Population genetics of the Schistosoma snail host Bulinus truncatus in Egypt

Genetic variation of the freshwater snail Indoplanorbis exustus (Gastropoda: Planorbidae) in Thailand, inferred from 18S and 28S rDNA sequences

Indoplanorbis exustus, a freshwater pulmonate snail, is widely distributed in tropical and subtropical zones and plays a significant role as an intermediate host for trematode parasites. Various genetic markers have been used for species identification and phylogenetic studies of this snail. However, there are limited studies about their molecular genetics based on nuclear ribosomal DNA (rDNA) genes. A genetic analysis of I. exustus in Thailand was conducted based on the nuclear 18S rDNA (339 bp) and 28S rDNA (1036 bp) genes. Indoplanorbis snails were collected from 29 localities in 21 provinces covering six regions of Thailand. Nucleotide sequences from 44 snails together with sequences from the GenBank database were examined for phylogenetic relationships and genetic diversity. All sequences of the selected nucleotide regions exhibited a high level of similarity (99%) to the sequences of I. exustus in the GenBank database. The maximum likelihood tree based on the 18S and 28S rDNA fragment sequences of I. exustus in Thailand revealed only one group with clear separation from another genus in the family Planorbidae. The I. exustus 28S rDNA sequences showed intraspecific genetic divergence ranging from 0 to 0.78% and were classified into 8 different haplotypes. Conversely, the 18S rDNA data showed lower variation than the 28S rDNA data and revealed a single haplotype and intraspecific distances of zero among all sampled individuals. The haplotype network of 28S rDNA sequences of I. exustus in Thailand revealed six unique haplotypes and two haplotypes shared by at least two regions. Overall, both markers were successful in the identification of I. exustus. However, these markers, particularly the 18S rDNA, may not be suitable for genetic analysis within the species, particularly for population genetic studies, due to their limited variation as seen in this study. In summary, this study not only enhances understanding of genetic variation in I. exustus but is also useful for the selection of molecular markers in future genetic research.

Large-scale and small-scale population genetic structure of the medically important gastropod species Bulinus truncatus (Gastropoda, Heterobranchia)

Background

Gastropod snails remain strongly understudied, despite their important role in transmitting parasitic diseases. Knowledge of their distribution and population dynamics increases our understanding of the processes driving disease transmission. We report the first study to use high-throughput sequencing (HTS) to elucidate the population genetic structure of the hermaphroditic snail Bulinus truncatus (Gastropoda, Heterobranchia) on a regional (17–150 km) and inter-regional (1000–5400 km) scale. This snail species acts as an intermediate host of Schistosoma haematobium and Schistosoma bovis, which cause human and animal schistosomiasis respectively.

Methods

Bulinus truncatus snails were collected in Senegal, Cameroon, Egypt and France and identified through DNA barcoding. A single-end genotyping-by-sequencing (GBS) library, comprising 87 snail specimens from the respective countries, was built and sequenced on an Illumina HiSeq 2000 platform. Reads were mapped against S. bovis and S. haematobium reference genomes to identify schistosome infections, and single nucleotide polymorphisms (SNPs) were scored using the Stacks pipeline. These SNPs were used to estimate genetic diversity, assess population structure and construct phylogenetic trees of B. truncatus.

Results

A total of 10,750 SNPs were scored and used in downstream analyses. The phylogenetic analysis identified five clades, each consisting of snails from a single country but with two distinct clades within Senegal. Genetic diversity was low in all populations, reflecting high selfing rates, but varied between locations due to habitat variability. Significant genetic differentiation and isolation by distance patterns were observed at both spatial scales, indicating that gene flow is not strong enough to counteract the effects of population bottlenecks, high selfing rates and genetic drift. Remarkably, the population genetic differentiation on a regional scale (i.e. within Senegal) was as large as that between populations on an inter-regional scale. The blind GBS technique was able to pick up parasite DNA in snail tissue, demonstrating the potential of HTS techniques to further elucidate the role of snail species in parasite transmission.

Conclusions

HTS techniques offer a valuable toolbox to further investigate the population genetic patterns of intermediate schistosome host snails and the role of snail species in parasite transmission.

