Complete sequence of the mitochondrial genome of Taenia saginata: comparison with T. solium and T. asiatica

Sympatric occurrence of Taenia saginata and Sarcocystis spp. in cattle from Narok County, Kenya: meat inspection findings with molecular validation

The epidemiological picture of Taenia saginata infections in Kenya is fragmented with limited available data. Although Sarcocystis species are significant meat-borne parasites, few studies have explored their occurrence in Kenya. This study aimed to estimate the occurrence of bovine cysticercosis and screen for the presence of Sarcocystis spp. A meat inspection-based survey was conducted in ten abattoirs in Narok County, Kenya, and inspection for T. saginata cysticerci was limited to the Triceps brachii muscle. The apparent occurrence of the parasite was 5.4% (95% CI, 3.8, 7.6, n=573). Molecular confirmation of T. saginata was done via nested polymerase chain reaction targeting the mitochondrial 12S ribosomal RNA gene and restricted fragment length polymorphism. Sarcocystis species were identified using a multiplex polymerase chain reaction method targeting the 18S ribosomal RNA gene sequences and the mitochondrial cytochrome c oxidase subunit I gene. Of the 31 cystic lesions tested, 26/31 (83.9%) were confirmed to be T. saginata.Sarcocystis cruzi and S. hominis were detected in 8/31 (25.8%) and 1/31 (3.2%) of the cystic lesions, respectively. Co-infections of S. cruzi and T. saginata were found in 6/31 lesions (19.4%). The confirmation of bovine cysticercosis and S. hominis is suggestive of the presence of risky culinary and sanitation practices that facilitate transmission. This is the first report and molecular confirmation of Sarcocystis spp. in cattle in the country. The presence of both zoonotic S. hominis and pathogenic S. cruzi highlights an underexplored concern of veterinary and human health significance, warranting further epidemiological investigation.

A rare case of human taeniasis caused by Taenia saginata with species undetermined cysticercosis

Taeniasis and cysticercosis, which are caused by Taenia saginata, Taenia solium and Taenia asiatica, are zoonotic parasitic infections with a significant disease burden worldwide. There is consensus amongst experts that T. saginata is a common tapeworm that causes taeniasis in humans as opposed to cysticercosis. This case study of a middle-aged Tibetan man conducted in 2021 challenges the prevailing notion that T. saginata exclusively causes taeniasis and not cysticercosis by documenting symptoms and laboratory studies related to both taeniasis and multiple cysticercosis. The patient's medical record with the symptoms of taeniasis and cysticercosis was reviewed, and the tapeworm's proglottids and cyst were identified from the patient by morphological evaluation, DNA amplification and sequencing. The patient frequently experienced severe headaches and vomiting. Both routine blood screenings and testing for antibodies against the most common parasites were normal. After anthelmintic treatment, an adult tapeworm was found in feces, and medical imaging examinations suggested multiple focal nodules in the brain and muscles of the patient. The morphological and molecular diagnosis of the proglottids revealed the Cestoda was T. saginata. Despite the challenges presented by the cyst's morphology, the molecular analysis suggested that it was most likely T. saginata. This case study suggests that T. saginata infection in humans has the potential to cause human cysticercosis. However, such a conclusion needs to be vetted by accurate genome-wide analysis in patients with T. saginata taeniasis associated with cysts. Such studies shall provide new insights into the pathogenicity of T. saginata.

Genetic Variation of Taenia Saginata Cyst Isolates from Iraq Based on Mitochondrial COX1 Sequences

The zoonotic parasite disease of economic and public health relevance is bovine cysticercosis, resulting from the larval stage of Taenia saginata. The presented research aims to identify intraspecific variation in T. saginata isolated from cattle in Iraq's Sulaymaniyah province using the mitochondrial cytochrome c oxidase subunit 1 (COX1) gene. Sequence analysis of the COX1 gene revealed that five distinct haplotypes were identified in 37 T. saginata specimens from Iraq. Four of the five T. saginata haplotypes may have been identified for the first time in the world. Phylogenetic research revealed that all T. saginata haplotypes had been clustered in a single clade, with Korean and Iranian isolates sharing a high degree of closeness. In addition, individual haplotypes related to COX1 had a pairwise evolutionary divergence of 0.005- 0.013, whereas the overall evolutionary divergence regarding all five haplotypes ranged between 0.000-0.018. It was concluded that added newly recorded data on T. saginata genetic variation could have substantial implications for taeniasis epidemiology and control.

Comparative Mitochondrial Genomic Analysis Robustly Supported That Cat Tapeworm Hydatigera taeniaeformis (Platyhelminthes: Cestoda) Represents a Species Complex

Hydatigera taeniaeformis is one of the most common intestinal tapeworms that has a worldwide distribution. In this study, we sequenced the complete mitochondrial (mt) genome of H. taeniaeformis from the leopard cat (designated HTLC) and compared it with those of H. taeniaeformis from the cat in China (designated HTCC) and Germany (designated HTCG). The complete mt genome sequence of HTLC is 13,814 bp in size, which is 167 bp longer than that of HTCC and is 74 bp longer than that of HTCG. Across the entire mt genome (except for the two non-coding regions), the sequence difference was 3.3% between HTLC and HTCC, 12.0% between HTLC and HTCG, and 12.1% between HTCC and HTCG. The difference across both nucleotide and amino acid sequences of the 12 protein-coding genes was 4.1 and 2.3% between the HTLC and HTCC, 13.3 and 10.0% between the HTLC and HTCG, and 13.8 and 10.6% between the HTCC and HTCG, respectively. Phylogenetic analysis based on concatenated amino acid sequences of 12 protein-coding genes showed the separation of H. taeniaeformis from different hosts and geographical regions into two distinct clades. Our analysis showed that the cat tapeworm H. taeniaeformis represents a species complex. The novel mt genomic datasets provide useful markers for further studies of the taxonomy and systematics of cat tapeworm H. taeniaeformis.

Expansion of Cyclophyllidea Biodiversity in Rodents of Qinghai-Tibet Plateau and the "Out of Qinghai-Tibet Plateau" Hypothesis of Cyclophyllideans

The Cyclophyllidea comprises the most species-rich order of tapeworms (Platyhelminthes, Cestoda) and includes species with some of the most severe health impact on wildlife, livestock, and humans. We collected seven Cyclophyllidea specimens from rodents in Qinghai-Tibet Plateau (QTP) and its surrounding mountain systems, of which four specimens in QTP were unsequenced, representing “putative new species.” Their complete mitochondrial (mt) genomes were sequenced and annotated. Phylogenetic reconstruction of partial 28S rDNA, cox1 and nad1 datasets provided high bootstrap frequency support for the categorization of three “putative new species,” assigning each, respectively, to the genera Mesocestoides, Paranoplocephala, and Mosgovoyia, and revealing that some species and families in these three datasets, which contain 291 species from nine families, may require taxonomic revision. The partial 18S rDNA phylogeny of 29 species from Taeniidae provided high bootstrap frequency support for the categorization of the “putative new species” in the genus Hydatigera. Combined with the current investigation, the other three known Taeniidae species found in this study were Taenia caixuepengi, T. crassiceps, and Versteria mustelae and may be widely distributed in western China. Estimates of divergence time based on cox1 + nad1 fragment and mt protein-coding genes (PCGs) showed that the differentiation rate of Cyclophyllidea species was strongly associated with the rate of change in the biogeographic scenarios, likely caused by the uplift of the QTP; i.e., species differentiation of Cyclophyllidea might be driven by host-parasite co-evolution caused by the uplift of QTP. We propose an “out of QTP” hypothesis for the radiation of these cyclophyllidean tapeworms.

