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Genomic approaches hold great promise for resolving unanswered questions about transmission patterns and responses to control efforts for schistosomiasis and other neglected tropical diseases. However, the cost of generating genomic data and the challenges associated with obtaining sufficient DNA from individual schistosome larvae (miracidia) from mammalian hosts have limited the application of genomic data for studying schistosomes and other complex macroparasites. Here, we demonstrate the feasibility of utilizing whole genome amplification and sequencing (WGS) to analyze individual archival miracidia. As an example, we sequenced whole genomes of 22 miracidia from 11 human hosts representing two villages in rural Sichuan, China, and used these data to evaluate patterns of relatedness and genetic diversity. We also down-sampled our dataset to test how lower coverage sequencing could increase the cost effectiveness of WGS while maintaining power to accurately infer relatedness. Collectively, our results illustrate that population-level WGS datasets are attainable for individual miracidia and represent a powerful tool for ultimately providing insight into overall genetic diversity, parasite relatedness, and transmission patterns for better design and evaluation of disease control efforts., Author summary Schistosomiasis is a neglected tropical disease caused by helminths within the genus Schistosoma, which affects over 200 million people globally. Here, we demonstrate the ability to obtain whole genome sequences from single S. japonicum miracidia that have been archived for years, and the promise of how these data may be used to answer major questions to understand and eventually help control schistosomiasis. To demonstrate the approach, we generated a moderate-sized dataset of 22 individual S. japonicum genomes and use these data to infer fine-scale patterns of relatedness among parasites from human hosts from two villages in Sichuan, China. We highlight how this type of genomic information may be useful for understanding the genetic variation among individual parasites with high precision, which could ultimately provide high resolution for understanding transmission pathways and inform control efforts with larger sample sizes. We also show that it is possible to use less data per individual than we obtained here, and still maintain high levels of accuracy; this would enable greater sample sizes by lowering individual sample cost. Collectively our results demonstrate that sampling genomes of individual schistosome parasites is now feasible on a population-level scale, opening new avenues for studying relatedness, tracing parasite spread, and studying parasite biology.

Background Microsatellites have been found to be useful in determining genetic diversities of various medically-important parasites which can be used as basis for an effective disease management and control program. In Asia and Africa, the identification of different geographical strains of Schistosoma japonicum, S. haematobium and S. mansoni as determined through microsatellites could pave the way for a better understanding of the transmission epidemiology of the parasite. Thus, the present study aims to apply microsatellite markers in analyzing the populations of S. japonicum from different endemic areas in the Philippines for possible strain differentiation. Methodology/ Principal findings Experimental mice were infected using the cercariae of S. japonicum collected from infected Oncomelania hupensis quadrasi snails in seven endemic municipalities. Adult worms were harvested from infected mice after 45 days of infection and their DNA analyzed against ten previously characterized microsatellite loci. High genetic diversity was observed in areas with high endemicity. The degree of genetic differentiation of the parasite population between endemic areas varies. Geographical separation was considered as one of the factors accounting for the observed difference between populations. Two subgroups have been observed in one of the study sites, suggesting that co-infection with several genotypes of the parasite might be present in the population. Clustering analysis showed no particular spatial structuring between parasite populations from different endemic areas. This result could possibly suggest varying degrees of effects of the ongoing control programs and the existing gene flow in the populations, which might be attributed to migration and active movement of infected hosts from one endemic area to another. Conclusions/ Significance Based on the results of the study, it is reasonable to conclude that genetic diversity could be one possible criterion to assess the infection status in highly endemic areas. Genetic surveillance using microsatellites is therefore important to predict the ongoing gene flow and degree of genetic diversity, which indirectly reflects the success of the control program in schistosomiasis-endemic areas., Author summary Schistosomiasis is one of the important neglected tropical diseases endemic in 78 countries throughout the world. The disease is caused by the parasitic worms known as schistosomes. In the Philippines, S. japonicum is the causative agent of the disease. The prevalence of the disease varies in endemic areas, suggesting that the parasite populations might differ in their genetic composition and infectivity to the human host. In this study, DNA samples of adult worms from seven endemic municipalities were analyzed. Characterization of S. japonicum samples in different endemic sites with varying prevalence provides information on the genetic diversity of the parasite. Results of this study showed that samples in high prevalence endemic areas like Irosin, Catarman and Socorro were genetically diverse as compared to other areas. Information on parasite genetic diversity is therefore important in planning disease control strategies. The results suggest ongoing parasite transmission across geographic endemic areas which should be monitored and used as reference for genetic diversity of the schistosomes attributed to geographic areas, thus a safeguarding precaution should be implemented to ensure localized elimination of the disease.