Graphical Abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s13071-022-05445-x.

Predicting the habitat suitability of Schistosoma intermediate host Bulinus truncatus, its predatory aquatic insect Odonata nymph, and the associated aquatic plant Ceratophyllum demersum using MaxEnt

Schistosomiasis is one of the most important parasitic diseases in tropical and subtropical areas. Its prevalence is associated with the distribution of freshwater snails, which are their intermediate hosts. Thus, control of freshwater snails is the solution to reduce the transmission of this disease. This will be achieved by understanding the relationship between the snails and their habitats including natural enemies and associated aquatic plants as well as the factors affecting their distribution. In this study, Maximum Entropy model (MaxEnt) was used for mapping and predicting the possible geographic distribution of Bulinus truncatus snail (the intermediate host of Schistosoma haematobium), Odonata nymph (predatory aquatic insect), and Ceratophyllum demersum (the associated aquatic plant) in Egypt based on topographic and climatic factors. The models of the investigated species were evaluated using the area under receiver operating characteristic curve. The results showed that the potential risk areas were along the banks of the Nile River and its irrigation canals. In addition, the MaxEnt models revealed some similarities in the distribution pattern of the vector, the predator, and the aquatic plant. It is obvious that the predictive distribution range of B. truncatus was affected by altitude, precipitation seasonality, isothermality, and mean temperature of warmest quarter. The presence of B. truncatus decreases with the increase of altitude and precipitation seasonality values. It could be concluded that the MaxEnt model could help introducing a predictive risk map for Schistosoma haematobium prevalence and performing better management strategies for 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.

DNA and eDNA-based tracking of the North African sharptooth catfish Clarias gariepinus

The African sharptooth catfish, Clarias gariepinus, contributes much to the River Nile ecosystem by its high omnivorosity, sturdiness, growth rates, and fecundity. It was globally appreciated as a key fluvial aquaculture species. Yet, it is also one of the top world freshwater aliens. Monitoring the genetic diversity of different economically and ecologically important species as well as development of markers that aid their tracing and abundance are fundamental. This is chiefly due to the growing international threats of environmental pollution, reduction, and loss of biodiversity. Herein, the genetic diversity of C. gariepinus along the River Nile in Egypt was assessed through sequencing of the mitochondrial cytochrome oxidase subunit I (COI). Also, a qPCR assay based on C. gariepinus 16srDNA was developed to assess the species abundance through environmental water DNA samples (eDNA). The results showed low genetic diversity of that species in Egypt. Moreover, its populations exhibited high rates of fixation. Testing its eDNA-based marker resulted in an unambiguous quantitative trend in situ, in agreement with reports of local fishermen. These eDNA signals were strong at least 1 Km upstream to the initial sampling areas, even where no C. gariepinus fishing activities are carried out. This possibly indicated a degree of homogenous species-abundance in each of the studied areas. Finally, the results identified a need for better conservation strategies for C. gariepinus, since its low diversity in the Egyptian River Nile may represent a threat against its persistence under the continuously changing environmental conditions. Moreover, using non-invasive sampling methods, e.g. based on aquatic eDNA quantification, can aid much the detection of areas of abundance of C. gariepinus, especially for both the economic importance it contributes and the invasive power it possesses.

Molecular diversity of Bulinus species in Madziwa area, Shamva district in Zimbabwe: implications for urogenital schistosomiasis transmission

Background

Bulinus species are freshwater snails that transmit the parasitic trematode Schistosoma haematobium. Despite their importance, the diversity of these intermediate host snails and their evolutionary history is still unclear in Zimbabwe. Bulinus globosus and B. truncatus collected from a urogenital schistosomiasis endemic region in the Madziwa area of Zimbabwe were characterized using molecular methods.

Methods

Malacological survey sites were mapped and snails were collected from water contact sites in four communities in the Madziwa area, Shamva district for a period of one year, at three-month intervals. Schistosoma haematobium infections in snails were determined by cercarial shedding and the partial mitochondrial cytochrome c oxidase subunit 1 gene (cox1) was used to investigate the phylogeny and genetic variability of the Bulinus spp. collected.

