Molecular characterization of pouched amphistome parasites (Trematoda: Gastrothylacidae) using ribosomal ITS2 sequence and secondary structures

Molecular characterization of Microphallus sp. (Digenea: Microphallidae) parasitic in freshwater crabs of Manipur, India

Freshwater crabs (Potamiscus manipuriensis), commonly consumed as local delicacies by the native people in the state of Manipur, were found to harbour metacercariae of Microphallus sp. (Family Microphyllidae), which were morphologically different from metacercariae of Microphallus spp reported earlier from different regions. So, PCR-based molecular characterization of this metacercaria was done utilizing rDNA marker regions: larger subunit (LSU) or 28S (D1-D3 region) and inter-transcribed spacer 2 (ITS2). Sequence and phylogenetic analyses confirmed that the taxon under study belonged to family Microphyllidae of genus Microphallus.

Amphistome Infection and Species Diversity of Freshwater Snails Collected from Selected Wildlife Drinking Water Sources in Matebeleland Region of Zimbabwe

This study aimed at determining the identity of freshwater snails collected from selected water habitats frequented by wildlife as source of drinking water in the Matebeleland region of Zimbabwe and further screening the identified snails for natural infections with amphistomes using PCR. A total of 487 freshwater snails were collected from six areas in the Matebeleland region of Zimbabwe for identification and screening of amphistome infection. Eight freshwater snail species were morphologically identified and Biomphalaria pfeifferi, Bul. tropicus, Bul. truncatus, Bul. globosus, and L. (R.) natalensis were confirmed using the COI gene. Bulinus tropicus and Phy. acuta were the most abundant species at 33.9% (165/487) and 31.2% (155/487), respectively. DNA of amphistome was detected in 11.9% (58/487) of the collected snails. The highest infection rate was detected in Bul. globosus (44.4%). West Nicholson recorded the highest infection rate (33.9%), and infection was not detected in L. (R.) natalensis, Phy. acuta, and Bellamya spp. Amphistome DNA from M. tuberculata was successfully sequenced and identified as Calicophoron microbothrium. An additional band was detected in M. tuberculata, Bul. tropicus, and Bul. trancatus, which showed a 96.42% similarity to Paragonimus sp. sequence in the GenBank.

Epidemiology of rumen fluke infection in selected buffalo farms in perak, malaysia: prevalence, molecular species identification, and associated risk factors

Rumen flukes cause heavy economic losses in the ruminant industry worldwide, especially in tropical and subtropical countries. This study estimated the prevalence of rumen flukes in buffaloes, identified the species diversity, and determined risk factors associated with rumen fluke prevalence in Perak, Peninsular Malaysia. A cross-sectional study was conducted, and 321 faecal samples were collected from six buffalo farms. A structured questionnaire was developed, and farmers were interviewed to obtain information regarding risk factors associated with rumen fluke infection. The faecal samples were examined using sedimentation and Flukefinder® techniques. Genomic DNA was extracted from the fluke eggs recovered using the Flukefinder® method, and the internal transcribed spacer 2 (ITS2) fragment was amplified and sequenced to facilitate species identification. The results showed that the overall prevalence of rumen fluke across the sampled farms was 40.2% (129/321). Three rumen fluke species were identified, namely, Fischoederius elongatus, F. cobboldi, and Orthocoelium streptocoelium. Several management factors had a significant association (P < 0.05) with rumen fluke prevalence, including production type, cleaning of the stable, drinking water system, flooding around the farm, grazing system, pasture sharing with other livestock, and deworming program. This work constitutes the first attempt to understand the epidemiology of rumen fluke infection in the region and suggests that good farm management, pasture management, choosing appropriate drugs, and proper husbandry practices may improve buffalo health and production in areas where rumen flukes are prevalent.

