2021-09-10 21:48:00 +02:00
<!DOCTYPE html>
< html lang = "" xml:lang = "" >
< head >
< meta charset = "utf-8" / >
< meta http-equiv = "X-UA-Compatible" content = "IE=edge" / >
< title > A New Instrument for Microbial Epidemiology< / title >
< meta name = "description" content = "This is the PhD thesis of the author." / >
< meta name = "generator" content = "bookdown 0.24 and GitBook 2.6.7" / >
< meta property = "og:title" content = "A New Instrument for Microbial Epidemiology" / >
< meta property = "og:type" content = "book" / >
< meta property = "og:description" content = "This is the PhD thesis of the author." / >
< meta name = "github-repo" content = "msberends/a_new_instrument_for_microbial_epidemiology" / >
< meta name = "twitter:card" content = "summary" / >
< meta name = "twitter:title" content = "A New Instrument for Microbial Epidemiology" / >
< meta name = "twitter:description" content = "This is the PhD thesis of the author." / >
< meta name = "author" content = "Matthijs S. Berends" / >
< meta name = "viewport" content = "width=device-width, initial-scale=1" / >
< meta name = "apple-mobile-web-app-capable" content = "yes" / >
< meta name = "apple-mobile-web-app-status-bar-style" content = "black" / >
2021-09-10 22:22:38 +02:00
< link rel = "next" href = "colophon.html" / >
2021-09-10 21:48:00 +02:00
< script src = "libs/header-attrs-2.10/header-attrs.js" > < / script >
< script src = "libs/jquery-3.6.0/jquery-3.6.0.min.js" > < / script >
< script src = "https://cdn.jsdelivr.net/npm/fuse.js@6.4.6/dist/fuse.min.js" > < / script >
< link href = "libs/gitbook-2.6.7/css/style.css" rel = "stylesheet" / >
< link href = "libs/gitbook-2.6.7/css/plugin-table.css" rel = "stylesheet" / >
< link href = "libs/gitbook-2.6.7/css/plugin-bookdown.css" rel = "stylesheet" / >
< link href = "libs/gitbook-2.6.7/css/plugin-highlight.css" rel = "stylesheet" / >
< link href = "libs/gitbook-2.6.7/css/plugin-search.css" rel = "stylesheet" / >
< link href = "libs/gitbook-2.6.7/css/plugin-fontsettings.css" rel = "stylesheet" / >
< link href = "libs/gitbook-2.6.7/css/plugin-clipboard.css" rel = "stylesheet" / >
< link href = "libs/anchor-sections-1.0.1/anchor-sections.css" rel = "stylesheet" / >
< script src = "libs/anchor-sections-1.0.1/anchor-sections.js" > < / script >
< style type = "text/css" >
pre > code.sourceCode { white-space: pre; position: relative; }
pre > code.sourceCode > span { display: inline-block; line-height: 1.25; }
pre > code.sourceCode > span:empty { height: 1.2em; }
.sourceCode { overflow: visible; }
code.sourceCode > span { color: inherit; text-decoration: inherit; }
pre.sourceCode { margin: 0; }
@media screen {
div.sourceCode { overflow: auto; }
}
@media print {
pre > code.sourceCode { white-space: pre-wrap; }
pre > code.sourceCode > span { text-indent: -5em; padding-left: 5em; }
}
pre.numberSource code
{ counter-reset: source-line 0; }
pre.numberSource code > span
{ position: relative; left: -4em; counter-increment: source-line; }
pre.numberSource code > span > a:first-child::before
{ content: counter(source-line);
position: relative; left: -1em; text-align: right; vertical-align: baseline;
border: none; display: inline-block;
-webkit-touch-callout: none; -webkit-user-select: none;
-khtml-user-select: none; -moz-user-select: none;
-ms-user-select: none; user-select: none;
padding: 0 4px; width: 4em;
color: #aaaaaa;
}
pre.numberSource { margin-left: 3em; border-left: 1px solid #aaaaaa; padding-left: 4px; }
div.sourceCode
{ }
@media screen {
pre > code.sourceCode > span > a:first-child::before { text-decoration: underline; }
}
code span.al { color: #ff0000; font-weight: bold; } /* Alert */
code span.an { color: #60a0b0; font-weight: bold; font-style: italic; } /* Annotation */
code span.at { color: #7d9029; } /* Attribute */
code span.bn { color: #40a070; } /* BaseN */
code span.bu { } /* BuiltIn */
code span.cf { color: #007020; font-weight: bold; } /* ControlFlow */
code span.ch { color: #4070a0; } /* Char */
code span.cn { color: #880000; } /* Constant */
code span.co { color: #60a0b0; font-style: italic; } /* Comment */
code span.cv { color: #60a0b0; font-weight: bold; font-style: italic; } /* CommentVar */
code span.do { color: #ba2121; font-style: italic; } /* Documentation */
code span.dt { color: #902000; } /* DataType */
code span.dv { color: #40a070; } /* DecVal */
code span.er { color: #ff0000; font-weight: bold; } /* Error */
code span.ex { } /* Extension */
code span.fl { color: #40a070; } /* Float */
