Regeneration of tunic cuticle is suppressed in edible ascidian Halocynthia roretzi contracting soft tunic syndrome.

Soft tunic syndrome is an infectious disease caused by the flagellate Azumiobodo hoyamushi, which severely damages the aquaculture of the edible ascidian Halocynthia roretzi. Tunic is a cellulosic extracellular matrix entirely covering the body in ascidians and other tunicates, and its dense cuticle layer covers the tunic surface as a physical barrier against microorganisms. When the tunic of intact H. roretzi individuals was cut into strips, electron-dense fibers (DFs) appeared on the cut surface of the tunic matrix and aggregated to regenerate a new cuticular layer in seawater within a few days. DF formation was partially or completely inhibited in individuals with soft tunic syndrome, and DF formation was also inhibited by the presence of some proteases, indicating the involvement of proteolysis in the process of tunic softening as well as cuticle regeneration. Using pure cultures of the causative flagellate A. hoyamushi, the expression of protease genes and secretion of some proteases were confirmed by RNA-seq analysis and a 4-methylcoumaryl-7-amide substrate assay. Some of these proteases may degrade proteins in the tunic matrix. These findings suggest that the proteases of A. hoyamushi is the key to understanding the mechanisms of cuticular regeneration inhibition and tunic softening.

Geography-Dependent Horizontal Gene Transfer from Vertebrate Predators to Their Prey.

Horizontal transfer (HT) of genes between multicellular animals, once thought to be extremely rare, is being more commonly detected, but its global geographic trend and transfer mechanism have not been investigated. We discovered a unique HT pattern of Bovine-B (BovB) LINE retrotransposons in vertebrates, with a bizarre transfer direction from predators (snakes) to their prey (frogs). At least 54 instances of BovB HT were detected, which we estimate to have occurred across time between 85 and 1.3 Ma. Using comprehensive transcontinental sampling, our study demonstrates that BovB HT is highly prevalent in one geographical region, Madagascar, suggesting important regional differences in the occurrence of HTs. We discovered parasite vectors that may plausibly transmit BovB and found that the proportion of BovB-positive parasites is also high in Madagascar where BovB thus might be physically transported by parasites to diverse vertebrates, potentially including humans. Remarkably, in two frog lineages, BovB HT occurred after migration from a non-HT area (Africa) to the HT hotspot (Madagascar). These results provide a novel perspective on how the prevalence of parasites influences the occurrence of HT in a region, similar to pathogens and their vectors in some endemic diseases.

Innate immunity in the edible ascidian Halocynthia roretzi developing soft tunic syndrome: Hemolymph can eliminate the causative flagellates and discriminate allogeneic hemocytes.

The infection of the kinetoplastid flagellate Azumiobodo hoyamushi causes soft tunic syndrome that often results in mass mortality in the aquaculture of the edible ascidian Halocynthia roretzi. In the diseased ascidian individuals, the flagellates are exclusively found in the tunic matrix that entirely cover the epidermis, and never invade into internal tissues, such as a mantle. The present study for the first time demonstrated that the ascidian blood plasma and hemolymph have an activity to agglutinate and disintegrate the flagellates, suggesting the innate immunity protects the internal tissue from the invasion of A. hoyamushi. This activity is indifferent between the healthy and the diseased individuals. Allo-specific recognition and cytotoxic reaction among ascidian hemocytes, so-called contact reaction, occur among the individuals of healthy-healthy, healthy-diseased, and diseased-diseased combination, and therefore, the hemocytes from diseased individuals still retain the allo-reactivity. Moreover, the allo-reactive combinations are not changed under the presence of the flagellates, indicating the flagellates neither suppress nor induce the effector system of the contact reaction. These results suggest that the infection of A. hoyamushi does not impair the innate immunity in the ascidian hemolymph.

Molecular and morphological description of a novel microsporidian Inodosporus fujiokai n. sp. infecting both salmonid fish and freshwater prawns.

