Mitochondrial and nuclear ribosomal DNA dataset supports that Paramphistomum leydeni (Trematoda: Digenea) is a distinct rumen fluke species

Morphological and molecular data confirm the occurrence of Paramphistomum leydeni (Trematoda: Paramphistomidae) in ruminants from Southern Brazil

Species belonging to the family Paramphistomidae Fischoeder, 1901, commonly known as "rumen flukes", are a group of parasites frequently related to Brazilian livestock production. They inhabit the digestive tract of ruminants and have recognized pathogenicity during the early stages of infection, which can be responsible for economic losses. These trematodes are often associated with Southern Brazil, a region heavily focused on animal farming, which also makes it ideal for the life cycle of paramphistomes. Despite their aforementioned importance, studies regarding their distribution, molecular taxonomy and biology are still scarce in the country. In the present study, rumen flukes collected from cattle (n = 22) and sheep (n = 3) from 9 batches of ruminants from the cities of Jaguarão, Pelotas and Rio Grande, state of Rio Grande do Sul, Brazil, between May and July 2022, were subjected to morphological and molecular study. The microscopic analysis of histological and manual cuts revealed diagnostical traits compatible with Paramphistomum leydeni Näsmark, 1937, including the presence of tegumental papillae, pharynx of the liorchis type and acetabulum of the leydeni type. Molecular data corroborated the morphological identification, with ITS-2 and cox-1 sequences here obtained presenting 100% and 96.8-99.8% similarity, respectively, to P. leydeni samples previously characterized in different countries from Asia, Europe, and South America. Intensity of infection ranged from 5 to 458 and 1 to3 specimens of P. leydeni in sampled cattle and sheep, respectively. The present study contributes to a better understanding of the taxonomy of the flukes involved in cattle and sheep paramphistomosis in Brazil, suggesting that P. leydeni could be the main paramphistome species found in ruminants in the studied region.

Next-generation sequencing technologies for helminth diagnostics and surveillance in ruminants: shifting diagnostic barriers

Helminth infections in grazing ruminants are a major issue for livestock farming globally, but are unavoidable in outdoor grazing systems and must be effectively managed to avoid deleterious effects to animal health, and productivity. Next-generation sequencing (NGS) technologies are transforming our understanding of the genetic basis of anthelmintic resistance (AR) and epidemiological studies of ruminant gastrointestinal parasites. They also have the potential to not only help develop and validate molecular diagnostic tests but to be directly used in routine diagnostics integrating species-specific identification and AR into a single test. Here, we review how these developments have opened the pathway for the development of multi-AR and multispecies identification in a single test, with widespread implications for sustainable livestock farming for the future.

Evolutionary affinities and morphological characterization of the enigmatic Zonocotyle bicaecata (Trematoda: Paramphistomoidea: Zonocotylidae) from the Upper Paraná River basin

Neotropical fish amphistomes represent a highly diverse group within the Paramphistomoidea, with wide distribution across major South American hydrological drainages. However, the limited molecular characterization of these taxa has impeded a comprehensive assessment of their evolutionary relationships and the systematic relevance of morphological features in classification schemes. Our study, based on the critical evaluation of the type material of both nominal species of Zonocotyle (type genus of the monotypic Zonocotylidae), and newly collected specimens of Zonocotyle bicaecata from Steindachnerina insculpta (Curimatidae) in the Upper Paraná River basin, Brazil, presents a morphological reappraisal of Z. bicaecata and provides molecular data (28S rDNA, ITS1-5.8S-ITS2 region, and COI mtDNA) to assess its phylogenetic relationships. Our phylogenetic analyses confirm this species belongs to the Paramphistomoidea. The most comprehensive analyses (based on 28S and COI) further indicate a close relationship with other fish amphistomes from the Neotropical region. Additionally, we emphasized the necessity for a new classification within Paramphistomoidea and briefly discussed the host range of Zonocotyle among curimatid fish hosts.

In-herd prevalence of Fasciola hepatica and Calicophoron / Paramphistomum spp. infections in German dairy cows with comparison of two coproscopical methods and establishment of real-time pyrosequencing for rumen fluke species differentiation

