Nonisotopic single-strand conformation polymorphism analysis of sequence variability in ribosomal DNA expansion segments within the genusTrichinella (Nematoda: Adenophorea)

Trichinella pseudospiralis in a wolverine (Gulo gulo) from the Canadian North

Species of Trichinella are a globally distributed assemblage of nematodes, often with distinct host ranges, which include people, domestic, and wild animals. Trichinella spp. are important in northern Canada, where dietary habits of people and methods of meat preparation (drying, smoking, fermenting as well as raw) increase the risk posed by these foodborne zoonotic parasites. Outbreaks in the arctic and subarctic regions of Canada and the United States are generally attributed to T. nativa (T2) or the T6 genotype, when genetic characterization is performed. We report the discovery of Trichinella pseudospiralis (T4), a non-encapsulated species, in a wolverine (Gulo gulo) from the Northwest Territories of Canada. This parasite has been previously reported elsewhere from both mammals and carnivorous birds, but our findings represent new host and geographic records for T. pseudospiralis. Multiplex PCR and sequencing of fragments of Cytochrome Oxidase Subunit I (COI) and D3 rDNA confirmed the identification. Phylogenetically, Canadian isolates linked with each other and others derived from Palearctic or Neotropical regions, but not elsewhere in the Nearctic (continental USA). We suggest that migratory birds might have played a role in the dispersal of this pathogen 1000's of km to northwestern Canada. Wolverines are not typically consumed by humans, and thus should not pose a direct food safety risk for trichinellosis. However, the current finding suggests that they may serve as an indicator of a broader distribution for T. pseudospiralis. Along with infection risk already recognized for T. nativa and Trichinella T6, our observations emphasize the need for further studies using molecular diagnostics and alternative methods to clarify if this is a solitary case, or if T. pseudospiralis and other freeze susceptible species of Trichinella (such as T. spiralis) circulate more broadly in wildlife in Canada, and elsewhere.

Mitochondrial genomes of Trichinella species and genotypes – a basis for diagnosis, and systematic and epidemiological explorations

In the present study we sequenced or re-sequenced, assembled and annotated 15 mitochondrial genomes representing the 12 currently recognised taxa of Trichinella using a deep sequencing-coupled approach. We then defined and compared the gene order in individual mitochondrial genomes (14 to 17.7 kb), evaluated genetic differences among species/genotypes and re-assessed the relationships among these taxa using the mitochondrial nucleic acid or amino acid sequence data sets. In addition, a rich source of mitochondrial genetic markers was defined that could be used in future systematic, epidemiological and population genetic studies of Trichinella. The sequencing-bioinformatic approach employed herein should be applicable to a wide range of eukaryotic parasites.

New pieces of the Trichinella puzzle

Contrary to our understanding of just a few decades ago, the genus Trichinella now consists of a complex assemblage of no less than nine different species and three additional genotypes whose taxonomic status remains in flux. New data and methodologies have allowed advancements in detection and differentiation at the population level which in turn have demonstrably advanced epidemiological, immunological and genetic investigations. In like manner, molecular and genetic studies have permitted us to hypothesise biohistorical events leading to the worldwide dissemination of this genus, and to begin crystalising the evolution of Trichinella on a macro scale. The identification of species in countries and continents otherwise considered Trichinella-free has raised questions regarding host adaptation and associations, and advanced important findings on the biogeographical histories of its members. Using past reviews as a backdrop, we have ventured to present an up-to-date assessment of the taxonomy, phylogenetic relationships and epidemiology of the genus Trichinella with additional insights on host species, survival strategies in nature and the shortcomings of our current understanding of the epidemiology of the genus. In addition, we have begun compiling information available to date on genomics, proteomics, transcriptomics and population studies of consequence in the hope we can build on this in years to come.

