PCR-linked Restriction Fragment Length Research Articles

Evidence for mitochondrial pseudogenes (numts) as a source of contamination in the phylogeny of human whipworms.

Trichuris trichiura and T. suis are whipworms of humans and pigs, respectively, but it has recently been suggested that humans may be infected with multiple genotypes or species of Trichuris and cross-infection with Trichuris of pig origin has also been reported. In addition, the species status of Trichuris in non-human primates is unsettled and it is unknown how many whipworm species we share with other primates. Herein, we inferred the phylogeny of Trichuris collected from human, baboon and pig based on nuclear (18S and beta-tubulin) and mitochondrial (cox1) genes and evaluated the use of three PCR linked restriction fragment length polymorphism (PCR-RFLP) to identify worms. We found that all baboon worms clustered with human worms and that all these primate worms are different from T. suis. In general, there was an agreement between the phylogeny established based on the nuclear and mtDNA genes. However, we found evidence for non-targeted cox1 gene amplification for a subset of the human worms and suggest the presence of mitochondrial pseudogenes (numts) of pig cox1 gene in the human Trichuris genome. In conclusion, phylogenetic characterization of human whipworm based on the cox1 gene alone may be problematic without suitable preceded measures to avoid the numts amplification.

Phylogenetic relationships among Toxocara spp. and Toxascaris sp. from different regions of the world

Toxocara and Toxascaris are parasitic nematodes that infect canids and felids although species of the genus Toxocara also infect humans. This work aimed to establish the phylogenetic and phylogeographic relationship between specimens of T. canis, T. cati, T. malaysiensis and Toxascaris leonina and to evaluate the degree of host specificity. In total, 437 samples (adults and pools of eggs) were collected from canids and felids from eight countries. Parasites were identified by morphology, PCR linked Restriction Fragment Length Polymorphism (PCR-RFLP) and partial sequencing of the mitochondrial gene cox1. Phylogenetic trees were constructed and genetic distance among isolates was estimated. Based on the molecular characterization all worms were identified in agreement with their respective hosts with the exception of three samples; two from cats and one from dogs identified as T. canis and T. cati, respectively. There was no clear geographical clustering of the samples despite this study including parasites from three continents. This is the first study, to our knowledge, to use molecular methods to identify T. canis in cats and T. cati in dogs with host specificity being the most common finding. Our developed PCR-RFLP method was found to be a facile and reliable method for identifying Toxocara species.

The use of genetically marked infection cohorts to study changes in establishment rates during the time course of a repeated Ascaridia galli infection in chickens

This study investigated the changes in establishment rates during the time course of a 6week trickle infection of chickens with Ascaridia galli at two different dose levels, using a molecular marker. To differentiate early and late infection, two different egg cohorts (haplotype a and haplotype b, genetically identified using PCR-linked restriction fragment length polymorphism on the cox1 gene of the mitochondrial DNA) were used. Cohort-specific egg batches were produced by harvesting eggs from the uteri of female worms of the specific cohort. Fifty-six 8week old Lohmann Brown Lite chickens were divided into seven groups and the infectivity of the egg batches was compared between two groups of chickens (P=0.6). The remaining chickens were allocated to four infection regimes and one control group. Group ab100 was trickle infected for 3weeks with 100 eggs of haplotype a (twice weekly) followed by the same dose of eggs of haplotype b for another 3weeks. Group ba100 was treated similarly but in the opposite order (haplotype b preceding a). A similar infection regime was applied for groups ab25 and ba25 but with a lower inoculation dose (25 eggs). All of the birds in these five groups (four infected and one control) were euthanased 2weeks after the last inoculation. It was found that in the low-dose groups both the early and late infections established equally well, whereas in the high-dose groups the early infection was recovered in a significantly (P<0.001) higher proportion of chickens than the late infection, irrespective of genetic cohorts. Moreover, relatively higher proportions of the larvae from both the early and late infections were found in the posterior section of the small intestine. This result indicates the presence of dose-dependent resistance against reinfection and this resistance seems to act by reducing the establishment of late infection and by relocating the larvae from early infection.