Comparative Characterization of Mitogenomes From Five Orders of Cestodes (Eucestoda: Tapeworms)

The recognized potential of using mitogenomics in phylogenetics and the more accessible use of high-throughput sequencing (HTS) offer an opportunity to investigate groups of neglected organisms. Here, we leveraged HTS to execute the most comprehensive documentation of mitogenomes for cestodes based on the number of terminals sequenced. We adopted modern approaches to obtain the complete mitogenome sequences of 86 specimens representing five orders of cestodes (three reported for the first time: Phyllobothriidea, “Tetraphyllidea” and Trypanorhyncha). These complete mitogenomes represent an increase of 41% of the mitogenomes available for cestodes (61–147) and an addition of 33% in the representativeness of the cestode orders. The complete mitochondrial genomes are conserved, circular, encoded in the same strand, and transcribed in the same direction, following the pattern observed previously for tapeworms. Their length varies from 13,369 to 13,795 bp, containing 36 genes in total. Except for the Trypanorhyncha specimen, the gene order of the other four cestode orders sequenced here suggests that it could be a synapomorphy for the acetabulate group (with a reversion for taenids). Our results also suggest that no single gene can tell all the evolutionary history contained in the mitogenome. Therefore, cestodes phylogenies based on a single mitochondrial marker may fail to capture their evolutionary history. We predict that such phylogenies would be improved if conducted under a total evidence framework. The characterization of the new mitochondrial genomes is the first step to provide a valuable resource for future studies on the evolutionary relationships of these groups of parasites.

Genotypes of Echinococcus Species from Cattle in Tanzania

Cystic echinococcosis is a zoonotic parasitic disease caused by Echinococcus species. Tanzania is one of the endemic countries with cystic echinococcosis. This study focussed on identifying genotypes of Echinococcus spp. in Tanzania. We collected 7 cysts from cattle in Mwanza municipal (n=4) and Loliondo district (n=3). The cysts from Mwanza were all E. ortleppi and fertile. In contrast, the cysts from Loliondo were all E. granulosus sensu stricto and sterile. Two from the 4 cysts were a new haplotype of E. ortleppi (G5). These results can improve the preventive and control programs for humans and livestock in Tanzania. To our knowledge, this study is considered the first to identify the genotype and haplotype of Echinococcus spp. in Tanzania.

Taenia saginata Infection Misdiagnosed as Acute Cholecystitis in a Tibetan Patient, in China

The present study reports a rare case of Taenia saginata infection, which was initially diagnosed as acute cholecystitis in a Tibetan patient at the Qinghai-Tibetan Plateau pastoral area, China. A 45-year-old female was initially diagnosed with acute cholecystitis at a hospital in China. She had a slight fever, weight loss and constipation and complained of pain in the upper abdomen and left back areas. Increase of monocyte, eosinophil and basophil levels were shown. Taenia sp. eggs were detected in a fecal examination. An adult tapeworm approximately 146 cm in length, whitish-yellow color, was collected from the patient after treatment with traditional Chinese medicine. The adult tapeworm had a scolex and proglottids with genital pores. The scolex was rectangular shape with 4 suckers and rostellum without hooklet. The cox1 gene sequence shared 99.5-99.8% homology with that of T. saginata from other regions in China. The patient was diagnosed finally infected with T. saginata by morphological and molecular charateristics.

Genetic Evolution and Implications of the Mitochondrial Genomes of Two Newly Identified Taenia spp. in Rodents From Qinghai-Tibet Plateau

The larva of Taeniidae species can infect a wide range of mammals, causing major public health and food safety hazards worldwide. The Qinghai-Tibet Plateau (QTP), a biodiversity hotspot, is home to many species of rodents, which act as the critical intermediate hosts of many Taeniidae species. In this study, we identified two new larvae of Taenia spp., named T. caixuepengi and T. tianguangfui, collected from the plateau pika (Ochotona curzoniae) and the Qinghai vole (Neodon fuscus), respectively, in QTP, and their mitochondrial genomes were sequenced and annotated. Phylogenetic trees based on the mitochondrial genome showed that T. caixuepengi has the closest genetic relationship with T. pisiformis, while T. tianguangfui was contained in a monophyletic group with T. crassiceps, T. twitchelli, and T. martis. Biogeographic scenarios analysis based on split time speculated that the speciation of T. caixuepengi (∼5.49 Mya) is due to host switching caused by the evolution of its intermediate host. Although the reason for T. tianguangfui (∼13.11 Mya) speciation is not clear, the analysis suggests that it should be infective to a variety of other rodents following the evolutionary divergence time of its intermediate host and the range of intermediate hosts of its genetically close species. This study confirms the species diversity of Taeniidae in the QTP, and speculates that the uplift of the QTP has not only a profound impact on the biodiversity of plants and animals, but also that of parasites.

Prevalence and genotyping of Echinococcus granulosus sensu lato from livestock in north-eastern Kenya

Cystic echinococcosis (CE) is a zoonotic disease of cosmopolitan distribution and caused by the larval stage of the dog tapeworm, Echinococcus granulosus sensu lato (s.l.). CE occurs in the wider African continent and in Kenya, notably in the Maasailand and Turkana regions; however, recent studies demonstrate its presence in other parts of Kenya. This study determined the occurrence of CE in livestock (camels, goats, sheep and cattle) in Isiolo, Garissa and Wajir counties, and characterized the species of E. granulosus s.l. present. An abattoir survey was used to determine the presence of CE in various organs in livestock. Polymerase chain reaction-restriction fragment length polymorphism and sequencing of the mitochondrial NADH dehydrogenase subunit 1 gene was used for genotyping. A total of 1368 carcasses from 687 goats, 234 camels, 329 sheep and 118 cattle were inspected for the presence of hydatid cysts. The overall proportion of infections was 29.1% in camels, 14.4% in cattle, 9.9% in goats and 8.2% in sheep. The liver was the most infected organ, while only the lung of camels harboured fertile cysts. Of the 139 cysts genotyped, 111 (79.9%) belonged to Echinococcus canadensis (G6/7) and 20 (14.4%) to E. granulosus sensu stricto. One and two cysts were identified as Taenia saginata and unknown Taenia species, respectively. There was a significant association between county of origin and species of the animal with occurrence of CE. This study reports, for the first time, the characterization of Echinococcus species in livestock from Garissa and Wajir counties, and the current situation in Isiolo county. The fertility of cysts in camels and frequency of E. canadensis (G6/7) in all livestock species indicate that camels play an important role in the maintenance of CE in the north-eastern counties of Kenya.