Detection of Trichinella spiralis DNA in mouse faeces during the early stage of infection

Trichinella spiralis is an etiological agent of trichinellosis, a parasitic disease present worldwide, affecting both animals and humans. The infection starts from the intestinal stage which usually lasts a few weeks and develops into the muscle phase when larvae enter the muscle cells and create a nurse cell-larva-complex. In animals, the infection is asymptomatic even if a high number of larvae is ingested. The aim of this work was to develop a sensitive test to monitor the early phase of trichinellosis in laboratory animals. T. spiralis DNA presence was assayed in faeces of mice during the first 21 days of experimental infection. The target gene fragment of the mitochondrial ATP6 synthase F0 subunit was amplified by PCR from faecal samples of mice infected with 50, 250 or 500 larvae per mouse (lpm). Trichinella DNA was detected in 45% (116) of the examined faecal samples from days 1 to 21 post infection (p.i.). The time of appearance of the parasite DNA in the faeces and the percentage of PCR positive results were dose dependent. In collective samples consisting of faeces from 3 mice average 80%, 83% and 90% of PCR positive results were obtained for 50, 250 and 500 lpm doses, respectively, throughout 21 days of the observation period. In individual mice faeces DNA was detected on days 2-19 and 9-18 p.i. for 250 lpm and 50 lpm doses, respectively. For both infective doses the highest probability of DNA detection was on day 11 p.i. Since the developed test is simple and non-invasive, it can be useful for monitoring the intestinal phase of Trichinella sp. infection in laboratory animals.

Cryptosporidium--biotechnological advances in the detection, diagnosis and analysis of genetic variation

Cryptosporidiosis is predominantly a gastrointestinal disease of humans and other animals, caused by various species of protozoan parasites representing the genus Cryptosporidium. This disease, transmitted mainly via the faecal-oral route (in water or food), is of major socioeconomic importance worldwide. The diagnosis and genetic characterization of the different species and population variants (usually recognised as "genotypes" or "subgenotypes") of Cryptosporidium is central to the prevention, surveillance and control of cryptosporidiosis, particularly given that there is presently no broadly applicable treatment regimen for this disease. Although traditional phenotypic techniques have had major limitations in the specific diagnosis of cryptosporidiosis, there have been major advances in the development of molecular analytical and diagnostic tools. This article provides a concise account of Cryptosporidium and cryptosporidiosis, and focuses mainly on recent advances in nucleic acid-based approaches for the diagnosis of cryptosporidiosis and analysis of genetic variation within and among species of Cryptosporidium. These advances represent a significant step toward an improved understanding of the epidemiology as well as the prevention and control of cryptosporidiosis.

Single-strand conformation polymorphism (SSCP) for the analysis of genetic variation

The accurate analysis of genetic variation has major implications in many areas of biomedical research, including the identification of infectious agents (such as parasites), the diagnosis of infections, and the detection of unknown or known disease-causing mutations. Mutation scanning methods, including PCR-coupled single-strand conformation polymorphism (SSCP), have significant advantages over many other nucleic acid techniques for the accurate analysis of allelic and mutational sequence variation. The present protocol describes the SSCP method of analysis, including all steps from the small-scale isolation of genomic DNA and PCR amplification of target sequences, through to the gel-based separation of amplicons and scanning for mutations by SSCP (either by the analysis of radiolabeled amplicons in mutation detection enhancement (MDE) gels or by non-isotopic SSCP using precast GMA gels). The subsequent sequence analysis of polymorphic bands isolated from gels is also detailed. The SSCP protocol can readily detect point mutations for amplicon sizes of up to 450-500 bp, and usually takes 1-2 days to carry out. This user-friendly, low-cost, potentially high-throughput platform has demonstrated the utility to study a wide range of pathogens and diseases, and has the potential to be applied to any gene of any organism.

The specific identification of anisakid larvae from fishes from the Yellow Sea, China, using mutation scanning-coupled sequence analysis of nuclear ribosomal DNA

Nematodes of the family Anisakidae parasitize fish, mammals, birds and reptiles, with the larval stages of some species causing severe clinical disease in humans. Therefore, the accurate identification of anisakid nematodes is a key component of disease surveillance and control. An epidemiological survey of 123 fishes comprising eight different species from the Yellow Sea in China revealed that more than 25% of fish were infected with the larvae of anisakids, 200 third-stage larvae (L3s) were collected from fish and then subjected to morphological and molecular study. Larvae identified as Anisakis type I (n=197) and Hysterothylacium sp. (n=3), based on morphological criteria were characterized genetically by mutation scanning, followed by targeted sequencing of the first and second internal transcribed spacers of nuclear ribosomal DNA. Comparison of the sequences obtained from a subset of 27 specimens with those available in public gene databases showed that all samples identified morphologically as Anisakis type I (n=197) were Anisakis pegreffii, whereas those identified as Hysterothylacium sp. (n=3) were Hysterothylacium aduncum. The approach used herein was an effective means of matching incompletely identifiable larval nematodes with identifiable reference sequences, and provides a basis for exploring the composition of populations of anisakid larvae in fish as well as their ecology, particularly their life cycles and transmission patterns.