Characterization of Toxascaris leonina and Tococara canis from cougar (Panthera leo) and common wolf (Canis lupus) by nuclear ribosomal DNA sequences of internal transcribed spacerss

In the present study, samples representing Toxascaris leonina and Tococara canis were collected from cougar (Panthera leo) and common wolf (Canis lupus ) from Harbin Northern Forest Zoo in Heilongjiang Province, China, and they were characterized by nuclear ribosomal DNA (rDNA) sequences of internal transcribed spacers (ITS). The ITS rDNA was amplified by polymerase chain reaction (PCR), then sequenced and compared with that of other members of ascaridida published in GenBankTM. Furthermore, the phylogenetic relationship was reconstructed using Maximum Parsimony and Bayesian analyses. For the T. leonina of cougar, the length of the ITS sequences was 698 bp (the ITS1 and ITS2 were 419 and 279 bp, respectively) and the corresponding sequences of T. canis from common wolf were 808 bp (the ITS1 and ITS2 were 485 and 323 bp, respectively). The identity of ITS sequences of T. leonina and T. canis from cougar and common wolf was 76%. The ITS sequences were analyzed by PCR-linked restriction fragment length polymorphism (PCR-RFLP) which was established for the unequivocal delineation of the T. leonina and T. canis with which were easily confused morphologically, using restriction endonuclease EcoRV and SalI. The valuable tool established in this study makes the molecular identification, the ecology and genetic structure studies of these two ascaridoids possible. Key words: Toxascaris leonina, Tococara canis, ribosomal DNA (rDNA), internal transcribed spacers (ITS), PCR-linked restriction fragment length polymorphism (PCR-RFLP)

Zoonotic Ascariasis, United Kingdom

Zoonotic Ascariasis, United Kingdom

Discrimination between Haemaphysalis longicornis and H. qinghaiensis based on the partial 16S rDNA and the second internal transcribed spacer (ITS-2)

In the present study, two hard tick species, Haemaphysalis longicornis and H. qinghaiensis from North-western China were characterized genetically by the second internal transcribed spacer (ITS-2) of nuclear ribosomal DNA and partial 16S rDNA. Based on a fragment within the hypervariable region of 16S rDNA with the length of approximately 453 bp, the phylogenetic trees were constructed by Neighbor-Joining and Maximum-parsimony methods. The results indicated that the phylogenetic status of H. qinghaiensis was distant from that of H. longicornis and closer to H. flava. Furthermore, the ITS-2 rDNA was amplified by PCR and sequenced from individual ticks. The length of ITS-2 is 1,606 bp for H. longicornis and 1,162 bp for H. qinghaiensis. Although sequence variation between the immature stages of H. longicornis was 0.1-0.4%, nucleotide differences between the tested species ranged 2.1-23.2%, indicating that ITS-2 rDNA sequences are genetic markers for the differentiation of the two hard ticks in China. Hence, a PCR-linked restriction fragment length polymorphism (RFLP) approach was developed for their unequivocal differentiation based on ITS-2 rDNA, which provides the foundation for further studies on ticks in China and has implications for studying the population genetic structure of the ticks and for identification and differentiation of closely related ticks.

Characterization of Bunostomum trigonocephalum and Bunostomum phlebotomum from sheep and cattle by internal transcribed spacers of nuclear ribosomal DNA

In the present study, samples representing Bunostomum trigonocephalum and Bunostomum phlebotomum from sheep and cattle in Heilongjiang Province, China, were characterized and grouped genetically by the first (ITS-1) and second (ITS-2) internal transcribed spacers (ITS) of nuclear ribosomal DNA (rDNA). The rDNA region including the ITS-1, 5.8S, ITS-2, and flanking 18S and 28S rDNA sequences was amplified by polymerase chain reaction (PCR), then sequenced and compared with that of other members of the hookworms available in GenBank™, and phylogenetic relationships between them were reconstructed using the Maximum-Parsimony method. The ITS-1, 5.8S, and ITS-2 sequences of the sheep hookworm were 381, 153, and 231 bp in length, respectively, and the corresponding sequences of the cattle hookworm were 392, 153, and 240 bp in length. The identity of ITS sequences of B. trigonocephalum and B. phlebotomum from sheep and cattle was 87.4%. A PCR-linked restriction fragment length polymorphism (PCR-RFLP) assay using restriction endonuclease Nde I was established for the unequivocal differentiation of the two hookworm species. Phylogenetic analyses based on the ITS sequences revealed that B. trigonocephalum and B. phlebotomum were closely related, but they represent two different species.

