Molecular biology techniques in parasite ecology

A review of in vitro attempts to develop the axenic culture of Treponema pallidum and genomics-based suggestions to achieve this elusive goal

To date, the axenic culture of Treponema pallidum remains a challenge in the field of microbiology despite countless attempts. Here, we conducted a comprehensive bibliographic analysis using several databases and search engines, namely Pubmed, Google scholar, Google, Web of Science and Scopus. Numerous unsuccessful empiric studies have been conducted and evaluated using as criteria dark-field microscopic observation of motile spiral shaped cells in the culture and virulence of the culture through rabbit infectivity. All of these studies failed to induce rabbit infectivity, even when deemed positive after microscopic observation leading to the misnomer of avirulent T. pallidum. In fact, this criterion was improperly chosen because not all spiral shaped cells are T. pallidum. However, these studies led to the formulation of culture media particularly favourable to the growth of several species of Treponema, including Oral Microbiology and Immunology, Zürich medium (OMIZ), Oral Treponeme Enrichment Broth (OTEB) and T-Raoult, thus allowing the increase in the number of cultivable strains of Treponema. The predicted metabolic capacities of T. pallidum show limited metabolism, also exhibited by other non-cultured and pathogenic Treponema species, in contrast to cultured Treponema species. The advent of next generation sequencing represents a turning point in this field, as the knowledge inferred from the genome can finally lead to the axenic culture of T. pallidum.

The complete mitochondrial genome of the beef cattle hookworm Bunostomum phlebotomum (Nematoda: Bunostominae)

The bovine hookworm Bunostomum phlebotomum (Nematoda: Bunostominae) is a blood-feeding nematode with important socioeconomic impact in the cattle breeding industry. In the present study, the complete mitochondrial genome sequence of a representative individual of B. phlebotomum from beef cattle in Southwest China was determined using the next generation sequencing technology. The genome was 13,799 bp in size and encoded 12 protein-coding genes, 22 tRNA genes and two rRNA genes. The phylogeny revealed that although B. phlebotomum from Chinese beef cattle and yaks were more closely related to each other than to that from Australian cows, these three bovine-originated B. phlebotomum grouped together and formed paraphyletic relationships with Bunostomum trigonocephalum (goat/sheep hookworm) and Necator americanus (human hookworm), supporting their sister-species relationships within Bunostominae. The cumulative mitochondrial DNA data provides a better understanding of phylogenetic relationships of this species in cattle.

The mitochondrial genome of the dog hookworm Ancylostoma caninum (Nematoda, Ancylostomatidae) from Southwest China

The dog hookworm Ancylostoma caninum (Nematoda, Ancylostomatidae) is a blood-feeding intestinal parasitic nematode and can cause ancylostomiasis in humans. In this study, the complete mitochondrial genome of this anthropozoonotic hookworm was sequenced through Illumina deep sequencing technology. The whole genome was 13,721 bp in length and encoded 36 genes including 12 protein-coding genes, 22 transfer RNAs, and 2 ribosomal RNAs. Phylogeny revealed that A. caninum grouped with species from Ancylostomatinae and separated from species of Bunostominae in the family Ancylostomatidae. Amongst the subfamily Ancylostomatinae, three dog-originated A. caninum, regardless of isolate origins, clustered together and were more closely related to the cat hookworm A. tubaeforme and the human hookworm A. duodenale than to the dog/cat hookworm A. ceylanicum and the sea lion hookworm Uncinaria sanguinis. Taken together, the cumulative mitochondrial DNA data provides insights into phylogenetic studies among Ancylostomatidae nematodes.