Infections with liver and rumen flukes are among the most frequent parasitic diseases in cattle worldwide. In Europe, the predominant liver fluke species is Fasciola hepatica, and the recently rapidly spreading rumen flukes are mostly Calicophoron daubneyi and occasionally Paramphistomum leydeni. In this study, 1638 faecal samples from individual dairy cows from 24 northern and 18 southern German farms as well as one central German farm, all preselected for potential F. hepatica infection, were examined to determine in-herd prevalences of liver and rumen fluke infections. Furthermore, individual faecal egg counts (FECs) were determined in the northern and central German cows. On farms with patent F. hepatica infections, the mean in-herd prevalence was 15.8% in northern Germany, 41.6% in southern Germany and 14.0% in the central German farm. Rumen fluke infections resulted in high in-herd prevalences in all regions with a mean prevalence of 46.0% in northern, 48.4% in southern and 40.0% in central Germany. Individual FECs varied between 0.1 and 4.1 (mean 0.4) eggs per gram faeces (EPG) for F. hepatica and between 0.1 and 292.4 (mean 16.9) EPG for rumen flukes. Mean in-herd prevalence and mean FECs did not differ significantly between mono- and coinfected farms for either fluke species. Comparison of the classical sedimentation technique and the Flukefinder® method on a subset of 500 faecal samples revealed a similar number of positive samples, however, Flukefinder® mean FECs were three to four times higher for liver and rumen fluke eggs, respectively, with an increasing gap between EPG levels with rising egg counts. Fluke egg size measurement confirmed P. leydeni eggs on average to be larger in length and width (161.0 µm x 87.1 µm) than those of C. daubneyi (141.8 µm x 72.9 µm). However, due to overlap of measurements, morphological species identification based on egg size proved unreliable. For accurate identification, a real-time pyrosequencing approach was established, offering the advantage over classical Sanger sequencing of unambiguously identifying rumen fluke mixed species infections. Real-time pyrosequencing confirmed C. daubneyi (78.1% [50/64]) as the predominant rumen fluke species in Germany, while P. leydeni was detected in 12.5% (8/64) of sampled cows. A total of 9.4% (6/64) cows were infected with both C. daubneyi and P. leydeni, representing the first finding of a mixed infection in domestic ruminants in Europe to date.

Phylogenetic relationship of Prohemistomum vivax to other trematodes based on the internal transcribed spacer region and mitochondrial genes

Prohemistomum vivax is a zoonotic small cyathocotylid trematode that inhabits the intestines of fish-eating birds and mammals. Here, we amplified the internal transcribed spacer (ITS) sequence and six mitochondrial protein-coding genes (PCGs) from P. vivax. The ITS region was 1389 base pairs long and had a partial 18S ribosomal RNA gene, a full ITS1, 5.8S rRNA, and ITS2 sequence, and a partial 28S rRNA gene. The ITS region of P. vivax showed a minimum pairwise distance (0.3-0.6%) from the ITS sequences of Cyathocotylidae sp. 1 and 2 metacercariae from Clarias gariepinus. This result suggests that these metacercariae belong to P. vivax metacercariae. We first amplified mitochondrial genes from P. vivax, including cytochrome c oxidase subunit III (cox3) partial sequence; tRNA-His, cytochrome b (cytb), and NADH dehydrogenase subunit 4L (nad4L) complete sequences; and NADH dehydrogenase subunit 4 (nad4), cytochrome c oxidase I (cox1), and NADH dehydrogenase subunit 5 (nad5) partial sequences. P. vivax was most closely related to Cyathocotyle prussica (NC_039780) and Holostephanus sp. (OP082179), with cox1, cox3, and cytb genes conserved among the three trematodes. The ML phylogenetic tree of ITS sequences supports the order Diplostomida, divided into two main clades (the superfamily Diplostomoidea and Schistosomatoidea). The phylogeny of concatenated amino acid sequences of P. vivax six PCGs revealed that diplostomoids and Clinostomum sp. evolved in a clade with Plagiorchiida members, away from Schistosoma species. These results may yield ribosomal and mitochondrial genetic markers for molecular epidemiological investigations of cyathocotylid intestinal flukes.

First Molecular Identification of Calicophoron daubneyi (Dinnik, 1962) and Paramphistomum leydeni (Nasmark, 1937) in Wild Ruminants from Romania

Rumen flukes are geographically widespread trematodes affecting wild and domestic ruminants. The juvenile forms, which are found in the small intestine, are more pathogenic compared to the adults. Severe diarrhoea and weight loss are the major clinical signs, and the disease might be fatal in severely infested individuals. In the last decade, paramphistomosis has been described as an emerging parasitic disease in Europe. This study aimed to identify the rumen fluke species in wild ruminants from western Romania. Fifty-two pre-stomachs obtained from roe deer (Capreolus capreolus) that were hunted on 14 hunting grounds from Timiș and Arad counties were examined for the presence of paramphistomes. Three (9.09%) out of 33 samples were positive in Timiș County, and one (5.26%) out of 19 samples was positive in Arad County. Subsequent PCR testing revealed that three samples were positive for Calicophoron daubneyi and one for Paramphistomum leydeni. The presence of C. daubneyi and P. leydeni in roe deer has not been previously reported in Romania. Two Paramphistomum species-C. daubneyi and P. leydeni-were revealed as the main species of rumen flukes in roe deer from forests in Romania.

