their harbor the mother ITS2 genotype) and as a consequence can only infect the mollusc of the maternal species. Offspring produced by male S. mansoni × female S. bovis pairing can only infect Bulinus truncatus whereas offspring produced by female S. mansoni × male S. bovis can only infect Biomphalaria glabrata snails. Evolutionary and epidemiological consequences are discussed.

Population genetic structure of Schistosoma haematobium and Schistosoma haematobium × Schistosoma bovis hybrids among school-aged children in Côte d'Ivoire

While population genetics of Schistosoma haematobium have been investigated in West Africa, only scant data are available from Côte d’Ivoire. The purpose of this study was to analyze both genetic variability and genetic structure among S. haematobium populations and to quantify the frequency of S. haematobium × S. bovis hybrids in school-aged children in different parts of Côte d’Ivoire. Urine samples were subjected to a filtration method and examined microscopically for Schistosoma eggs in four sites in the western and southern parts of Côte d’Ivoire. A total of 2692 miracidia were collected individually and stored on Whatman^® FTA cards. Of these, 2561 miracidia were successfully genotyped for species and hybrid identification using rapid diagnostic multiplex mitochondrial cox1 PCR and PCR Restriction Fragment Length Polymorphism (PCR-RFLP) analysis of the nuclear ITS2 region. From 2164 miracidia, 1966 (90.9%) were successfully genotyped using at least 10 nuclear microsatellite loci to investigate genetic diversity and population structure. Significant differences were found between sites in all genetic diversity indices and genotypic differentiation was observed between the site in the West and the three sites in the East. Analysis at the infrapopulation level revealed clustering of parasite genotypes within individual children, particularly in Duekoué (West) and Sikensi (East). Of the six possible cox1-ITS2 genetic profiles obtained from miracidia, S. bovis cox1 × S. haematobium ITS2 (42.0%) was the most commonly observed in the populations. We identified only 15 miracidia (0.7%) with an S. bovis cox1 × S. bovis ITS2 genotype. Our study provides new insights into the population genetics of S. haematobium and S. haematobium × S. bovis hybrids in humans in Côte d’Ivoire and we advocate for researching hybrid schistosomes in animals such as rodents and cattle in Côte d’Ivoire.

Genomic analysis of a parasite invasion: Colonization of the Americas by the blood fluke Schistosoma mansoni

Schistosoma mansoni, a snail-borne, blood fluke that infects humans, was introduced into the Americas from Africa during the Trans-Atlantic slave trade. As this parasite shows strong specificity to the snail intermediate host, we expected that adaptation to South American Biomphalaria spp. snails would result in population bottlenecks and strong signatures of selection. We scored 475,081 single nucleotide variants in 143 S. mansoni from the Americas (Brazil, Guadeloupe and Puerto Rico) and Africa (Cameroon, Niger, Senegal, Tanzania, and Uganda), and used these data to ask: (i) Was there a population bottleneck during colonization? (ii) Can we identify signatures of selection associated with colonization? (iii) What were the source populations for colonizing parasites? We found a 2.4- to 2.9-fold reduction in diversity and much slower decay in linkage disequilibrium (LD) in parasites from East to West Africa. However, we observed similar nuclear diversity and LD in West Africa and Brazil, suggesting no strong bottlenecks and limited barriers to colonization. We identified five genome regions showing selection in the Americas, compared with three in West Africa and none in East Africa, which we speculate may reflect adaptation during colonization. Finally, we infer that unsampled populations from central African regions between Benin and Angola, with contributions from Niger, are probably the major source(s) for Brazilian S. mansoni. The absence of a bottleneck suggests that this is a rare case of a serendipitous invasion, where S. mansoni parasites were pre-adapted to the Americas and able to establish with relative ease.

Population Genetic Structure and Hybridization of Schistosoma haematobium in Nigeria

Background: Schistosomiasis is a major poverty-related disease caused by dioecious parasitic flatworms of the genus Schistosoma with a health impact on both humans and animals. Hybrids of human urogenital schistosome and bovine intestinal schistosome have been reported in humans in several of Nigeria’s neighboring West African countries. No empirical studies have been carried out on the genomic diversity of Schistosoma haematobium in Nigeria. Here, we present novel data on the presence and prevalence of hybrids and the population genetic structure of S. haematobium. Methods: 165 Schistosoma-positive urine samples were obtained from 12 sampling sites in Nigeria. Schistosoma haematobium eggs from each sample were hatched and each individual miracidium was picked and preserved in Whatman® FTA cards for genomic analysis. Approximately 1364 parasites were molecularly characterized by rapid diagnostic multiplex polymerase chain reaction (RD-PCR) for mitochondrial DNA gene (Cox1 mtDNA) and a subset of 1136 miracidia were genotyped using a panel of 18 microsatellite markers. Results: No significant difference was observed in the population genetic diversity (p > 0.05), though a significant difference was observed in the allelic richness of the sites except sites 7, 8, and 9 (p < 0.05). Moreover, we observed two clusters of populations: west (populations 1−4) and east (populations 7−12). Of the 1364 miracidia genotyped, 1212 (89%) showed an S. bovis Cox1 profile and 152 (11%) showed an S. haematobium cox1 profile. All parasites showed an S. bovis Cox1 profile except for some at sites 3 and 4. Schistosoma miracidia full genotyping showed 59.3% of the S. bovis ITS2 allele. Conclusions: This study provides novel insight into hybridization and population genetic structure of S. haematobium in Nigeria. Our findings suggest that S. haematobium x S. bovis hybrids are common in Nigeria. More genomic studies on both human- and animal-infecting parasites are needed to ascertain the role of animals in schistosome transmission.