Diversity of Taenia and Hydatigera (Cestoda: Taeniidae) in domestic dogs in Kenya

Taenia species of domestic dogs can cause cysticercosis and coenurosis in a wide range of intermediate hosts including humans. Most taeniids of dogs are globally distributed, but some wildlife-transmitted species can be specific for certain regions. Generally, little information exists on the species composition and frequency in most regions of the world, which impairs risk assessment and control strategies. This study determined the range of taeniid species in dogs in four widely spaced areas of Kenya by genetic identification of eggs in faeces collected from the environment. Individual taeniid eggs were characterised by nested polymerase chain reaction of NADH dehydrogenase subunit 1 and cytochrome C oxidase 1 genes, restriction fragment length polymorphism and partial sequencing. Overall 79/1621 (4.9%) faecal samples contained eggs of Taenia or Hydatigera (8.0% in Turkana, 4.8% in Isiolo, 3.8% in Maasai Mara and 1.3% in Meru). Taenia hydatigena and T. multiceps were the most frequent, found in 36 and 15 samples, respectively. Other eggs found in the faeces belonged to T. serialis (sensu lato), T. madoquae (the first record in domestic dogs), T. ovis, T. saginata and Hydatigera taeniaeformis. Polymorphism of nad1 sequences revealed 22 and 8 haplotypes of T. hydatigena and T. multiceps, respectively. The results show the involvement of dogs in both domestic and sylvatic transmission cycles. In addition to the species range, this study provides data on the intraspecific diversity of T. hydatigena and T. multiceps in Kenya, which will serve as baseline information for further studies into cysticercosis and coenurosis in livestock and humans in the region.

Molecular Identification of Taenia hydatigena from Sheep in Khartoum, Sudan

The cestode Taenia hydatigena uses canids, primarily dogs, as definitive hosts, while the metacestode larval stage cysticercus infects a range of intermediate hosts, including domestic animals such as goats, sheep, and pigs. Cysticercosis due to T. hydatigena has large veterinary and economic drawbacks. Like other taeniids, e.g., Echinococcus, intraspecific variation is found among the members of the genus Taenia. In Africa, few studies are available on the epidemiology and distribution of T. hydatigena, and even fewer studies are available on its genetic variation. In this study, we molecularly identified 11 cysticerci from sheep in Sudan and demonstrated the genetic variation based on the NADH dehydrogenase subunit 1 (nad1) and cytochrome c oxidase subunit 1 (cox1) mitochondrial genes. The isolates were correctly identified as T. hydatigena with more than 99% similarity to those in the GenBank database. Low diversity indices and insignificant neutrality indices were observed, with 3 and 2 haplotypes for the nad1 and cox1 genes, respectively. The results suggest the presence of unique T. hydatigena haplotypes in Sudan, as haplotypes with 100% similarity were not found in the GenBank database. With few available studies on the genetic variation of T. hydatigena in Africa, this report represents the first insights into the genetic variation of T. hydatigena in Sudan and constitutes useful data.

Taenia asiatica: Historical overview of taeniasis and cysticercosis with molecular characterization

Asian Taenia is a human-infecting Taenia tapeworm known as Taenia asiatica following morphological examination of adult and larval stages of the tapeworm by Eom and Rim (1993). The life cycle of T. asiatica differs from that of T. saginata in its intermediate host (pigs versus cattle) as well as in the infected organs (liver versus muscle). T. asiatica can be differentiated from T. solium and T. saginata by examination of morphological characteristics such as the scolex, mature and gravid proglottids in the adult stage, and the scolex and bladder surface in the larval stage. T. asiatica has been identified in Korea, Taiwan, the Philippines, China, Thailand, Indonesia, Vietnam, Japan, Lao PDR, Nepal and India. The molecular tools employed for T. asiatica identification have been developed to differentiate T. asiatica from other human-infecting Taenia tapeworms based on genetic information such as nucleotide sequence of mitochondrial genes, nuclear ribosomal genes and nuclear genes that lead to development of the subsequent molecular techniques, such as PCR-RFLP, PCR-RAPD, BESST-base, LAMP and qPCR. Investigation of the phylogenetic relationships among human Taenia species revealed that T. asiatica is a sister species with T. saginata, which is genetically more similar than other Taenia species in terms of the nucleotide sequences of cox1, nad1 and 28S rDNA. The mitochondrial genomes of human Taenia tapeworms comprise 13,703bp (T. asiatica), 13,670bp (T. saginata) and 13,709bp (T. solium), and contain 36 genes including 12 protein-coding genes, 2 ribosomal RNAs (rRNAs, a small and a large subunit), and 22 transfer RNAs (tRNAs). Sequence differences in the full genome of T. asiatica and T. saginata mitochondria is 4.6%, while T. solium differs by 11%. Hox gene orthology in T. asiatica was established by comparative analysis with Platyhelminthes Hox genes. T. asiatica Hox revealed six Hox orthologs including two lab/Hox1, two Hox3, one Dfd/Hox4 and one Lox/Lox4. Hybridization between T. asiatica and T. saginata was definitely observed in these species which are sympatrically endemic in the regions of Korea, Thailand, China and Lao PDR. Comparative analyses of T. asiatica, T. saginata and T. solium genomes were also reported with genome features. Taenia asiaticus nomen novum was proposed for T. asiaticaEom and Rim, 1993 which is a homonym of T. asiatica Linstow, 1901 (Davaineidae).

A new species of Clinostomum Leidy, 1856 in East Asia based on genomic and morphological data

Metacercariae of Clinostomum Leidy, 1856 are frequently encountered in freshwater fish. In 2015, a provisional species of Clinostomum in People's Republic of China (PRC) was distinguished from C. complanatum (Rudolphi, 1819) in Europe based on divergent cytochrome c oxidase I (CO1). However, in subsequent studies in East Asia, the same divergent CO1 genotype was identified as C. complanatum. These matching sequences suggest that either the provisional East Asian species was incorrectly distinguished from C. complanatum in 2015 or that C. complanatum in East Asia was misidentified in later studies. We tested these alternatives by sequencing the mitochondrial genome of C. complanatum in Italy, which was 5.7% divergent from a previously published sequence from Clinostomum in PRC, including differences in 80 of 3390 (2.4%) translated amino acids. Partial CO1 sequences of specimens from PRC and those from Italy, Romania, and Turkey also each formed reciprocally monophyletic clades. Partial CO1 from the East Asian clade varied by mean 3.6% (range 2.4-4.8%) from C. complanatum from Italy, Romania, and Turkey; mean intra-clade CO1 variation was 0.3% (range 0-1.9%). Metacercariae from Europe and East Asia display significant morphometric variation, and data from the literature suggest morphological differences in the genital complex of adults. Although sequences of nuclear rDNA did not differ between isolates from the west and East Asia, taken together, these results lead us to describe a new species of Clinostomum.

A cross-talk on compositional dynamics and codon usage patterns of mitochondrial CYB gene in Echinodermata

Codon usage bias (CUB) refers to a phenomenon in which some synonymous codons are used in mature mRNA at a higher frequency than other members codifying the same amino acid. CUB is mainly determined by mutation pressure and natural selection. We used bioinformatic tools to analyze the protein coding sequences of mitochondrial CYB gene in different classes of Echinodermata to understand the patterns of codon usage. The ENC values of CYB gene in five different classes of Echinodermata were 41.64, 30.33, 43.63, 41.11, and 41.33, which suggested that the CUB of this gene was low. The relative synonymous codon usage (RSCU) values showed that the patterns of over-represented and under-represented codons were different among different classes. Correspondence analysis indicated that the plots of CYB gene were different across classes, suggesting that the pattern of codon usage was also different among five classes under study. Highly significant correlation (p < .01) between overall nucleotide composition and its 3rd codon position indicated that both mutational pressure and natural selection had an influence on the codon usage bias of CYB gene. Furthermore, PR-2 bias plot analysis showed that both mutation pressure and natural selection might have affected the pattern of codon usage in CYB gene of Echinodermata.

