Chapter 8 : Molecular Epidemiology

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Molecular Epidemiology, Page 1 of 2

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Molecular epidemiology is often confused with another related but distinct microbiology discipline: molecular taxonomy. The use of nucleic acid hybridization techniques and the analysis of housekeeping gene sequences have greatly improved our understanding of microbial evolution. Compared to taxonomy and phylogeny, molecular epidemiology is the study of more recent population dynamics. In molecular epidemiology, molecular methods are used for detection, identification, virulence characterization, and subtyping, i.e., to generate isolate-specific molecular fingerprints for assessment of epidemiological relatedness. This chapter is an introduction to molecular epidemiology and basic molecular epidemiological concepts. A nonexhaustive list of subtyping methods that are commonly used now or are under development and are anticipated to supplement or replace the currently used ones is given. Subtyping method development including validation and quality control is discussed. The selection of methods appropriate in different contexts and the manner in which the choice of method and the epidemiological context influence the interpretation of data are also dealt with. Since the DNA arrays and sequencing methods are organism specific to a very great extent, traditional methods will still be needed to detect and identify new and reemerging pathogens.

Citation: Gerner-Smidt P, Hyytiä-trees E, Rota P. 2011. Molecular Epidemiology, p 100-123. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch8
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A hypothetical example of the subtype distribution of 100 epidemiologically unrelated microbial strains generated by two subtyping methods.

Citation: Gerner-Smidt P, Hyytiä-trees E, Rota P. 2011. Molecular Epidemiology, p 100-123. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch8
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Image of FIGURE 2

Procedural principles of some commonly used non-target-specific subtyping methods. “w.” indicates “with.”

Citation: Gerner-Smidt P, Hyytiä-trees E, Rota P. 2011. Molecular Epidemiology, p 100-123. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch8
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PFGE profiles of STEC O157 strains in PulseNet, showing the most common sporadic pattern EXHX01.0047 and the outbreak-associated pattern EXHX01.1264 (A) and their occurrence during the outbreak period (B).

Citation: Gerner-Smidt P, Hyytiä-trees E, Rota P. 2011. Molecular Epidemiology, p 100-123. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch8
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Generic image for table

Definitions commonly used in molecular epidemiology

Adapted in part from references and .

Citation: Gerner-Smidt P, Hyytiä-trees E, Rota P. 2011. Molecular Epidemiology, p 100-123. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch8
Generic image for table

Characteristics and application of a number of subtyping methods

Items on left and right of slash (/) refer to manual and automated versions, respectively.

Citation: Gerner-Smidt P, Hyytiä-trees E, Rota P. 2011. Molecular Epidemiology, p 100-123. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch8