Identities of two Paragonimus species from Sri Lanka inferred from molecular sequences

Paragonimiasis

Paragonimiasis is a zoonotic disease caused by lung flukes of the genus Paragonimus. Humans usually become infected by eating freshwater crabs or crayfish containing encysted metacercariae of these worms. However, an alternative route of infection exists: ingestion of raw meat from a mammalian paratenic host. Adult worms normally occur in pairs in cysts in the lungs from which they void their eggs via air passages. The pulmonary form is typical in cases of human infection due to P. westermani, P. heterotremus, and a few other species. Worms may occupy other sites in the body, notably the brain, but lung flukes have made their presence felt in almost every organ. Ectopic paragonimiasis is particularly common when infection is due to members of the P. skrjabini complex. Human paragonimiasis occurs primarily in the tropics and subtropics of Asia, Africa, and the Americas, with different species being responsible in different areas (Table 6.1).

Polyphyly of the Dinurinae Looss, 1907 (Digenea: Hemiuridae) and resurrection of the Mecoderinae Skrjabin & Guschanskaja, 1954 based on novel collection of Tubulovesicula laticaudi Parukhin, 1969 from marine elapid snakes in Sri Lanka

With one exception, the only known hemiurid trematodes that do not use teleost fishes as definitive hosts instead occur in marine elapid snakes. These comprise six species across four genera and three subfamilies, and so presumably indicate at least three independent invasions of marine snakes from teleost fishes. Here, one of these taxa, Tubulovesicula laticaudi Parukhin, 1969 (= T. orientalis Chattopadhyaya, 1970 n. syn.) is reported from Sri Lanka, collected from Shaw's sea snake Hydrophis curtus (Shaw) (Elapidae: Hydrophiinae: Hydrophinii), the annulated sea snake H. cyanocinctus Daudin and the yellow sea snake H. spiralis (Shaw) off Nayaru in the Bay of Bengal, and from H. spiralis in Portugal Bay, Gulf of Mannar. Novel molecular data, for COI mtDNA and ITS2 and 28S rDNA, are the first for a species of Tubulovesicula Yamaguti, 1934. Nominally, Tubulovesicula belongs in the Dinurinae Looss, 1907, but in phylogenetic analyses based on 28S rDNA, our sequences for T. laticaudi resolved relatively distant from that for representatives of Dinurus Looss, 1907, the type-genus, rendering the subfamily polyphyletic. Tubulovesicula laticaudi resolved closest to data for the type-species of the Plerurinae Gibson & Bray, 1979, but that subfamily is also polyphyletic. These findings lead us to re-evaluate an alternative classification considered by Gibson & Bray (1979). We propose restricting the Dinurinae for forms with a permanent sinus-organ (Dinurus, Ectenurus Looss, 1907; Erilepturus Woolcock, 1935; Paradinurus Vigueras, 1958; Qadriana Bilqees, 1971) and resurrect the Mecoderinae Skrjabin & Guschanskaja, 1954 for forms with a temporary sinus-organ (Mecoderus Manter, 1940, Allostomachicola Yamaguti, 1958, Stomachicola Yamaguti, 1934 and Tubulovesicula).

Paragonimus and paragonimiasis in Asia: An update

Paragonimiasis, or lung fluke disease, is a typical food-borne parasitic zoonosis caused by infection with trematodes belonging to the genus Paragonimus. More than 50 species of Paragonimus have been reported throughout the world, of which seven valid species infect humans, an estimated one million people annually worldwide. Among the seven species, P. westermani, P. heterotremus, and P. skrjabini/P. s. miyazakii, distributed in Asia, are the most important species as the cause of paragonimiasis. Humans acquire infection through the ingestion of raw, pickled or undercooked freshwater crustaceans, 2nd intermediate hosts, or consuming raw meat of wild boar or deer, paratenic hosts. Infections often occur clustered in foci where dietary habits allow transmission of the parasites. Paragonimiasis typically causes a subacute to chronic inflammatory disease of the lungs. The symptoms, including chronic cough, chest pain, dyspnea and hemoptysis, mimic those of tuberculosis and lung cancer. Serologic tests are commonly used for the diagnosis of paragonimiasis, and Praziquantel is the treatment of choice. In this review, the current status of Paragonimus and paragonimiasis in Asia is outlined based on the latest information and findings. We also summarize current trends of paragonimiasis in Japan, which is one of the most endemic area of paragonimiasis in the world, for the better understanding and control of paragonimiasis.