Molecular characterization of hard ticks from Romania by sequences of the internal transcribed spacers of ribosomal DNA

In the present study, four hard tick species and one soft tick species, namely, Dermacentor marginatus, Haemaphysalis punctata, Haemaphysalis parva, Ixodes ricinus, and Dermanyssus gallinae, from south-western Romania were characterized genetically by the first (ITS-1) and second (ITS-2) internal transcribed spacers (ITS) of nuclear ribosomal DNA (rDNA), using a hard tick, Haemaphysalis longicornis, from China for comparative purposes. The ITS rDNA was amplified by polymerase chain reaction (PCR) and sequenced from individual ticks. The lengths of the ITS-1 sequences were 238–1819 bp, and the lengths of ITS-2 were 137–1695 bp, respectively, for all ticks sequenced. While sequence variation within a hard tick species was 0–1.5%, nucleotide differences between hard tick species ranged 2–25.2%, indicating that ITS rDNA sequences provide genetic markers for the differentiation of hard ticks from Romania. Hence, a PCR-linked restriction fragment length polymorphism approach was developed for their unequivocal differentiation based on ITS-1 rDNA. This is the first characterization of ticks from Romania using a genetic approach, which provides the foundation for further studies on ticks in Romania and has implications for studying the population genetic structure of the Romanian ticks and for identification and differentiation of closely related ticks.

Molecular characterization of hard and soft ticks from Romania by sequences of the internal transcribed spacers of ribosomal DNA

In the present study, four hard tick species and one soft tick species, namely, Dermacentor marginatus, Haemaphysalis punctata, Haemaphysalis parva, Ixodes ricinus, and Dermanyssus gallinae, from south-western Romania were characterized genetically by the first (ITS-1) and second (ITS-2) internal transcribed spacers (ITS) of nuclear ribosomal DNA (rDNA), using a hard tick, Haemaphysalis longicornis, from China for comparative purposes. The ITS rDNA was amplified by polymerase chain reaction (PCR) and sequenced from individual ticks. The lengths of the ITS-1 sequences were 238-1819 bp, and the lengths of ITS-2 were 137-1695 bp, respectively, for all ticks sequenced. While sequence variation within a hard tick species was 0-1.5%, nucleotide differences between hard tick species ranged 2-25.2%, indicating that ITS rDNA sequences provide genetic markers for the differentiation of hard ticks from Romania. Hence, a PCR-linked restriction fragment length polymorphism approach was developed for their unequivocal differentiation based on ITS-1 rDNA. This is the first characterization of ticks from Romania using a genetic approach, which provides the foundation for further studies on ticks in Romania and has implications for studying the population genetic structure of the Romanian ticks and for identification and differentiation of closely related ticks.

Characterization of the second internal transcribed spacer of ribosomal DNA of Calicophoron daubneyi from various hosts and locations in southern Italy

Isolates of the rumen fluke Calicophoron daubneyi (Digenea: Paramphistomidae) from various hosts and three locations in southern Italy were characterized genetically. The second internal transcribed spacer (ITS-2) of ribosomal DNA (rDNA) plus flanking 5.8S and 28S sequence (ITS-2+) was amplified from individual rumen flukes by PCR. PCR-linked restriction fragment length polymorphism (PCR-RFLP) analysis was performed using four different restriction endonucleases, and PCR products were sequenced. The PCR analyses from all the C. daubneyi specimens produced identical fragments, and the PCR-RFLP analyses did not show, with respect to any of the four restriction endonucleases, any differences between the C. daubneyi specimens. The sequence analyses of the ITS-2+ from each of the C. daubneyi specimens showed them all to be 428 bp, and composed of the entire ITS-2 sequence (282 bp) plus the two partial flanking conserved sequences, 5.8S (99 bp) and 28S (47 bp). No intra-specific variation was observed in the nucleotide composition of the ITS-2+ (homology = 100%). There was, however, an observable inter-specific variation between the ITS-2+ of C. daubneyi and the ITS-2+ of both Calicophoron calicophorum (homology = 97.2 %) and Calicophoron microbothrioides (homology = 97.4 %) , both previously deposited in the GenBank™. The finding of the present study shows that, as has already demonstrated for other parasitic helminths, ITS-2 can serve as an effective genetic marker for the molecular identification of paramphistomes, and as a useful tool for developing molecular epidemiological techniques for the study of C. daubneyi transmission patterns and prevalence in definitive and intermediate hosts.