The complete mitochondrial genome of Ogmocotyle ailuri: gene content, composition and rearrangement and phylogenetic implications

Trematodes of the genus Ogmocotyle are intestinal flukes that can infect a variety of definitive hosts, resulting in significant economic losses worldwide. However, there are few studies on molecular data of these trematodes. In this study, the mitochondrial (mt) genome of Ogmocotyle ailuri isolated from red panda (Ailurus fulgens) was determined and compared with those from Pronocephalata to investigate the mt genome content, genetic distance, gene rearrangements and phylogeny. The complete mt genome of O. ailuri is a typical closed circular molecule of 14 642 base pairs, comprising 12 protein-coding genes (PCGs), 22 transfer RNA genes, 2 ribosomal RNA genes and 2 non-coding regions. All genes are transcribed in the same direction. In addition, 23 intergenic spacers and 2 locations with gene overlaps were determined. Sequence identities and sliding window analysis indicated that cox1 is the most conserved gene among 12 PCGs in O. ailuri mt genome. The sequenced mt genomes of the 48 Plagiorchiida trematodes showed 5 types of gene arrangement based on all mt genome genes, with the gene arrangement of O. ailuri being type I. Phylogenetic analysis using concatenated amino acid sequences of 12 PCGs revealed that O. ailuri was closer to Ogmocotyle sikae than to Notocotylus intestinalis. These data enhance the Ogmocotyle mt genome database and provide molecular resources for further studies of Pronocephalata taxonomy, population genetics and systematics.

Identification and prevalence of fluke infection in yak and Tibetan sheep around Qinghai Lake, China

Liver flukes (Fasciola spp.) and rumen flukes (Paramphistomum spp.) are significant parasites in livestock worldwide, and Fasciola spp. are considered an important zoonotic parasite. To our knowledge, there are no reports on fluke species identification and epidemiological prevalence in yak and Tibetan sheep around Qinghai Lake, China. Therefore, this study aimed to identify the major fluke species and determine the prevalence of fluke infections among yak and Tibetan sheep in this area. A total of 307 fecal samples were collected and fluke eggs identified using morphology and molecular methods. Our study is the first to display that the predominant fluke species were F. hepatica and P. leydeni in yak and Tibetan sheep around Qinghai Lake. The overall prevalence of fluke infections in yak and Tibetan sheep was 57.7% (177/307). Specifically, the prevalences of F. hepatica and P. leydeni were 15.0% (46/307) and 31.6% (97/307), respectively, and the co-infection of both species was 11.1% (34/307). No significant difference existed in the prevalence of overall fluke infection between yak and Tibetan sheep (p < 0.05). However, F. hepatica prevalence was significantly different in yak and Tibetan sheep (p < 0.05) but not P. leydeni. The findings of this study provide useful information about the current status of natural fluke invasion in yak and Tibetan sheep around Qinghai Lake, which could be important for monitoring and controlling these parasites in the region.

Characterization of the complete mitochondrial genome of Plagiorchis multiglandularis (Digenea, Plagiorchiidae): Comparison with the members of Xiphidiatan species and phylogenetic implications

Plagiorchis multiglandularis Semenov, 1927 is a common fluke of birds and mammals, with significant impacts on animals and also human health. However, the systematics of Plagiorchiidae remain ambiguous. In the present study, the complete mitochondrial (mt) genome of P. multiglandularis cercariae was sequenced and compared with other digeneans in the order Xiphidiata. The complete circular mt genome of P. multiglandularis was 14,228 bp in length. The mitogenome contains 12 protein-coding genes and 22 transfer RNA genes. The 3' end of nad4L overlaps the 5' end of nad4 by 40 bp, while the atp8 gene is absent. Twenty-one transfer RNA genes transcribe products with conventional cloverleaf structures, while one transfer RNA gene has unpaired D-arms. Comparative analysis with related digenean trematodes revealed that A + T content of mt genome of P. multiglandularis was significantly higher among all the xiphidiatan trematodes. Phylogenetic analyses demonstrated that Plagiorchiidae formed a monophyletic branch, in which Plagiorchiidae are more closely related to Paragonimidae than Prosthogonimidae. Our data enhanced the Plagiorchis mt genome database and provides molecular resources for further studies of Plagiorchiidae taxonomy, population genetics and systematics.