A new microsporidian disease of cultured rainbow trout Oncorhynchus mykiss has recently been confirmed in Japan, and the causative species was tentatively designated as Microsporidium sp. RBT-2021. Involvement of common prawn Palaemon paucidens in its transmission was suggested based on the previous feeding trials, although the microsporidian infection in P. paucidens was not confirmed. In this study, P. paucidens in Lake Biwa, Japan was investigated for microsporidian infection and 4 types of spores (types 1-4) were newly found. The nucleotide sequence of the small subunit ribosomal RNA gene was identical between type 1 and Microsporidium sp. RBT-2021, indicating they are conspecific. However, intriguingly, the spore morphology and the mode of development in fish and prawn were strikingly different. Morphological observations revealed type 1 in the prawn possesses characteristics of the genus Inodosporus Overstreet and Weidner, 1974, while Microsporidium sp. RBT-2021 in the trout exhibited the characteristics of the genus Kabatana Lom, Dyková and Tonguthai, 2000. In the phylogeny, type 1 was placed within a clade comprising Kabatana spp. and Inodosporus octosporus. Based on the morphological and molecular analyses, we describe Microsporidium sp. RBT-2021 as Inodosporus fujiokai n. sp. Together with the success of the previous prawn-feeding trials, this study strongly suggests I. fujiokai n. sp. has a multi-host life cycle utilizing fish and crustacean hosts and different modes of development in each host. Such polymorphic life cycle has barely been known among fish microsporidians. This study also suggests that the genus Kabatana is a junior synonym of the genus Inodosporus.

Isolation and molecular characterization of Polychromophilus spp. (Haemosporida: Plasmodiidae) from the Asian long-fingered bat (Miniopterus fuliginosus) and Japanese large-footed bat (Myotis macrodactylus) in Japan.

Bats (order, Chiroptera) account for more than one-fifth of all mammalian species in the world and are infected by various intra-erythrocytic parasites of the family Plasmodiidae (Apicomplexa: Haemosporida), including Polychromophilus Dionisi, 1899. Recent advance in the molecular characterization of haemosporidian isolates has enabled their accurate identification, particularly in the last decade. Studies are actively conducted in tropical regions, Europe, and Australia; however, data on haemosporidian infection in bats in Asian temperate areas, including Japan, remain limited. In this study, 75 bats of 4 species (Miniopterus fuliginosus, Myotis macrodactylus, Rhinolophus nippon, and Rhinolophus cornutus) were captured at three sites in western Japan (Yamaguchi Prefecture), and haemosporidian parasites were screened microscopically and molecularly via nested polymerase chain reaction (PCR) targeting the cytochrome b (cytb), cytochrome c oxidase subunit I (cox-1), apicoplast caseinolytic protease C (clpc), and nuclear elongation factor 2 (EF2) genes. The survey detected Polychromophilus melanipherus in 15 (40.5%) miniopterid bats (M. fuliginosus) and Polychromophilus murinus in 6 (46.2%) vespertilionid bats (M. macrodactylus), whereas none of the 25 rhinolophid bats (R. nippon and R. cornutus) was infected, indicating the robust host specificity for miniopterid (P. melanipherus) and vespertilionid (P. murinus) bats regardless of orthotopic nesting. The 15 Polychromophilus cytb sequences obtained from 11 miniopterid and 4 vespertilionid bats were classified into six cytb haplotypes (three for each species), showing no region-specific variation in a phylogenetic tree of Polychromophilus isolates in the Old World. Similarly, multiple haplotypes (seven for cox-1 and nine for clpc) and genotypes (three for EF2) were characterized for the Japanese isolates of Polychromophilus, and the results were consistent with those based on a haemosporidian cytb analysis. Bat flies (Nycteribia allotopa and another undetermined Nycteribia sp.) collected from the body surface of bats harbored Polychromophilus oocysts on the external surface of the midgut. This is the first study to report the isolation and molecular characterization of Polychromophilus spp. in miniopterid and vespertilionid bats in the temperate area of Asia (western Japan). Future studies should evaluate the global prevalence of haemosporidian infections in bats.

