In this chapter, the contribution of molecular tools in understanding the aetiology and ecology of infectious diseases is
examined in the context of molecular epidemiology (ME). ME is seen as providing the ‘tools’, both laboratory and
analytical, which have predictive significance in epidemiological investigations of the causation of disease. A diversity of
questions can be addressed with these tools which can conveniently be viewed as particular regions of DNA and grouped
according to the different hierarchical levels of specificity by which infectious agents can be characterized. These groupings
and the applications of the different molecular tools are described, and consideration given to the most appropriate methods
of analysing data from ME investigations.