INESC-ID   Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa
technology from seed


Knowledge Discovery and Bioinformatics
Inesc-ID Lisboa

Microbial typing methods: databases and quantitative correspondence between typing methods results

04/12/2007 - 16:30
04/12/2007 - 17:30

Typing methods are major tools for the epidemiological characterization of bacterial pathogens, allowing the determination of the clonal relationships between isolates based on their genotypic or phenotypic characteristics. Recent technological advances have resulted in a shift from classical phenotypic typing methods, such as serotyping, biotyping and antibiotic resistance typing, to molecular methods such as restriction fragment length polymorphisms (RFLP), pulsed-field gel electrophoresis (PFGE), and PCR serotyping . With the availability of affordable sequencing methods, another shift occurred towards sequence based typing methods such as multilocus sequence typing (MLST) and emm sequence typing. Sequence based methods have a large appeal since they provide unambiguous data and are intrinsically portable, allowing the creation of databases that, if publicly available through the internet, enable the comparison of local data with that of previous studies in different geographical locations. Ideally an analysis of each typing method, in terms of discriminatory power, reproducibility, typeability, feasibility, and other characteristics, should be performed to better determine which method is appropriate in a given setting. Several molecular epidemiology studies of clinically relevant microorganisms provide a characterization of isolates based on different typing methods. Frequently these studies focus on a comparison between the assigned types of different typing methods, from a qualitative point of view, i.e., indicating correspondences between the types of the different methods. Although this may be useful for the comparison of the genetic backgrounds of the particular set of isolates under study, it does not allow for a broader view of how the results of the different typing methods are related. In this seminar we present the recent work on a online database for a new sequence-based typing method for Staphylococcus aureus and an online tool that implements a framework of measures that allow the quantitative assessment of the congruence for different typing methods results.