Parasites, people and policy: infectious diseases and the Millennium Development Goals

Compilation of parasitic immunogenic proteins from 30 years of published research using machine learning and natural language processing

The World Health Organisation reported in 2020 that six of the top 10 sources of death in low-income countries are parasites. Parasites are microorganisms in a relationship with a larger organism, the host. They acquire all benefits at the host’s expense. A disease develops if the parasitic infection disrupts normal functioning of the host. This disruption can range from mild to severe, including death. Humans and livestock continue to be challenged by established and emerging infectious disease threats. Vaccination is the most efficient tool for preventing current and future threats. Immunogenic proteins sourced from the disease-causing parasite are worthwhile vaccine components (subunits) due to reliable safety and manufacturing capacity. Publications with ‘subunit vaccine’ in their title have accumulated to thousands over the last three decades. However, there are possibly thousands more reporting immunogenicity results without mentioning ‘subunit’ and/or ‘vaccine’. The exact number is unclear given the non-standardised keywords in publications. The study aim is to identify parasite proteins that induce a protective response in an animal model as reported in the scientific literature within the last 30 years using machine learning and natural language processing. Source code to fulfil this aim and the vaccine candidate list obtained is made available.

THE ZOONOTIC CITY: Urban Political Ecology and the Pandemic Imaginary

In the context of the Covid-19 pandemic this article takes a longer view of the evolving relationship between urbanization and the range of zoonotic diseases that have spread from animals to humans. I suggest that the existing interpretation of epidemiological transitions remains overly Eurocentric and requires a more nuanced conception of global environmental history. Similarly, the conceptualization of urban space within these teleological schemas has relied on a narrow range of examples and has failed to fully engage with networked dimensions to urbanization. At an analytical level I consider the potential for extending the conceptual framework offered by urban political ecology to take greater account of the epidemiological dimensions to contemporary urbanization and its associated pandemic imaginary. I examine how contemporary health threats intersect with complex patterns of environmental change, including the destruction of biodiversity (and trade in live animals), the co-evolutionary dynamics of viruses and other pathogens, and wider dimensions to the global technosphere, including food production, infrastructure networks, and the shifting topographies of peri- or ex-urban contact zones.

Comparative analyses of parasites with a comprehensive database of genome-scale metabolic models

Protozoan parasites cause diverse diseases with large global impacts. Research on the pathogenesis and biology of these organisms is limited by economic and experimental constraints. Accordingly, studies of one parasite are frequently extrapolated to infer knowledge about another parasite, across and within genera. Model in vitro or in vivo systems are frequently used to enhance experimental manipulability, but these systems generally use species related to, yet distinct from, the clinically relevant causal pathogen. Characterization of functional differences among parasite species is confined to post hoc or single target studies, limiting the utility of this extrapolation approach. To address this challenge and to accelerate parasitology research broadly, we present a functional comparative analysis of 192 genomes, representing every high-quality, publicly-available protozoan parasite genome including Plasmodium, Toxoplasma, Cryptosporidium, Entamoeba, Trypanosoma, Leishmania, Giardia, and other species. We generated an automated metabolic network reconstruction pipeline optimized for eukaryotic organisms. These metabolic network reconstructions serve as biochemical knowledgebases for each parasite, enabling qualitative and quantitative comparisons of metabolic behavior across parasites. We identified putative differences in gene essentiality and pathway utilization to facilitate the comparison of experimental findings and discovered that phylogeny is not the sole predictor of metabolic similarity. This knowledgebase represents the largest collection of genome-scale metabolic models for both pathogens and eukaryotes; with this resource, we can predict species-specific functions, contextualize experimental results, and optimize selection of experimental systems for fastidious species.