Discovery of evocalcet, a next-generation calcium-sensing receptor agonist for the treatment of hyperparathyroidism.

The calcium-sensing receptor (CaSR) plays an important role in sensing extracellular calcium ions and regulating parathyroid hormone secretion by parathyroid gland cells, and the receptor is a suitable target for the treatment of hyperparathyroidism. Cinacalcet hydrochloride is a representative CaSR agonist which widely used for the hyperparathyroidism. However, it has several issues to clinical use, such as nausea/vomiting and strong inhibition of CYP2D6. We tried to improve these issues of cinacalcet for a new pharmaceutical agent as a preferable CaSR agonist. Optimization from cinacalcet resulted in the identification of pyrrolidine compounds and successfully led to the discovery of evocalcet as an oral allosteric CaSR agonist. Evocalcet, which exhibited highly favorable profiles such as CaSR agonistic activity and good DMPK profiles, will provide a novel therapeutic option for secondary hyperparathyroidism.

Measurement of Tunic Hardness in an Edible Ascidian, Halocynthia roretzi, with Remarks on Soft Tunic Syndrome.

The infection caused by a kinetoplastid flagellate, Azumiobodo hoyamushi, in an ascidian, Halocynthia roretzi, results in softening of the tunic, and finally death. This disease is usually recognized using palpation of the softening tunic, and A. hoyamushi infection is detectable using microscopy or PCR amplification of specific gene fragments. The present study is the first quantitative evaluation of the symptoms of soft tunic syndrome by measuring the amount of bending (bending) and the peak force required to pierce the tunic (force). There was a strong correlation between bending and force. Correlation analyses among other parameters (ascidian total weight, tunic thickness, and tunic water content) indicated that larger ascidians had harder and thicker tunics with a higher water content. As compared to the tunic of healthy individuals, softened tunic was thinner and had lower water content. Infected tunics thus possibly lose water and become softer and thinner. Mechanisms for maintaining the appropriate water level content may be crucial for preventing tunic softening.

First report of Kudoa species in the somatic muscle of the Japanese parrotfish Calotomus japonicus (Scaridae) and a description of Kudoa igami, n. sp. (Myxozoa: Multivalvulida).

Three species of the Kudoid parasite (Myxozoa: Multivalvulida) were observed in the somatic muscle of Japanese parrotfish Calotomus japonicus caught off the coast of western Japan. All three species formed pseudocysts in myofibers and caused subclinical infections. The three Kudoa species were distinguished by spore morphology, as well as their 18S and 28S rDNA sequences. We identified a previously undescribed taxa Kudoa igami n. sp. with spores that were stellate with rounded peripheral edges and five to six polar capsules (prevalence 29.3%). Kudoa igami n. sp. were morphologically most similar to Kudoa neothunni but were distinguishable by a more rounded shape in the apical view. Molecular analyses demonstrated that the K. igami n. sp. is closely related to Kudoa thalassomi; however, the similarity in the 28S rDNA sequence was <96% and the spore morphology was different. We found Kudoa thalassomi in one sample (prevalence 2.4%), which is a new host and geographical record for this species. Kudoa lateolabracis, which causes postmortem myoliquefaction in Chinese sea bass Lateolabrax sp. and olive flounder Paralichthys olivaceus was found in Japanese parrotfish (prevalence 41.5%) for the first time, but did not cause myoliquefaction. We also expanded the host record for the brain-infecting Kudoa yasunagai (prevalence 94.1%). In addition, an unidentified microsporidia was observed in the somatic muscle (prevalence 23.3%).