Analysis of COI and ITS2 regions of DNA obtained from Paragonimus westermani eggs in ancient coprolites on Joseon dynasty mummies

The genetic information of ancient Paragonimus westermani, the oriental lung fluke infecting over 20 million people worldwide, has not been thoroughly investigated thus far. We analysed genetic markers (COI and ITS2) of P. westermani from coprolite specimens (n = 6) obtained from 15th to 18th century Korean mummies. Our results indicated that all P. westermani sequences were generally distinct from the other species of the genus Paragonimus. The sequences were clustered into three groups: Group I for East Asia; Group II for South and Southeast Asia; and Group III for India and Sri Lanka. In this study, we found that ancient P. westermani sequences in Korea belong to Group I, adding invaluable information to the existing knowledge of Paragonimus paleogenetics.

Paragonimiasis

Paragonimiasis is a zoonotic disease caused by lung flukes of the genus Paragonimus. Humans usually become infected by eating freshwater crabs or crayfish containing encysted metacercariae of these worms. However, an alternative route of infection exists: ingestion of raw meat from a mammalian paratenic host. Adult worms normally occur in pairs in cysts in the lungs from which they void their eggs via air passages. The pulmonary form is typical in cases of human infection due to P. westermani, P. heterotremus, and a few other species (Table 5.1). Worms may occupy other sites in the body, notably the brain, but lung flukes have made their presence felt in almost every organ. Ectopic paragonimiasis is particularly common when infection is due to members of the P. skrjabini complex (Table 5.1). Human paragonimiasis occurs primarily in the tropics and subtropics of Asia, Africa, and the Americas, with different species being responsible in different areas (Table 5.1).

Gene flow analysis method, the D-statistic, is robust in a wide parameter space

Background

We evaluated the sensitivity of the D-statistic, a parsimony-like method widely used to detect gene flow between closely related species. This method has been applied to a variety of taxa with a wide range of divergence times. However, its parameter space and thus its applicability to a wide taxonomic range has not been systematically studied. Divergence time, population size, time of gene flow, distance of outgroup and number of loci were examined in a sensitivity analysis.

Result

The sensitivity study shows that the primary determinant of the D-statistic is the relative population size, i.e. the population size scaled by the number of generations since divergence. This is consistent with the fact that the main confounding factor in gene flow detection is incomplete lineage sorting by diluting the signal. The sensitivity of the D-statistic is also affected by the direction of gene flow, size and number of loci. In addition, we examined the ability of the f-statistics, \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$ {\widehat{f}}_G $$\end{document}f^G and \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$ {\widehat{f}}_{hom} $$\end{document}f^hom, to estimate the fraction of a genome affected by gene flow; while these statistics are difficult to implement to practical questions in biology due to lack of knowledge of when the gene flow happened, they can be used to compare datasets with identical or similar demographic background.

Conclusions

The D-statistic, as a method to detect gene flow, is robust against a wide range of genetic distances (divergence times) but it is sensitive to population size. The D-statistic should only be applied with critical reservation to taxa where population sizes are large relative to branch lengths in generations.

Electronic supplementary material

The online version of this article (10.1186/s12859-017-2002-4) contains supplementary material, which is available to authorized users.

Paragonimiasis

Paragonimiasis is a zoonotic disease caused by lung flukes of the genus Paragonimus. Humans usually become infected by eating freshwater crabs or crayfish containing encysted metacercariae of these worms. However, an alternative route of infection exists: ingestion of raw meat from a mammalian paratenic host. Adult worms normally occur in pairs in cysts in the lungs from which they void their eggs via air passages. The pulmonary form is typical in cases of human infection due to P. westermani, P. heterotremus, and a few other species (Table 5.1). Worms may occupy other sites in the body, notably the brain, but lung flukes have made their presence felt in almost every organ. Ectopic paragonimiasis is particularly common when infection is due to members of the P. skrjabini complex (Table 5.1). Human paragonimiasis occurs primarily in the tropics and subtropics of Asia, Africa, and the Americas, with different species being responsible in different areas (Table 5.1).