Hybridization increases genetic diversity in Schistosoma haematobium populations infecting humans in Cameroon

Background

Hybrids between Schistosoma haematobium (Sh) and S. bovis (Sb) have been found in several African countries as well as in Europe. Since the consequences of this hybridization are still unknown, this study aims to verify the presence of such hybrids in Cameroonian humans, to describe the structure of S. haematobium populations on a large geographic scale, and to examine the impact of these hybrids on genetic diversity and structure of these populations.

Methods

From January to April 2019, urine from infected children was collected in ten geographically distinct populations. Miracidia were collected from eggs in this urine. To detect the presence of hybrids among these miracidia we genotyped both Cox1 (RD-PCR) and ITS2 gene (PCR-RFLP). Population genetic diversity and structure was assessed by genotyping each miracidium with a panel of 14 microsatellite markers. Gene diversity was measured using both heterozygosity and allelic richness indexes, and genetic structure was analyzed using paired Fst, PCA and Bayesian approaches.

Results

Of the 1327 miracidia studied, 88.7% were identified as pure genotypes of S. haematobium (Sh_Sh/Sh) while the remaining 11.3% were hybrids (7.0% with Sh_Sh/Sb, 3.7% with Sb_Sb/Sh and 0.4% with Sb_Sh/Sb). No miracidium has been identified as a pure genotype of S. bovis. Allelic richness ranged from 5.55 (Loum population) to 7.73 (Matta-Barrage) and differed significantly between populations. Mean heterozygosity ranged from 53.7% (Loum) to 59% (Matta Barrage) with no significant difference. The overall genetic differentiation inferred either by a principal component analysis or by the Bayesian approach shows a partial structure. Southern populations (Loum and Matta Barrage) were clearly separated from other localities but genetic differentiation between northern localities was limited, certainly due to the geographic proximity between these sites.

Conclusions

Hybrids between S. haematobium and S. bovis were identified in 11.3% of miracidia that hatched from eggs present in the urine of Cameroonian schoolchildren. The percentages of these hybrids are correlated with the genetic diversity of the parasite, indicating that hybridization increases genetic diversity in our sampling sites. Hybridization is therefore a major biological process that shapes the genetic diversity of S. haematobium.

Graphical Abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s40249-022-00958-0.

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.

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.

Genome-wide insights into adaptive hybridisation across the Schistosoma haematobium group in West and Central Africa

Schistosomiasis remains a public health concern across sub-Saharan Africa; current control programmes rely on accurate mapping and high mass drug administration (MDA) coverage to attempt disease elimination. Inter-species hybridisation can occur between certain species, changing epidemiological dynamics within endemic regions, which has the potential to confound control interventions. The impact of hybridisation on disease dynamics is well illustrated in areas of Cameroon where urogenital schistosomiasis, primarily due to Schistosoma haematobium and hybrid infections, now predominate over intestinal schistosomiasis caused by Schistosoma guineensis. Genetic markers have shown the ability to identify hybrids, however the underlying genomic architecture of divergence and introgression between these species has yet to be established. In this study, restriction site associated DNA sequencing (RADseq) was used on archived adult worms initially identified as; Schistosoma bovis (n = 4), S. haematobium (n = 9), S. guineensis (n = 3) and S. guineensis x S. haematobium hybrids (n = 4) from Mali, Senegal, Niger, São Tomé and Cameroon. Genome-wide evidence supports the existence of S. guineensis and S. haematobium hybrid populations across Cameroon. The hybridisation of S. guineensis x S. haematobium has not been demonstrated on the island of São Tomé, where all samples showed no introgression with S. haematobium. Additionally, all S. haematobium isolates from Nigeria, Mali and Cameroon indicated signatures of genomic introgression from S. bovis. Adaptive loci across the S. haematobium group showed that voltage-gated calcium ion channels (Cav) could play a key role in the ability to increase the survivability of species, particularly in host systems. Where admixture has occurred between S. guineensis and S. haematobium, the excess introgressive influx of tegumental (outer helminth body) and antigenic genes from S. haematobium has increased the adaptive response in hybrids, leading to increased hybrid population fitness and viability.