Prevalence and geographical distribution of amphistomes of African wild ruminants: A scoping review

This review summarizes published records on the prevalence, species diversity, geographical distribution, mixed infections, co-infections with other trematodes and intermediate hosts (IHs) of amphistomes (rumen flukes) of wild ruminants in Africa. Literature search was conducted on Google Scholar, PubMed and JSTOR, using a combination of predetermined search terms and Boolean operators. Of the 54 African countries searched, results showed that occurrence of amphistome infections in wild ruminants have only been reported in 23 countries. A total of 38 amphistome species consisting of the following 11 genera were recorded, viz Bilatorchis, Calicophoron, Carmyerius, Choerecotyloides, Cotylophoron, Explanatum, Gastrothylax, Gigantocotyle, Leiperocotyle, Paramphistomum and Stephanopharynx. These were recorded in 39 wild ruminant species, belonging to the Bovidae family. The genus Carmyerius recorded the highest number of species (n = 13) across nine countries Africa. However, Calicophoron species (n = 9) were more widely distributed, occurring in 17 countries across all regions of Africa. Species of this genus collectively infected 27 wild ruminant species. However, at a species level, Cotylophoron cotylophorum infected the highest number of wild ruminant species. Prevalence of infection based on post-mortem examination ranged from 1.89% in African Buffalo to 100% in Defassa waterbuck from Egypt and Zambia, respectively. The most common mixed infections recorded were those between amphistomes of the same or different genus. Snail intermediate hosts (IHs) were described for 10/38 amphistome species, and these were predominantly species from Plarnobidae family. Despite the richness in diversity of amphistomes infecting wild ruminants in Africa, there is need to further confirm identity of snail IHs and the amphistome species using both morphological and molecular techniques. Furthermore, more studies are recommended to assess the burden of amphistomosis in commercially reared wildlife/game farming, mixed game and livestock farming systems in Africa.

Amphistomes

Amphistomes, commonly referred to as 'stomach' or 'rumen' flukes because of the localization of these flukes in the stomach of ruminants, are digenetic trematodes distinguished by the absence of an oral sucker and the position of the ventral sucker or acetabulum at the posterior end of the body. The body is characterized by a leaf-like fleshy structure, pink or red with a large posterior sucker. Amphistomes are an important group of parasites since they cause 'amphistomiasis' (variously known as paramphistomosis/amphistomosis), a serious disease of great economic importance in ruminants worldwide. These parasites have a broad spectrum of definitive hosts together with a wide geographical distribution. Though they form a continuous evolutional lineage from fishes to mammals, amphistomes mainly inhabit the rumen and reticulum of ruminant mammals, while some species occur in the large intestine or parenteric sites of ruminants, pigs, equines and man.

Morphological and molecular description of Dictyocaulus xanthopygus sp. nov. (Nematoda: Trichostrongyloidea) from the Manchurian wapiti Cervus elaphus xanthopygus

Dictyocaulus xanthopygus sp. nov. (Nematoda: Trichostrongyloidea) was isolated from the lungs of the Manchurian wapiti in Primorsky kray, Russia. The newly described species exhibits morphological characteristics of Dictyocaulus but is distinct from congeneric species based on morphological (lengths of body and esophagus, distances from the anterior end to nerve ring and to excretory pore, the thickness of the buccal capsule, etc.) and molecular features. High levels of genetic divergence as well as Bayesian phylogenetic analyses based on 18S rRNA nuclear and cox1 mitochondrial genes supported the independence of Dictyocaulus xanthopygus sp. nov. Secondary structures of helix 39 of 18S rRNA were identical, while ES9 adjacent to the helix has a unique conformation for newly described worms. Energy-efficient conformational rearrangements of rRNA secondary structures can be applicable in studies on the pathogenesis, epidemiology, taxonomy and evolutionary biology of parasites. Additionally, bracketed dichotomous keys to six valid species of Dictyocaulus were prepared.