The Complete Mitochondrial Genome and Expression Profile of Mitochondrial Protein-Coding Genes in the Bisexual and Parthenogenetic Haemaphysalis longicornis

The tick Haemaphysalis longicornis is widely distributed in eastern Asia, New Zealand and Australia, and is well-known as a vector of multiple zoonotic pathogens. This species exhibits two reproductive strategies, bisexual and obligate parthenogenetic reproduction. Hence, in the current study, the complete mitochondrial genomes of the bisexual and parthenogenetic populations were assembled and analyzed, and the expression of the mitochondrial protein-coding genes was evaluated and compared between the two reproductive populations. The results indicated that the length of the mitochondrial genomes of the two reproductive populations is 14,694 and 14,693 bp in the bisexual and parthenogenetic populations, respectively. The AT content in the mitochondrial genome of the bisexual and obligate parthenogenetic population reached 77.22 and 77.34%, respectively. The phylogenetic tree was constructed combining 13 protein-coding genes, which showed that the genetic distance between the bisexual and parthenogenetic populations was less than that between the subspecies. The expression of the mitochondrial protein-coding genes was quantitatively analyzed at different feeding status for the bisexual and parthenogenetic populations, and the results showed significant differences in the expression patterns of these genes, suggesting that they might trigger specific energy utilization mechanisms due to their different reproductive strategies and environmental pressures.

Helminth parasites of howler and spider monkeys in Mexico: Insights into molecular diagnostic methods and their importance for zoonotic diseases and host conservation

The majority of the parasite assessments of New World primates have been conducted through the identification of the eggs found in faeces, though many species of parasites have very similar eggs, leaving uncertainty in the diagnosis. Here, we present the results of a parasite survey of the three species of primates distributed in Mexico, combining non-invasive sampling with molecular techniques via DNA extraction of the eggs found in the faeces. Mitochondrial and ribosomal DNA were employed for species identification and Bayesian phylogenetic analysis. Nine parasite taxa were found in the three primate species: the nematodes Trypanoxyuris minutus, T. multilabiatus, T. pigrae, T. atelis, T. atelophora, Strongyloides sp., unidentified Ancylostomatid, unidentified Ascarid, and the trematode Controrchis biliophilus. We were able to extract and amplify DNA from the eggs of the five species of Trypanoxyuris reported for Mexican primates, two morphologically different trematode eggs, and Strongyloides sp. Phylogenetic analysis confirmed that the two types of trematode eggs belong to Controrchis biliophilus, a member of the family Dicrocoeliidae. For Strongyloides sp., phylogenetic analysis and genetic divergence showed an association between our samples and S. fuelleborni; however, no species could be established due to the lack of more DNA sequences from Strongyloides sp. occurring in Neotropical primates. The use of molecular and phylogenetic methods could help to overcome the limitations imposed by traditional non-invasive sampling because eggs are primarily obtained from the faeces; however, its utility relies on the extant genetic library and the contributions that expand such library. The information presented here could serve as a basis for future research on primate parasitology, allowing a more accurate parasite diagnosis and a more precise evaluation of their zoonotic potential.

Dermacentor everestianus Hirst, 1926 (Acari: Ixodidae): phylogenetic status inferred from molecular characteristics

Dermacentor everestianus Hirst, 1926, is only reported in Northwestern China and Nepal. Few researches about this species have been involved, especially for molecular characteristics. The taxonomy studies of D.everestianus are mainly based on morphological features, and its taxonomic status is an ongoing controversy. To clarify the molecular characteristics and phylogenetic status of D.everestianus and other related species, the sequences of mitochondrial 16S ribosomal DNA (rDNA) and cox1 fragments were analyzed in the present study. Analysis of 16S rDNA and cox1 sequences showed 99.3-100% identity within D.everestianus individuals, with the genetic divergence among them was 0-0.0086. The interspecific distance of 16S rDNA and cox1 between D.everestianus and some other Palaearctic species including D. silvarum, D. nuttalli, and D. marginatus was much smaller than that between D.everestianus and Nearctic Dermacentor ticks (D.albipictus, D.nitens, and D.variabilis). Such relationships of these ticks were also verified in the phylogenetic analysis. Two major clades were recovered within Dermacentor spp. with more than 90% bootstrap support in the phylogenetic trees. D.everestianus together with D.silvarum, D.nuttalli, and D.marginatus were included in the clade I (Eurasia lineage). Other analyzed tick species including D.variabilis, D.nitens, and D.albipictus formed clade II, which are distributed in Nearctic realm. These indicated that the genus Dermacentor was at least composed of two lineages. Thus, further researches including additionally molecular markers on all Dermacentor species globally should be taken to precisely resolve relationships within Dermacentor.