Hybridized Zoonotic Schistosoma Infections Result in Hybridized Morbidity Profiles: A Clinical Morbidity Study amongst Co-Infected Human Populations of Senegal

Hybridization of infectious agents is a major emerging public and veterinary health concern at the interface of evolution, epidemiology, and control. Whilst evidence of the extent of hybridization amongst parasites is increasing, their impact on morbidity remains largely unknown. This may be predicted to be particularly pertinent where parasites of animals with contrasting pathogenicity viably hybridize with human parasites. Recent research has revealed that viable zoonotic hybrids between human urogenital Schistosoma haematobium with intestinal Schistosoma species of livestock, notably Schistosoma bovis, can be highly prevalent across Africa and beyond. Examining human populations in Senegal, we found increased hepatic but decreased urogenital morbidity, and reduced improvement following treatment with praziquantel, in those infected with zoonotic hybrids compared to non-hybrids. Our results have implications for effective monitoring and evaluation of control programmes, and demonstrate for the first time the potential impact of parasite hybridizations on host morbidity.

Natural Intra- and Interclade Human Hybrid Schistosomes in Africa with Considerations on Prevention through Vaccination

Causal agents of schistosomiasis are dioecious, digenean schistosomes affecting mankind in 76 countries. Preventive measures are manifold but need to be complemented by vaccination for long-term protection; vaccine candidates in advanced pre-clinical/clinical stages include Sm14, Sm-TSP-2/Sm-TSP-2Al^®, Smp80/SchistoShield^®, and Sh28GST/Bilhvax^®. Natural and anthropogenic changes impact on breaking species isolation barriers favoring introgressive hybridization, i.e., allelic exchange among gene pools of sympatric, interbreeding species leading to instant large genetic diversity. Phylogenetic distance matters, thus the less species differ phylogenetically the more likely they hybridize. PubMed and Embase databases were searched for publications limited to hybridale confirmation by mitochondrial cytochrome c oxidase (COX) and/or nuclear ribosomal internal transcribed spacer (ITS). Human schistosomal hybrids are predominantly reported from West Africa with clustering in the Senegal River Basin, and scattering to Europe, Central and Eastern Africa. Noteworthy is the dominance of Schistosoma haematobium interbreeding with human and veterinary species leading due to hybrid vigor to extinction and homogenization as seen for S. guineensis in Cameroon and S. haematobium in Niger, respectively. Heterosis seems to advantage S. haematobium/S. bovis interbreeds with dominant S. haematobium-ITS/S. bovis-COX1 profile to spread from West to East Africa and reoccur in France. S. haematobium/S. mansoni interactions seen among Senegalese and Côte d’Ivoirian children are unexpected due to their high phylogenetic distance. Detecting pure S. bovis and S. bovis/S. curassoni crosses capable of infecting humans observed in Corsica and Côte d’Ivoire, and Niger, respectively, is worrisome. Taken together, species hybridization urges control and preventive measures targeting human and veterinary sectors in line with the One-Health concept to be complemented by vaccination protecting against transmission, infection, and disease recurrence. Functional and structural diversity of naturally occurring human schistosomal hybrids may impact current vaccine candidates requiring further research including natural history studies in endemic areas targeted for clinical trials.

The detection of Schistosoma bovis in livestock on Pemba Island, Zanzibar: A preliminary study

Schistosoma bovis is a parasitic trematode of ungulates transmitted by freshwater snails in Sub-Saharan Africa causing bovine intestinal schistosomiasis that leads to chronic morbidity and significant agricultural economic losses. The recently reported occurrence of Bulinus globosus infected with S. bovis for the first time on Pemba Island (Zanzibar, United Republic of Tanzania) is a cause of concern for livestock/wildlife health and complicates the surveillance of Schistosoma haematobium. To confirm that local cattle are infected with S. bovis, fresh faecal samples were collected from six adult cows surrounding two schistosomiasis transmission sites in Kinyasini, Pemba Island. Schistosome eggs were concentrated, egg hatching stimulated and miracidia were individually captured and identified by analysis of the partial mitochondrial cytochrome c oxidase subunit 1 (cox1) and the partial nuclear internal transcribed spacer region (ITS1+5.8S+ITS2). Two S. bovis miracidia were collected from one faecal sample with two cox1 haplotypes, one matching cox1 data obtained from S. bovis cercariae, collected previously at the same site in Pemba, the other matching S. bovis cox1 data originating from coastal Tanzania. The findings conclude that S. bovis transmission has been established on Pemba Island and is likely to have been imported through livestock trade with East Africa. Increasing the sensitivity of non-invasive diagnostics for bovine schistosomiasis, together with wider sampling, will enable a better assessment on the epidemiology of S. bovis on Pemba Island.

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The bovine schistosome Schistosoma bovis is detected for the first time from cattle in Zanzibar.

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Local transmission of S. bovis is confirmed on Pemba Island.

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Bovine schistosomes complicate the xenomonitoring and surveillance of human urogenital schistosomiasis.

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Bovine schistosomiasis could lead to chronic morbidity of cattle and agricultural economic losses.