Multi-detection for paramphistomes using novel manually designed PAR-LAMP primers and its application in a lateral flow dipstick (LAMP-LFD) system

Loop-mediated isothermal amplification (LAMP) has been applied for the detection of various parasites, and its application in lateral flow dipstick (LFD) can improve the convenience of point-of-care diagnosis. A novel PAR-LAMP probe and primers were designed by manual selection from a region of low variation in the ITS-2 DNA sequence. Up to six species of rumen fluke were detected by LAMP and LAMP-LFD in this study. Target specificity and sensitivity were tested, revealing a high target specificity (accuracy) and a low limit of detection (sensitivity). Different target sensitivities of paramphistome were presented, including 5 pg for Gastrothylax crumenifer and Carmyerius sp.; 1 pg for Fischoederius elongatus, Orthocoelium parvipapillatum, and O. dicranocoelium; and 0.1 pg for Paramphistomum epiclitum. LAMP-LFD can detect a paramphistome egg even in contaminated in feces that was spiked with the egg under laboratory conditions. In addition, natural paramphistome infection in cattle from Surat Thani and Khon Kaen provinces, Thailand, was evaluated by detection of egg contamination in fecal specimens using PAR-LAMP primers. The PAR-LAMP detection result was also statistically evaluated by microscopic examination of feces. This study presents the application of novel manually designed primers in a LAMP-LFD system for improving performance in detection and diagnosis assays for paramphistomosis.

Morphology and Mitochondrial Genome of Fischoederius sp. 1 in Thailand

A rumen fluke Fischoederius elongatus is assigned to the type species of genus Fischoederius, family Gastrothylacidae. However, the mitochondrial sequences recently published are thought to be of inconsistent species, suggesting that several morphologically similar but genetically distinct species might be classified as Fischoederius elongatus. Thus, mentions of F. elongatus from South, Southeast, and East Asia might unintentionally refer to different species. The present work describes morphology and a full mitochondrial genome sequence of one of these species. The fluke specimens were collected from 2 infected cattle in Thailand. An interesting finding was the presence of a second tRNA-Asp gene next to a partial ND1 gene. It is suggested that these duplicated sequences are the remnants of non-reciprocal recombination events caused by inverted repeats located between ND2 and ND1 mitochondrial genes.

Fischoederius elongatus (Poirier, 1883) Stiles & Goldberger, 1910, a cryptic species of pouched amphistome (Gastrothylacidae)?

Rumen flukes in the genus Fischoederius are neglected foodborne parasites of cattle in Asia. Fischoederius elongatus, first described in 1883 from a sample collected in Indonesia is the type-species of the genus and is found from South to East Asia. In this study Fischoederius spp were collected from cattle in Thailand. The flukes resembled F. elongatus and images of 48 specimens were taken and their DNA was isolated. The mtDNA sequence of the cytochrome c oxidase subunit I (COX1) gene was amplified by PCR and used for restriction analysis with MseI. Nine restriction patterns (A-I) were observed and the COX1 mtDNA sequence for each pattern was determined. Phylogenetic analysis clustered the nine COX1 sequences into five groups with 4.6-9.6 % sequence differences between the groups. This is beyond intragenic variation observed for the COX1 gene in other organisms and suggested that the analyzed specimens represented several species. A comparative transcriptome analysis of specimens with COX1 MseI patterns A, C, E supported this finding. The observed median base differences, both absolute and relative, in the protein coding sequences of 999 orthologs were similar to those between distinct fruit fly species. It is proposed that the genus Fischoederius contains undescribed species that follow the classic description of F. elongatus.

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.