Profile analysis of C. elegans rheotaxis behavior using a microfluidic device

The directed motility of organisms in response to fluid velocity, which is called rheotaxis, is important in the life cycle of C. elegans, enabling them to navigate their environment and maintain their positions in the presence of adverse flow. Thus, to study the mechanism underlying rheotaxis behavior and reveal information on parasitic diseases, the profile analysis of the rheotaxis response in worm populations with high resolution in well-defined fluid environments is highly desirable. In this work, we presented a rapid and robust microfluidic approach to quantitatively analyze the rheotaxis behavior of worms in response to velocity. The flow-based microfluidic chip contained six helical spline microchannels for generating six flow streams with different flow velocities. Since the worms loaded in the chip would swim upstream into channels, the distribution of the worms in response to the different flow velocities was successfully monitored for the quantitative analysis of their rheotaxis behavior using this microfluidic chip. The results indicated that the rate range of around 50 μm s-1 was the most favorable flow velocity for the wild-type worms. Further, we analyzed ASH neuron-blocked worms and found that the functionally defective ASH neurons inhibited their sensitivity to flow rate. In addition, the rheotaxis analysis of the mutant worms indicated that TRP mechanosensory channels and serotonin signals also play a regulatory role in the rheotaxis response of these worms. Thus, our microfluidic method provides a useful platform to study the rheotaxis behaviors in C. elegans and can be further applied for anti-parasitic drug tests.

Genetic susceptibility to infectious diseases: Current status and future perspectives from genome-wide approaches

Genome-wide association studies (GWASs) have been widely applied to identify genetic factors that affect complex diseases or traits. Presently, the GWAS Catalog includes > 2800 human studies. Of these, only a minority have investigated the susceptibility to infectious diseases or the response to therapies for the treatment or prevention of infections. Despite their limited application in the field, GWASs have provided valuable insights by pinpointing associations to both innate and adaptive immune response loci, as well as novel unexpected risk factors for infection susceptibility. Herein, we discuss some issues and caveats of GWASs for infectious diseases, we review the most recent findings ensuing from these studies, and we provide a brief summary of selected GWASs for infections in non-human mammals. We conclude that, although the general trend in the field of complex traits is to shift from GWAS to next-generation sequencing, important knowledge on infectious disease-related traits can be still gained by GWASs, especially for those conditions that have never been investigated using this approach. We suggest that future studies will benefit from the leveraging of information from the host's and pathogen's genomes, as well as from the exploration of models that incorporate heterogeneity across populations and phenotypes. Interactions within HLA genes or among HLA variants and polymorphisms located outside the major histocompatibility complex may also play an important role in shaping the susceptibility and response to invading pathogens.

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Relatively few GWASs for infectious diseases were performed.

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Phenotype heterogeneity and case/control misclassification can affect GWAS power.

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Adaptive and innate immunity loci were identified in several infectious disease GWASs.

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Unexpected loci (e.g., lncRNAs) were also associated with infection susceptibility.

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GWASs should integrate host and pathogen diversity and use complex association models.

A hydrodynamic mechanism for attraction of undulatory microswimmers to surfaces (bordertaxis)

Although small nematodes significantly impact human and animal health, agriculture, and ecology, little is known about the role of hydrodynamics in their life cycles. Using the nematode Caenorhabditis elegans as a model undulatory microswimmer, we have observed that animals are attracted to and swim along surfaces. The attraction to surfaces does not require mechanosensory neuron function. In dilute swarms, swimmers aggregate near surfaces. Using resistive force-based theory, symmetry arguments, and direct hydrodynamic simulations, we demonstrate that forces resulting from the interaction between the swimmer-induced flow field and a nearby surface cause a short-range hydrodynamic torque that stirs the swimmers towards the surface. When combined with steric forces, this causes locomotion along the surface. This surface attraction may affect nematode mate and food finding behaviour and, in the case of parasitic nematodes, may facilitate host penetration. Surface attraction must be accounted for when studying animals' responses to various stimuli, and suggests means of controlling undulatory microswimmers.

Quantitative analyses and modelling to support achievement of the 2020 goals for nine neglected tropical diseases

Quantitative analysis and mathematical models are useful tools in informing strategies to control or eliminate disease. Currently, there is an urgent need to develop these tools to inform policy to achieve the 2020 goals for neglected tropical diseases (NTDs). In this paper we give an overview of a collection of novel model-based analyses which aim to address key questions on the dynamics of transmission and control of nine NTDs: Chagas disease, visceral leishmaniasis, human African trypanosomiasis, leprosy, soil-transmitted helminths, schistosomiasis, lymphatic filariasis, onchocerciasis and trachoma. Several common themes resonate throughout these analyses, including: the importance of epidemiological setting on the success of interventions; targeting groups who are at highest risk of infection or re-infection; and reaching populations who are not accessing interventions and may act as a reservoir for infection,. The results also highlight the challenge of maintaining elimination 'as a public health problem' when true elimination is not reached. The models elucidate the factors that may be contributing most to persistence of disease and discuss the requirements for eventually achieving true elimination, if that is possible. Overall this collection presents new analyses to inform current control initiatives. These papers form a base from which further development of the models and more rigorous validation against a variety of datasets can help to give more detailed advice. At the moment, the models' predictions are being considered as the world prepares for a final push towards control or elimination of neglected tropical diseases by 2020.