Characterization of the complete mitochondrial genomes of Diplodiscus japonicus and Diplodiscus mehari (Trematoda: Diplodiscidae): Comparison with the members of the superfamily Paramphistomoidea and phylogenetic implication

Diplodiscus japonicus and Diplodiscus mehari (Trematoda: Diplodiscidae) are two important parasites in wood frogs, which have large infection rates and essential importance of ecology, economy and society. In this study, the complete mitochondrial (mt) genomes of D. japonicus and D. mehari were sequenced, then compared with other related trematodes in the superfamily Paramphistomoidea. The complete circular mt sequence of D. japonicus and D. mehari were 14,210 bp and 14,179 bp in length, respectively. Both mt genomes comprised 36 functional subunits, consisting of 12 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and one non-coding region. The mt genes of D. japonicus and D. mehari were transcribed in the same direction, and the gene arrangements were identical to those of Paramphistomoidea trematodes. In the 12 PCGs, GTG was the most common initiation codon, whereas TAG was the most common termination codon. All tRNAs had a typical cloverleaf structure except tRNA Ser1. A comparison with related Paramphistomoidea trematode mt genomes suggested that the cox1 gene of D. mehari was the longest in these trematodes. Phylogenetic analyses revealed that Paramphistomoidea trematodes formed a monophyletic branch, Paramphistomidae and Gastrothylacidae were more closely related than Diplodiscidae. And the further analysis with Pronocephalata branch found that the flukes parasitic in amphibians (frogs) formed one group, and the flukes from ruminants (cattle, sheep, ect) formed another group. Our study demonstrated the importance of sequencing mt genomes of D. japonicus and D. mehari, which will provide significant molecular resources for further studies of Paramphistomoidea taxonomy, population genetics and systematics.

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The complete mt genomes of Diplodiscus japonicus and D. mehari were determined first time.

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There is only one NCR in Diplodiscus japonicus and D. mehari complete mt genomes.

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Phylogenetic analyses revealed two monophyletic groups for the flukes parasitic in amphibians and ruminants.

The mitogenome of Ophidascaris wangi isolated from snakes in China

Different species of the genus Ophidascaris (Baylis, 1921; Nematoda: Ascaridida, Ascaridoidea) are intestinal parasites of various snake species. More than 30 Ophidascaris species have been reported worldwide; however, few molecular genetic studies have been conducted on this genus. We sequenced the complete mitogenome of Ophidascaris wangi parasitizing two snake species of the family Colubridae, i.e., Elaphe carinata (Günther, 1864) and Dinodon rufozonatum. The mitogenome sequence of O. wangi was approximately 14,660 base pairs (bp) long and encoded 36 genes, including 12 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes, and 22 transfer RNA genes. Gene arrangement, genome content, and transcription direction were in line with those in Toxascaris leonina (Linstow, 1902; Ascaridida: Ascarididae). Phylogenetics of O. wangi and other ascaridoids were reconstructed based on the concatenated amino acid sequences of 12 PCGs, and on nucleotide sequences of 12 PCGs and two rRNA genes. Phylogenetic analyses were performed using maximum likelihood and Bayesian inference methods, and the results suggested that O. wangi constitutes a sister clade of Ascaris, Parascaris, Baylisascaris, and Toxascaris within the family Ascarididae, which is a sister clade of Toxocaridae. The mitogenome sequence of O. wangi obtained from the present study will be useful for future identification of the nematode worms in the genus Ophidascaris and will increase the understanding of population genetics, molecular epidemiology, and phylogenetics of ascaridoid nematodes in snakes.

A Universal Approach to Molecular Identification of Rumen Fluke Species Across Hosts, Continents, and Sample Types

Rumen fluke are parasitic trematodes that affect domestic and wild ruminants across a wide range of countries and habitats. There are 6 major genera of rumen fluke and over 70 recognized species. Accurate species identification is important to investigate the epidemiology, pathophysiology and economic impact of rumen fluke species but paramphistomes are morphologically plastic, which has resulted in numerous instances of misclassification. Here, we present a universal approach to molecular identification of rumen fluke species, including different life-cycle stages (eggs, juvenile and mature fluke) and sample preservation methods (fresh, ethanol- or formalin-fixed, and paraffin wax-embedded). Among 387 specimens from 173 animals belonging to 10 host species and originating from 14 countries on 5 continents, 10 rumen fluke species were identified based on ITS-2 intergenic spacer sequencing, including members of the genera Calicophoron, Cotylophoron, Fischeroedius, Gastrothylax, Orthocoelium, and Paramphistomum. Pairwise comparison of ITS-2 sequences from this study and GenBank showed >98.5% homology for 80% of intra-species comparisons and <98.5% homology for 97% of inter-species comparisons, suggesting that some sequence data may have been entered into public repositories with incorrect species attribution based on morphological analysis. We propose that ITS-2 sequencing could be used as a universal tool for rumen fluke identification across host and parasite species from diverse technical and geographical origins and form the basis of an international reference database for accurate species identification.