Results

Among the 1570 Bulinus spp. snails collected, 30 (1.9%) B. globosus were shedding morphologically identified schistosomes. None of the B. truncatus snails were shedding. The mitochondrial cox1 data from 166 and 16 samples for B. globosus and B. truncatus, respectively, showed genetically diverse populations within the two species. Twelve cox1 haplotypes were found from the 166 B. globosus samples and three from the 16 B. truncatus samples with phylogenetic analysis showing that the haplotypes fall into well-supported clusters within their species groups. Both B. truncatus and B. globosus clustered into two distinct lineages. Overall, significant negative values for both Tajima’s D statistic and the Fu’s Fs statistic were observed for B. globosus and B. truncatus.

Conclusions

The study provided new insights into the levels of genetic diversity within B. globosus and additional information on B. truncatus collected from a small geographical area in Zimbabwe. Low prevalence levels of infection observed in the snails may reflect the low transmission level of urogenital schistosomiasis in the area. Our results contribute towards the understanding of the distribution and population genetic structure of Bulinus spp. supporting the mapping of the transmission or risk of transmission of urogenital schistosomiasis, particularly in Zimbabwe.

Molecular identification of Bulinus spp. intermediate host snails of Schistosoma spp. in crater lakes of western Uganda with implications for the transmission of the Schistosoma haematobium group parasites

Background

Human schistosomiasis is the second most important tropical disease and occurs in two forms in Africa (intestinal and urogenital) caused by the digenetic trematodes Schistosoma mansoni and Schistosoma haematobium, respectively. A proposed recent shift of schistosomiasis above a previously established altitudinal threshold of 1400 m above sea level in western Ugandan crater lakes has triggered more research interest there.

Methods

Based on extensive field sampling in western Uganda and beyond and employing an approach using sequences of the mitochondrial barcoding gene cytochrome c oxidase subunit 1 (cox1) this study aims were: (i) identification and establishment of the phylogenetic affinities of Bulinus species as potential hosts for Schistosoma spp.; (ii) determining diversity, frequency and distribution patterns of Bulinus spp.; and (iii) establishing genetic variability and phylogeographical patterns using Bayesian inference and parsimony network analyses.

Results

Out of the 58 crater lakes surveyed, three species of Bulinus snails were found in 34 crater lakes. Bulinus tropicus was dominating, Bulinus forskalii was found in two lakes and Bulinus truncatus in one. The latter two species are unconfirmed potential hosts for S. haematobium in this region. However, Bulinus tropicus is an important species for schistosomiasis transmission in ruminants. Bulinus tropicus comprised 31 haplotypes while both B. forskalii and B. truncatus exhibited only a single haplotype in the crater lakes. All species clustered with most of the haplotypes from surrounding lake systems forming source regions for the colonization of the crater lakes.

Conclusions

This first detailed malacological study of the crater lakes systems in western Uganda revealed presence of Bulinus species that are either not known or not regionally known to be hosts for S. haematobium, the causing agent of human urogenital schistosomiasis. Though this disease risk is almost negligible, the observed dominance of B. tropicus in the crater lakes shows that there is a likelihood of a high risk of infections with Schistosoma bovis. Thus, extra attention should be accorded to safeguard wild and domestic ruminants in this region as the population benefits from these animals.

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.

RETRACTED: Diversity and Compatibility of Human Schistosomes and Their Intermediate Snail Hosts

This article has been retracted: please see Elsevier Policy on Article Withdrawal (https://www.elsevier.com/about/our-business/policies/article-withdrawal) This article has been retracted at the request of the authors: Benjamin Sanogo, Dongjuan Yuan, Xin Zeng, Yanhua Zhang, and Zhongdao Wu. Our article reviews the evolution, geography, diversity, genetics and host-compatibility of human schistosomes and their hosts. It has come to our attention that readers have found some of the content in the article to be confusing or misleading. As authors, we have tried our best to share our scientific discovery and understanding faithfully, but we also agree that scientific reports should stand up to doubt and discussion. After serious consideration, to avoid confusion in the Schistosoma research community, we are retracting the Review. We apologize to the community for any inconvenience we have caused.