Paragonimus heterotremus Chen et Hsia, 1964 (Digenea: Paragonimidae): species identification based on the biological and genetic criteria, and pathology of infection

As a result of the experimental infection of rats with metacercariae of Paragonimus heterotremus Chen et Hsia, 1964 from crabs (Potamiscus tannanti) caught in Yen Bai province, Vietnam, it was found that worms migrated into the lungs, to the liver and less frequently to the tissue that lines body cavities of the hosts, where they reached the adult stage, but in the muscles, worms stayed at the larval stage. Studies have shown that for P. heterotremus, rats can simultaneously play the role of the final and paratenic host; herewith, an infection with the trematode of this species can lead to the development of three forms of paragonimiasis: pulmonary, hepatic and muscular. Eggs from the adult worms localised in the liver, unlike eggs from the adult worms localised in the lungs, were not excreted into the external environment, but accumulated inside the organ. Histology and description of changes, which take place on the external surface of organs affected with P. heterotremus, are given in this study. Based on the behavioural characteristics of worms during rat infection and molecular genetic data, we established that worms from Vietnam and India should be assigned to different species of Paragonimus. P. heterotremus distribution is limited to the territory of the Southeast China, Northern Vietnam, Laos and Thailand.

Morphological, Molecular, and Pathological Appraisal of Hymenolepis nana (Hymenolepididae) Infecting Laboratory Mice (Mus musculus)

Hymenolepis nana, typically a parasite found in conventionally established mouse colonies, has zoonotic potential characterized by autoinfection and direct life cycle. The objective of this study was to determine the rate of parasite infection in laboratory mice. The hymenolepidide cestode infected 40% of the 50 mice sampled. The rate of infection in males (52%) was higher than in females (28%). Morphological studies on the cestode parasite showed that worms had a globular scolex with four suckers, a retractable rostellum with 20-30 hooks, and a short unsegmented neck. In addition, the remaining strobila consisted of immature, mature, and gravid proglottids, irregularly alternating genital pores, lobulated ovaries, postovarian vitelline glands, and uteri with up to 200 eggs in their gravid proglottids. The parasite taxonomy was confirmed by using molecular characterization based on the sequence analysis of the mitochondrial cytochrome c oxidase subunit 1 (mtCOX1) gene. The parasite recovered was up to 80% identical to other species in GenBank. High blast scores and low divergence were noted between the isolated parasite and previously described H. nana (gb| AP017666.1). The phylogenetic analysis using the COX1 sequence places this hymenolepidid species of the order Cyclophyllidea.

Molecular characterization of Hymenolepis nana based on nuclear rDNA ITS2 gene marker

Introduction

Hymenolepis nana is a zoonotic tapeworm with widespread distribution. The goal of the present study was to identify the parasite in the specimens collected from NorthWestern regions of Iran using PCR-sequencing method.

Methods

A total of 1521 stool samples were collected from the study individuals. Initially, the identification of hymenolepis nana was confirmed by parasitological method including direct wet-mount and formalin-ethyl acetate concentration methods. Afterward, PCR-sequencing analysis of ribosomal ITS2 fragment was targeted to investigate the molecular identification of the parasite.

Results

Overall, 0.65% (10/1521) of the isolates were contaminated with H. nana in formalin-ethyl acetate concentration. All ten isolates were succefully amplified by PCR and further sequenced. The determined sequences were deposited in GenBank under the accession numbers MH337810 -MH337819.

Conclusion

Our results clarified the presence of H. nana among the patients in the study areas. In addition, the molecular technique could be accessible when the human eggs are the only sources available to identify and diagnose the parasite.

Morphological and molecular characterization of six Indian Tetracotyle type metacercariae (Digenea: Strigeidae Railliet, 1919), using ribosomal and mitochondrial DNA