Viability of developmental stages of Schistosoma mansoni quantified with xCELLigence worm real-time motility assay (xWORM)

Infection with helminth parasites causes morbidity and mortality in billions of people and livestock worldwide. Where anthelmintic drugs are available, drug resistance is a major problem in livestock parasites, and a looming threat to public health. Monitoring the efficacy of these medicines and screening for new drugs has been hindered by the lack of objective, high-throughput approaches. Several cell monitoring technologies have been adapted for parasitic worms, including video-, fluorescence-, metabolism enzyme- and impedance-based tools that minimize the screening bottleneck. Using the xCELLigence impedance-based system we previously developed a motility-viability assay that is applicable for a range of helminth parasites. Here we have improved substantially the assay by using diverse frequency settings, and have named it the xCELLigence worm real-time motility assay (xWORM). By utilizing strictly standardized mean difference analysis we compared the xWORM output measured with 10, 25 and 50 kHz frequencies to quantify the motility of schistosome adults (human blood flukes) and hatching of schistosome eggs. Furthermore, we have described a novel application of xWORM to monitor movement of schistosome cercariae, the developmental stage that is infectious to humans. For all three stages, 25 kHz was either optimal or near-optimal for monitoring and quantifying schistosome motility. These improvements in methodology sensitivity should enhance the capacity to screen small compound libraries for new drugs both for schistosomes and other helminth pathogens at large.

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25 kHz on the xCELLigence system dramatically improves the schistosome xWORM assay.

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xWORM assay can efficiently determine viability of Schistome adults or eggs.

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First time cercariae have been incorporated into an automated viability assay.

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Other helminth monitoring may benefit from alternate xCELLigence frequency options.

Propensity of undulatory swimmers, such as worms, to go against the flow

The ability to orient oneself in response to environmental cues is crucial to the survival and function of diverse organisms. One such orientation behavior is the alignment of aquatic organisms with (negative rheotaxis) or against (positive rheotaxis) fluid current. The questions of whether low-Reynolds-number, undulatory swimmers, such as worms, rheotax and whether rheotaxis is a deliberate or an involuntary response to mechanical forces have been the subject of conflicting reports. To address these questions, we use Caenorhabditis elegans as a model undulatory swimmer and examine, in experiment and theory, the orientation of C. elegans in the presence of flow. We find that when close to a stationary surface the animal aligns itself against the direction of the flow. We elucidate for the first time to our knowledge the mechanisms of rheotaxis in worms and show that rheotaxis can be explained solely by mechanical forces and does not require sensory input or deliberate action. The interaction between the flow field induced by the swimmer and a nearby surface causes the swimmer to tilt toward the surface and the velocity gradient associated with the flow rotates the animal to face upstream. Fluid mechanical computer simulations faithfully mimic the behavior observed in experiments, supporting the notion that rheotaxis behavior can be fully explained by hydrodynamics. Our study highlights the important role of hydrodynamics in the behavior of small undulating swimmers and may assist in developing control strategies to affect the animals' life cycles.

Network epidemiology and plant trade networks

Models of epidemics in complex networks are improving our predictive understanding of infectious disease outbreaks. Nonetheless, applying network theory to plant pathology is still a challenge. This overview summarizes some key developments in network epidemiology that are likely to facilitate its application in the study and management of plant diseases. Recent surveys have provided much-needed datasets on contact patterns and human mobility in social networks, but plant trade networks are still understudied. Human (and plant) mobility levels across the planet are unprecedented-there is thus much potential in the use of network theory by plant health authorities and researchers. Given the directed and hierarchical nature of plant trade networks, there is a need for plant epidemiologists to further develop models based on undirected and homogeneous networks. More realistic plant health scenarios would also be obtained by developing epidemic models in dynamic, rather than static, networks. For plant diseases spread by the horticultural and ornamental trade, there is the challenge of developing spatio-temporal epidemic simulations integrating network data. The use of network theory in plant epidemiology is a promising avenue and could contribute to anticipating and preventing plant health emergencies such as European ash dieback.

