New Frontiers of Molecular Epidemiology of Infectious Diseases
Molecular epidemiology has recently broaden its focuses due to the development of molecular tools but also by incorporating advances of other fields such as mathematical epidemiology, molecular ecology, population genetics and evolution. Facing new risks
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Molecular Typing of Bacterial Pathogens: A Tool for the Epidemiological Study and Control of Infectious Diseases Marie Hallin, Ariane Deplano, and Marc J. Struelens
Abstract Molecular typing is nowadays an integral part of the public health microbiology toolbox. It indexes subspecies genotypic or phenotypic characters to estimate the genetic relatedness of microbial isolates and infer from it their probability of belonging to the same chain of transmission. Typing is used both to investigate outbreaks and enhance the resolution of disease surveillance at different population levels: (i) locally, in hospitals or the community, by clinical or public health laboratories; (ii) nationally, by reference laboratories or (iii) globally, through international surveillance networks. This chapter provides an overview of currently available and emerging technologies for typing human bacterial pathogens, discusses their suitability to different levels of use and reviews examples of integrated typing in advanced surveillance systems.
2.1 Introduction Microbial typing allows the differentiation of epidemiological related from unrelated isolates of the same bacterial species. It is used to elucidate the source and route of transmission of micro-organisms causing outbreaks of infectious diseases. It can also be applied to basic research including in depth investigations of infectious disease pathogenesis, bacterial population structures and microbial genetic diversity in diverse ecosystems (van Belkum et al. 2007).
M. Hallin (*) • A. Deplano Laboratoire de Microbiologie et Laboratoire de Référence des Staphylocoques-MRSA, Hôpital Erasme, 808 route de Lennik, 1070 Brussels, Belgium e-mail: [email protected] M.J. Struelens Scientific Advice Unit, European Centre for Disease Prevention and Control, 17183 Stockholm, Sweden
S. Morand et al. (eds.), New Frontiers of Molecular Epidemiology of Infectious Diseases, DOI 10.1007/978-94-007-2114-2_2, © Springer Science+Business Media B.V. 2012
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A typing method (TM) should ideally be rapid, robust and produce objective and portable data enabling subspecies discrimination of microbial isolates to trace pathogen transmission unambiguously across various population and time scales. Even though next generation whole genome sequencing has become the ultimate reference technology (Harris et al. 2010; Lewis et al. 2010), high cost and complex data analysis hurdles must still be overcome to make it routinely applicable for epidemiological typing. Therefore, less comprehensive microbial typing methods (TM) still have to be carefully chosen with respect to analytical performance and convenience criteria according to the pathogen and application of interest (Struelens and ESGEM 1996; van Belkum et al. 2007). TM can be classified according to the nature of the character they explore, where “phenotypic” TM are opposed to “genotypic” TM or following their standardisation and portability of results they produce, where “comparative” TM are opposed to “definitive (library) t
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