Population Genetics and Molecular Epidemiology of Eukaryotes

Molecular epidemiology uses the distribution and organization of a pathogen's DNA to understand the distribution and determinants of disease. Since the biology of DNA for eukaryotic pathogens differs substantially from that of bacteria, the analytic approach to their molecular epidemiology can also differ. While many of the genotyping techniques presented earlier in this series, "Advances in Molecular Epidemiology of Infectious Diseases," can be applied to eukaryotes, the output must be interpreted in the light of how DNA is distributed from one generation to the next. In some cases, parasite populations can be evaluated in ways reminiscent of bacteria. They differ, however, when analyzed as sexually reproducing organisms, where all individuals are unique but the genetic composition of the population does not change unless a limited set of events occurs. It is these events (migration, mutation, nonrandom mating, selection, and genetic drift) that are of interest. At a given time, not all of them are likely to be equally important, so the list can easily be narrowed down to understand the driving forces behind the population as it is now and even what it will look like in the future. The main population characteristics measured to assess these events are differentiation and diversity, interpreted in the light of what is known about the population from observation. The population genetics of eukaryotes is important for planning and evaluation of control measures, surveillance, outbreak investigation, and monitoring of the development and spread of drug resistance. *This article is part of a curated collection.

Genetic Characterization of Taenia saginata Cyst Isolates from Germany

The beef tapeworm Taenia saginata, which causes taeniosis in humans and cysticercosis in cattle, is of medical and economic importance. Understanding the parasite's genetic population structure may help to analyze transmission patterns and aid in the development of control measures. As information on sequence variability is scarce for European isolates, this study aimed to elucidate the intraspecific genetic variability of T. saginata cysts from German cattle by sequence comparison of the mitochondrial cytochrome c oxidase subunit 1 (cox1) and NADH dehydrogenase subunit 5 (nad5) genes, in relationship to sequences from other geographical origins. Cysts were collected from northern German, Swiss, and Belgian cattle. Moreover, proglottids from an adult T. saginata specimen from Palestine were included. Amplification and Sanger sequencing of the cox1 gene was successful for 57 samples (45 German, 9 Swiss, 2 Belgian, 1 Palestinian), whereas 32 sequences were obtained for the nad5 gene (21 German, 10 Swiss, 1 Palestinian). For German isolates, sequence comparison revealed minor genetic variability with two polymorphic sites and mutations in both genes. Three haplotypes with haplotype diversity of 0.088 for cox1 and 0.186 for nad5, as well as nucleotide diversities of 0.00028 and 0.00095, respectively, were observed. Comparison of the cox1 gene sequence of German isolates with other European, African, American, and Asian isolates obtained from National Center for Biotechnology Information (total of 71 sequences) raised 11 polymorphic sites and mutations as well as 10 haplotypes (haplotype diversity: 0.239; nucleotide diversity: 0.00097). Although nad5 sequence comparison comprised less sequences (N = 33), analyses revealed 11 polymorphic sites, 12 mutation sites, and 7 haplotypes (haplotype diversity: 0.335, nucleotide diversity: 0.00391), indicating a better resolution of genetic variability compared to cox1. Thus, nad5 may be particularly useful for in-depth studies on genetic divergence of T. saginata.

Complete sequence and characterization of the mitochondrial genome of Diphyllobothrium stemmacephalum, the type species of genus Diphyllobothrium (Cestoda: Diphyllobothriidae), using next generation sequencing

We first constructed and characterized the complete mitochondrial genome (mitogenome) sequence of Diphyllobothrium stemmacephalum, the type species of genus Diphyllobothrium, using next generation sequencing (NGS). The mitogenome of D. stemmacephalum was 13,716bp, including 12 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 2 longer intergenic non-coding regions, and has features common to mitogenomes of other cestodes. Although it has been accepted that tRNA for serine (trnS2_(UCN)) in Platyhelminthes lacks a D arm, the trnS2_(UCN) of D. stemmacephalum was predicted to have a paired D arm as in Diplogonoporus balaenopterae. The non-coding region 2 contained eight tandem repeat units (34nucleotides/unit). This study also corroborated that D. stemmacephalum is phylogenetically more closely related to Dip. balaenopterae than to Diphyllobothrium latum and Diphyllobothrium nihonkaiense. As demonstrated here, mitogenome sequence data obtained using NGS is useful for gaining a better understanding of the systematics, phylogeny and taxonomic revisions involving valuable specimens preserved in museums, universities or research institutes for which sequence data are not yet available, and also for making diagnoses based on clinical samples.

Epidemiological Survey and Phylogenetic Characterization of Cysticercus tenuicollis Isolated from Tibetan Pigs in Tibet, China

Cysticercus tenuicollis, commonly known as "water bell," is a larva of Taenia hydatigena, which is the most significant parasite of pigs. However, until now very few information is available regarding the prevalence and genetic characterization of the Cysticercus tenuicollis in Tibetan pigs. Therefore, the aim of this study was to investigate the prevalence and phylogenetic analysis of Cysticercus tenuicollis in Tibetan pigs. For this purpose, the COX2 gene of Cysticercus tenuicollis was amplified and sequenced for the first time in Tibetan pigs. The overall prevalence of Cysticercus tenuicollis was 43.93% in Tibetan pigs, with further distribution of 42.86% in 2014 and 45.35% in 2015. In Tibetan male and female pigs, the prevalence of Cysticercus tenuicollis was 43.39% and 44.56%, respectively. The prevalence of Cysticercus tenuicollis in different growing stages (juveniles, subadults, and adults) varied from 30.20% to 63.79%. The phylogenetic analysis of the Cysticercus tenuicollis isolates showed very close resemblance to 16 reference strains, isolates from Gansu, Hunan, and Sichuan provinces of China. To the best of our knowledge, this is the first report on the prevalence and genetic characterization of Cysticercus tenuicollis derived from Tibetan pigs. The data of present study provides baseline information for controlling cysticerci infections in pigs in Tibetan Plateau, China.

Moniezia benedeni and Moniezia expansa are distinct cestode species based on complete mitochondrial genomes

Moniezia spp. parasitize the intestines of ruminants, causing monieziasis. In this study, the complete mitochondrial (mt) genomes of M. benedeni and M. expansa have been determined, characterized and employed to test the hypothesis that M. benedeni and M. expansa are distinct species by phylogenetic analysis based on the concatenated amino acid sequences derived from 12 protein-coding genes, inferred with Bayesian and Maximum-likelihood methods. The complete mt genomes of M. benedeni and M. expansa were 13,958bp and 13,934bp in size, respectively. Nucleotide sequence identity between the two mt genomes was 83.4%. Each of the two circular mt genomes encodes 36 genes including two ribosomal RNA genes, 22 transfer RNA genes and 12 protein-coding genes, which are transcribed from the same direction. The gene orders of the two mt genomes are identical to those of Anoplocephala spp. (Anoplocephalidae), Hymenolepis spp. (Hymenolepididae) and Dipylidium caninum (Dipylidiidae), but distinct from the species of the Taeniidae family. Phylogenetic analysis confirmed that M. benedeni and M. expansa are taxonomically valid species and have a sister relationship, regardless of the analytical method employed. Furthermore, comparing the cox1 gene sequences of Moniezia spp. from the NCBI deposited sequences and the ones obtained in the present study revealed that the nucleotide sequence differences were 12.5% for M. benedeni and 6.2% for M. expansa, respectively, suggesting the existence of cryptic species in these parasites. The complete mt genome sequences reported herein will be valuable in further studies of diagnoses, molecular ecology and population genetics of Moniezia spp. of socio-economic importance.