Comparative analyses of complete ribosomal DNA sequences of Clonorchis sinensis and Metorchis orientalis: IGS sequences may provide a novel genetic marker for intraspecific variation

Both Clonorchis sinensis and Metorchis orientalis are the fish-borne zoonotic trematodes, and have a wide distribution of southeastern Asia, especially in China. Due to the similar morphology, life cycle, and parasitic positions are difficult to differentiate between both metacercariae. In the present study, the complete rDNA sequences of five C. sinensis and five M. orientalis were obtained and compared for the first time. And the IGS rDNA sequences were tested as a genetic marker. The results showed complete rDNA lengths of C. sinensis were range from 8049 bp to 8391 bp, including 1991 bp, 1116 bp, 3854 bp, and 1088-1430 bp belonging to 18S, ITS, 28S and IGS, respectively. And the complete rDNA lengths of M. orientalis were range from 7881 bp to 9355 bp, including 1991 bp, 1077 bp, 3856 bp, and 957-2431 bp belonging to 18S, ITS, 28S and IGS, respectively. Comparative analyses reveal length difference main in IGS, which has higher intraspecific and interspecific variations than other ribosomal regions. Forty four repeat (forward and inverted) sequences were found in the complete rDNAs of C. sinensis and M. orientalis. The phylogenetic analyses showed that the sequences of ITS1, ITS2, 18S and 28S could be used as different level genetic markers. In IGS phylogenetic tree, Opisthorchiidae, Paramphistomidae, Dicrocoeliidae, and Schistosomatidae formed monophyletic groups, and the same length sequences were clustered together in the same species. These findings of the present study provide the new molecular data for studying the complete rDNA of C. sinensis and M. orientalis, and indicate IGS sequences may used as a novel genetic marker for studying intraspecific variation in trematodes.

Mitochondrial genome evidence suggests Cooperia sp. from China may represent a distinct species from Cooperia oncophora from Australia

Cooperia spp. are parasitic nematodes parasitizing in small intestine of ruminants with a worldwide distribution. Infection of ruminants with Cooperia species can cause severe enteritis, causing significant socio-economic losses to the livestock industry. However, it is yet to know whether there is genetic diversity in mitochondrial (mt) DNA sequences of Cooperia nematodes from different geographic regions. The objective of the present study was to examine sequence difference in mt genomes between Cooperia sp. from China and other Cooperia species. We determined the sequences of the internal transcribed spacer (ITS-1 and ITS-2) of nuclear ribosomal DNA (rDNA) of 11 Cooperia specimens collected from the small intestine of a Tianzhu White yak in Gansu Province, northwestern China, which had 99% similarity with that of C. oncophora from Brazil (GenBank accession Number: AJ544290) in ITS-1, and 99% similarity with those from Denmark (AB245040), Scotland and Australia (AJ000032) in ITS-2, indicating that specimens used in the present study should at least represent parasites in Cooperia. We then determined the complete mt genome sequences of one representative specimen of Cooperia sp. from China (CspC), compared the mt DNA sequences with that of C. oncophora from Australia (COA, GQ888713), and conducted phylogenetic analysis with selected nematodes using both maximum likelihood (ML) and Bayesian inference (BI) methods based on both concatenated 12 PCGs, rrnL and rrnS sequences and partial cox2 sequences. The complete mt genome sequence of CspC (KY769271) is 13, 583 bp in length, which is 91 bp shorter than that from COA. The sequence difference over the entire mt genome between CspC and COA was 12.2% in nucleotide and 6.3% in inferred amino acids, with nad4L and nad1 being the most variable and the most conserved PCGs, respectively. Phylogenetic analysis indicated that CspC and COA were closely-related but distinct taxa. The determination of mt genome sequences for Cooperia sp. from China also provides novel resources for further studies of taxonomy, systematics and population genetics of Cooperia from different geographical locations.

