Publisher Summary Molecular tools enhance outbreak investigation and surveillance, facilitate description of the transmission system, and increase understanding of the epidemiology. Molecular tools enhance case definitions, increasing specificity and reducing misclassification, and are now a standard tool in outbreak investigations. Although it is assumed during an outbreak that a single microbe is causing the clinical symptoms, it is possible that a microbe of the same genus and species but different strain is causing disease during the same time period. Molecular typing can distinguish between outbreak and nonoutbreak strains. Molecular tools also facilitate estimating parameters key to understanding the transmission system, including the incidence, prevalence, transmission probability, duration of carriage, effective dose, and probability of effective contact. Molecular tools enable one to trace the dissemination of a particular subtype across time and space and thus develop theories of transmission and dissemination, determine the origin of an epidemic and test theories about reservoirs and evolution of a particular pathogen, follow the emergence of new infections as they cross species, testing the hypotheses about the apparent transmissibility and rate of evolution, and follow mobile genetic elements conferring antimicrobial resistance or virulence between strains within a species or between species, and so develop theories about evolution and transmission within the populations of pathogens.
Chapter 3 Applications of Molecular Tools to Infectious Disease Epidemiology