The molecular epidemiology of parasite infections: Tools and applications

Fish Health Unit, School of Veterinary and Biomedical Sciences, Murdoch University, Murdoch WA 6150, Australia.
Molecular and Biochemical Parasitology (Impact Factor: 1.79). 02/2012; 181(2):102-16. DOI: 10.1016/j.molbiopara.2011.10.006
Source: PubMed


Molecular epidemiology, broadly defined, is the application of molecular genetic techniques to the dynamics of disease in a population. In this review, we briefly describe molecular and analytical tools available for molecular epidemiological studies and then provide an overview of how they can be applied to better understand parasitic disease. A range of new molecular tools have been developed in recent years, allowing for the direct examination of parasites from clinical or environmental samples, and providing access to relatively cheap, rapid, high throughput molecular assays. At the same time, new analytical approaches, in particular those derived from coalescent theory, have been developed to provide more robust estimates of evolutionary processes and demographic parameters from multilocus, genotypic data. To date, the primary application of molecular epidemiology has been to provide specific and sensitive identification of parasites and to resolve taxonomic issues, particularly at the species level and below. Population genetic studies have also been used to determine the extent of genetic diversity among populations of parasites and the degree to which this diversity is associated with different host cycles or epidemiologically important phenotypes. Many of these studies have also shed new light on transmission cycles of parasites, particularly the extent to which zoonotic transmission occurs, and on the prevalence and importance of mixed infections with different parasite species or intraspecific variants (polyparasitism). A major challenge, and one which is now being addressed by an increasing number of studies, is to find and utilize genetic markers for complex traits of epidemiological significance, such as drug resistance, zoonotic potential and virulence.

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Available from: Alan Lymbery, Feb 24, 2014
    • "Increasing evidence from experimental and human studies has shown that polymerase chain reaction (PCR) and PCRcoupled methods improve the diagnosis of Schistosoma infection as well as the identification of Schistosoma species (Gobert et al. 2005; Sandoval et al. 2006; Kato-Hayashi et al. 2010; Lv et al. 2015). Although these techniques are useful and effective, the electrophoresis or sequencing analysis can be, in some cases, quite time consuming and expensive , rendering such tools impracticable for large-scale molecular epidemiological studies (Lymbery and Thompson 2012). "
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    ABSTRACT: Schistosomiasis, caused by blood flukes belonging to several species of the genus Schistosoma, is a serious and widespread parasitic disease. Accurate and rapid differentiation of these etiological agents of animal and human schistosomiasis to species level can be difficult. We report a real-time PCR assay coupled with a high-resolution melt (HRM) assay targeting a portion of the nuclear 18S rDNA to detect, identify, and distinguish between four major blood fluke species (Schistosoma japonicum, Schistosoma mansoni, Schistosoma haematobium, and Schistosoma mekongi). Using this system, the Schistosoma spp. was accurately identified and could also be distinguished from all other trematode species with which they were compared. As little as 10(-5) ng genomic DNA from a Schistosoma sp. could be detected. This process is inexpensive, easy, and can be completed within 3 h. Examination of 21 representative Schistosoma samples from 15 geographical localities in seven endemic countries validated the value of the HRM detection assay and proved its reliability. The melting curves were characterized by peaks of 83.65 °C for S. japonicum and S. mekongi, 85.65 °C for S. mansoni, and 85.85 °C for S. haematobium. The present study developed a real-time PCR coupled with HRM analysis assay for detection and differential identification of S. mansoni, S. haematobium, S. japonicum, and S. mekongi. This method is rapid, sensitive, and inexpensive. It has important implications for epidemiological studies of Schistosoma.
    Parasitology Research 08/2015; 114(11). DOI:10.1007/s00436-015-4660-3 · 2.10 Impact Factor
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    • "The simplified morphology entailed in the adoption of a parasitic way of life is one of the main reasons for the difficulties associated with carrying out exhaustive systematic appraisals of many parasite groups. This research field has benefitted significantly from the development of molecular tools which allow a more comprehensive evaluation of parasite diversity (McManus and Bowles, 1996; Lymbery and Thompson, 2012). Avian haemosporidians (Phylum Apicomplexa, Order Haemosporida ) are among those parasite groups whose study has greatly improved with the advent of molecular techniques. "
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    ABSTRACT: Despite the ecological significance and appeal of birds of prey, many aspects of their biology remain poorly known, including the diversity of parasites infecting them in the wild. We studied the diversity and prevalence of haemosporidian parasites infecting the two species of kites of the genus Milvus, aiming to describe the phylogenetic relationships among them and with other haemosporidians, as well as their distribution in the two host species. Black kites, Milvus migrans, harboured a more diverse community of parasites, including three haplotypes of each of the three genera Plasmodium, Haemoproteus and Leucocytozoon, which also occurred at a higher prevalence than in red kites. In red kites, Milvus milvus. only three haplotypes of Leucocytozoon were found. Kite parasites were not closely related to one another nor were they kite-specific: their diversity spanned various branches of the haemosporidian phylogenetic tree, and their closest relatives were found in other species (including various avian orders), although some Leucocytozoon and Haemoproteus haplotypes clustered within apparently raptor-specific parasite clades. Remarkably, Plasmodium spp. and Haemoproteus spp. infected adult black kites only, an observation which supports the hypothesis that they are transmitted at the African wintering grounds, while Leucocytozoon spp. is putatively transmitted only in Europe. Intercontinental migration of the black kite might explain the divergence of parasite diversity between these two sister species.
    International journal for parasitology 01/2013; 43(5). DOI:10.1016/j.ijpara.2012.12.007 · 3.87 Impact Factor
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    • "Regardless of taxonomy, these deep divergences need to be taken into careful consideration in experimental studies with P. vinckei. More broadly, the correct identification of independently evolving lineages (species) is of critical epidemiological relevance, as it can enable interbreeding populations to be identified, which is essential for the management of disease [30]. "
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    ABSTRACT: Background Over the last 6 decades, rodent Plasmodium species have become key model systems for understanding the basic biology of malaria parasites. Cell and molecular parasitology have made much progress in identifying genes underpinning interactions between malaria parasites, hosts, and vectors. However, little attention has been paid to the evolutionary genetics of parasites, which provides context for identifying potential therapeutic targets and for understanding the selective forces shaping parasites in natural populations. Additionally, understanding the relationships between species, subspecies, and strains, is necessary to maximize the utility of rodent malaria parasites as medically important infectious disease models, and for investigating the evolution of host-parasite interactions. Results Here, we collected multi-locus sequence data from 58 rodent malaria genotypes distributed throughout 13 subspecies belonging to P. berghei, P. chabaudi, P. vinckei, and P. yoelii. We employ multi-locus methods to infer the subspecies phylogeny, and use population-genetic approaches to elucidate the selective patterns shaping the evolution of these organisms. Our results reveal a time-line for the evolution of rodent Plasmodium and suggest that all the subspecies are independently evolving lineages (i.e. species). We show that estimates of species-level polymorphism are inflated if subspecies are not explicitly recognized, and detect purifying selection at most loci. Conclusions Our work resolves previous inconsistencies in the phylogeny of rodent malaria parasites, provides estimates of important parameters that relate to the parasite’s natural history and provides a much-needed evolutionary context for understanding diverse biological aspects from the cross-reactivity of immune responses to parasite mating patterns.
    BMC Evolutionary Biology 11/2012; 12(1):219. DOI:10.1186/1471-2148-12-219 · 3.37 Impact Factor
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