[Molecular epidemiology of infectious diseases: analytical methods and results interpretation].
Molecular typing and fingerprinting of microbial pathogens represent an essential tool for the epidemiological surveillance, outbreak detection and control of infectious diseases. Indeed, epidemiological investigation without genotyping data may not provide comprehensive information to allow the most appropriate interventions; despite this consideration, some barriers still hamper the routine application and interpretation of molecular typing data. In this paper, the most important methods currently used for characterization of pathogenic microorganisms for microbial source tracking and for the identification of clonal relationships among different isolates, are described according to their principles, advantages and limitations. Criteria for their evaluation and guidelines for the correct interpretation of results are also proposed. Molecular typing methods can be grouped into four categories based on different methodological principles, which include the characterization of restriction sites in genomic or plasmid DNA; the amplification of specific genetic targets; the restriction enzyme digestion and the subsequent amplification; sequence analysis. Although the development and the extensive use of molecular typing systems have greatly improved the understanding of the infectious diseases epidemiology, the rapid diversification, partial evaluation and lack of comparative data on the methods have raised significant questions about the selection of the most appropriate typing method, as well as difficulties for the lack of consensus about the interpretation of the results and nomenclature used for interpretation. Several criteria should be considered in order to evaluate the intrinsic performance and practical advantages of a typing system. However none of the available genotyping methods fully meets all these requirements. Therefore, the combined use of different approaches may lead to a more precise characterization and discrimination of isolates than a single method, especially if used in a hierarchical manner. The interpretation of the molecular results differs according to the typing system's characteristics: for example in the restriction fragments-based analysis, the divergences or the similarity percentages among the profiles are evaluated, whilst the differences in terms of number and intensity of bands are analyzed in the amplification-based approaches. Moreover, a correct interpretation of molecular results significantly depends by other critical factors, such as the comprehension of the typing system and data quality, the microbial diversity, and the epidemiological context in which the method is used. The analysis of PFGE data, considered as the "gold standard", is based on the differences of the number and position of bands patterns, although recent recommendations are now available from the Centers for Diseases Control and Prevention (CDC) for a more accurate interpretation, which also include the evaluation of the gel quality, the genetic diversity of the microorganism, the time and geographical scale of an epidemic event. Future advances in the molecular typing technologies indeed will provide rapid methodological improvements, such as a greater degree of automation, better resolution, higher throughput, and a greater availability of dedicated bioinformatics tools. These factors will all contribute to an increasing application of genotyping methods to better understand the epidemiology of infectious diseases, and to implement, along with the strengthened international and interdisciplinary partnerships, more effective control and prevention strategies for Public Health improvements.
Cattedra di Igiene, Dipartimento di Medicina e di Scienze della Salute, Università degli Studi del Molise.
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Sammarco
Cattedra di Igiene, Dipartimento di Medicina e di Scienze della Salute, Università degli Studi del Molise.
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Ripabelli
Cattedra di Igiene, Dipartimento di Medicina e di Scienze della Salute, Università degli Studi del Molise.
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Tamburro
D003141:Communicable Diseases / Q000453:epidemiology* / Q000235:genetics*; D005784:Gene Amplification; D005838:Genotype; D006801:Humans; D017720:Molecular Epidemiology / Q000379:methods; D058889:Molecular Typing; D015183:Restriction Mapping; D017422:Sequence Analysis, DNA