Classification of Mycoplasma synoviae strains using single-strand conformation polymorphism and high-resolution melting-curve analysis of the vlhA gene single-copy region

Mycoplasma synoviae is an economically important pathogen of poultry worldwide, causing respiratory infection and synovitis in chickens and turkeys. Identification of M. synoviae isolates is of critical importance, particularly in countries in which poultry flocks are vaccinated with the live attenuated M. synoviae strain MS-H. Using oligonucleotide primers complementary to the single-copy conserved 5' end of the variable lipoprotein and haemagglutinin gene (vlhA), amplicons of approximately 400 bp were generated from 35 different M. synoviae strains/isolates from chickens and subjected to mutation scanning analysis. Analysis of the amplicons by single-strand conformation polymorphism (SSCP) revealed 10 distinct profiles (A-J). Sequencing of the amplicons representing these profiles revealed that each profile related to a unique sequence, some differing from each other by only one base-pair substitution. Comparative high-resolution melting (HRM) curve analysis of the amplicons using SYTO 9 green fluorescent dye also displayed profiles which were concordant with the same 10 SSCP profiles (A-J) and their sequences. For both mutation detection methods, the Australian M. synoviae strains represented one of the A, B, C or D profiles, while the USA strains represented one of the E, F, G, H, I or J profiles. The results presented in this study show that the PCR-based SSCP or HRM curve analyses of vlhA provide high-resolution mutation detection tools for the detection and identification of M. synoviae strains. In particular, the HRM curve analysis is a rapid and effective technique which can be performed in a single test tube in less than 2 h.

Multilocus mutation scanning for the analysis of genetic variation within Malassezia (Basidiomycota: Malasseziales)

Members of the genus Malassezia are budding yeasts, characterized by a thick cell wall. Recently, these yeasts have received attention as emerging pathogens. They are common commensals on the skin of animals and can become pathogenic under the influence of various predisposing factors. Central to studying their taxonomy, systematics, and ecology and to diagnosis is the accurate identification of species or operational taxonomic units. To overcome the limitations of current phenotypic and biochemical methods of identification, a PCR-coupled SSCP approach, utilizing sequence variation (0.4-33.5%) in short regions (approximately 250-270 bp) of the first internal transcribed spacer (ITS-1) of nuclear ribosomal DNA and the chitin synthase-2 gene (chs-2), was assessed for the identification and differentiation of different species/genotypes of Malassezia, characterized previously by DNA sequencing. Genomic DNA samples (n = 30) from Malassezia isolates cultured from canine skin scrapings were assessed by SSCP analysis of the two different genetic loci, and unequivocal delineation between genotypes and species was achieved. This SSCP approach is considered to provide a practical tool for the rapid and reliable genetic characterization of Malassezia genotypes/species from dogs and for investigating their population genetics and ecology. It will also provide a powerful tool for studies of Malassezia isolates from other animal species.

Nucleotide alterations in the D3 domain of the large subunit of ribosomal DNA among 21 species of equine strongyle

