Microbial typing methods: databases and quantitative correspondence between typing methods results
João Carriço,
Inesc-ID –
Abstract:
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.
Date: 2007-Apr-12 Time: 16:30:00 Room: 336
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Workshop “Metabolism and mathematical models: Two for a tango” – 2nd Edition
Title: Workshop Metabolism and mathematical models: Two for a tango – 2nd Edition
Dates: October 25-26, 2022
Location: This workshop will be held in a virtual way
The topic of this workshop is metabolism in general, with a special focus, although not exclusive, on parasitology. Besides an exploration of the biological, biochemical and biomedical aspects, the workshop will also aim at presenting some of the mathematical modelling, algorithmic theory and software development that have become crucial to explore such aspects.
This workshop is being organised in the context of two projects, both with the Inria European Team Erable. One of the projects involves a partnership with the University of São Paulo (USP), in São Paulo, Brazil, more specifically the Institute of Mathematics and Statistics (IME) and the Institute of Biomedical Sciences – Inria Associated Team Capoeira – and the other involves the Inesc-ID/IST in Portugal, ETH in Zürich and EMBL in Heidelberg – H2020 Twinning Project Olissipo.
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