Differential diagnosis of Taenia saginata and Taenia saginata asiatica taeniasis through PCR

New multiplex-PCR and PCR-linked restriction fragment length polymorphism protocols, derived from Taenia saginata HDP2 DNA sequence (AccN#AJ133740), have been designed that allow the simultaneous and specific identification of T. saginata and Taenia saginata asiatica. Proglottids expelled from 20 different Spanish taeniasis patients, previously diagnosed as T. saginata by both morphological identification and multiplex HDP2-PCR, were also examined by the newly developed PCR protocols, and the original diagnosis of T. saginata infection was confirmed. All of the 20 T. saginata samples were negative in the T. saginata asiatica–specific PCR. Three authentic T. saginata asiatica samples were unambiguously identified as such in the T. saginata asiatica PCR. These new protocols have immediate potential for the specific, sensitive, and rapid identification of T. saginata asiatica and may assist in taxonomic studies.

Characterisation of Fasciola species from Mainland China by ITS-2 ribosomal DNA sequence

Isolates of Fasciola (Platyhelminthes: Trematoda: Digenea) from different host species and geographical locations in Mainland China were characterised genetically. The second internal transcribed spacer (ITS-2) of nuclear ribosomal DNA (rDNA) was amplified from individual trematodes by polymerase chain reaction (PCR), and the representative amplicons were cloned and sequenced. The length of the ITS-2 sequences was 361–362 bp for all Chinese Fasciola specimens sequenced. While there was no variation in length or composition of the ITS-2 sequences among multiple specimens from France, Sichuan and Guangxi, sequence difference of 1.7% (6/362) was detected between specimens from France and Sichuan, and those from Guangxi. Based on ITS-2 sequence data, it was concluded that the Fasciola from Sichuan represented Fasciola hepatica, the one from Guangxi represented Fasciola gigantica and the one from sheep from Heilongjiang may represent an “intermediate genotype”, as its ITS-2 sequences were unique in that two different ITS-2 sequences exist in the rDNA array within a single Fasciola worm. One of the sequences is identical to that of F. hepatica, and the other is almost identical to that of F. gigantica in that nucleotides at five of the six polymorphic positions represent F. gigantica. This microheterogeneity is possibly due to sequence polymorphism among copies of the ITS-2 array within the same worm. Based on the sequence differences, a PCR-linked restriction fragment length polymorphism (PCR-RFLP) assay was established for the unequivocal delineation of the Fasciola spp. from Mainland China using restriction endonuclease Hsp92II or RcaI. This assay should provide a valuable tool for the molecular identification and for studying the ecology and population genetic structures of Fasciola spp. from Mainland China and elsewhere.

Single-strand conformation polymorphism-based analysis reveals genetic variation within Spirometra erinacei (Cestoda: Pseudophyllidea) from Australia

This study examined genetic variability within Spirometra erinacei (Cestoda: Pseudophyllidea) from different host species and geographical origins in Australia using a polymerase chain reaction (PCR)-based mutation detection approach, followed by DNA sequencing. Part of the cytochrome c oxidase subunit 1 gene (p cox 1) was amplified by PCR, scanned for sequence variation by single-strand conformation polymorphism (SSCP), and representative samples from different host species were selected for DNA sequencing. While no variation in SSCP profiles was detected among S. erinacei samples from dog, fox, cat, tiger snake and python, they differed in profile from 5 specimens from the green tree frog (Litoria caerulea). This was supported by sequence data which demonstrated that p cox 1 sequences of samples from the latter host species differed at 8 of 393 (2%) nucleotide positions from those from the non-amphibian host. Using a nucleotide difference in the p cox 1 sequence, a PCR-linked restriction fragment length polymorphism (RFLP) could be employed to unequivocally delineate between samples from non-amphibian and amphibian hosts. These findings demonstrate the existence of at least two genotypes within S. erinacei, which may have important implications for studying the epidemiology, ecology and systematics of this cestode.