The expansion segments or divergent (D) domains in the large subunit (LSU) of the ribosomal DNA have been suggested as genetic markers for taxonomic and/or phylogenetic studies of parasites. In the present study, we assessed the degree of sequence variation in the D3 domain and flanking core regions of the LSU for 21 species of equine strongyles (Strongylida: Strongylidae) and determined which positions in the secondary structure of the LSU were associated with the nucleotide alterations. No intraspecific sequence variation was detected in 17 species, for which multiple individual worms were available. Mutations in sequence among species were detected at 19 nucleotide positions, most of which were located in the D3 domain. Fifteen alterations were transitions, three were transversions and one represented a site of multiple mutations. In relation to the secondary structure element of D3, 26% of these mutations were located in unpaired regions (i.e., end of loops, or in bulges of helices) and thus did not appear to alter the pairing arrangement in the helices of the secondary structure. Many of the other mutations represented partial or complete compensatory base pair changes. The magnitude of interspecific nucleotide variation in the D3 domain (0-4%) was considerably less than that recorded for some other nematode groups (enoplids and thelastomatoids), indicating that this region alone is of limited value for taxonomic and phylogenetic studies for strongyles of equids but is interesting in relation to the evolution of ribosomal DNA.

Systematics and epidemiology of trichinella

In this review, we describe the current knowledge on the systematics, ecology and epidemiology of Trichinella and trichinellosis, and the impact of recent research discoveries on the understanding of this zoonosis. The epidemiology of this zoonosis has experienced important changes over the past two decades, especially with regard to the importance of the sylvatic cycle and the sylvatic species. Outbreaks of trichinellosis due to Trichinella spiralis from domestic swine, while still frequent, increasingly are caused by other Trichinella spp. infecting hosts such as horses, dogs, wild boars, bears and walruses. The latter revelations have occurred as a result of a series of discoveries on the systematics of Trichinella spp., facilitated by new molecular tools. As a consequence, the genus is now composed of two clades, an encapsulated group (five species and three genotypes) and a non-encapsulated one (three species). This has sparked renewed investigations on the host range of these parasites and their epidemiological features. Most dramatic, perhaps, is the recognition that reptiles may also serve as hosts for certain species. This new knowledge base, in addition to having an important relevance for food safety policies and protection measures, is raising important questions on the phylogeny of Trichinella spp., the ecological characteristics of the species and their geographic histories. Answers to these questions may have great value for the understanding of the evolutionary biology for other parasitic helminths, and may increase the value of this genus as models for research on parasitism in general.

Differentiation of Entamoeba histolytica from Entamoeba dispar by PCR-coupled nonisotopic SSCP analysis

Entamoeba histolytica is a pathogenic protozoan parasite, which causes amoebic colitis, dysentery and liver abscesses in humans. Since the cyst and small trophozoite stages of this parasite are indistinguishable by light microscopy from Entamoeba dispar (which is nonpathogenic), specific diagnosis is compromised. To overcome this limitation, a PCR-coupled SSCP approach, utilising a sequence difference of 4.6% in a short region ( approximately 173-174 bp) of the small subunit of nuclear ribosomal DNA, was evaluated for the differentiation of the two species of Entamoeba. Including a range of well-defined control DNA samples (n = 67) to evaluate the specificity of the PCR, 45 DNA samples representing E. histolytica and E. dispar from human faecal samples were tested by SSCP, and unequivocal delineation between the species was achieved. This SSCP approach should provide a practical tool for the specific diagnosis of E. histolytica in humans and for investigating its epidemiology.

Experimental infections of pigs and mice with selected genotypes of Ascaris

Extending a previous investigation of the genotypic variability within Ascaris from humans and pigs, experimental infections of mice and pigs with selected genotypes of Ascaris were performed in the present study to explore possible host affiliation. Initial findings indicate that there is a significant difference in the ability of Ascaris eggs of genotype G1 (derived from human) and G3 (derived from pig) to infect and establish as larvae in mice and as adults in pigs, supporting the difference in the frequencies of the genotypes reported previously in natural Ascaris populations in pigs and humans in areas in China endemic for ascariasis.

Recent advances on the taxonomy, systematics and epidemiology of Trichinella

Since Owen first described Trichinella as a human pathogen in 1835, the number of organisms comprising this genus has grown dramatically. Where it was once thought to be a monospecific group, this genus is now comprised of eight species and three additional genotypic variants that have yet to be taxonomically defined. Along with the growth in the genus and description of the parasites has come a concomitant increase in our understanding of the epidemiology and geographical distribution of these organisms. Recent expansion of the non-encapsulated group to include three species biologically defined by their unique host ranges encompassing mammals, birds and reptiles, has raised substantial questions as to the term, 'Trichinella-free' as it applies to geographical localities. A true appreciation of the adaptability of this genus to host and environmental selection factors, as well as its dissemination to the far reaches of the world can best be appreciated by reviewing what we know and what we hope to know about this ancient and elusive parasite. The review herein consolidates our current understanding of the taxonomy, epidemiology, and phylogeny of the genus Trichinella, and identifies areas where data are lacking and our knowledge requires additional clarification.