Comparative genomics reveals adaptive evolution of Asian tapeworm in switching to a new intermediate host

Taenia saginata, Taenia solium and Taenia asiatica (beef, pork and Asian tapeworms, respectively) are parasitic flatworms of major public health and food safety importance. Among them, T. asiatica is a newly recognized species that split from T. saginata via an intermediate host switch ∼1.14 Myr ago. Here we report the 169- and 168-Mb draft genomes of T. saginata and T. asiatica. Comparative analysis reveals that high rates of gene duplications and functional diversifications might have partially driven the divergence between T. asiatica and T. saginata. We observe accelerated evolutionary rates, adaptive evolutions in homeostasis regulation, tegument maintenance and lipid uptakes, and differential/specialized gene family expansions in T. asiatica that may favour its hepatotropism in the new intermediate host. We also identify potential targets for developing diagnostic or intervention tools against human tapeworms. These data provide new insights into the evolution of Taenia parasites, particularly the recent speciation of T. asiatica.

Only one of the three Taenia species causing taeniasis in humans was previously sequenced. Here the authors provide draft genomes of Taenia saginata and Taenia asiatica, analyse genome evolution of all three species, and identify potential targets for developing diagnostic markers or intervention tools.

Complete Mitochondrial Genome of Anoplocephala magna Solidifying the Species

The 2 species of the genus Anoplocephala (Anoplocephalidae), A. perfoliata and A. magna, are among the most important equine cestode parasites. However, there is little information about their differences at the molecular level. The present study revealed that the mitochondrial (mt) genome of A. magna was 13,759 bp in size and 700 bp shorter than that of A. perfoliata. The 2 species includes 2 rRNA, 22 tRNA, and 12 protein-coding genes each. The size of each of the 36 genes was the same as that of A. perfoliata, except for cox1, rrnL, trnC, trnS2(UCN), trnG, trnH, trnQ, and trnP. In the full mitochondrial genome, the sequence similarity was 87.1%. The divergence in the nucleotide and amino acid sequences of individual protein-coding genes ranged from 11.1% to 16% and 6.8% to 16.4%, respectively. The 2 noncoding regions of the mt genome of A. magna were 199 bp and 271 bp in length, while the equivalent regions in A. perfoliata were 875 bp and 276 bp, respectively. The results of this study support the proposal that A. magna and A. perfoliata are separate species, consistent with previous morphological analyses.

The Increase of Exotic Zoonotic Helminth Infections: The Impact of Urbanization, Climate Change and Globalization

Zoonotic parasitic diseases are increasingly impacting human populations due to the effects of globalization, urbanization and climate change. Here we review the recent literature on the most important helminth zoonoses, including reports of incidence and prevalence. We discuss those helminth diseases which are increasing in endemic areas and consider their geographical spread into new regions within the framework of globalization, urbanization and climate change to determine the effect these variables are having on disease incidence, transmission and the associated challenges presented for public health initiatives, including control and elimination.

Novel PCRs for differential diagnosis of cestodes

Cestodes or tapeworms belong to a diverse group of helminths. The adult Taenia saginata and Taenia solium tapeworm can infest the human gut and the larval stage of Echinococcus spp. and T. solium can infect tissues of the human body, causing serious disease. Molecular diagnostics can be performed on proglottids, eggs and on cyst fluids taken by biopsy. Detection of cestodes when a helminthic infection is suspected is of vital importance and species determination is required for appropriate patient care. For routine diagnostics a single test that is able to detect and type a range of cestodes is preferable. We sought to improve our diagnostic procedure that used to rely on PCR and subsequent sequencing of the Cox1 and Nad1 genes. We have compared these PCRs with novel PCRs on the 12S rRNA and Nad5 gene and established the sensitivity and specificity. A single PCR on the 12S gene proved to be very suitable for detection and specification of Taenia sp. and Echinococcus sp. Both targets harbour enough polymorphic sites to determine the various Echinococcus species. The 12S PCR was most sensitive of all tested.

The complete mitochondrial genome of the dwarf tapeworm Hymenolepis nana--a neglected zoonotic helminth

Hymenolepis nana, commonly known as the dwarf tapeworm, is one of the most common tapeworms of humans and rodents and can cause hymenolepiasis. Although this zoonotic tapeworm is of socio-economic significance in many countries of the world, its genetics, systematics, epidemiology, and biology are poorly understood. In the present study, we sequenced and characterized the complete mitochondrial (mt) genome of H. nana. The mt genome is 13,764 bp in size and encodes 36 genes, including 12 protein-coding genes, 2 ribosomal RNA, and 22 transfer RNA genes. All genes are transcribed in the same direction. The gene order and genome content are completely identical with their congener Hymenolepis diminuta. Phylogenetic analyses based on concatenated amino acid sequences of 12 protein-coding genes by Bayesian inference, Maximum likelihood, and Maximum parsimony showed the division of class Cestoda into two orders, supported the monophylies of both the orders Cyclophyllidea and Pseudophyllidea. Analyses of mt genome sequences also support the monophylies of the three families Taeniidae, Hymenolepididae, and Diphyllobothriidae. This novel mt genome provides a useful genetic marker for studying the molecular epidemiology, systematics, and population genetics of the dwarf tapeworm and should have implications for the diagnosis, prevention, and control of hymenolepiasis in humans.

The complete mitochondrial genome of Anoplocephala perfoliata, the first representative for the family Anoplocephalidae

Background

Mitochondrial (mt) genome sequences are widely used to understand phylogenetic relationships among parasites. However, no complete mt genome sequence is available in the family Anoplocephalidae to date. This study sequenced and annotated the complete mt genome of Anoplocephala perfoliata (Anoplocephalidae), and investigated its phylogenetic relationships with other species from the families Hymenolepididae, Dipylidiidae and Taeniidae of the order Cyclophyllidea using the amino acid sequences of the 12 proteins in their mt genomes.

Methods

The complete mt genome of A. perfoliata was amplified by Long-range PCR, sequenced using primer walking and annotated by comparing with those of other cestodes. Its phylogenetic relationship with the species from the families Hymenolepididae, Dipylidiidae and Taeniidae was inferred using the 12 protein sequences based on Maximum likelihood and Bayesian methods.

Results

The complete circular mt genome sequence for A. perfoliata is 14,459 bp in size, and includes 12 protein-coding genes, 2 rRNA genes and 22 tRNA genes. The mt gene arrangement of A. perfoliata is identical to those of previously reported Hymenolepis diminuta (Hymenolepididae) and Dipylidium caninum (Dipylidiidae), but slightly different from those of other taeniids due to an order switch between tRNA(S2) and tRNA(L1). The phylogenetic analyses showed that the Dipylidiidae was more closely related to Anoplocephalidae and Hymenolepididae than to Taeniidae. The relationship among the four families obtained by Maximum likelihood and Bayesian inferences based on predicted amino acid sequences of protein-coding genes is consistent with that based on their mt gene arrangement similarities.

Conclusions

This study determined the first mt genome for the family Anoplocephalidae, providing rich sources for selecting useful molecular markers for ecological and phylogenetic studies. Analyses on mt genome sequences of the four families of cestodes provide novel insights into their phylogenetic relationships. Of couse, more taxon sampling is necessary for future phylogenetic studies of these cestodes using mt genome sequences.

Electronic supplementary material

The online version of this article (doi:10.1186/s13071-015-1172-z) contains supplementary material, which is available to authorized users.