Electrophoretic detection of population variation within Contracaecum ogmorhini (Nematoda: Ascaridoidea: Anisakidae).

This study examined genetic variation among specimens of Contracaecum ogmorhini from different otariid hosts and geographical origins using a polymerase chain reaction (PCR)-based mutation detection approach. The first (ITS-1) and second (ITS-2) internal transcribed spacers (ITS) of ribosomal DNA (rDNA) were amplified individually by PCR, scanned for sequence variation by single-strand conformation polymorphism (SSCP), and samples displaying variable SSCP profiles were subjected to cycle sequencing. While C. ogmorhini individuals from Arctocephalus pusillus pusillus (CoAPP) from South Africa and those from Arctocephalus pusillus doriferus (CoAPD) from Australia had very similar SSCP profiles for both ITS-1 and ITS-2, individuals of C. ogmorhini from Zalophus californianus (CoZC) from Pacific Canada could be unequivocally distinguished based on their profiles. In accordance with SSCP results, both CoAPP and CoAPD had identical ITS consensus sequences, whereas CoZC differed in sequence from both CoAPP and CoAPD populations by 0.2% (one base in the ITS-1) and 0.7% (two bases in the ITS-2). Based on the nucleotide difference in the ITS-2 sequence, a PCR-linked restriction fragment length polymorphism (RFLP) could be employed to distinguish individuals representing CoZC from those of both CoAPP and CoAPD. The findings suggest that C. ogmorhini may represent a complex of at least two species.

Elucidation of Schistosoma japonicum population dynamics in pigs using PCR-based identification of individuals representing distinct cohorts

The study reported here investigated the interactions of successive infections and acquired resistance of pigs to challenge infections of Schistosoma japonicum. Two morphologically indistinguishable geographical isolates from China (from Anhui and Zhejiang provinces) were used for the infections. The worms of the two isolates were distinguishable by PCR-linked restriction fragment length polymorphism analysis of the nicotinamide adenine dinucleotide phosphate dehydrogenase I gene of the mitochondrial genome. Thirty-two pigs divided into seven groups were used in the experiment. Two groups received a single infection by either the Anhui or the Zhejiang isolate. In Challenge Groups 1, 4, 6, 8 and 12, a primary infection of the Zhejiang isolate was followed by a challenge infection with the Anhui isolate at week 1, 4, 6, 8 or 12 after the primary infection. In this way it was possible to determine whether worms recovered by perfusion originated from the primary or the challenge infection. Only the challenge infection at week 1 resulted in a higher worm burden when compared with a single primary infection with the Zhejiang isolate. The results showed that challenge worms were able to establish, and that the proportion of worms originating from challenge infection increased at the later challenge infections, however without an increase in the total number of worms. In addition, mixed pairs of the two isolates were found in all challenge-infected groups. The results indicate that pigs are able to mount a partial resistance against re-infection with S. japonicum by 4 weeks after a primary infection, but that worms of the challenge infections eventually replace the primary infection. The finding of mixed pairs of the two isolates indicates that worms of S. japonicum are either polygamous or able to wait in solitude for up to 12 weeks for a partner.

Intraspecific and interspecific variation in the second internal transcribed spacer sequence for Metastrongylus (Nematoda: Metastrongyloidea) detected by high resolution PCR-linked restriction fragment length polymorphism

Metastrongylus species are important parasites of free-range pigs and wild boar, but little is known about the genetic make-up of natural populations. This study was undertaken to examine sequence variation in internal transcribed spacer 2 of ribosomal DNA within and among three species of Metastrongylus using PCR-linked restriction fragment length polymorphism analysis. In contrast to many other species of bursate nematodes, significant intraspecific variation was detected in restriction fragment length polymorphism profiles among individual worms. In spite of this, it was possible to identify the three species by their distinctive restriction profiles. The findings suggest that the internal transcribed spacer 2 region should be useful for analysing population variation within Metastrongylus species.