Molecular characterization of Thelastomatoidea (Nematoda: Oxyurida) from cockroaches in Australia

A molecular approach was used to genetically characterize 5 species (Aoruroides queenslandensis, Blattophila sphaerolaima, Cordonicola gibsoni, Desmicola ornata and Leidynemella fusiformis) belonging to the superfamily Thelastomatoidea (Nematoda: Oxyurida), a group of pinworms that parasitizes terrestrial arthropods. The D3 domain of the large subunit of nuclear ribosomal RNA (LSU) was sequenced for individual specimens, and the analysis of the sequence data allowed the genetic relationships of the 5 species to be studied. The sequence variation in the D3 domain within individual species (0-1.8%) was significantly less than the differences among species (4.3-12.4%). Phylogenetic analyses, using maximum parsimony, maximum likelihood, and neighbour-joining, tree-building methods, established relationships among the 5 species of Thelastomatoidea and Oxyuris equi (a species of the order Oxyurida). The molecular approach employed provides the prospect for developing DNA tools for the specific identification of the Thelastomatoidea, irrespective of developmental stage and sex, as a basis for systematic, ecological and/or population genetic investigations of members within this superfamily.

Trichinella britovi etiological agent of sylvatic trichinellosis in the Republic of Guinea (West Africa) and a re-evaluation of geographical distribution for encapsulated species in Africa

In West Africa, Trichinella infection was documented in humans and animals from Senegal in the 1960s, and the biological characters of one isolate showed a lower infectivity to domestic pigs and rodents when compared with that of a Trichinella spiralis pig isolate from Europe. To identify the Trichinella species present in West Africa, a survey was conducted in a total of 160 wild animals in the Republic of Guinea. Three Viverridae, one true civet (Viverra civetta) and two African palm civets (Nandinia binotata) from the Fouta Djallon Massif, Pilimini Subprefecture, were found positive by artificial digestion of muscle samples. Trichinella larvae from these three viverrids were identified as Trichinella britovi and no difference was detected in three examined sequences from these African isolates and the reference strain of T. britovi from Europe, indicating common ancestry, an historically continuous geographic distribution, and recent isolation for African and European populations. The detection of T. britovi in West Africa modifies our knowledge about the distribution of encapsulated species of Trichinella in Africa. Thus, Trichinella nelsoni is now considered to have a distribution limited to the Eastern part of the Afrotropical region from Kenya to South Africa. This provides a plausible explanation for the presence of Trichinella T8 in Namibia and South Africa, and further suggests that T. britovi could be the Trichinella species circulating among wild animals of Northern Africa.

Molecular tools--advances, opportunities and prospects

Modern molecular technologies are having a substantial impact in many fundamental and applied areas of parasitology. In particular, polymerase chain reaction (PCR)-coupled approaches have found broad applicability because their sensitivity permits the enzymatic amplification of gene fragments from minute quantities of nucleic acids from tiny amounts of parasite material. Also, high-resolution electrophoretic and genomic methods are finding increased utility. This paper briefly discusses some developments and applications of DNA methods to parasites and highlights their usefulness or potential for those of veterinary importance. Selected examples of applications with implications in fundamental (systematics, population genetics, epidemiology and ecology) and applied (diagnosis, prevention and control) areas are presented. The focus is mainly on tools for the accurate identification of parasitic nematodes and protozoa of socio-economic importance, the diagnosis of infections and the detection of genetic variability using PCR-coupled mutation scanning technology.