A review of molecular approaches for investigating patterns of coevolution in marine host-parasite relationships

Parasites and their relationships with hosts play a crucial role in the evolutionary pathways of every living organism. One method of investigating host-parasite systems is using a molecular approach. This is particularly important as analyses based solely on morphology or laboratory studies of parasites and their hosts do not take into account historical evolutionary interactions that can shape the distribution, abundance and population structure of parasites and their hosts. However, the predominant host-parasite coevolution literature has focused on terrestrial hosts and their parasites, and there still is a lack of studies in marine environments. Given that marine systems are generally more open than terrestrial ones, they provide fascinating opportunities for large-scale (as well as small-scale) geographic studies. Further, patterns and processes of genetic structuring and systematics are becoming more available across many different taxa (but especially fishes) in many marine systems, providing an excellent basis for examining whether parasites follow host population/species structure. In this chapter, we first highlight the factors and processes that challenge our ability to interpret evolutionary patterns of coevolution of hosts and their parasites in marine systems at different spatial, temporal and taxonomic scales. We then review the use of the most commonly utilized genetic markers in studying marine host-parasite systems. We give an overview and discuss which molecular methodologies resolve evolutionary relationships best and also discuss the applicability of new approaches, such as next-generation sequencing and studies utilizing functional markers to gain insights into more contemporary processes shaping host-parasite relationships.

Morphological, biological and molecular characteristics of bisexual and parthenogenetic Haemaphysalis longicornis

The reproductive mechanism of Haemaphysalis longicornis is quite different from many other animal species. In this article, several characteristics of parthenogenetic and bisexual populations of H. longicornis were analyzed, including some important micro-structures, synchronized life cycle feature and sequences of mitochondrial 16S rRNA gene. The results suggested even though many observations of the two populations were similar to each other, some important differences also existed. The genital apron of parthenogenetic females was wider than that of bisexual females. Parthenogenetic individuals (except engorged females) were significantly larger in weight than bisexual individuals (p<0.01; unfed nymph p<0.05); the difference of nymphal premoulting, female feeding and preoviposition, and egg incubation periods between the two populations were significant (p<0.01); hatch percentage of parthenogenesis was lower than that of bisexual population (69% and 73%, respectively); parthenogenetic individuals had a slightly longer development cycle than bisexual individuals (134 and 129 days, respectively). Hybridization attempts failed between them. Comparing to the two strains of bisexual H. longicornis, parthenogenetic strain of H. longicornis inserted two nucleotides of thymine, though the genetic distance of 16S rDNA between the bisexual and parthenogenetic populations was 0. In order to clarify the relationships of the two reproductive populations of H. longicornis, the sequences of 16S rDNA of four strains of two other species were also analyzed. The divergence between Hebei and Xinjiang strains of Rhipicephalus sanguineus was 0, and the sequences were totally identical between them. The divergence between the two subspecies of Hyalomma asiaticum was 0.01. The results indicated that the relationship between bisexual and parthenogenetic H. longicornis was certainly closer than that between subspecies, but farther than that between the same reproductive populations of conspecies.