Strigeids have a cup-shaped fore body, containing a holdfast organ with two lobes and hind body. The species diversity of strigeids remains incomplete, especially in the Indian sub-continent. Here, we described six Tetracotyle type metacercariae (T. muscularis, T. fausti, T. lucknowensis, T. xenentodoni, T. mathuraensis and T. glossogobii) from five fresh water fish, collected at Lucknow (India). Next, we characterized these metacercariae using ribosomal (18S, 28S, ITS2) and mitochondrial DNA (COI) to determine their systematic and phylogenetic position. Molecular identification using inter-specific variation range for all four molecular markers revealed 1.9-4.9% (18S); 3.3-8.8% (28S); 6.8-12.9% (ITS2), and 3.5-9.4% (COI) among six Tetracotyle type metacercariae. In phylogenetic analysis, constructed by neighbour-joining (NJ) and maximum likelihood (ML) methods, T. fausti, T. glossogobii, T. xenentodoni, T. lucknowensis and T. mathuraenis nested as sister groups with the member of strigeids for all four markers used; T. muscularis, however, formed a basal clade. Furthermore, phylogenetic placement states the monophyly of the Tetracotyle type of metacercariae in all the markers (18S, 28S, COI), except ITS2.

Amphistomes

Amphistomes, commonly referred to as 'stomach' or 'rumen' flukes because of the localization of these flukes in the stomach of ruminants, are digenetic trematodes distinguished by the absence of an oral sucker and the position of the ventral sucker or acetabulum at the posterior end of the body. The body is characterized by leaf-like fleshy structure, pink or red in colour with a large posterior sucker. Amphistomes are an important group of parasites since they cause 'amphistomiasis' (variously known as paramphistomosis/amphistomosis), a serious disease of great economic importance in ruminants worldwide. These parasites have a broad spectrum of definitive hosts together with a wide geographical distribution. Though, they form a continuous evolutional lineage from fishes to mammals, amphistomes mainly inhabit the rumen and reticulum of ruminant mammals, while some species occur in the large intestine or parenteric sites of ruminants, pigs, equines and man.

Morphological and molecular characterization of Paramphistomum epiclitum of small ruminants

Morphological and molecular identification can pave the way to design the most effective control measures against the Paramphistomum epiclitum in small ruminants. Morphology of the flukes had described the features of Paramphistomum genus. Body was conical with concave ventral and convex dorsal surface, tegumental spines all around the body in the immature stage, terminal funnel shape oral sucker, sub-terminal acetabulum, blind caeca with a serpentine course touching the anterior level of the acetabulum. Vitelline glands were at the lateral margins of the body extended from the pharynx to the posterior sucker. Testes were lobed and tandem, wavy post-testicular uterus and genital pore behind intestinal bifurcation. Sequence analyses of internal transcribed spacer (ITS)-2+ (PCR products of approximately 500 bp) of 10 flukes yielded 2 genotypes, Navsari isolate 1 and 2. In BLAST analysis, ITS-2+ genotypes were 97.3-99% similar with published sequences (KF564870, JF834888, KF642983 and JX678254) of P. epiclitum of Paramphistomatidae. Two genotypes depicted 4 single nucleotide polymorphisms (NPs) in the form of transitions (C-T at 10 and 18; G-A at 255; A-G at 367 locus), 1 triple NPs (CGT-GAA between 21-23 loci) and missing A base at codon 40 in the genotype 1. Average AT and GC content was 49.61% and 50.38%, respectively. Trees topology inferred by Neighbor Joining and Maximum Likelihood methods of ITS2+ of trematodes were similar, with small difference of bootstrap values. Navsari genotypes formed a tight cluster with the P. epiclitum, originated from different location with high bootstrap value and 0.004-0.011 estimated evolutionary divergence.

Incidence of amphistome infection in sheep from Mhow, Madhya Pradesh

A total of 445 faecal samples and 128 rumens of sheep collected from Slaughter house, Mhow (Madhya Pradesh) were examined for a period of 1 year from February 2011 to January 2012. Faecal sample examination based, incidence of amphistomes was found to be 23.37% from the study area. The incidence of amphistomes was significantly higher (p < 0.01) during summer (36.75%) than winter (27.74%) and monsoon (3.52%). Age-wise, non-significantly higher infection was observed in ≥1 year-old animals (23.61%) than <1 year-old animals (23.11%). Non-significantly higher rate of infection was recorded in case of females (25.63%) than that of males (19.64%). Out of 128, 49 (38.28%) rumens were found positive for amphistomes. The prevalence of Paramphistomum cervi (27.34%) was found to be significantly (p < 0.01) higher than Gastrothylax crumenifer (10.94%).