Three Unicapsula species (Myxosporea: Trilosporidae) of Asian marine fishes, including the description of Unicapsula setoensis n. sp. in the yellowfin goby (Acanthogobius flavimanus) from the Inland Sea of Japan.

The myxosporean genus Unicapsula (Multivalvulida: Trilosporidae) is defined as having a spore with three unequal shell valves and polar capsules, of which one is prominent and the two other polar capsules are rudimentary. Genetic characterization of members of the genus, currently 11 nominal species, is, at present, unsatisfactory yet when comparing to the closely related genus Kudoa (Multivalvulida: Kudoidae). In the present study, we characterized long ribosomal RNA gene (rDNA) sequences of three Unicapsula spp., namely Unicapsula pyramidata, Unicapsula seriolae, and a novel myxosporean species, Unicapsula setoensis n. sp., from Asian fishes. Elongated plasmodia of U. pyramidata were found in the trunk muscle of Japanese threadfin breams, Nemipterus japonicus, fished off northern Vietnam in the South China Sea. Semitriangular spores, 5.5-6.4 µm in length and 5.6-9.6 µm in width, consisted of three shell valves with two caudal appendages, 7.2-7.4 µm in length. One prominent polar capsule, 2.0-2.4 µm in diameter, was located in the apical shell valve and two rudimentary polar capsules, 0.4-0.5 µm in diameter, in each caudal shell valve. Elongated plasmodia of U. seriolae were found in the trunk muscle of a greater yellowtail, Seriola dumerili, aquacultured in Japan. Semispherical spores, 5.9-7.4 µm in length and 6.3-7.4 µm in width, also consisted of three shell valves and one prominent polar capsule, 3.4-3.8 µm in diameter, with two rudimentary polar capsules, 0.7-1.0 µm in diameter. Plasmodia of U. setoensis n. sp. were found in the trunk muscle of yellowfin gobies, Acanthogobius flavimanus, fished off Hofu, Yamaguchi Prefecture, in the Inland Sea of Japan. Semispherical spores, 5.6-6.9 µm in diameter, displayed three shell valves and one prominent and two rudimentary polar capsules. The former functional polar capsule was 1.9-2.5 µm in diameter and extruded a 9.4-13.8-µm-long polar filament. Nearly the whole length of the 18S rDNA and more than 2,200 bp of the 28S rDNA of the three Unicapsula spp. were sequenced along with nucleotide sequences of the 5.8S rDNA and internal transcribed spacer-1 and spacer-2 of U. pyramidata and U. setoensis n. sp. Molecular genetic analyses supported the morphological species differentiation of U. pyramidata and U. seriolae, and the distinctness of U. setoensis n. sp. from hitherto known species.

Recent situation of taeniasis in Mongolia (2002-2012).

Epidemiological situation of taeniasis in Mongolia was assessed based on mitochondrial DNA identification of the parasite species. Multiplex PCR was used on a total of 194 proglottid specimens of Taenia species and copro-PCR and loop-mediated isothermal amplification (LAMP) assays were utilized for detection of copro-DNA of 37 fecal samples from taeniasis patients submitted to the Mongolian National Center for Communicable Diseases (NCCD) from 2002 to 2012. In addition, 4 out of 44 calcified cysts in beef kept in formalin since 2003 were evaluated for histopathological confirmation of cattle cysticercosis. All proglottid specimens and stool samples were confirmed to be Taenia saginata by multiplex PCR and by copro-PCR and LAMP, respectively. Cysts collected from cattle were morphologically confirmed to be metacestodes of Taenia species. T. saginata taeniasis was identified from almost all ages from a 2-year-old boy up to a 88-year-old woman and most prominently in 15-29 age group (37%, 74/198) followed by 30-44 age group (34.8%, 69/198 ) from 15 of Mongolia's 21 provinces, while cattle cysticerci were found from 12 provinces. The highest proportion of taeniasis patients was in Ulaanbaatar, the capital of Mongolia.