Morphological and molecular characterization of Paragonimus westermani in northeastern India

Evidence for the presence of lung flukes of the Paragonimus westermani in India remains scant. In particular, evidence based on morphology of adult worms is lacking. Metacercariae of the genus Paragonimus, recovered from crabs in two regions of northeastern India, were raised to adulthood in laboratory rats. Morphologically, these worms appear to be P. westermani. DNA sequences from the second internal transcribed spacer (ITS2) and a portion of the ribosomal large subunit gene (28S) of the nuclear ribosomal RNA gene repeat, as well as fragments of the mitochondrial cytochrome c oxidase subunit 1 (cox1) and NADH dehydrogenase subunit 1 (nad1) genes, all supported this identification. Molecular phylogenetic methods were used for studying the relatedness of these Indian flukes with counterparts from southeast and far-east Asia. Molecular data showed that Indian representatives of the P. westermani complex represent a distinct lineage. It is unclear whether the Indian form can cause disease in humans as some members of the complex do elsewhere.

North American paragonimiasis (Caused by Paragonimus kellicotti) in the context of global paragonimiasis

Paragonimus species are highly evolved parasites with a complex life cycle that involves at least three different hosts, i.e., snails, crustaceans, and mammals. The adult forms of Paragonimus species reside and mate in the lungs of a variety of permissive mammalian hosts, including humans. Although human paragonimiasis is uncommonly encountered in North America, both autochthonous and imported disease may be encountered. Paragonimus kellicotti, the species endemic to North America, is a well-known pathogen in wild and domestic animals. Five patients with North American paragonimiasis have been reported in the recent medical literature. The biologic, clinical, radiologic, and laboratory features of paragonimiasis are reviewed, with emphasis on North American paragonimiasis whenever possible.

The first intermediate host of Paragonimus westermani in Sri Lanka

Freshwater snails (family Paludomidae, genus Paludomus) were collected from streams in Hedeniya and Peradeniya (the campus of Peradeniya University), Kandy district, Central Province, Sri Lanka, and found to harbor rediae and cercariae of a Paragonimus sp. These larvae were identified as Paragonimus westermani by using ITS2 DNA sequences. The infection rates of P. westermani in Paludomus sp. in Hedeniya and Peradeniya were 0.1% (one of 1014) and 0.2% (two of 1006), respectively. The snail has not been identified to species in the present study. This is the first report of the snail host of Paragonimus in Sri Lanka.

Advances and Trends in the Molecular Systematics of the Parasitic Platyhelminthes

The application of molecular systematics to the parasitic Platyhelminthes (Cestoda, Digenea and Monogenea) over the last decade has advanced our understanding of their interrelationships and evolution substantially. Here we review the current state of play and the early works that led to the molecular-based hypotheses that now predominate in the field; advances in their systematics, taxonomy, classification and phylogeny, as well as trends in species circumscription, molecular targets and analytical methods are discussed for each of the three major parasitic groups. A by-product of this effort has been an ever increasing number of parasitic flatworms characterized genetically, and the useful application of these data to the diagnosis of animal and human pathogens, and to the elucidation of life histories are presented. The final section considers future directions in the field, including taxon sampling, molecular targets of choice, and the current and future utility of mitochondrial and nuclear genomics in systematic study.

The Use and Implications of Ribosomal DNA Sequencing for the Discrimination of Digenean Species

In just over a decade, the use of molecular approaches for the recognition of parasites has become commonplace. For trematodes, the internal transcribed spacer region of ribosomal DNA (ITS rDNA) has become the default region of choice. Here, we review the findings of 63 studies that report ITS rDNA sequence data for about 155 digenean species from 19 families, and then review the levels of variation that have been reported and how the variation has been interpreted. Overall, complete ITS sequences (or ITS1 or ITS2 regions alone) usually distinguish trematode species clearly, including combinations for which morphology gives ambiguous results. Closely related species may have few base differences and in at least one convincing case the ITS2 sequences of two "good" species are identical. In some cases, the ITS1 region gives greater resolution than the ITS2 because of the presence of variable repeat units that are generally lacking in the ITS2. Intraspecific variation is usually low and frequently apparently absent. Information on geographical variation of digeneans is limited but at least some of the reported variation probably reflects the presence of multiple species. Despite the accepted dogma that concerted evolution makes the individual representative of the entire species, a significant number of studies have reported at least some intraspecific variation. The significance of such variation is difficult to assess a posteriori, but it seems likely that identification and sequencing errors account for some of it and failure to recognise separate species may also be significant. Some reported variation clearly requires further analysis. The use of a "yardstick" to determine when separate species should be recognised is flawed. Instead, we argue that consistent genetic differences that are associated with consistent morphological or biological traits should be considered the marker for separate species. We propose a generalised approach to the use of rDNA to distinguish trematode species.