View Item 
        •   Utrecht University Student Theses Repository Home
        • UU Theses Repository
        • Theses
        • View Item
        •   Utrecht University Student Theses Repository Home
        • UU Theses Repository
        • Theses
        • View Item
        JavaScript is disabled for your browser. Some features of this site may not work without it.

        Browse

        All of UU Student Theses RepositoryBy Issue DateAuthorsTitlesSubjectsThis CollectionBy Issue DateAuthorsTitlesSubjects

        Examining the multitude of available methods for attributing sources to molecular infection and antimicrobial resistance

        Thumbnail
        View/Open
        Writing Assignment - Tristan Schadron - 6669980 - Examing the multitude of available methods for attributing sources to molecular infection and antimicrobial resistance(1).pdf (247.4Kb)
        Publication date
        2022
        Author
        Schadron, Tristan
        Metadata
        Show full item record
        Summary
        In order to counteract disease outbreaks, monitor pathogen populations, and allow preventive measures to be put in place against pathogens, pathogens need to be attributed to putative sources. To this extent source attribution may look at phenotypical and genotypical characteristics of the pathogen to link it to a source. Proper designation to a source requires overcoming problems related to the pathogen and sources characteristic, which may erase recognizable patterns differentiating one serovar strain from another. However, no standard approach to source attribution exists, which overcomes the problems and limitations inherent therein. No standard approach to all source attribution tasks is likely to exist, however by combining different genotyping approaches using WGS data pathogens can be attributed with a higher resolution. Here biological problems and technical problems associated with source attribution, among which host range, host switching behavior, genome plasticity, source designation, metadata annotation, problems with data, and spatio-temporal dynamics are evaluated. These technical and biological problems are placed in context of different phenotyping, genotyping and genotype-based microbial source attribution approaches to give an intuitive overview of the strengths and weaknesses of the aforementioned approaches. Agreeing with previous papers, we find that a combination of genotyping approaches is the best way forward. However, WGS genotyping approaches require standardization before universal application. We hope to highlight possible research directions, such as to what extent genetic signals are associated with adaptation, and by proxy attributable to a source. Additionally, we stressed the relevance of spatio-temporal data to expand source attribution capabilities.
        URI
        https://studenttheses.uu.nl/handle/20.500.12932/41495
        Collections
        • Theses

        Related items

        Showing items related by title, author, creator and subject.

        • Naïve Bayes classifier: normally distributed continuous attributes versus the discretized version of those attributes 

          Majoor, I.A.G. (2017)
          In this paper, the differences between training a Naïve Bayes classifier on normally distributed continuous attributes and training a Naïve Bayes classifier on the discretized version of those continuous attributes have ...
        • Performance of Specific Source and Common Source Bayes Factors for Trace-Reference Problems 

          Boudens, Emilie (2022)
        • Beached Debris from Fisheries at the Gal ́apagos Islands: can we identify sources? Ocean Pathways, Source Identification, and an Investigation into the Predictability of Fishing Activity 

          Nagler, Ina (2022)
        Utrecht university logo