Discrimination between E. granulosus sensu stricto, E. multilocularis and E. shiquicus Using a Multiplex PCR Assay

BACKGROUND

Infections of Echinococcus granulosus sensu stricto (s.s), E. multilocularis and E. shiquicus are commonly found co-endemic on the Qinghai-Tibet plateau, China, and an efficient tool is needed to facilitate the detection of infected hosts and for species identification.

METHODOLOGY/PRINCIPAL FINDINGS

A single-tube multiplex PCR assay was established to differentiate the Echinococcus species responsible for infections in intermediate and definitive hosts. Primers specific for E. granulosus, E. multilocularis and E. shiquicus were designed based on sequences of the mitochondrial NADH dehydrogenase subunit 1 (nad1), NADH dehydrogenase subunit 5 (nad5) and cytochrome c oxidase subunit 1 (cox1) genes, respectively. This multiplex PCR accurately detected Echinococcus DNA without generating nonspecific reaction products. PCR products were of the expected sizes of 219 (nad1), 584 (nad5) and 471 (cox1) bp. Furthermore, the multiplex PCR enabled diagnosis of multiple infections using DNA of protoscoleces and copro-DNA extracted from fecal samples of canine hosts. Specificity of the multiplex PCR was 100% when evaluated using DNA isolated from other cestodes. Sensitivity thresholds were determined for DNA from protoscoleces and from worm eggs, and were calculated as 20 pg of DNA for E. granulosus and E. shiquicus, 10 pg of DNA for E. multilocularis, 2 eggs for E. granulosus, and 1 egg for E. multilocularis. Positive results with copro-DNA could be obtained at day 17 and day 26 after experimental infection of dogs with larval E. multilocularis and E. granulosus, respectively.

CONCLUSIONS/SIGNIFICANCE

The multiplex PCR developed in this study is an efficient tool for discriminating E. granulosus, E. multilocularis and E. shiquicus from each other and from other taeniid cestodes. It can be used for the detection of canids infected with E. granulosus s.s. and E. multilocularis using feces collected from these definitive hosts. It can also be used for the identification of the Echinococcus metacestode larva in intermediate hosts, a stage that often cannot be identified to species on visual inspection.

Mitochondrial Genome Sequences of Spirometra erinaceieuropaei and S. decipiens (Cestoidea: Diphyllobothriidae)

The present study was performed to compare the mitochondrial genomes between 2 Spirometra tapeworms, Spirometra erinaceieuropaei and Spirometra decipiens (Cestoidea: Diphyllobothriidae), which larval stages are important etiological agents of sparganosis in humans. For each species, the full mitochondrial genome was amplified in 8 overlapping fragments using total genomic DNA purified from a single worm as the template. The mitochondrial genomes were 13,643 bp (S. erinaceieuropaei) and 13,641 bp (S. decipiens) in length and contained 36 genes; 12 protein-coding genes, 2 ribosomal RNA (rRNA, small and large subunits), and 22 transfer RNAs (tRNAs). The 12 protein-coding genes constituted 10,083 bp (S. erinaceieuropaei) and 10,086 bp (S. decipiens) of their respective mitochondrial genomes. The tRNA genes, ranging in length from 56 to 70 bp, were identified based on putative secondary structures such as the typical cloverleaf shape. A total of 23 intergenic sequences, varying from 1 to 204 bp in size, were interspersed in S. erinaceieuropaei (total, 504 bp) and S. decipiens (total, 496 bp) mtDNA. The 12 protein-coding genes of S. erinaceieuropaei and S. decipiens differed by 12.4%, whereas the overall difference in mtDNA sequence between S. erinaceieuropaei and S. decipiens was 12.9%. Thus, from the standpoint of the mitochondrial genome, S. decipiens represents a valid species that can be distinguished from S. erinaceieuropaei.

Multiplex real-time PCR monitoring of intestinal helminths in humans reveals widespread polyparasitism in Northern Samar, the Philippines

The global socioeconomic importance of helminth parasitic disease is underpinned by the considerable clinical impact on millions of people. While helminth polyparasitism is considered common in the Philippines, little has been done to survey its extent in endemic communities. High morphological similarity of eggs between related species complicates conventional microscopic diagnostic methods which are known to lack sensitivity, particularly in low intensity infections. Multiplex quantitative PCR diagnostic methods can provide rapid, simultaneous identification of multiple helminth species from a single stool sample. We describe a multiplex assay for the differentiation of Ascaris lumbricoides, Necator americanus, Ancylostoma, Taenia saginata and Taenia solium, building on our previously published findings for Schistosoma japonicum. Of 545 human faecal samples examined, 46.6% were positive for at least three different parasite species. High prevalences of S. japonicum (90.64%), A. lumbricoides (58.17%), T. saginata (42.57%) and A. duodenale (48.07%) were recorded. Neither T. solium nor N. americanus were found to be present. The utility of molecular diagnostic methods for monitoring helminth parasite prevalence provides new information on the extent of polyparasitism in the Philippines municipality of Palapag. These methods and findings have potential global implications for the monitoring of neglected tropical diseases and control measures.

Evolutionary analysis of mitogenomes from parasitic and free-living flatworms

Mitochondrial genomes (mitogenomes) are useful and relatively accessible sources of molecular data to explore and understand the evolutionary history and relationships of eukaryotic organisms across diverse taxonomic levels. The availability of complete mitogenomes from Platyhelminthes is limited; of the 40 or so published most are from parasitic flatworms (Neodermata). Here, we present the mitogenomes of two free-living flatworms (Tricladida): the complete genome of the freshwater species Crenobia alpina (Planariidae) and a nearly complete genome of the land planarian Obama sp. (Geoplanidae). Moreover, we have reanotated the published mitogenome of the species Dugesia japonica (Dugesiidae). This contribution almost doubles the total number of mtDNAs published for Tricladida, a species-rich group including model organisms and economically important invasive species. We took the opportunity to conduct comparative mitogenomic analyses between available free-living and selected parasitic flatworms in order to gain insights into the putative effect of life cycle on nucleotide composition through mutation and natural selection. Unexpectedly, we did not find any molecular hallmark of a selective relaxation in mitogenomes of parasitic flatworms; on the contrary, three out of the four studied free-living triclad mitogenomes exhibit higher A+T content and selective relaxation levels. Additionally, we provide new and valuable molecular data to develop markers for future phylogenetic studies on planariids and geoplanids.

Genetic variability of Taenia saginata inferred from mitochondrial DNA sequences

Taenia saginata is an important tapeworm, infecting humans in many parts of the world. The present study was undertaken to identify inter- and intraspecific variation of T. saginata isolated from cattle in different parts of Iran using two mitochondrial CO1 and 12S rRNA genes. Up to 105 bovine specimens of T. saginata were collected from 20 slaughterhouses in three provinces of Iran. DNA were extracted from the metacestode Cysticercus bovis. After PCR amplification, sequencing of CO1 and 12S rRNA genes were carried out and two phylogenetic analyses of the sequence data were generated by Bayesian inference on CO1 and 12S rRNA sequences. Sequence analyses of CO1 and 12S rRNA genes showed 11 and 29 representative profiles respectively. The level of pairwise nucleotide variation between individual haplotypes of CO1 gene was 0.3-2.4% while the overall nucleotide variation among all 11 haplotypes was 4.6%. For 12S rRNA sequence data, level of pairwise nucleotide variation was 0.2-2.5% and the overall nucleotide variation was determined as 5.8% among 29 haplotypes of 12S rRNA gene. Considerable genetic diversity was found in both mitochondrial genes particularly in 12S rRNA gene.