Rapid differentiation of Fusarium oxysporum isolates using PCR-SSCP with the combination of pH-variable electrophoretic medium and low temperature

Differentiation of Fusarium oxysporum is significantly important for unraveling the pathogenetic mechanism of Fusaria wilts. In this study, isolates of F. oxysporum were screened from the soils in the rhizosphere of watermelon plant by Komada medium and differentiated by SSCP approach with the combination of pH-variable electrophoretic medium (Tris-MES-EDTA (TME), pH 6.1) and low temperature (9 degrees C). We found that TME was a good electrophoretic medium and its pH value was variable over the course of electrophoresis in our apparatus. The pH-variable electrophoretic medium made more contribution for the better differentiation of F. oxysporum isolates than low temperature. The combination of TME pH 6.1 and low temperature showed an improved effect on resolution of ssDNAs. Leaving partial nondenatured dsDNA for SSCP was advantageous for differentiation of F. oxysporum isolates. The SSCP patterns of F. oxysporum isolates proved to be highly reproducible. Sequencing data confirmed that this SSCP method could detect one single base change within the 550 bp PCR fragment from the ribosomal internal transcribed spacer region of F. oxysporum.

Analysis of genetic variability within Thelazia callipaeda (Nematoda: Thelazioidea) from Europe and Asia by sequencing and mutation scanning of the mitochondrial cytochrome c oxidase subunit 1 gene

This study investigated genetic variability within the 'eyeworm'Thelazia callipaeda (Nematoda: Thelazioidea) from Europe and Asia by polymerase chain reaction (PCR)-coupled sequencing and mutation scanning of the mitochondrial cytochrome c oxidase subunit 1 gene (cox 1). Eight different sequence variants of cox 1 (haplotypes) were determined for the 50 individual adult specimens of T. callipaeda (from dogs, foxes or cats from Italy, Germany and the Netherlands and from dogs from China and Korea). Nucleotide variation (0.3--2%) was detected at 23 of 649 positions in the cox 1. Six of these positions were invariable among all 37 individuals from Europe and among the 13 individuals from Asia (irrespective of host origin) but differed (five G<-->A and one C<-->T changes) between Europe and Asia. PCR-based single-strand conformation polymorphism (SSCP) analysis of the most variable portion (v-cox 1) of the cox 1 was validated (for a subset of samples) as a tool to rapidly screen for genetic (haplotypic) variability. The results for the SSCP analysis and sequencing were concordant, indicating that the mutation scanning approach provides a useful tool for investigating the population genetics and molecular ecology of T. callipaeda.

Definition of genetic markers in nuclear ribosomal DNA for a neglected parasite of primates, Ternidens deminutus (Nematoda: Strongylida) – diagnostic and epidemiological implications

Ternidens deminutus (Strongylida) is a parasitic nematode infecting non-human and human primates in parts of Africa, Asia and the Pacific islands. The present study genetically characterized T. deminutus and defined genetic markers in nuclear ribosomal DNA (rDNA) as a basis for developing molecular-diagnostic tools. The sequences of the second internal transcribed spacer (ITS-2) of rDNA were determined for adult specimens of T. deminutus (Nematoda: Strongylida: Oesophagostominae) from the Olive baboon and the Mona monkey. The length and G+C content of the ITS-2 sequences was 216 bp and approximately 43%, respectively. While there was no sequence variation among individual T. deminutus specimens from the baboon, 6 (2.8%) nucleotide differences were detected in the ITS-2 between the parasite from baboon and that of the Mona monkey, which is similar to the difference (3.2%) between 2 other species of Oesophagostominae (Oesophagostomum bifurcum and O. stephanostomum) from non-human primates, suggesting significant population variation or the existence of cryptic (i.e. hidden) species within T. deminutus . Pairwise comparisons of the ITS-2 sequences of the 2 operational taxonomic units of T. deminutus with previously published ITS-2 sequences for selected members of the subfamilies Oesophagostominae and Chabertiinae indicated that species from primates (including those representing the subgenera Conoweberia and Ihleia) are closely related, in accordance with previous morphological studies. The sequence differences (27-48.3%) in the ITS-2 between the 2 taxonomic units of T. deminutus and hookworms (superfamily Ancylostomatoidea) enabled their identification and delineation by polymerase chain reaction (PCR)-based mutation scanning. The genetic markers in the ITS-2 provide a foundation for improved, PCR-based diagnosis of T. deminutus infections and for investigating the life-cycle, transmission patterns and ecology of this parasite.