Genetic divergence of human pathogens Nanophyetus spp. (Trematoda: Troglotrematidae) on the opposite sides of the Pacific Rim

Human and animal nanophyetiasis is caused by intestinal flukes belonging to the genus Nanophyetus distributed on both North American and Eurasian coasts of Northern Pacific. In spite of the wide geographical distribution and medical and veterinary importance of these flukes, the intra-generic taxonomy of Nanophyetus spp. remains unresolved. The two most widely distributed nominal species, Nanophyetus salmincola and Nanophyetus schikhobalowi, both parasitizing humans and carnivorous mammals, were described from North America and eastern Eurasia, respectively. However, due to their high morphological similarity their interrelationships remained unclear and taxonomic status unstable. In this study, we explored genetic diversity of Nanophyetus spp. from the Southern Russian Far East in comparison with that of samples from North America based on the sequence variation of the nuclear ribosomal gene family (18S, internal transcribed spacers, ITS1-5·8S-ITS2 and 28S). High levels of genetic divergence in each rDNA region (nucleotide substitutions, indels, alterations in the secondary structures of the ITS1 and ITS2 transcripts) as well as results of phylogenetic analysis provided strong support for the status of N. salmincola and N. schikhobalowi as independent species.

Loads of trematodes: discovering hidden diversity of paramphistomoids in Kenyan ruminants

Paramphistomoids are ubiquitous and widespread digeneans that infect a diverse range of definitive hosts, being particularly speciose in ruminants. We collected adult worms from cattle, goats and sheep from slaughterhouses, and cercariae from freshwater snails from ten localities in Central and West Kenya. We sequenced cox1 (690 bp) and internal transcribed region 2 (ITS2) (385 bp) genes from a small piece of 79 different adult worms and stained and mounted the remaining worm bodies for comparisons with available descriptions. We also sequenced cox1 and ITS2 from 41 cercariae/rediae samples collected from four different genera of planorbid snails. Combining morphological observations, host use information, genetic distance values and phylogenetic methods, we delineated 16 distinct clades of paramphistomoids. For four of the 16 clades, sequences from adult worms and cercariae/rediae matched, providing an independent assessment for their life cycles. Much work is yet to be done to resolve fully the relationships among paramphistomoids, but some correspondence between sequence- and anatomically based classifications were noted. Paramphistomoids of domestic ruminants provide one of the most abundant sources of parasitic flatworm biomass, and because of the predilection of several species use Bulinus and Biomphalaria snail hosts, have interesting linkages with the biology of animal and human schistosomes to in Africa.

Differential diagnosis and molecular characterization of Hymenolepis nana and Hymenolepis diminuta (Cestoda: Cyclophyllidea: Hymenolepididae) based on nuclear rDNA ITS2 gene marker

Given the widespread distribution and medical implication of members of the genus Hymenolepis, specific identification of the aetiological agent becomes imperative. For precise diagnosis of the species, molecular techniques such as PCR and RFLP of the nuclear ribosomal internal transcribed spacer 2 (rDNA-ITS2) gene marker were carried out. The results showed distinct restriction patterns for both Hymenolepis nana and Hymenolepis diminuta when digested with either of the enzymes RsaI, HaeIII or HhaI. The annotated rDNA-ITS2 sequences from the two species revealed differences in the length; the folded secondary structure also depicted clear demarcation between the two species with variations in length of the helices, pyrimidine-pyrimidine mismatches and sites where motifs occur. In phylogenetic analysis of the evolutionary relationship between the two species as well as with other members of the family Hymenolepididae, the species causing human hymenolepiasis were found to be distantly related as they diverged independently from the ancestral lineage.