UDP-galactopyranose mutases from Leishmania species that cause visceral and cutaneous leishmaniasis

Leishmaniasis is a vector-borne, neglected tropical disease caused by parasites from the genus Leishmania. Galactofuranose (Galf) is found on the cell surface of Leishmania parasites and is important for virulence. The flavoenzyme that catalyzes the isomerization of UDP-galactopyranose to UDP-Galf, UDP-galactopyranose mutase (UGM), is a validated drug target in protozoan parasites. UGMs from L. mexicana and L. infantum were recombinantly expressed, purified, and characterized. The isolated enzymes contained tightly bound flavin cofactor and were active only in the reduced form. NADPH is the preferred redox partner for both enzymes. A kcat value of 6 ± 0.4s(-1) and a Km value of 252 ± 42 μM were determined for L. infantum UGM. For L. mexicana UGM, these values were ∼4-times lower. Binding of UDP-Galp is enhanced 10-20 fold in the reduced form of the enzymes. Changes in the spectra of the reduced flavin upon interaction with the substrate are consistent with formation of a flavin-iminium ion intermediate.

A model framework to estimate impact and cost of genetics-based sterile insect methods for dengue vector control

Vector-borne diseases impose enormous health and economic burdens and additional methods to control vector populations are clearly needed. The Sterile Insect Technique (SIT) has been successful against agricultural pests, but is not in large-scale use for suppressing or eliminating mosquito populations. Genetic RIDL technology (Release of Insects carrying a Dominant Lethal) is a proposed modification that involves releasing insects that are homozygous for a repressible dominant lethal genetic construct rather than being sterilized by irradiation, and could potentially overcome some technical difficulties with the conventional SIT technology. Using the arboviral disease dengue as an example, we combine vector population dynamics and epidemiological models to explore the effect of a program of RIDL releases on disease transmission. We use these to derive a preliminary estimate of the potential cost-effectiveness of vector control by applying estimates of the costs of SIT. We predict that this genetic control strategy could eliminate dengue rapidly from a human community, and at lower expense (approximately US$ 2∼30 per case averted) than the direct and indirect costs of disease (mean US$ 86–190 per case of dengue). The theoretical framework has wider potential use; by appropriately adapting or replacing each component of the framework (entomological, epidemiological, vector control bio-economics and health economics), it could be applied to other vector-borne diseases or vector control strategies and extended to include other health interventions.

The emergence of human-evolutionary medical genomics

In this review, I describe how evolutionary genomics is uniquely suited to spearhead advances in understanding human disease risk, owing to the privileged position of genes as fundamental causes of phenotypic variation, and the ability of population genetic and phylogenetic methods to robustly infer processes of natural selection, drift, and mutation from genetic variation at the levels of family, population, species, and clade. I first provide an overview of models for the origins and maintenance of genetically based disease risk in humans. I then discuss how analyses of genetic disease risk can be dovetailed with studies of positive and balancing selection, to evaluate the degree to which the 'genes that make us human' also represent the genes that mediate risk of polygenic disease. Finally, I present four basic principles for the nascent field of human evolutionary medical genomics, each of which represents a process that is nonintuitive from a proximate perspective. Joint consideration of these principles compels novel forms of interdisciplinary analyses, most notably studies that (i) analyze tradeoffs at the level of molecular genetics, and (ii) identify genetic variants that are derived in the human lineage or in specific populations, and then compare individuals with derived versus ancestral alleles.

A novel high throughput assay for anthelmintic drug screening and resistance diagnosis by real-time monitoring of parasite motility

Background

Helminth parasites cause untold morbidity and mortality to billions of people and livestock. Anthelmintic drugs are available but resistance is a problem in livestock parasites, and is a looming threat for human helminths. Testing the efficacy of available anthelmintic drugs and development of new drugs is hindered by the lack of objective high-throughput screening methods. Currently, drug effect is assessed by observing motility or development of parasites using laborious, subjective, low-throughput methods.

Methodology/Principal Findings

Here we describe a novel application for a real-time cell monitoring device (xCELLigence) that can simply and objectively assess anthelmintic effects by measuring parasite motility in real time in a fully automated high-throughput fashion. We quantitatively assessed motility and determined real time IC₅₀ values of different anthelmintic drugs against several developmental stages of major helminth pathogens of humans and livestock, including larval Haemonchus contortus and Strongyloides ratti, and adult hookworms and blood flukes. The assay enabled quantification of the onset of egg hatching in real time, and the impact of drugs on hatch rate, as well as discriminating between the effects of drugs on motility of drug-susceptible and –resistant isolates of H. contortus.

