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 thedirect examinationofparasites fromclinical or environmental samples, andproviding
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 ofthese 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.