The genomic Echinococcus microsatellite EmsB sequences: from a molecular marker to the epidemiological tool

In the field of molecular and epidemiological parasitology, characterization of fast evolving genetic markers appears as an important challenge to consider the diversity and genetic structure of parasites. The study of respective populations can help us to understand their adaptive strategies to survive and perpetuate the species within different host populations, all trying to resist infection. In the past, the relative monomorphic features of Echinococcus multilocularis, the causative agent of alveolar echinococcosis and a severe human parasitic disease, did not stimulate studies dealing with the genetic variability of Echinococcus species or respective populations. A recently developed, characterized and validated original multilocus microsatellite, named EmsB, tandemly repeated in the genome, offered an additional opportunity for this line of investigation. We have compiled in this review new insights brought by this molecular tracker on the transmission activity of Echinococcus among different hosts and at different geographical scales.

Multi-locus microsatellite analysis supports the hypothesis of an autochthonous focus of Echinococcus multilocularis in northern Italy

Echinococcus multilocularis is characterised by a wide geographical distribution, encompassing three continents (North America, Asia and Europe) yet very low genetic variability is documented. Recently, this parasite has been detected in red foxes (Vulpes vulpes) circulating in an Alpine region of Italy, close to Austria. This finding raised the question as to whether an autochthonous cycle exists in Italy or whether the infected foxes originated from the neighbouring regions of Austria. Studies have shown that multi-locus microsatellite analysis can identify genomic regions carrying mutations that result in a local adaptation. We used a tandem repeated multi-locus microsatellite (EmsB) to evaluate the genetic differences amongst adult worms of E. multilocularis collected in Italy, worms from neighbouring Austria and from other European and extra-European countries. Fluorescent PCR was performed on a panel of E. multilocularis samples to assess intra-specific polymorphism. The analysis revealed four closed genotypes for Italian samples of E. multilocularis which were unique compared with the other 25 genotypes from Europe and the five genotypes from Alaska. An analysis in the Alpine watershed, comparing Italian adult worms with those from neighbouring areas in Austria, showed a unique cluster for Italian samples. This result supports the hypothesis of the presence of an autochthonous cycle of E. multilocularis in Italy. EmsB can be useful for 'tracking' the source of infection of this zoonotic parasite and developing appropriate measures for preventing or reducing the risk of human alveolar echinococcosis.

A quantitative real-time PCR assay for Ehrlichia ruminantium using pCS20

Heartwater is a tick borne disease that affects ruminants and wild animals in Africa south of the Sahara. It is caused by Ehrlichia ruminantium and transmitted by the tick Amblyomma hebraeum. The protocols currently used to detect heartwater take several days to complete. Here, we describe the development of a pCS20 quantitative real-time PCR TaqMan probe assay to detect E. ruminantium in livestock blood and ticks from the field. The assay is based on the conserved pCS20 gene region of E. ruminantium that contains two overlapping genes, rnc and ctaG [Collins, N.E., Liebenberg, J., De Villiers, E.P., Brayton, K.A., Louw, E., Pretorius, A., Faber, F.E., Van Heerden, H., Josemans, A., Van Kleef, M., Steyn, H.C., Van Strijp, M.F., Zweygarth, E., Jongejan, F., Maillard, J.C., Berthier, D., Botha, M., Joubert, F., Corton, C.H., Thomson, N.R., Allsopp, M.T., Allsopp, B.A., 2005. The genome of the heartwater agent Ehrlichia ruminantium contains multiple tandem repeats of actively variable copy number. PNAS 102, 838-843]. The pCS20 quantitative real-time PCR TaqMan probe was compared to the currently used pCS20 PCR and PCR/32P-probe test with regards to sensitivity, specificity and the ability to detect DNA in field samples and in blood from experimentally infected sheep. This investigation showed that the pCS20 quantitative real-time PCR TaqMan probe was the most sensitive assay detecting seven copies of DNA/mul of cell culture. All three assays, however, cross react with Ehrlichia canis and Ehrlichia chaffeensis. The pCS20 real-time PCR detected significantly more positive field samples. Both the PCR and pCS20 real-time PCR could only detect E. ruminantium parasites in the blood of experimentally infected sheep during the febrile reaction. The PCR/32P-probe assay, however, detected the parasite DNA 1 day before and during the febrile reaction. Thus, because this new quantitative pCS20 real-time PCR TaqMan probe assay was the most sensitive and can be performed within 2h it is an effective assay for epidemiological surveillance and monitoring of infected animals.