Conclusions/Significance

Our findings indicate that this technique will be suitable for discovery and development of new anthelmintic drugs as well as for detection of phenotypic resistance to existing drugs for the majority of helminths and other pathogens where motility is a measure of pathogen viability. The method is also amenable to use for other purposes where motility is assessed, such as gene silencing or antibody-mediated killing.

Parasitic worms cause untold morbidity and mortality on billions of people and livestock. Drugs are available but resistance is problematic in livestock parasites and is a looming threat for human helminths. Currently, new drug discovery and resistance monitoring is hindered as drug efficacy is assessed by observing motility or development of parasites using laborious, subjective, low-throughput methods evaluated by eye using microscopy. Here we describe a novel application for a cell monitoring device (xCELLigence) that can simply and objectively assess real time anti-parasite efficacy of drugs on eggs, larvae and adults in a fully automated, label-free, high-throughput fashion. This technique overcomes the current low-throughput bottleneck in anthelmintic drug development and resistance detection pipelines. The widespread use of this device to screen for new therapeutics or emerging drug resistance will be an invaluable asset in the fight against human, animal and plant parasitic helminths and other pathogens that plague our planet.

Important helminth infections in Southeast Asia diversity, potential for control and prospects for elimination

Besides the 'big three'-HIV/AIDS, malaria and tuberculosis-there are a host of diseases that, by comparison, are truly neglected. These so-called neglected tropical diseases (NTDs), many of which caused by helminths, are intimately linked with poverty and are rampant where housing is poor; access to clean water and adequate sanitation is lacking; hygiene and nutrition is substandard and populations are marginalized and vulnerable. More than a billion people are affected by NTDs, mainly in remote rural and deprived urban settings of the developing world. An overview of papers published in two special thematic volumes of the Advances in Parasitology is provided here under the umbrella of current status of research and control of important helminth infections. A total of 25 comprehensive reviews are presented, which summarise the latest available data pertaining to the diagnosis, epidemiology, pathogenesis, prevention, treatment, control and eventual elimination of NTDs in Southeast Asia and neighbourhood countries. The focus of the first volume provides the current regional status of schistosomiasis, lymphatic filariasis, food-borne trematodiases, echinococcosis and cysticercosis/taeniasis, less common parasitic diseases that can cause epidemic outbreaks and helminth infections affecting the central nervous system. The second volume deals with the tools and strategies for control, including diagnostics, drugs, vaccines and cutting-edge basic research (e.g. the '-omics' sciences). Moreover, cross-cutting themes such as multiparasitism, social sciences, capacity strengthening, geospatial health technologies, health metrics and modelling the potential impact of climate change on helminthic diseases are discussed. Hopefully, these two volumes will become useful for researchers and, most importantly, disease control managers for integrated and sustainable control, rigorous monitoring and eventual elimination of NTDs in Southeast Asia and elsewhere.

Landscape genetics reveals focal transmission of a human macroparasite

Macroparasite infections (e.g., helminths) remain a major human health concern. However, assessing transmission dynamics is problematic because the direct observation of macroparasite dispersal among hosts is not possible. We used a novel landscape genetics approach to examine transmission of the human roundworm Ascaris lumbricoides in a small human population in Jiri, Nepal. Unexpectedly, we found significant genetic structuring of parasites, indicating the presence of multiple transmission foci within a small sampling area (∼14 km²). We analyzed several epidemiological variables, and found that transmission is spatially autocorrelated around households and that transmission foci are stable over time despite extensive human movement. These results would not have been obtainable via a traditional epidemiological study based on worm counts alone. Our data refute the assumption that a single host population corresponds to a single parasite transmission unit, an assumption implicit in many classic models of macroparasite transmission. Newer models have shown that the metapopulation-like pattern observed in our data can adversely affect targeted control strategies aimed at community-wide impacts. Furthermore, the observed metapopulation structure and local mating patterns generate an excess of homozygotes that can accelerate the spread of recessive traits such as drug resistance. Our study illustrates how molecular analyses complement traditional epidemiological information in providing a better understanding of parasite transmission. Similar landscape genetic approaches in other macroparasite systems will be warranted if an accurate depiction of the transmission process is to be used to inform effective control strategies.