code span.fu { color: #06287e; } /* Function */
code span.im { } /* Import */
code span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Information */
code span.kw { color: #007020; font-weight: bold; } /* Keyword */
code span.op { color: #666666; } /* Operator */
code span.ot { color: #007020; } /* Other */
code span.pp { color: #bc7a00; } /* Preprocessor */
code span.sc { color: #4070a0; } /* SpecialChar */
code span.ss { color: #bb6688; } /* SpecialString */
code span.st { color: #4070a0; } /* String */
code span.va { color: #19177c; } /* Variable */
code span.vs { color: #4070a0; } /* VerbatimString */
code span.wa { color: #60a0b0; font-weight: bold; font-style: italic; } /* Warning */
< / style >
< link rel = "stylesheet" href = "style.css" type = "text/css" / >
< / head >
< body >
< div class = "book without-animation with-summary font-size-2 font-family-1" data-basepath = "." >
< div class = "book-summary" >
< nav role = "navigation" >
< ul class = "summary" >
< li > < a href = "./" > A New Instrument for Microbial Epidemiology< / a > < / li >
< li class = "divider" > < / li >
2021-09-10 22:22:38 +02:00
< li class = "chapter" data-level = "" data-path = "index.html" > < a href = "index.html" > < i class = "fa fa-check" > < / i > Preamble< / a >
< ul >
< li class = "chapter" data-level = "" data-path = "index.html" > < a href = "index.html#short-summary-250-words" > < i class = "fa fa-check" > < / i > Short summary (250 words)< / a > < / li >
< / ul > < / li >
< li class = "chapter" data-level = "" data-path = "colophon.html" > < a href = "colophon.html" > < i class = "fa fa-check" > < / i > Colophon< / a > < / li >
< li class = "chapter" data-level = "1" data-path = "introduction.html" > < a href = "introduction.html" > < i class = "fa fa-check" > < / i > < b > 1< / b > Introduction< / a > < / li >
2021-09-10 21:48:00 +02:00
< li class = "divider" > < / li >
< li > < a href = "https://github.com/rstudio/bookdown" target = "blank" > Published with bookdown< / a > < / li >
< / ul >
< / nav >
< / div >
< div class = "book-body" >
< div class = "body-inner" >
< div class = "book-header" role = "navigation" >
< h1 >
< i class = "fa fa-circle-o-notch fa-spin" > < / i > < a href = "./" > A New Instrument for Microbial Epidemiology< / a >
< / h1 >
< / div >
< div class = "page-wrapper" tabindex = "-1" role = "main" >
< div class = "page-inner" >
< section class = "normal" id = "section-" >
< div id = "header" >
< 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 >
< / div >
2021-09-10 22:22:38 +02:00
< div id = "preamble" class = "section level1 unnumbered" >
< h1 > Preamble< / h1 >
< p > This is the integral PhD thesis ‘ ’ < 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 ‘ ’ < / p >
< div id = "short-summary-250-words" class = "section level3 unnumbered" >
< 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 >
< / div >
2021-09-10 21:48:00 +02:00
< / div >
< / section >
< / div >
< / div >
< / div >
2021-09-10 22:22:38 +02:00
< a href = "colophon.html" class = "navigation navigation-next navigation-unique" aria-label = "Next page" > < i class = "fa fa-angle-right" > < / i > < / a >
2021-09-10 21:48:00 +02:00
< / div >
< / div >
< script src = "libs/gitbook-2.6.7/js/app.min.js" > < / script >
< script src = "libs/gitbook-2.6.7/js/clipboard.min.js" > < / script >
< script src = "libs/gitbook-2.6.7/js/plugin-search.js" > < / script >
< script src = "libs/gitbook-2.6.7/js/plugin-sharing.js" > < / script >
< script src = "libs/gitbook-2.6.7/js/plugin-fontsettings.js" > < / script >
< script src = "libs/gitbook-2.6.7/js/plugin-bookdown.js" > < / script >
< script src = "libs/gitbook-2.6.7/js/jquery.highlight.js" > < / script >
< script src = "libs/gitbook-2.6.7/js/plugin-clipboard.js" > < / script >
< script >
gitbook.require(["gitbook"], function(gitbook) {
gitbook.start({
"sharing": {
"github": false,
"facebook": true,
"twitter": true,
"linkedin": false,
"weibo": false,
"instapaper": false,
"vk": false,
"whatsapp": false,
"all": ["facebook", "twitter", "linkedin", "weibo", "instapaper"]
},
"fontsettings": {
"theme": "white",
"family": "sans",
"size": 2
},
"edit": {
"link": null,
"text": null
},
"history": {
"link": null,
"text": null
},
"view": {
"link": null,
"text": null
},
"download": ["a_new_instrument_for_microbial_epidemiology.pdf", "a_new_instrument_for_microbial_epidemiology.epub"],
"search": {
"engine": "fuse",
"options": null
},
"toc": {
"collapse": "subsection"
}
});
});
< / script >
< / body >
< / html >
