The molecular epidemiology of parasite infections: Tools and applications

Abstract

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 utilise genetic markers for complex traits of epidemiological significance, such as drug resistance, zoonotic potential and virulence.

Biology and Systematics of Echinococcus

“…As such, research on the horse and sheep strains of E. granulosus led to similar studies on Echinococcus of cattle, pig, camel and cervid origin with the description and characterization of several new strains/genotypes (Thompson and McManus, 2002;Thompson, 2008, Table 2). These studies not only confirmed the existence of a number of host-adapted life cycles in different parts of the world but also provided additional data on developmental differences between strains which may impact on control (Lymbery and Thompson, 2012;Thompson, 2001Thompson, , 2008Thompson and Lymbery, 1988;Thompson and McManus, 2002). These informal groupings were retained for many years but with the advent of molecular characterization they were shown to be genetically distinct (Thompson and McManus, 2001).…”

“…The term strain was introduced during the period of taxonomic uncertainty to refer to intraspecific variants of Echinococcus with defined phenotypic and subsequently genotypic characteristics (Lymbery and Thompson, 2012;Lymbery, 1990, 1996). The term strain has largely been replaced by genotype as this enabled a numerical system to be developed to refer to the different strains (Table 2).…”

“…What has been clear, however, from the earliest descriptions of the parasite is that the genus exhibits considerable variability at the species level in terms of host specificity, morphology, antigenicity, development rate, and cycles of transmission (Lymbery and Thompson, 2012;Thompson and Lymbery, 1988;McManus, 2001, 2002;Thompson, 2008). However, concerns about the genetic basis of phenotypic differences, particularly with respect to morphology, intermediate host specificity and evidence of reproductive isolation, have been the principle reasons for questioning the taxonomic status of some species (also see Chapter 3…”

“…The results demonstrated that there were fundamental physiological differences between E. granulosus of sheep and horse origin and the coining of the term 'physiological strain differences' (Smyth and Davies, 1974b;Smyth, 1982). This had a broad influence beyond Echinococcus, and in particular the importance of combining phenotypic and genetic differences in the characterization and description of parasites at the intraspecific level (Lymbery and Thompson, 2012;Lymbery, 1990, 1996;. p0040…”

“…The outcomes of this research caused an attitudinal shift in studies on Echinococcus that were not constrained by taxonomic issues with the growing realization that a 'strain' was an acceptable term when describing variability at the phenotypic, and subsequently genotypic levels within species of parasites (Lymbery and Thompson, 2012;Lymbery, 1990, 1996). As such, research on the horse and sheep strains of E. granulosus led to similar studies on Echinococcus of cattle, pig, camel and cervid origin with the description and characterization of several new strains/genotypes (Thompson and McManus, 2002;Thompson, 2008, Table 2).…”