First report of Pleistophora hyphessobryconis infection in medaka Oryzias latipes, an important ornamental and laboratory fish in Japan.

Medaka Oryzias latipes is a small freshwater fish widely distributed in Japan. It is a popular ornamental fish and now has been recognized as an important model organism in many areas of biological research. Here we report microsporidian infections for the first time in medaka, from 2 research facilities and a wild population. Infected medaka exhibited abnormal appearance with whitish trunk muscle, and microsporidian spores were detected from the affected tissue. The size of spores was similar in all the three cases: 7.0 µm in length and 3.7-4.2 µm in width. In the histological observation, numerous sporophorous vesicles containing spores or other developmental stages were observed within the myocytes of the trunk muscle. Nucleotide sequence of the ribosomal RNA gene was determined and it was identical among all three cases. A BLAST search revealed it shared 99.5-99.6% identity with Pleistophora hyphessobryconis, a microsporidian known to infect >20 freshwater fish species. Light microscopic observation of spores and histological features also indicated the microsporidian infection in medaka is caused by P. hyphessobryconis. This is the first record of the microsporidian species from medaka and from Japan.

Mitochondrial phylogeny of the genus Echinococcus (Cestoda: Taeniidae) with emphasis on relationships among Echinococcus canadensis genotypes.

The mitochondrial genomes of the genus Echinococcus have already been sequenced for most species and genotypes to reconstruct their phylogeny. However, two important taxa, E. felidis and E. canadensis G10 genotype (Fennoscandian cervid strain), were lacking in the published phylogeny. In this study, the phylogeny based on mitochondrial genome sequences was completed with these taxa. The present phylogeny highly supports the previous one, with an additional topology showing sister relationships between E. felidis and E. granulosus sensu stricto and between E. canadensis G10 and E. canadensis G6/G7 (closely related genotypes referred to as camel and pig strains, respectively). The latter relationship has a crucial implication for the species status of E. canadensis. The cervid strain is composed of two genotypes (G8 and G10), but the present phylogeny clearly suggests that they are paraphyletic. The paraphyly was also demonstrated by analysing the complete nucleotide sequences of mitochondrial cytochrome c oxidase subunit 1 (cox1) of E. canadensis genotypes from various localities. A haplotype network analysis using the short cox1 sequences from worldwide isolates clearly showed a close relatedness of G10 to G6/G7. Domestic and sylvatic life cycles based on the host specificity of E. canadensis strains have been important for epidemiological considerations. However, the taxonomic treatment of the strains as separate species or subspecies is invalid from a molecular cladistic viewpoint.

Echinococcus species from red foxes, corsac foxes, and wolves in Mongolia.

The small intestines of 420 wild canids (111 corsac foxes, 191 red foxes and 118 wolves) from Mongolia, were examined for adult worms of the genus Echinococcus. The Mongolian genotype of Echinococcus multilocularis was found in fifteen red foxes and four wolves, whereas two genotypes (G6/7 and G10) of Echinococcus canadensis were found in two and three wolves, respectively. No adult Echinococcus worms were found in the corsac foxes examined. The genotypes of E. multilocularis and E. canadensis are discussed in terms of host specificity and distribution in Mongolia. The importance of wolves in the completion of the life cycle of Echinococcus spp. is also discussed.

Genotypic relationships between Taenia saginata, Taenia asiatica and their hybrids.

Partial sequences of the DNA polymerase delta (pold) gene from Taenia saginata-like adult worms were sequenced. Phylogenetic analysis revealed that pold gene sequences were clearly divided into two clades, differing from each other in five to seven nucleotides. There is little doubt that T. saginata and Taenia asiatica were once separated into two distinct taxa as has been concluded in previous studies. On the other hand, most of the adult worms, which were identified as T. asiatica using mitochondrial DNA, were homozygous for an allele that originated from the allele of T. saginata via single nucleotide substitution. These results indicate that most of the adult worms, which had been called T. asiatica, are not actually 'pure T. asiatica' but instead originated from the hybridization of 'pure T. saginata' and 'pure T. asiatica'.