The complete mitochondrial genome of Echinostoma miyagawai: Comparisons with closely related species and phylogenetic implications

Echinostoma miyagawai (Trematoda: Echinostomatidae) is a common parasite of poultry that also infects humans. Es. miyagawai belongs to the "37 collar-spined" or "revolutum" group, which is very difficult to identify and classify based only on morphological characters. Molecular techniques can resolve this problem. The present study, for the first time, determined, and presented the complete Es. miyagawai mitochondrial genome. A comparative analysis of closely related species, and a reconstruction of Echinostomatidae phylogeny among the trematodes, is also presented. The Es. miyagawai mitochondrial genome is 14,416 bp in size, and contains 12 protein-coding genes (cox1-3, nad1-6, nad4L, cytb, and atp6), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and one non-coding region (NCR). All Es. miyagawai genes are transcribed in the same direction, and gene arrangement in Es. miyagawai is identical to six other Echinostomatidae and Echinochasmidae species. The complete Es. miyagawai mitochondrial genome A + T content is 65.3%, and full-length, pair-wise nucleotide sequence identity between the six species within the two families range from 64.2-84.6%. The Es. miyagawai sequences is most similar to Echinostoma caproni. Sequence difference are 15.0-33.5% at the nucleotide level, and 8.6-44.2% at the amino acid level, among the six species, for the 12 protein-coding genes. ATG and TAG are the most common initiation and termination codons, respectively. Twenty of the Es. miyagawai transfer RNA genes transcribe products of the conventional cloverleaf structure, while two of the transfer RNA genes, namely trnS1^(AGC) and trnS2^(UGA), have unpaired D-arms. Phylogenetic analyses using our mitochondrial data indicate that Es. miyagawai is closely related to other Echinostomatidae species, except for Echinostoma hortense, which forms a distinct paraphyletic branch, and Echinochasmus japonicus, which is outside the clade containing all other Echinostomatidae species. These phylogenetic results support the elevation of subfamily Echinostomatidae. Our dataset also provides a significant resource of molecular markers to study the taxonomy, population genetics, and systematics of the echinostomatids.

Characterization of the mitochondrial genome sequences of the liver fluke Amphimerus sp. (Trematoda: Opisthorchiidae) from Ecuador and phylogenetic implications

Amphimerus Barker, 1911 is a liver fluke infecting several animal species and humans. Being a digenetic trematode of the Opisthorchiidae family, Amphimerus is closely related to the genera Metorchis, Clonorchis and Opisthorchis. Recently, a high prevalence of Amphimerus infection in humans, cats, and dogs had been demonstrated in a tropical Pacific region of Ecuador. Hence, we determined and characterized the entire mt genome sequences of adult liver flukes, morphologically identified as Amphimerus, collected in the endemic region of Ecuador, and examined its phylogenetic relationships with flukes in the Opisthorchiidae family using Bayesian inference (BI) based on the concatenated amino acid sequences and partial cox1 sequences. The complete mt genome sequence (15, 151 bp in length) of the Amphimerus sp. contains 35 genes, including 12 protein-coding genes (PCGs, without atp8), two rRNAs (rrnL and rrnS) and 21 tRNAs, lacking trnG. The gene content and arrangement of the Ecuadorian Amphimerus mt genome was similar to those of other trematodes in the Opisthorchiidae family. All genes in the circular mt genome of Amphimerus sp. are transcribed from the same strand in one direction, with the A + T content of 60.77%. Genetic distances between Amphimerus sp. and other genera in Opisthorchiidae were rather high, ranging from 26.86% to 28.75% at nucleotide level and 29.37%-31.12% at amino acid level. Phylogenetic analysis placed the Ecuadorian Amphimerus within the branch of Opisthorchiidae, but very distinct from Opisthorchis. Our results indicate that the liver fluke Amphimerus from Ecuador does not belong to the genus Opisthorchis, and that it should be assigned under the genus Amphimerus. The determination of the mt genome of the Ecuadorian Amphimerus provides a new genetic resource for future studies on taxonomy and molecular epidemiology of Opisthorchiidae trematodes.

The complete mitochondrial genome of Paragonimus ohirai (Paragonimidae: Trematoda: Platyhelminthes) and its comparison with P. westermani congeners and other trematodes

We present the complete mitochondrial genome of Paragonimus ohirai Miyazaki, 1939 and compare its features with those of previously reported mitochondrial genomes of the pathogenic lung-fluke, Paragonimus westermani, and other members of the genus. The circular mitochondrial DNA molecule of the single fully sequenced individual of P. ohirai was 14,818 bp in length, containing 12 protein-coding, two ribosomal RNA and 22 transfer RNA genes. As is common among trematodes, an atp8 gene was absent from the mitogenome of P. ohirai and the 5' end of nad4 overlapped with the 3' end of nad4L by 40 bp. Paragonimusohirai and four forms/strains of P. westermani from South Korea and India, exhibited remarkably different base compositions and hence codon usage in protein-coding genes. In the fully sequenced P. ohirai individual, the non-coding region started with two long identical repeats (292 bp each), separated by tRNAGlu . These were followed by an array of six short tandem repeats (STR), 117 bp each. Numbers of the short tandem repeats varied among P. ohirai individuals. A phylogenetic tree inferred from concatenated mitochondrial protein sequences of 50 strains encompassing 42 species of trematodes belonging to 14 families identified a monophyletic Paragonimidae in the class Trematoda. Characterization of additional mitogenomes in the genus Paragonimus will be useful for biomedical studies and development of molecular tools and mitochondrial markers for diagnostic, identification, hybridization and phylogenetic/epidemiological/evolutionary studies.

