Which typing method? This really is the million dollar question in molecular epidemiological research. The choice of typing approach should firstly be driven by three aspects:

1. The ecologic and evolutionary scale of the research question (e.g. outbreak investigation or long-term global spread)
2. How rapidly does the pathogen evolve (e.g. rapidly evolving RNA virus)
3. Assumption of the (genetic) method

Secondly performance criteria of available typing approaches need to be assessed. These include:

1. Typeability
2. Reproducibility
3. Stability
4. Discriminatory power

The importance of the choice of typing method is illustrated by the below graph. Assume that for example the typing approach using Marker A has a higher discriminatory power than Marker B. The discriminatory power is the average probability that the typing system will assign a different type to two unrelated strains randomly sampled in the microbial population. Depending on your choice of approach your findings will diverge, either showing that Strain 1-3 are identical or different.

[This figure was taken from Tibayrenc 1998]

This illustrates how crucial the choice of an appropriate techniques as well as the interpretation of the experimental data within a sound theoretical framework are.

It is important to underline in this context that an ideal typing system for universal use does not exist. We will explore each of the four performance criteria in detail in future articles.

Sources and Resources:

Zadoks, R. N., and Y. H. Schukken. 2006. Use of molecular epidemiology in veterinary practice. Veterinary Clinics of North America-Food Animal Practice 22:229-261.

Riley, L. W. 2004. Molecular Epidemiology of Infectious Diseases - Principles and Practices. ASM Press, Washington, DC.

Tibayrenc M. Beyond strain typing and molecular epidemiology: Integrated genetic epidemiology of infectious diseases. Parasitology Today 1998; 14: 323-329.

Struelens MJ, Members of the European Study Group on Epidemiological Markers (ESGEM) of the European Society for Clinical Microbiology and Infectious Diseases (ESCMID). Consensus guidelines for appropriate use and evaluation of microbial epidemiologic typing systems. Clinical Microbiology and Infection 1996; 2: 2-11.