EmsB, a tandem repeated multi-loci microsatellite, new tool to investigate the genetic diversity of Echinococcus multilocularis

In order to explore the genetic diversity within Echinococcus multilocularis (E. multilocularis), the cestode responsible for the alveolar echinococcosis (AE) in humans, a microsatellite, composed of (CA) and (GA) repeats and designated EmsB, was isolated and characterized in view of its nature and potential field application. PCR-amplification with specific primers exhibited a high degree of size polymorphism between E. multilocularis and Echinococcus granulosus sheep (G1) and camel (G6) strains. Fluorescent-PCR was subsequently performed on a panel of E. multilocularis isolates to assess intra-species polymorphism level. EmsB provided a multi-peak profile, characterized by tandemly repeated microsatellite sequences in the E. multilocularis genome. This "repetition of repeats" feature provided to EmsB a high discriminatory power in that eight clusters, supported by bootstrap p-values larger than 95%, could be defined among the tested E. multilocularis samples. We were able to differentiate not only the Alaskan from the European samples, but also to detect different European isolate clusters. In total, 25 genotypes were defined within 37 E. multilocularis samples. Despite its complexity, this tandem repeated multi-loci microsatellite possesses the three important features for a molecular marker, i.e. sensitivity, repetitiveness and discriminatory power. It will permit assessing the genetic polymorphism of E. multilocularis and to investigate its spatial distribution in detail.

Real-time PCR investigation of parasite ecology: in situ determination of oyster parasite Perkinsus marinus transmission dynamics in lower Chesapeake Bay

Perkinsus marinus is a severe pathogen of the oyster Crassostrea virginica on the East Coast of the United States. Transmission dynamics of this parasite were investigated in situ for 2 consecutive years (May through October) at 2 lower Chesapeake Bay sites. Compared to previous studies where seasonal infection patterns in oysters were measured, this study also provided parasite water column abundance data measured using real-time PCR. As previously observed, salinity and temperature modulated parasite transmission dynamics. Using regression analysis, parasite prevalence, oyster mortalities and parasite water column abundance were significantly positively related to salinity. Perkinsus marinus weighted prevalence in wild oysters and parasite water column abundance both were significantly related to temperature, but the responses lagged 1 month behind temperature. Parasite water column abundance was the highest during August (up to 1,200 cells/l) and was significantly related to P. marinus weighted prevalence in wild oysters, and to wild oyster mortality suggesting that parasites are released in the environment via both moribund and live hosts (i.e. through feces). Incidence was not significantly related to parasite water column abundance, which seems to indicate the absence of a linear relationship or that infection acquisition is controlled by a more complex set of parameters.

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.

Genetic variation in Taenia solium

Neurocysticercosis is a major zoonotic larval cestode infection that has a worldwide distribution and is of significant public health importance. Knowledge of the genetic structure of Taenia solium can be applied to the epidemiology and transmission of this disease, since genetic variants may differ in infectivity and pathogenicity. Molecular epidemiological approaches can also enable detailed studies of transmission. On a global scale, mitochondrial markers have differentiated between T. solium isolates from Asia and isolates from Africa/Latin America. Intraspecific variation in T. solium has been detected to some extent, using RAPD markers to differentiate between T. solium populations from different regions within Mexico. Markers currently available for T. solium have not been used to analyse genetic variation at the community or local level. The development of highly polymorphic markers such as microsatellites in T. solium can provide the means to examine genetic heterogeneity of tapeworm infection at the household, community and regional level. Preliminary studies suggest it is possible to analyse population genetic variation in communities using a range of polymorphic markers.

