1 - An Introduction to the Generation and Analysis of Microbial Typing Data

Abstract

Typing is used to describe a microbial isolate in such a way that it can be distinguished from other isolates. Thus, typing can be an identifying method in which a given character, e.g., a serotype, is used to identify an isolate as one already included in an existing typing scheme. Typing can also be done comparatively, which implies that microbial isolates of a defined set are compared to each other for similarity, without any reference to other isolates not included in the set and without reference to existing classification schemes. This chapter deals with general aspects of typing, including data management and analysis, as well as quality control. Typing methods can be grouped in different categories, including phenotypic vs. genotypic methods and comparative vs. definitive (absolute or identifying) methods. The most commonly used analytical method, cluster or pattern analysis, involves the pairwise comparison of isolates or objects, followed by their grouping on the basis of similarity, and their subsequent depiction in a tree-like structure termed a dendrogram. Cluster analysis can be applied to both genotypic and phenotypic data, including DNA fragment electrophoretic patterns, profiles generated by mass spectrometry or gas chromatography, or biochemical profiles.