Detection of human taeniases in Tibetan endemic areas, China.

Detection of taeniasis carriers of Taenia solium is essential for control of cysticercosis in humans and pigs. In the current study, we assessed the positive detection rate of a self-detection tool, stool microscopy with direct smear and coproPCR for taeniasis carriers in endemic Tibetan areas of northwest Sichuan. The self-detection tool through questioning about a history of proglottid expulsion within the previous one year showed an overall positive detection rate of more than 80% for Taenia saginata, T. solium and T. asiatica. The positive detection rate was similar for T. saginata and T. solium. In 132 taeniid tapeworm carriers, 68 (51·5%) were detected by microscopy and 92 (69·7%) were diagnosed by coproPCR. A combination of microscopy and coproPCR increased the positive detection rate to 77·3%. There remained 10 cases (7·6%) coproPCR negative but microscopy positive. Due to the high cost and complicated process, coproPCR is required for the identification of Taenia species only when necessary, though it had a significant higher positive detection rate than microscopy. Combined use of self-detection and stool microscopy are recommended in community-based mass screening for taeniases in this Tibetan area or in other situation-similar endemic regions.

Advances in diagnosis and spatial analysis of cysticercosis and taeniasis.

Human cysticercosis, caused by accidental ingestion of eggs of Taenia solium, is one of the most pathogenic helminthiases and is listed among the 17 WHO Neglected Tropical Diseases. Controlling the life-cycle of T. solium between humans and pigs is essential for eradication of cysticercosis. One difficulty for the accurate detection and identification of T. solium species is the possible co-existence of two other human Taenia tapeworms (T. saginata and T. asiatica, which do not cause cysticercosis in humans). Several key issues for taeniasis/cysticercosis (T/C) evidence-based epidemiology and control are reviewed: (1) advances in immunological and molecular tools for screening of human and animals hosts and identification of Taenia species, with a focus on real-time detection of taeniasis carriers and infected animals in field community screenings, and (2) spatial ecological approaches that have been used to detect geospatial patterns of case distributions and to monitor pig activity and behaviour. Most recent eco-epidemiological studies undertaken in Sichuan province, China, are introduced and reviewed.

Genetic diversity of Echinococcus spp. in Russia.

In Russia, both alveolar and cystic echinococcoses are endemic. This study aimed to identify the aetiological agents of the diseases and to investigate the distribution of each Echinococcus species in Russia. A total of 75 Echinococcus specimens were collected from 14 host species from 2010 to 2012. Based on the mitochondrial DNA sequences, they were identified as Echinococcus granulosus sensu stricto (s.s.), E. canadensis and E. multilocularis. E. granulosus s.s. was confirmed in the European Russia and the Altai region. Three genotypes, G6, G8 and G10 of E. canadensis were detected in Yakutia. G6 was also found in the Altai region. Four genotypes of E. multilocularis were confirmed; the Asian genotype in the western Siberia and the European Russia, the Mongolian genotype in an island of Baikal Lake and the Altai Republic, the European genotype from a captive monkey in Moscow Zoo and the North American genotype in Yakutia. The present distributional record will become a basis of public health to control echinococcoses in Russia. The rich genetic diversity demonstrates the importance of Russia in investigating the evolutionary history of the genus Echinococcus.

Serological and molecular characteristics of the first Korean case of Echinococcus multilocularis.

