The process of subtyping is epidemiologically important for recognizing outbreaks of diseases, detecting the cross-transmission of nosocomial pathogens, determining the source of infection, and in some cases recognizing particularly virulent strains of organisms.
Subtyping or strain classification has been accomplished by a number of different approaches. In recent years, the development and extensive use of highresolution molecular typing systems based on direct analysis of genomic polymorphism have greatly improved the understanding of the epidemiology of infectious diseases.[1'2] These molecular typing methods can be applied to answer a number of different questions, such as:
In an outbreak, what is the extent and mode of transmission of the epidemic clone(s)?
In long-term surveillance, what is the prevalence over time and the geographic spread of epidemic and endemic clones in the population?
A large number of molecular typing methods are available for a wide range of microorganisms and can provide a good epidemiological tool. However, the rapid diversification and incomplete comparative evaluation of some of these methods leave the microbiologist and the epidemiologist faced with a number of questions dealing with selection of appropriate typing system(s), to address a particular problem, as well as a lack of consensus about interpretation and communication of results.
Several criteria have been proposed for evaluating the performance of typing systems.[1,2] These criteria include typeability, reproducibility, stability, and discriminatory power.
• Typeability. Typeability refers to the proportion of isolates that can be scored in the typing system and assigned to a type.
• Reproducibility. Reproducibility refers to the ability of the typing system to assign the same type on repeated testing of the same strain.
• Stability. Stability is based on the biological features of clonally derived isolates to express constant markers over time and generations.
• Discriminatory power. This is a key characteristic of typing systems, as it estimates the probability that isolates sharing identical or closely related types are truly clonal and part of the same chain of transmission.
Additional comparative studies are needed to establish the relative value of systems currently used for typing microbial pathogens. Moreover, there are important variations in the performance of any given method depending on the species and on modifications of the procedure as applied by different investigators.
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