Chapter 10 : Molecular Epidemiology

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Molecular epidemiology may be defined as the application of molecular, i.e., nucleic acid or protein based, methods to study the transmission of microbial pathogens in human populations. In molecular epidemiology, molecular methods are used for detection, identification, virulence characterization, and subtyping, i.e., to generate isolate-specific profiles or fingerprints for assessment of epidemiological relatedness. Molecular methods have gradually replaced old phenotypic methods, starting with the introduction of plasmid profiling in the 1970s and reaching the most recent resolution with the emergence of next-generation sequencing techniques during the latter part of the past decade. This chapter describes the most commonly used methods, together with their strengths, weaknesses, and applications in the context of molecular epidemiology. The appropriate process for method selection, development, and validation is discussed, along with the factors that may affect data interpretation. Finally, we provide examples of the reference libraries that are available for molecular methods.

Citation: Trees E, Rota P, MacCannell D, Gerner-Smidt P. 2015. Molecular Epidemiology, p 131-160. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch10
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Hypothetical example of the subtype distribution of 100 epidemiologically unrelated microbial strains generated by two subtyping methods. doi:10.1128/9781555817381.ch10.f1

Citation: Trees E, Rota P, MacCannell D, Gerner-Smidt P. 2015. Molecular Epidemiology, p 131-160. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch10
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Procedural principles of some commonly used non-target-specific subtyping methods. doi:10.1128/9781555817381.ch10.f2

Citation: Trees E, Rota P, MacCannell D, Gerner-Smidt P. 2015. Molecular Epidemiology, p 131-160. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch10
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Image of FIGURE 3

Procedural principles of some commonly used target-specific subtyping methods. doi:10.1128/9781555817381.ch10.f3

Citation: Trees E, Rota P, MacCannell D, Gerner-Smidt P. 2015. Molecular Epidemiology, p 131-160. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch10
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Image of FIGURE 4

Heat map showing the SNPs among 10 STEC O157 isolates belonging to the same outbreak. In order to elucidate the genetic relationships among the outbreak isolates, high-quality SNPs were called against the outbreak reference strain (index case) that appears at the far left. A total of nine SNPs were detected among the outbreak isolates. doi:10.1128/9781555817381.ch10.f4

Citation: Trees E, Rota P, MacCannell D, Gerner-Smidt P. 2015. Molecular Epidemiology, p 131-160. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch10
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Image of FIGURE 5

PFGE profiles of two STEC O157 strains, namely, the most common sporadic pattern, EXHX01.0047, and the outbreak-associated pattern, EXHX01.1264, and their distribution during the 2002 outbreak period. doi:10.1128/9781555817381.ch10.f5

Citation: Trees E, Rota P, MacCannell D, Gerner-Smidt P. 2015. Molecular Epidemiology, p 131-160. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch10
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Generic image for table

Definitions commonly used in molecular epidemiology

Citation: Trees E, Rota P, MacCannell D, Gerner-Smidt P. 2015. Molecular Epidemiology, p 131-160. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch10
Generic image for table

Characteristics and application of a number of subtyping methods

Citation: Trees E, Rota P, MacCannell D, Gerner-Smidt P. 2015. Molecular Epidemiology, p 131-160. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch10
Generic image for table

Definitions commonly used in bioinformatics

Citation: Trees E, Rota P, MacCannell D, Gerner-Smidt P. 2015. Molecular Epidemiology, p 131-160. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch10

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