In December 2011, we reported an autochthonous case of Echinococcus multilocularis infection in a 42-year-old woman in Korea. The diagnosis was based on histopathological findings of the surgically resected liver cyst. In the present study, we evaluated the serological and molecular characteristics of this Korean E. multilocularis case. The patient's serum strongly reacted with affinity-purified native Em18 and recombinant Em18 antigens (specific for E. multilocularis) but negative for recombinant antigen B8/1 (reactive for Echinococcus granulosus). In immunoaffinity chromatography, the serum also strongly reacted with E. multilocularis and only weakly positive for E. granulosus. We determined the whole nucleotide sequence of cox1 (1,608 bp) using the paraffin-embedded cystic tissue which was compared with E. multilocularis isolates from China, Japan, Kazakhstan, Austria, France, and Slovakia. The Korean case showed 99.8-99.9% similarity with isolates from Asia (the highest similarity with an isolate from Sichuan, China), whereas the similarity with European isolates ranged from 99.5 to 99.6%.

Phylogenetic relationships within Echinococcus and Taenia tapeworms (Cestoda: Taeniidae): an inference from nuclear protein-coding genes.

The family Taeniidae of tapeworms is composed of two genera, Echinococcus and Taenia, which obligately parasitize mammals including humans. Inferring phylogeny via molecular markers is the only way to trace back their evolutionary histories. However, molecular dating approaches are lacking so far. Here we established new markers from nuclear protein-coding genes for RNA polymerase II second largest subunit (rpb2), phosphoenolpyruvate carboxykinase (pepck) and DNA polymerase delta (pold). Bayesian inference and maximum likelihood analyses of the concatenated gene sequences allowed us to reconstruct phylogenetic trees for taeniid parasites. The tree topologies clearly demonstrated that Taenia is paraphyletic and that the clade of Echinococcus oligarthrus and Echinococcusvogeli is sister to all other members of Echinococcus. Both species are endemic in Central and South America, and their definitive hosts originated from carnivores that immigrated from North America after the formation of the Panamanian land bridge about 3 million years ago (Ma). A time-calibrated phylogeny was estimated by a Bayesian relaxed-clock method based on the assumption that the most recent common ancestor of E. oligarthrus and E. vogeli existed during the late Pliocene (3.0 Ma). The results suggest that a clade of Taenia including human-pathogenic species diversified primarily in the late Miocene (11.2 Ma), whereas Echinococcus started to diversify later, in the end of the Miocene (5.8 Ma). Close genetic relationships among the members of Echinococcus imply that the genus is a young group in which speciation and global radiation occurred rapidly.

Origin of the pork tapeworm Taenia solium in Bali and Papua, Indonesia.

Global distributions of zoonotic pathogens have been strongly affected by the history of human dispersal and domestication of livestock. The pork tapeworm Taenia solium is distributed worldwide as the cause of neurocysticercosis, one of the most serious neglected tropical diseases. T. solium has been reported in Indonesia but only endemic to restricted areas such as Bali and Papua. Previous studies indicated the distinctiveness of a mitochondrial haplotype confirmed in Papua, but only one isolate has been examined to date. In this study, genetic characterization of T. solium and pigs in Bali and Papua was conducted to clarify the distributional history of the parasite. Mitochondrial haplotype network analysis clearly showed that Indonesian T. solium comprises a unique haplogroup which was the first to diverge among Asian genotypes, indicating its single origin and the fact that it was not introduced in the recent past from other area in Asia in which it is endemic. Although phylogenetic analysis based on the mitochondrial D-loop revealed multiple origins of pigs in Bali and Papua, the majority of pigs belonged to the Pacific Clade, which is widely dispersed throughout the Island Southeast Asia (ISEA) and Oceania due to Neolithic human dispersal. Given the results of our network analysis, it is likely that the Pacific Clade pigs played a key role in the dispersal of T. solium. The data suggest that T. solium was introduced from mainland Asia into Western Indonesia, including Bali, by modern humans in the late Pleistocene, or in the early to middle Holocene along with the Pacific Clade pigs. Introduction into New Guinea most likely occurred in the late Holocene through the spread of Pacific Clade pigs. Over time, T. solium has been eradicated from most of Indonesia through the middle to modern ages owing to religious and cultural practices.