Ribosomal DNA analysis of isolates of the liver fluke Opisthorchis pedicellata (Verma, 1927) from two siluroid fish species in India

The aim of this paper was to evaluate the genetic relationship between two isolates of Opisthorchis (O. pedicellata sp. 1, O. pedicellata sp. 2) from two siluroid fish hosts, based on three nuclear DNA (18S, internal transcribed spacer 1 (ITS1) and ITS2). Molecular analysis revealed that both isolates of 18S sequences showed low intraspecific variability (1.6%), while this was 1.9% for ITS1 and 2.6% for ITS2. The secondary structure of the ITS2 region exhibited a remarkable four-helix model, with helices 1 and 4 being relatively short, three U–U mismatches in helix 2 and the longest helix (3) having two UGGG motifs. The phylogenetic analyses, using neighbour–joining (NJ) and maximum parsimony (MP) methods of MEGA 6, demonstrate that both isolates form a sister clade with significant support (100%). Therefore, we concluded that both the isolates of O. pedicellata are of the same species but some variations may be due to the sympatric environment of variant hosts.

Molecular analysis of selected paramphistome isolates from cattle in southern Africa

Paramphistomes are parasites of domestic and wild ruminants, the effects of which in animal health remain underestimated. Very few studies in Africa have been done using molecular techniques to resolve situations associated with taxonomical groupings and epidemiology of these parasites. In this study, the genetic variability of nine representative paramphistome isolates collected from southern African countries, namely Botswana, South Africa, Zambia and Zimbabwe, was assessed using both morphological and internal transcribed spacer 2 (ITS2) rDNA sequence data. Morphological characterization and identification were carried out using median sagittal sections of the paramphistomes. DNA of the individual paramphistomes was isolated, the ITS2 rDNA was amplified, purified and sequenced. The sequences were submitted to GenBank, which assigned them the following accession numbers: KP639631, KP639630, KP639632, KP639633, KP639634, KP639635, KP639636, KP639637 and KP639638. These sequences were used for phylogenetic analysis using MEGA 6. Morphological characterization revealed three species of paramphistomes belonging to three different sub-families: one Stephanopharynx compactus isolate, a member of the Stephanopharyngidae sub-family; one Carmyerius dollfusi isolate, a member of the Gastrothylacidae sub-family; and seven Calicophoron microbothrium isolates belonging to the Paramphistomidae sub-family. ITS2 sequence analysis using BlastN results indicated that this is the first report of S. compactus (KP639630) and C. dollfusi (KP639636). Phylogenetic reconstruction of the paramphistome isolates revealed three separate clades representing the three species. However, the clade with all the C. microbothrium isolates was the only one that was supported by a higher bootstrap value of 92%, although there was no differentiation of the isolates according to geographical locations. The low divergence values on the ITS2 sequences of the C. microbothrium isolates indicate that ITS rDNA sequences can be used as a molecular tool to infer knowledge for resolving taxonomic groupings.

Molecular characterization of Gastrothylax crumenifer (Platyhelminthes: Gastrothylacidae) from goats in the western part of India by LSU of nuclear ribosomal DNA

The rumen parasite, Gastrothylax crumenifer (Platyhelminthes: Gastrothylacidae), is a highly pathogenic trematode parasite of goat (Capra hircus). It sucks blood that causes acute disease like anemia, and severe economic losses occur due to morbidity and mortality of the ruminant infected by these worms. The study of these rumen paramphistomes, their infection, and public health importance remains unclear in India especially in the western part of state Uttar Pradesh (U.P.), Meerut, India, where the goat meat consumption is very high. This paper provides the molecular characterization of G. crumenifer recovered from the rumen of Capra hircus from Meerut, U.P., India by the partial sequence of 28S rDNA. Nucleotide sequence similarity searching on BLAST of 28S rDNA from parasites showed the highest identity with those of G. crumenifer from the same host Capra hircus. This is the first report of molecular identification of G. crumenifer from this part of India.

