Pramod Kumar Prasad

Molecular identification of the Indian liver fluke, Fasciola (Trematoda: Fasciolidae) based on the ribosomal internal transcribed spacer regions

The species of liver flukes of the genus Fasciola (Platyhelminthes: Digenea: Fasciolidae) are obligate parasitic trematodes residing in the large biliary ducts of herbivorous mammals. While Fasciola hepatica has a cosmopolitan distribution, the other major species, i.e., Fasciola gigantica is reportedly prevalent in the tropical and subtropical regions of Africa and Asia. To determine the phylogenic location of Fasciola sp. of Assam (India) origin based on rDNA molecular data, ribosomal ITS regions were sequenced and compared with other species of trematodes in the family Fasciolidae. NCBI databases were used for sequence homology analysis using BLAST and ClustalW programs. The phylogenetic trees constructed based upon the ITS (1 and 2) sequences revealed a close relationship with isolates of F. gigantica from China, Indonesia, Japan, Egypt, and Zambia, the isolate from China with significant bootstrap values being the closest. Using the novel approach of molecular morphometrics that is based on ITS2 secondary structure homologies, phylogenetic relationships of the various isolates of fasciolid species have also been discussed. While comparing ITS1, the sequence of another Indian isolate designated as F. gigantica (accession no. EF198867) showed almost absolute match with F. hepatica. Hence, this particular isolate should be identified as F. hepatica and not F. gigantica.

Surface fine topography and PCR-based determination of metacercaria of Paragonimus sp. from edible crabs in Arunachal Pradesh, Northeast India

In several mountainous regions of Northeastern India, foci of Paragonimus infection reportedly involving species that are known to prevail in China have been identified. The present study was undertaken to demonstrate the surface fine topography and sequence analysis of the ribosomal deoxyribonucleic acid (rDNA; second internal transcribed spacer, ITS2) of the metacercarial stages of the lung fluke collected from a mountain stream of the area (Miao, Changlang District in Arunachal Pradesh). The encysted metacercariae were oval in shape and had a smooth surface. The newly excysted metacercaria had a ventral sucker larger than the oral; the body surface was covered with numerous single-pointed and thorn-like tegumentary spines, of which those on the anterior part of the body were bigger in size and showed a gradual reduction in length and number towards the posterior end; dome-shaped papillae in variable numbers were seen around the rim of the oral sucker and were sparsely distributed all over the body surface. The polymerase chain reaction-amplified rDNA ITS2 sequences of the metacercariae were aligned with known sequences for the various species of Paragonimus, and the expectation value was found to be most significant with P. westermani, revealing an absolute match. The surface topography including the number and distribution of papillae and spination patterns and the ITS2 sequences of the metacercariae strongly suggest that the Paragonimus species, prevalent in the region of India, is in fact P. westermani.

PCR-based determination of internal transcribed spacer (ITS) regions of ribosomal DNA of giant intestinal fluke, Fasciolopsis buski (Lankester, 1857) Looss, 1899

Fasciolopsis buski, the zoonotic intestinal flukes of pigs in South and Southeast Asia, is commonly prevalent in regions across Northeast India. Populations of the fluke collected from different parts of the region exhibit variations in morphology. The main objective of our study was to provide molecular characterization of the parasite so as to supplement morphological criteria, using ribosomal DNA cluster (rDNA), which is flanked by more conserved internal transcribed spacer (ITS) regions. We describe herein the ITS sequences of the parasite collected from swine hosts of Assam region. The ITS sequences of both egg and adult origins were found to be identical in length and composition. Phylogenetically, F. buski resembles closely the other members of family Fasciolidae, showing significant expectation value in the alignment. The results corroborate that the ITS sequences are not stage specific and are conserved through different stages of development of the fluke, and thus could be used as species markers.

Use of sequence motifs as barcodes and secondary structures of internal transcribed spacer 2 (ITS2, rDNA) for identification of the Indian liver fluke, Fasciola (Trematoda: Fasciolidae).

Most phylogenetic studies using current methods have focused on primary DNA sequence information. However, RNA secondary structures are particularly useful in systematics because they include characteristics that give “morphological” information which is not found in the primary sequence. Also DNA sequence motifs from the internal transcribed spacer (ITS) of the nuclear rRNA repeat are useful for identification of trematodes. The species of liver flukes of the genus Fasciola (Platyhelminthes: Digenea: Fasciolidae) are obligate parasitic trematodes residing in the large biliary ducts of herbivorous mammals. While Fasciola hepatica has a cosmopolitan distribution, the other major species, i.e., F. gigantica is reportedly prevalent in the tropical and subtropical regions of Africa and Asia. To determine the Fasciola sp. of Assam (India) origin based on rDNA molecular data, ribosomal ITS2 region was sequenced (EF027103) and analysed. NCBI databases were used for sequence homology analysis and the phylogenetic trees were constructed based upon the ITS2 using MEGA and a Bayesian analysis of the combined data. The latter approach allowed us to include both primary sequence and RNA molecular morphometrics and revealed a close relationship with isolates of F. gigantica from China, Indonesia and Japan, the isolate from China with significant bootstrap values being the closest. ITS2 sequence motifs allowed an accurate in silico distinction of liver flukes. The data indicate that ITS2 motifs (≤ 50 bp in size) can be considered promising tool for trematode species identification. Using the novel approach of molecular morphometrics that is based on ITS2 secondary structure homologies, phylogenetic relationships of the various isolates of fasciolid species have been discussed.

PCR-based molecular characterization and insilico analysis of food-borne trematode parasites Paragonimus westermani, Fasciolopsis buski and Fasciola gigantica from Northeast India using ITS2 rDNA.

