**2. Genotypic methods**

The application of molecular biology tools to infectious disease epidemiology is perhaps just as revolutionary in advancing knowledge and concepts in epidemiology. Genotypic typing methods assess genome variation in bacterial isolates.

The advantages of nucleic acid-based typing systems lie in that they are less likely to be affected by growth conditions or the laboratory manipulations to which organisms are subjected. Undoubtedly, genetic materials undergo changes due to natural or artificial selective pressures, but this mechanism is exactly the basis for their typeability.

Compared to the classical phenotypic typing techniques, genotypic typing techniques have several advantages such as general applicability and a high discriminatory power.

A molecular technique must take into consideration the relative accumulation of variation (short or long term) of a targeted set of genes in a pathogen. Nearly all the typing systems can be grouped into variants of just three basic analytical procedures: (i) PCR, (ii) the use of restriction enzymes, and (iii) nucleic acid sequencing. These procedures allow for the use of common equipment and standard reagents to analyze many different types of infectious agents. In addition, genotypic characterization of pathogens facilitates standardization of information storage and data analyses, interpretation, and communication, which are all amenable to computer-assisted manipulations.