Currently, knowledge of transmission patterns of human helminth parasites is based on traditional epidemiological data such as the number of parasites within hosts. Genetic markers can greatly facilitate our understanding of the transmission process because they provide an indirect means to infer dispersal. Here, we apply novel landscape genetics methods to examine the transmission dynamics of the world's most common human macroparasite, Ascaris lumbricoides. Specifically, we tested for both the presence of multiple transmission foci in a single human village in Nepal and the epidemiological factors associated with such infection foci. On this very local scale, we were surprised to find multiple transmission foci that were centered on households and that reinfections were occurring from the same foci. Thus, our study illustrates the utility of population genetics analyses in epidemiology. Furthermore, our study challenges current dogma by revealing fragmentation of transmission rather than homogeneous parasite mixing within a single human community. Thus, the results have important implications for drug resistance evolution and parasite control.

Neglected and endemic zoonoses

Endemic zoonoses are found throughout the developing world, wherever people live in close proximity to their animals, affecting not only the health of poor people but often also their livelihoods through the health of their livestock. Unlike newly emerging zoonoses that attract the attention of the developed world, these endemic zoonoses are by comparison neglected. This is, in part, a consequence of under-reporting, resulting in underestimation of their global burden, which in turn artificially downgrades their importance in the eyes of administrators and funding agencies. The development of cheap and effective vaccines is no guarantee that these endemic diseases will be eliminated in the near future. However, simply increasing awareness about their causes and how they may be prevented-often with very simple technologies-could reduce the incidence of many endemic zoonoses. Sustainable control of zoonoses is reliant on surveillance, but, as with other public-sector animal health services, this is rarely implemented in the developing world, not least because of the lack of sufficiently cheap diagnostics. Public-private partnerships have already provided advocacy for human disease control and could be equally effective in addressing endemic zoonoses.

Herd immunity acquired indirectly from interactions between the ecology of infectious diseases, demography and economics

Patterns of morbidity and mortality around the globe are determined by interactions between infectious diseases and systematic human socioeconomic processes. The most obvious of these patterns is that the greatest burdens of infectious diseases are found among the poor, who lack the basic resources for disease prevention and treatment. Yet, it is becoming increasingly clear that many infectious diseases are themselves causes of poverty owing to their effects on labour productivity. A particularly subtle phenomenon that receives little attention in the epidemiology literature and is especially important for poor communities is the role of the birth rate as an important direct cause of high disease burdens. Because of their high rates of transmission and life-long immunity, the persistence of many child diseases such as measles relies on high rates of reproduction as their source of susceptible individuals. Thus, there are significant direct health benefits of lower fertility rates, which are further enhanced by interactions with economic processes. Indeed, fertility, poverty and disease all interact with each other in important and predictable ways that can be built into traditional disease ecology models. We present such a model here that provides insights into the long-term effect of policy interventions. For example, because of indirect income effects, herd immunity may be acquired with lower vaccine coverage than previously thought. Reductions in the disease burden can also occur through lower fertility. Our model thus provides a disease ecology framework that is useful for the analysis of demographic transitions.

Genomic linkage map of the human blood fluke Schistosoma mansoni

BACKGROUND

Schistosoma mansoni is a blood fluke that infects approximately 90 million people. The complete life cycle of this parasite can be maintained in the laboratory, making this one of the few experimentally tractable human helminth infections, and a rich literature reveals heritable variation in important biomedical traits such as virulence, host-specificity, transmission and drug resistance. However, there is a current lack of tools needed to study S. mansoni's molecular, quantitative, and population genetics. Our goal was to construct a genetic linkage map for S. mansoni, and thus provide a new resource that will help stimulate research on this neglected pathogen.

RESULTS

We genotyped grandparents, parents and 88 progeny to construct a 5.6 cM linkage map containing 243 microsatellites positioned on 203 of the largest scaffolds in the genome sequence. The map allows 70% of the estimated 300 Mb genome to be ordered on chromosomes, and highlights where scaffolds have been incorrectly assembled. The markers fall into eight main linkage groups, consistent with seven pairs of autosomes and one pair of sex chromosomes, and we were able to anchor linkage groups to chromosomes using fluorescent in situ hybridization. The genome measures 1,228.6 cM. Marker segregation reveals higher female recombination, confirms ZW inheritance patterns, and identifies recombination hotspots and regions of segregation distortion.

CONCLUSIONS

The genetic linkage map presented here is the first for S. mansoni and the first for a species in the phylum Platyhelminthes. The map provides the critical tool necessary for quantitative genetic analysis, aids genome assembly, and furnishes a framework for comparative flatworm genomics and field-based molecular epidemiological studies.