Characterisation of Ascaris from human and pighosts by nuclear ribosomal DNA sequences

The sequences of the nuclear ribosomal DNA region spanning the first internaltranscribed spacer, the 5.8S rRNA gene and the second internal transcribed spacer weredetermined for Ascaris samples from pigs and humans from different geographicalregions. The sequences of the 5.8S gene and the second internal transcribed spacer were the samefor all samples examined, whereas all Ascaris samples from humans had six (1.3%)nucleotide differences in the first internal transcribed spacer compared with those from pigs.These differences provided some support for the existence of separate species of Ascarisor population variation within this genus. Using a nucleotide difference within a site for therestriction enzyme HaeIII, a PCR-linked restriction fragment length polymorphismmethod was established which allowed the delineation of the Ascaris samples from pigsand humans used herein. Exploiting the sequence differences in the first internal transcribedspacer, a PCR-based single-strand conformation polymorphism method was established for futureanalysis of the genetic structure of pig and human Ascaris populations in sympatric andallopatric zones. © 1999 Australian Society for Parasitology. Published by Elsevier Science Ltd.All rights reserved. Ascaris; Internal transcribed spacer; Ribosomal DNA; Polymerasechain reaction; Restriction fragment length polymorphism; Single-strand conformationpolymorphism

Use of the ITS rDNA for elucidation of some life-cycles of Mesometridae (Trematoda, Digenea)

Identification of larval stages is crucial for elucidating the life-cycles of various Digenea. However, in many digenean species, the larvae lack distinctive morphological features and it is impossible to establish the affiliation between the larval and adult stages by using morphological criteria. Molecular methods, based on DNA sequencing or PCR–restriction fragment length polymorphism analysis, can offer a new tool for larval-stage identification. In this study, the sequences of internal transcribed spacer of the ribosomal DNA were used to identify the cercariae of three out of five species of the family Mesometridae ( Centroderma spinosissima, Elstia stossichianum and Wardula capitellata). The three species differ from one another by number of repeats in the region of internal transcribed spacer 1. The phylogeny of Mesometridae was inferred from their internal transcribed spacer ribosomal DNA sequences. The PCR-linked restriction fragment length polymorphism approach was developed for future life-cycle and ecological studies of this family.

Strongylus asini (Nematoda, Strongyloidea): Genetic relationships with other strongylus species determined by ribosomal DNA

Genomic DNA was isolated from adult Strongylus asini collected from zebra. The second ribosomal transcribed spacer (ITS-2) was amplified and sequenced using polymerase chain reaction (PCR) based techniques. The DNA sequence was compared with previously published data for 3 related Strongylus species. A PCR-linked restriction fragment length polymorphism method allowed the 4 species to be differentiated unequivocally. The ITS-2 sequence of S. asini was found to be more similar to those of S. edentatus (87.1%) and S. equinus (95.3%) than to that of S. vulgaris (73.9%). This result confirms that S. asini and S. vulgaris represent separate species and supports the retention of the 4 species within 1 genus.

Differences in a ribosomal DNA sequence of Strongylus species allows identification of single eggs

In the current study, molecular techniques were evaluated for the species identification of individual strongyle eggs. Adult worms of Strongylus edentatus, S. equinus and S. vulgaris were collected at necropsy from berses from Australia and the U.S.A. Genomic DNA was isolated and a ribosomal trameribed spacer (ITS-2) amplified and sequenced using polymerase chain reaction (PCR) techniques. The length of the ITS-2 sequence of S. edentatus, S. equinus and S. vulgaris ranged between 217 and 235 nucleotides. Extensive sequence analysis demonstrated a low degree (0 – 0.9%) of intraspecific variation in the ITS-2 for the Strongylus species examined, whereas the levels of interspecific differences (13–29%) were significantly greater. Interspecific differences in the ITS-2 sequences allowed unequivocal species identification of single worms and eggs using PCR-linked restriction fragment length polymorphism. These results demonstrate the potential of the ribosomal spacers as genetic markers for species identification of single strongyle eggs from horse faeces.