Utilizing ribosomal DNA gene marker regions to characterize the metacercariae (Trematoda: Digenea) parasitizing piscine intermediate hosts in Manipur, Northeast India

Freshwater fishes in Manipur, Northeast India frequently harbour several types of metacercariae, which based on morphological criteria were identified as Clinostomoides brieni, Euclinostomum heterostomum (Clinostomidae) and Polylekithum sp. (Allocreadiidae). Molecular techniques utilizing PCR amplification of rDNA regions of larger subunit (LSU or 28S), smaller subunit (SSU or 18S) and inter transcribed spacers (ITS1, 2) were used for molecular characterization of these types. Sequences generated from the metacercariae were compared with their related sequences available in public databases; an analysis of the identity matrices and phylogenetic trees constructed was also carried out, which confirmed their identification. Similarly, the sequences generated from Polylekithum sp. were found to be highly similar to the species of the same genus. The rDNA ITS2 secondary structure provided additional confirmation of the robustness of the molecular marker as a tool for taxon-specific characterization.

Utility of divergent domains of 28S ribosomal RNA in species discrimination of paramphistomes (Trematoda: Digenea: Paramphistomoidea)

Among the digenetic trematodes, paramphistomes are known to be the causative agent of "amphistomiasis" or the stomach fluke disease of domestic and wild animals, mainly ruminants. The use of 28S (divergent domains) and 18S rRNA for phylogenetic inference is significantly warranted for these flukes since it is as yet limited to merely the exploration of the second internal transcribed spacer (ITS2) region. The present study intended to explore the divergent domains (D1-D3) of 28S rRNA and simultaneously equate the phylogenetic information with 18S rRNA in paramphistomes. Divergence of the 28S rRNA domains was evident amongst the divergent (D) domains, where D1 domain emerged as the most variable and D2, the most robust domain, since the latter could provide a higher resolution of the species. D2 was the only domain that comprised compensatory mutations in the helices of its structural constraints; this domain is thus well suited for species distinction and may be considered a potential DNA barcode complementary to mitochondrial DNA. 28S (D1 + D2 + D3) rRNA provided a significant resolution of the taxa corroborating with the taxonomy of these flukes and thus proved to be more robust as a phylogenetic marker for lower levels than 18S rRNA. Phylogenetic inferences of paramphitomes are still scarcely explored; additional data from other taxa belonging to this family may estimate better the biodiversity of these flukes.

Molecular characterization of the Indian poultry nodular tapeworm, Raillietina echinobothrida (Cestoda: Cyclophyllidea: Davaineidae) based on rDNA internal transcribed spacer 2 region

The nodular tapeworm, Raillietina echinobothrida is a well studied avian gastrointestinal parasite of family Davaineidae (Cestoda: Cyclophyllidea). It is reported to be the largest in size and second most prevalent species infecting chicken in north-east India. In the present study, morphometrical methods coupled with the molecular analysis of the second internal transcribed spacer (ITS2) region of ribosomal DNA were employed for precise identification of the parasite. The annotated ITS2 region was found to be 446 bp long and further utilized to elucidate the phylogenetic relationships and its species-interrelationships at the molecular level. In phylogenetic analysis similar topology was observed among the trees obtained by distance-based neighbor-joining as well as character-based maximum parsimony tree building methods. The query sequence R. echinobothrida is well aligned and placed within the Davaineidae group, with all Raillietina species well separated from the other cyclophyllidean (taeniid and hymenolepid) cestodes, while Diphyllobothrium latum (Pseudophyllidea: Diphyllobothriidae) was rooted as an out-group. Sequence similarities indeed confirmed our hypothesis that Raillietina spp. are neighboring the position with other studied species of order Cyclophyllidea against the out-group order Pseudophyllidea. The present study strengthens the potential of ITS2 as a reliable marker for phylogenetic reconstructions.