The complete mitochondrial genome of Neobenedenia melleni (Platyhelminthes: Monogenea): mitochondrial gene content, arrangement and composition compared with two Benedenia species

The complete mitochondrial (mt) genome sequences of Neobenedenia melleni were determined and compared with those of Benedenia seriolae and B. hoshinai. This circular genome comprises 13,270 bp and includes all 36 typical mt genes found in flatworms. Total AT content of N. melleni is 75.9 %. ATG is the most common start codon, while nad4L is initiated by GTG. All protein-coding genes are predicted to terminate with TAG and TAA. N. melleni has the trnR with a TCG anticodon, which is the same to B. seriolae but different from B. hoshinai (ACG). The mt gene arrangement of N. melleni is similar to that of B. seriolae and B. hoshinai with the exception of three translocations (trnF, trnT and trnG). The overlapped region between nad4L and nad4 was found in the N. melleni mt genome, which was also reported for the published Gyrodactylus species, but it was not found in those of B. seriolae and B. hoshinai, which are non-coding regions instead. The present study provides useful molecular characters for species or strain identification and systematic studies of this parasite.

Genetic characteristics of Chinese isolates of the tapeworm Taenia pisiformis based on two mitochondrial genes

Cysticercosis is caused by infections with embryonated eggs of the tapeworm Taenia pisiformis. Knowledge of the genetic characteristics of T. pisiformis could be applied to study the epidemiology and transmission of this parasite. In this study, 61 isolates of intraperitoneal cysticerci from eight geographically distinct regions in Sichuan province, China, were subjected to a molecular analysis in order to determine their intra-regional genetic characteristics. Partial sequences of the mitochondrial cytochrome c oxidase subunit I (cox1, 1427 bp) and NADH dehydrogenase 1 (nad1, 738 bp) were concatenated. Five haplotypes were identified, and 89.04% of total genetic variation was found in collections of T. pisiformis isolates from a single region. According to the phylogenetic reconstruction, the T. pisiformis isolates from eight regions did not form geographical clusters. Our study highlights the genetic characteristics of T. pisiformis with the aim of accelerating the genetic research and control of cysticercosis.

Epidemiology and genetic diversity of Taenia asiatica: a systematic review

Taenia asiatica has made a remarkable journey through the scientific literature of the past 50 years, starting with the paradoxical observation of high prevalences of T. saginata-like tapeworms in non-beef consuming populations, to the full description of its mitochondrial genome. Experimental studies conducted in the 1980s and 1990s have made it clear that the life cycle of T. asiatica is comparable to that of T. saginata, except for pigs being the preferential intermediate host and liver the preferential location of the cysts. Whether or not T. asiatica can cause human cysticercosis, as is the case for Taenia solium, remains unclear. Given the specific conditions needed to complete its life cycle, in particular the consumption of raw or poorly cooked pig liver, the transmission of T. asiatica shows an important ethno-geographical association. So far, T. asiatica has been identified in Taiwan, South Korea, Indonesia, the Philippines, Thailand, south-central China, Vietnam, Japan and Nepal. Especially this last observation indicates that its distribution is not restricted to South-East-Asia, as was thought so far. Indeed, the molecular tools developed over the last 20 years have made it increasingly possible to differentiate T. asiatica from other taeniids. Such tools also indicated that T. asiatica is related more closely to T. saginata than to T. solium, feeding the debate on its taxonomic status as a separate species versus a subspecies of T. saginata. Furthermore, the genetic diversity within T. asiatica appears to be very minimal, indicating that this parasite may be on the verge of extinction. However, recent studies have identified potential hybrids between T. asiatica and T. saginata, reopening the debate on the genetic diversity of T. asiatica and its status as a separate species.

Complete mitochondrial genome of Haplorchis taichui and comparative analysis with other trematodes

Mitochondrial genomes have been extensively studied for phylogenetic purposes and to investigate intra- and interspecific genetic variations. In recent years, numerous groups have undertaken sequencing of platyhelminth mitochondrial genomes. Haplorchis taichui (family Heterophyidae) is a trematode that infects humans and animals mainly in Asia, including the Mekong River basin. We sequenced and determined the organization of the complete mitochondrial genome of H. taichui. The mitochondrial genome is 15,130 bp long, containing 12 protein-coding genes, 2 ribosomal RNAs (rRNAs, a small and a large subunit), and 22 transfer RNAs (tRNAs). Like other trematodes, it does not encode the atp8 gene. All genes are transcribed from the same strand. The ATG initiation codon is used for 9 protein-coding genes, and GTG for the remaining 3 (nad1, nad4, and nad5). The mitochondrial genome of H. taichui has a single long non-coding region between trnE and trnG. H. taichui has evolved as being more closely related to Opisthorchiidae than other trematode groups with maximal support in the phylogenetic analysis. Our results could provide a resource for the comparative mitochondrial genome analysis of trematodes, and may yield genetic markers for molecular epidemiological investigations into intestinal flukes.

Evolution of parasitism along convergent lines: from ecology to genomics

SUMMARY From hundreds of independent transitions from a free-living existence to a parasitic mode of life, separate parasite lineages have converged over evolutionary time to share traits and exploit their hosts in similar ways. Here, we first summarize the evidence that, at a phenotypic level, eukaryotic parasite lineages have all converged toward only six general parasitic strategies: parasitoid, parasitic castrator, directly transmitted parasite, trophically transmitted parasite, vector-transmitted parasite or micropredator. We argue that these strategies represent adaptive peaks, with the similarities among unrelated taxa within any strategy extending to all basic aspects of host exploitation and transmission among hosts and transcending phylogenetic boundaries. Then, we extend our examination of convergent patterns by looking at the evolution of parasite genomes. Despite the limited taxonomic coverage of sequenced parasite genomes currently available, we find some evidence of parallel evolution among unrelated parasite taxa with respect to genome reduction or compaction, and gene losses or gains. Matching such changes in parasite genomes with the broad phenotypic traits that define the convergence of parasites toward only six strategies of host exploitation is not possible at present. Nevertheless, as more parasite genomes become available, we may be able to detect clear trends in the evolution of parasitic genome architectures representing true convergent adaptive peaks, the genomic equivalents of the phenotypic strategies used by all parasites.

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.

Molecular approaches to Taenia asiatica

Taenia solium, T. saginata, and T. asiatica are taeniid tapeworms that cause taeniasis in humans and cysticercosis in intermediate host animals. Taeniases remain an important public health concerns in the world. Molecular diagnostic methods using PCR assays have been developed for rapid and accurate detection of human infecting taeniid tapeworms, including the use of sequence-specific DNA probes, PCR-RFLP, and multiplex PCR. More recently, DNA diagnosis using PCR based on histopathological specimens such as 10% formalin-fixed paraffin-embedded and stained sections mounted on slides has been applied to cestode infections. The mitochondrial gene sequence is believed to be a very useful molecular marker for not only studying evolutionary relationships among distantly related taxa, but also for investigating the phylo-biogeography of closely related species. The complete sequence of the human Taenia tapeworms mitochondrial genomes were determined, and its organization and structure were compared to other human-tropic Taenia tapeworms for which complete mitochondrial sequence data were available. The multiplex PCR assay with the Ta4978F, Ts5058F, Tso7421F, and Rev7915 primers will be useful for differential diagnosis, molecular characterization, and epidemiological surveys of human Taenia tapeworms.