Fasciolopsis buski (Digenea: Fasciolidae) from China and India may represent distinct taxa based on mitochondrial and nuclear ribosomal DNA sequences

Background

Fasciolopsis buski is a zoonotic intestinal fluke infecting humans and pigs, but it has been seriously neglected. It is yet to know whether there is any genetic diversity among F. buski from different geographical locations, particularly in sequences of nuclear ribosomal DNA (rDNA) and mitochondrial (mt) DNA. Therefore, we determined the sequences of partial 18S, the complete internal transcribed spacer (ITS) rDNA and the complete mt genome of F. buski from China, compared the rDNA and mtDNA sequences with those of isolates from India and Vietnam, and assessed the phylogenetic relationships of this fluke and related fasciolid trematodes based on the mtDNA dataset.

Results

The complete mt genome sequence of F. buski from China is 14,833 bp, with 36 genes, including 12 protein-coding genes (PCGs), 22 tRNA genes, and two rRNA genes (rrnL and rrnS). The AT content of F. buski from China is 65.12%. The gene content and arrangement of the F. buski mt genome is similar to that of Fascioloides magna. Genetic distances between isolates of F. buski from China and India were high (28.2% in mtDNA, 13.2% in ITS-1 and 9.8% in ITS-2) and distinctly higher than the interspecific differences between Fasciola hepatica and Fasciola gigantica. The rDNA and mtDNA datasets for F. buski from China (isolate from pigs) and Vietnam (isolates from humans) were identical. The intergeneric differences in amino acid and nucleotide sequences among the genera Fasciolopsis, Fascioloides and Fasciola ranged between 24.64–25.56% and 26.35–28.46%, respectively.

Conclusions

Our results indicate that F. buski from China and India may represent distinct taxa, while F. buski in Vietnam and China represent the same species. These findings might have implications for the implementation of appropriate control strategies in different regions. Further studies are needed to decode mtDNA and rDNA sequences of F. buski from various geographical isolates for the better understanding of the species complex of F. buski.

Electronic supplementary material

The online version of this article (doi:10.1186/s13071-017-2039-2) contains supplementary material, which is available to authorized users.

Molecular identification of the rumen flukes Paramphistomum leydeni and Paramphistomum cervi in a concurrent infection of the red deer Cervus elaphus

Paramphistomosis, caused by paramphistomid flukes, is a gastrointestinal parasitic disease of domestic and wild ruminants. Originally thought to be limited to the tropics and subtropics, the disease has recently been reported in temperate regions. Here we describe the concurrent infection of a red deer doe (Cervus elaphus) with Paramphistomum leydeni and Paramphistomum cervi. This is the first report of P. leydeni in Croatia. Flukes were identified on the basis of morphological keys (tegumental papillae) and sequencing of the internal transcribed spacer region 2 in ribosomal DNA. Our results confirm that the absence of tegumental papillae allows P. cervi to be differentiated morphologically from other paramphistomid species in Europe based on incident light stereomicroscopy. Nevertheless the limitations of morphological identification and taxonomic issues suggest that previous findings on paramphistomid infection should be interpreted carefully. The possible worldwide distribution of these pathogens means that paramphistomosis may be more common and its economic impact greater than previously thought.

Complete mitochondrial genome of the giant liver fluke Fascioloides magna (Digenea: Fasciolidae) and its comparison with selected trematodes

Background

Representatives of the trematode family Fasciolidae are responsible for major socio-economic losses worldwide. Fascioloides magna is an important pathogenic liver fluke of wild and domestic ungulates. To date, only a limited number of studies concerning the molecular biology of F. magna exist. Therefore, the objective of the present study was to determine the complete mitochondrial (mt) genome sequence of F. magna, and assess the phylogenetic relationships of this fluke with other trematodes based on the mtDNA dataset.

Findings

The complete F. magna mt genome sequence is 14,047 bp. The gene content and arrangement of the F. magna mt genome is similar to those of Fasciola spp., except that trnE is located between trnG and the only non-coding region in F. magna mt genome. Phylogenetic relationships of F. magna with selected trematodes using Bayesian inference (BI) was reconstructed based on the concatenated amino acid sequences for 12 protein-coding genes, which confirmed that the genus Fascioloides is closely related to the genus Fasciola; the intergeneric differences of amino acid composition between the genera Fascioloides and Fasciola ranged 17.97–18.24 %.

