This is my full PhD thesis in R Markdown (using the bookdown package), containing a PDF and EPUB file, and a website in the ‘docs’ folder with the integral content of the book. https://git.io/PhDthesisAMR
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<i class="fa fa-circle-o-notch fa-spin"></i><a href="./">A New Instrument for Microbial Epidemiology</a>
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<h1 class="title">A New Instrument for Microbial Epidemiology</h1>
<h2 class="subtitle"><em>Empowering Antimicrobial Resistance Data Analysis</em></h2>
<p class="author"><em>Matthijs S. Berends</em></p>
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<h1>Preamble</h1>
<p>This is the integral PhD thesis ‘A New Instrument for Microbial Epidemiology’ (DOI <a href="https://doi.org/10.33612/diss.177417131">10.33612/diss.177417131</a>) by <a href="https://www.rug.nl/staff/m.s.berends">Matthijs S. Berends</a>, which was defended publicly at the University of Groningen, the Netherlands, on 25 August 2021.</p>
<p>All texts were copied from the printed version ‘as is’; no modifications were made.</p>
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<h3>Short summary (250 words)</h3>
<p>Treating infectious diseases requires insights into the microorganisms causing infectious diseases. Antimicrobial resistance (AMR) in microorganisms limits treatment possibilities and poses an enormous healthcare problem worldwide. The spread and AMR patterns of microorganisms, risk factors for infection, and preventive and control measures of infectious disease are studied within the field of Microbial Epidemiology, a cross-over field between Epidemiology and Clinical Microbiology. For analysing the spread and AMR patterns of microorganisms, however, no standardised method previously existed. This thesis showcases the development and applied use of a new instrument to analyse AMR data: the AMR package for R. From multiple viewpoints, the AMR package and its advantages are put into perspective: from a technical viewpoint, from an infection management viewpoint and from a clinical viewpoint. These combined provide a common ground for comprehending what the AMR package could yield in the field and how it can set a new empowered starting point for future applications of microbial epidemiology, in clinical and research settings alike. This thesis subsequently elaborates on these multiple viewpoints by illustrating the use of this new instrument in epidemiological research projects in the Dutch-German cross-border region to better understand the occurrence and AMR patterns of microorganisms on a (eu)regional level. In conclusion, this thesis shows the added value of a consistent data-analytical instrument to prepare and analyse AMR data in a full-region approach, that can also be used in clinical settings to obtain novel insights on AMR patterns.</p>
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