Molecular identification of Taenia spp. in the Eurasian lynx (Lynx lynx) from Finland

Cestodes of the genus Taenia are parasites of mammals, with mainly carnivores as definitive and herbivores as intermediate hosts. Various medium-sized cats, Lynx spp., are involved in the life cycles of several species of Taenia. The aim of the present study was to identify Taenia tapeworms in the Eurasian lynx (Lynx lynx) from Finland. In total, 135 tapeworms from 72 lynx were subjected to molecular identification based on sequences of 2 mtDNA regions, the cytochrome c oxidase subunit 1 and the NADH dehydrogenase subunit 1 genes. Available morphological characters of the rostellar hooks and strobila were compared. Two species of Taenia were found: T. laticollis (127 samples) and an unknown Taenia sp. (5 samples). The latter could not be identified to species based on mtDNA, and the rostellar hooks were short relative to those described among other Taenia spp. recorded in felids from the Holarctic region. In the phylogenetic analyses of mtDNA sequences, T. laticollis was placed as a sister species of T. macrocystis, and the unknown Taenia sp. was closely related to T. hydatigena and T. regis. Our analyses suggest that these distinct taeniid tapeworms represent a putative new species of Taenia. The only currently recognized definitive host is L. lynx and the intermediate host is unknown.

Mitochondrial genes and genomes support a cryptic species of tapeworm within Taenia taeniaeformis

Taenia taeniaeformis is a globally distributed cestode, which uses felids as definitive and rodents as intermediate hosts. The complete mitochondrial DNA (mtDNA) of T. taeniaeformis from Germany (Tt-GER) was sequenced, and compared with that of another isolate from China (GenBank NC_014768; Tt-CHN), both taken from cats. Analysis of the two mtDNAs indicated that the isolates are significantly different from one another with 12.6% and 9.9% nucleotide and amino acid divergence between them, for concatenated protein-coding genes; overall difference based on a pairwise nucleotide alignment of complete mtDNAs was 11.8%. A phylogenetic analysis based on the 12 protein-coding genes of all available taeniid mtDNAs confirmed the two T. taeniaeformis isolates as sister taxa (likely separate species) and early divergent members of the genus, as suggested previously by morphology. Phylogenetic analysis of published fragments of mt genes rrnS, cox1 and nad1, which represent multiple geographic isolates of T. taeniaeformis also resolve two distinct clades that at present do not seem to be geographically isolated. Mean pairwise (nucleotide) differences between the two clades of T. taeniaeformis were approximately 11%, 10% and 13% in partial rrnS (182bp), cox1 (371bp) and nad1 (459bp) genes, respectively. Differences between entire mtDNAs and partial mt genes of the two T. taeniaeformis isolates are of a similar magnitude between established taeniid sister species. Tt-CHN differs from all other Taenia mtDNAs in lacking a short (∼69bp) non-coding region between trnY and trnL1. Partial mt fragment analysis highlighted likely misidentifications of T. taeniaeformis on GenBank.

The complete mitochondrial genomes of three cestode species of Taenia infecting animals and humans

Mitochondrial (mt) genome sequences provide useful markers for investigating population genetic structures, systematics and phylogenetics of organisms. Although Taenia multiceps, T. hydatigena, and T. taeniaeformis are common taeniid tapeworms of ruminants, pigs, dogs, or cats, causing significant economic losses, no published study on their mt genomes is available. The complete mt genomes of T. multiceps, T. hydatigena, and T. taeniaeformis were amplified in two overlapping fragments and then sequenced. The sizes of the entire mt genome were 13700 bp for T. multiceps, 13489 bp for T. hydatigena, and 13647 bp for T. taeniaeformis. Each of the three genomes contains 36 genes, consisting of 12 genes for proteins, 2 genes for rRNA, and 22 genes for tRNA, which are the same as the mt genomes of all other cestode species studied to date. All genes are transcribed in the same direction and have a nucleotide composition high in A and T. The contents of A+T of the complete genomes are 71.3% for T. multiceps, 70.8% for T. hydatigena, and 73.0% for T. taeniaeformis. The AT bias had a significant effect on both the codon usage pattern and amino acid composition of proteins. T. multiceps and T. hydatigena had two noncoding regions, but T. taeniaeformis had only one. Phylogenetic analyses based on concatenated amino acid sequences of 12 protein-coding genes revealed that T. multiceps, T. hydatigena, and T. taeniaeformis were more closely related to the other members of the Taenia genus, consistent with results of previous morphological and molecular studies. The present study determined the complete mt genome sequences for three Taenia species of animal and human health significance, providing useful markers for studying the systematics, population genetics, and molecular epidemiology of these cestode parasites of animals and humans.

Complete mitochondrial genomes of Taenia multiceps, T. hydatigena and T. pisiformis: additional molecular markers for a tapeworm genus of human and animal health significance

Background

Mitochondrial genomes provide a rich source of molecular variation of proven and widespread utility in molecular ecology, population genetics and evolutionary biology. The tapeworm genus Taenia includes a diversity of tapeworm parasites of significant human and veterinary importance. Here we add complete sequences of the mt genomes of T. multiceps, T. hydatigena and T. pisiformis, to a data set of 4 published mtDNAs in the same genus. Seven complete mt genomes of Taenia species are used to compare and contrast variation within and between genomes in the genus, to estimate a phylogeny for the genus, and to develop novel molecular markers as part of an extended mitochondrial toolkit.

Results

The complete circular mtDNAs of T. multiceps, T. hydatigena and T. pisiformis were 13,693, 13,492 and 13,387 bp in size respectively, comprising the usual complement of flatworm genes. Start and stop codons of protein coding genes included those found commonly amongst other platyhelminth mt genomes, but the much rarer initiation codon GTT was inferred for the gene atp6 in T. pisiformis. Phylogenetic analysis of mtDNAs offered novel estimates of the interrelationships of Taenia. Sliding window analyses showed nad6, nad5, atp6, nad3 and nad2 are amongst the most variable of genes per unit length, with the highest peaks in nucleotide diversity found in nad5. New primer pairs capable of amplifying fragments of variable DNA in nad1, rrnS and nad5 genes were designed in silico and tested as possible alternatives to existing mitochondrial markers for Taenia.

Conclusions

With the availability of complete mtDNAs of 7 Taenia species, we have shown that analysis of amino acids provides a robust estimate of phylogeny for the genus that differs markedly from morphological estimates or those using partial genes; with implications for understanding the evolutionary radiation of important Taenia. Full alignment of the nucleotides of Taenia mtDNAs and sliding window analysis suggests numerous alternative gene regions are likely to capture greater nucleotide variation than those currently pursued as molecular markers. New PCR primers developed from a comparative mitogenomic analysis of Taenia species, extend the use of mitochondrial markers for molecular ecology, population genetics and diagnostics.

Geographical distribution of Taenia asiatica and related species

Geographical information of Taenia asiatica is reviewed together with that of T. solium and T. saginata. Current distribution of T. asiatica was found to be mostly from Asian countries: the Republic of Korea, China, Taiwan, Indonesia, and Thailand. Molecular genotypic techniques have found out more countries with T. asiatica from Japan, the Philippines, and Vietnam. Specimens used in this paper were collected from around the world and mostly during international collaboration projects of Korean foundations for parasite control activities (1995-2009) in developing countries.