Conclusions

The determination of F. magna mt genome sequence provides a valuable resource for further investigations of the phylogeny of the family Fasciolidae and other trematodes, and represents a useful platform for designing appropriate molecular markers.

Electronic supplementary material

The online version of this article (doi:10.1186/s13071-016-1699-7) contains supplementary material, which is available to authorized users.

Rumen fluke in Irish sheep: prevalence, risk factors and molecular identification of two paramphistome species

BACKGROUND

Rumen flukes are trematode parasites found globally; in tropical and sub-tropical climates, infection can result in paramphistomosis, which can have a deleterious impact on livestock. In Europe, rumen fluke is not regarded as a clinically significant parasite, recently however, the prevalence of rumen fluke has sharply increased and several outbreaks of clinical paramphistomosis have been reported. Gaining a better understanding of rumen fluke transmission and identification of risk factors is crucial to improve the control of this parasitic disease. In this regard, a national prevalence study of rumen fluke infection and an investigation of associated risk factors were conducted in Irish sheep flocks between November 2014 and January 2015. In addition, a molecular identification of the rumen fluke species present in Ireland was carried out using an isolation method of individual eggs from faecal material coupled with a PCR. After the DNA extraction of 54 individual eggs, the nuclear fragment ITS-2 was amplified and sequenced using the same primers.

RESULTS

An apparent herd prevalence of 77.3 % was determined. Several risk factors were identified including type of pasture grazed, regional variation, and sharing of the paddocks with other livestock species. A novel relationship between the Suffolk breed and higher FEC was reported for the first time. The predominant rumen fluke species found was C. daubneyi. Nevertheless, P. leydeni was unexpectedly identified infecting sheep in Ireland for the first time.

CONCLUSIONS

An exceptionally high prevalence of rumen fluke among Irish sheep flocks has been highlighted in this study and a more thorough investigation is necessary to analyse its economic impact. The isolation of individual eggs coupled with the PCR technique used here has proven a reliable tool for discrimination of Paramphistomum spp. This technique may facilitate forthcoming studies of the effects of paramphistomosis on livestock production. The most noteworthy finding was the identification of P. leydeni affecting sheep in Ireland, however further studies are required to clarify its implications. Also, a significant relationship between Suffolk breed and a heavier infection was found, which can be used as a starting point for future research on control strategies of rumen fluke infection.

The complete mitochondrial genomes of Gnathostoma doloresi from China and Japan

Gnathostoma doloresi is one of the neglected pathogens causing gnathostomiasis. Although this zoonotic parasite leads to significant socioeconomic concerns globally, little is known of its genetics and systematics. In the present study, we sequenced and characterized the complete mitochondrial (mt) genomes of G. doloresi isolates from China and Japan. The lengths of the mt genomes of the G. doloresi China and Japan isolates are 13,809 and 13,812 bp, respectively. Both mt genomes encode 36 genes, including 12 protein-coding genes (PCGs), 2 ribosomal RNA genes, and 22 transfer RNA genes. The gene order, transcription direction, and genome content are identical with its congener G. spinigerum. Phylogenetic analyses based on concatenated amino acid sequences of 12 PCGs by Bayesian inference (BI) indicated that G. doloresi are closely related to G. spinigerum. Our data provide an invaluable resource for studying the molecular epidemiology, phylogenetics, and population genetics of Gnathostoma spp. and should have implications for further studies of the diagnosis, prevention, and control of gnathostomiasis in humans and animals.

Mitochondrial genome of Ogmocotyle sikae and implications for phylogenetic studies of the Notocotylidae trematodes

Ogmocotyle spp. (Trematoda: Digenea: Notocotylidae) are neglected but important trematodes that can infect numerous mammal species, causing significant economic losses to livestock industries. However, there have been few studies on the molecular ecology of these trematodes. We amplified and sequenced the complete mitochondrial (mt) genome of Ogmocotyle sikae (14,307 bp). The gene content and gene arrangement of O. sikae mt genome was similar to that of Dicrocoelium chinensis, except that trnE and trnG were reversed. Phylogenetic analysis of O. sikae and selected parasites using Bayesian inference was performed based on concatenated amino acid sequence datasets conceptually translated from the 12 protein-coding genes. The results indicated that the family Notocotylidae is related to the family Paramphistomatidae. Our description of O. sikae mt genome provides a significant resource of molecular markers for future comparative studies of the Notocotylidae and other trematodes.