Food-borne fluke infections/trematodiases are emerging as a major public health problem worldwide with over 40 million people affected and over 10% of world population at risk of infection. The major concentration of these infections is in Southeast Asian and Western Pacific Regions, where the epidemiological factors (including the prevalent socio-cultural food habits) are conducive for transmission of these infections. The preponderance of these infections is usually in food deficit poor communities that lack access to proper sanitary infrastructure. While targeting health for all, especially the poor rural tribal communities, it is imperative to take these infections into account. Bayesian analysis phylogeny of food-borne trematode parasites under study showed that they are closely related phylogenetic groups. To focus the control strategies at the target populations, the aim of the present study was to establish molecular methods for accurate discrimination between common food-borne trematodes parasites Paragonimus (lung fluke), Fasciolopsis (giant intestinal fluke) and Fasciola (liver fluke), the infections of which commonly prevail in NE India. In the first step, we amplified and sequenced the second internal transcribed spacer (ITS2) region of ribosomal DNA, utilizing nucleotide differences between the multiple sequence alignments of the parasites under study. Based upon the differences in nucleotide sequences of conserved regions, we designed species-specific primers that can unequivocally discriminate one species from another. ITS2 sequence motifs allowed an accurate in-silico distinction of the trematodes. The data indicate that ITS2 motifs (≤ 50 bp in size) can be considered promising tool for trematode species identification. Using molecular morphometrics that is based on ITS2 secondary structure homologies, phylogenetic relationships with various isolates of several trematode species have been discussed. The present results suggest that the ITS2 specific primers can be used for epidemiological investigations of the prevalence of trematodiasis.

Molecular characterization of Gastrodiscoides hominis (Platyhelminthes: Trematoda: Digenea) inferred from ITS rDNA sequence analysis.

Gastrodiscoides hominis (Digenea: Paramphistomata: Gastrodiscidae) is an amphistomid intestinal fluke of pigs causing gastrodiscoidiosis. With the use of molecular tools assisting the conventional diagnostic procedures, we aimed at finding out molecular characterization of G. hominis using PCR amplifications of rDNA ITS (1, 2) sequences. The sequences obtained (GenBank accession numbers EF027096, EF027097, EF027098, EU887294, and EU887295) were compared with available sequences of other digenean parasites, particularly those having a zoonotic potential in the northeastern region of India. The BLAST search revealed a close similarity with members of the family Paramphistomidae, showing maximum similarity with the amphistome, Homalogaster paloniae (subfamily Paramphistominae). Based on various tree construction methods, phylogeny of G. hominis is discussed.

Morphological and molecular identification of the metacestode parasitizing the liver of rodent hosts in bamboo growing areas of mizoram, northeast India.

In Mizoram (Northeast India), rodent outbreaks are known to occur periodically with the onset of bamboo flowering causing a tremendous destruction to food grains and as per the folk belief, often resulting in famine. In an exploratory survey of rodent pests in bamboo growing atreas for their helminth parasite spectrum, metacestodes of tapeworms were frequently encountered infecting the liver lobes and body cavity of the host. The morphological criteria were found to be closely consistent with the metacestode of Taenia species. In molecular characterization of the parasite, the ribosomal DNA (ITS1, ITS2) and mitochondrial COI were amplified and sequenced. Based upon both morphological data and molecular analysis using bioinformatic tools, the metacestode is identified as confirmed to be representing Cysticercus fasciolaris. The adult form of which (Taenia taeniaeformis) commonly occurs in felid and canid mammalian hosts.

Reconstructing the Phylogenetic Relationships of the Cyclophyllidean Cestodes: A Case Study Using ITS2 rDNA and Sequence-Structure Alignment

Different authors have subscribed to varied opinions on the phylogenetic relationships and systematic position of cyclophyllidean cestodes owing to high degree of non-significant morphological variations among these taxa. Molecular phylogenetic analysis based on ITS2 rDNA of 16 representatives spanning 6 different families (Mesocestoididae, Davaineidae, Anoplocephalidae, Taeniidae, Dipylidiidae and Hymenolepididae) of the Order Cyclophyllidea and one out group from the family Diphyllobothriidae of the Order Pseudophyllidea revealed the order Order Cyclophyllidea to be a monophyletic clade. The results were further validated by bayesian analysis, primary sequence-structure alignment and subsequent molecular morphometrics analysis. A consistent support for all the major nodes was seen across all the phylogenetic trees. Interestingly, the genus Mesocestoides, in which the genital pores are ventral in position, a feature of the Order Pseudophyllidea, was accommodated within Cyclophyllidea and served as a sister clade close to the families Taeniidae, Anoplocephalidae, Hymenolepididae and Dipylidiidae.

Crustacean-borne infections with microphallid metacercariae (Digenea: Microphallidae) from focal areas in Meghalaya, north-east India.

During a survey of edible Crustacea for recovery of infective stages (metacercariae) of potential helminthozoonoses of trematode origin in north-east India, the crab species Barytelphusa lugubris mansoniana, collected from suspected foci of lungfluke infection in Meghalaya and Assam, was found to harbour metacercarial cysts that were different from the earlier reported infection, in which the lungfluke Paragonimus was confirmed to be implicated. Using morphological criteria, this metacercaria was identified as Microphallus indicus Mukherjee & Ghosh, 1967 of the trematode family Microphallidae. The present study extends the previous work by providing molecular characterization of this parasite using ribosomal internal transcribed spacer regions (rDNA ITS1 and ITS2) and the partial large ribosomal subunit DNA, lsr. These target regions were amplified by polymerase chain reaction (PCR) using trematode universal primers and sequenced. In BLAST analysis the query sequences were found close to members of Microphallidae and closest to the genus Microphallus.