Molecular epidemiology: A multidisciplinary approach to understanding parasitic zoonoses

Sound application of molecular epidemiological principles requires working knowledge of both molecular biological and epidemiological methods. Molecular tools have become an increasingly important part of studying the epidemiology of infectious agents. Molecular tools have allowed the aetiological agent within a population to be diagnosed with a greater degree of efficiency and accuracy than conventional diagnostic tools. They have increased the understanding of the pathogenicity, virulence, and host-parasite relationships of the aetiological agent, provided information on the genetic structure and taxonomy of the parasite and allowed the zoonotic potential of previously unidentified agents to be determined. This review describes the concept of epidemiology and proper study design, describes the array of currently available molecular biological tools and provides examples of studies that have integrated both disciplines to successfully unravel zoonotic relationships that would otherwise be impossible utilising conventional diagnostic tools. The current limitations of applying these tools, including cautions that need to be addressed during their application are also discussed.

Nucleic acid amplification-based techniques for pathogen detection and identification

Nucleic acid amplification techniques have revolutionised diagnostic and research industries. Current technologies that allow the detection of amplification in real-time are fast becoming industry standards, particularly in a diagnostic context. In this review, we describe and explore the application of numerous real-time detection chemistries and amplification techniques for pathogen detection and identification, including the polymerase chain reaction, nucleic acid sequence-based amplification, strand displacement amplification and the ligase chain reaction. The emergence of newer technologies, such as lab-on-a-chip devices and photo-cleavable linkers, is also discussed.

Emerging technologies for the detection and genetic characterization of protozoan parasites

The development and adaptation of new technologies for the genetic characterization and identification of parasites continue to accelerate, providing an increasing number of research and analytical tools. We review emerging technologies that have applications in this area, including real-time PCR and microarrays, and discuss the fundamental principles of some of these technologies and how they are applied to characterize parasites. We give special consideration to the application of genetic data to biological questions, where selection of the most appropriate technique depends on the biological question posed by the investigator.

GEOGRAPHIC DISTRIBUTION OF THE MUSCLE-DWELLING NEMATODE PARELAPHOSTRONGYLUS ODOCOILEI IN NORTH AMERICA, USING MOLECULAR IDENTIFICATION OF FIRST-STAGE LARVAE

Molecular identification of dorsal-spined larvae (DSL) from fecal samples indicates that the protostrongylid parasite Parelaphostrongylus odocoilei occupies a broader geographic range in western North America than has been previously reported. We analyzed 2,124 fecal samples at 29 locations from thinhorn sheep (Ovis dalli dalli and O. d. stonei), bighorn sheep (Ovis canadensis canadensis and O. c. californiana), mountain goats (Oreamnos americanus), woodland caribou (Rangifer tarandus caribou), mule deer (Odocoileus hemionus hemionus), and black-tailed deer (O. h. columbianus). The DSL were recovered from populations of thinhorn sheep south, but not north, of the Arctic Circle, and they were not recovered from any of the bighorn sheep populations that we examined. In total, DSL were recovered from 20 locations in the United States and Canada (Alaska, Yukon Territory, Northwest Territories, British Columbia, Alberta, and California). The DSL were identified as P. odocoilei by comparing sequences of the second internal transcribed spacer (ITS2) region of ribosomal RNA among 9 protostrongylid species validated by adult comparative morphology. The ITS2 sequences were markedly different between Parelaphostrongylus and other protostrongylid genera. Smaller fixed differences served as diagnostic markers for the 3 species of Parelaphostrongylus. The ITS2 sequences (n = 60) of P. odocoilei were strongly conserved across its broad geographic range from California to Alaska. Polymorphism at 5 nucleotide positions was consistent with multiple copies of the ITS2 within individual specimens of P. odocoilei. This work combines extensive fecal surveys, comparative morphology, and molecular diagnostic techniques to describe comprehensively the host associations and geographic distribution of a parasitic helminth.